Biochemistry – Nature17
Biology and Chemistry
Biochemistry
Carbohydrates, Lipids, Proteins,
Pigments, Vitamins, Nucleic Acids, and
Xenobiotics
Nature17
|Page
Biochemistry – Nature17
Table of Contents
Table of Figures ................................................................................................................................................................. iii
Objectives ........................................................................................................................................................................... vi
Carbohydrates .................................................................................................................................................................... 1
Outline .............................................................................................................................................................................. 1
Monosaccharides ............................................................................................................................................................ 1
Types of Glucose ....................................................................................................................................................... 3
Shape of Carbohydrates ......................................................................................................................................... 6
Monosaccharide Reactions....................................................................................................................................... 8
Detecting Reducing Sugars ................................................................................................................................... 13
Disaccharides ............................................................................................................................................................... 13
Erythro and Threo Sugars ..................................................................................................................................... 14
Polysaccharides ........................................................................................................................................................... 15
Structural Polysaccharides .................................................................................................................................... 16
Glycosaminoglycans and Proteoglycans ........................................................................................................... 17
Lipids .................................................................................................................................................................................. 18
Outline ........................................................................................................................................................................... 18
Lipids.............................................................................................................................................................................. 19
Fats................................................................................................................................................................................. 21
Rancidity of Triglycerides ..................................................................................................................................... 22
Phospholipids ............................................................................................................................................................... 23
Phospholipids in Archaeal Membranes .............................................................................................................. 25
Glycolipids ................................................................................................................................................................... 26
Steroids ......................................................................................................................................................................... 26
Soaps and Detergents ............................................................................................................................................... 27
Wax............................................................................................................................................................................... 29
Prostaglandins, Thromboxanes, and Leukotrienes ................................................................................................ 29
Terpenes and Terpenoids .......................................................................................................................................... 30
Lipoproteins .................................................................................................................................................................. 31
Proteins .............................................................................................................................................................................. 32
Outline ........................................................................................................................................................................... 32
Amino Acids .................................................................................................................................................................. 34
Synthesis of Amino Acids ........................................................................................................................................... 42
Protein Function............................................................................................................................................................ 43
Protein Structure .......................................................................................................................................................... 43
Protein Models ............................................................................................................................................................. 48
i|Page
Biochemistry – Nature17
Protein Misfolding ....................................................................................................................................................... 49
Enzymes ......................................................................................................................................................................... 49
Types of Enzymes ................................................................................................................................................... 50
Gibbs Free Energy and Activation Energy........................................................................................................ 51
Enzyme Kinetics and Activity ................................................................................................................................ 52
Analysis of Proteins ..................................................................................................................................................... 56
Reaction with Ninhydrin ......................................................................................................................................... 57
Protein Assays ......................................................................................................................................................... 58
Motor Proteins.............................................................................................................................................................. 58
Proteomes ..................................................................................................................................................................... 59
Pigments............................................................................................................................................................................. 59
Outline ........................................................................................................................................................................... 59
Pigments ........................................................................................................................................................................ 60
Porphyrins ..................................................................................................................................................................... 60
Chlorophyll............................................................................................................................................................... 60
Hemoglobin and Myoglobin................................................................................................................................. 61
Cytochromes ............................................................................................................................................................ 63
Carotenoids .................................................................................................................................................................. 63
Anthocyanins ................................................................................................................................................................ 64
Analysis of Pigments ................................................................................................................................................... 65
Vitamins ............................................................................................................................................................................. 65
Outline ........................................................................................................................................................................... 65
Vitamins ......................................................................................................................................................................... 66
Vitamin B-complex ...................................................................................................................................................... 66
Vitamin C ...................................................................................................................................................................... 69
Vitamin A ...................................................................................................................................................................... 69
Vitamin D ...................................................................................................................................................................... 69
Vitamin K....................................................................................................................................................................... 69
Vitamin E ....................................................................................................................................................................... 70
Malnutrition................................................................................................................................................................... 70
Nucleic Acids ..................................................................................................................................................................... 71
Outline ........................................................................................................................................................................... 71
Nucleic Acid Function .................................................................................................................................................. 72
Nucleotides ................................................................................................................................................................... 73
Pentose Sugar ......................................................................................................................................................... 73
Nitrogenous Base.................................................................................................................................................... 74
ii | P a g e
Biochemistry – Nature17
Nucleosides and Nucleotides ............................................................................................................................... 75
Nucleic Acid Bond Formation................................................................................................................................ 76
DNA and RNA.............................................................................................................................................................. 77
Types of DNA .............................................................................................................................................................. 79
ATP ................................................................................................................................................................................. 81
Nucleotide Synthesis ................................................................................................................................................... 82
DNA Expression (An Overview)................................................................................................................................ 88
Xenobiotics ........................................................................................................................................................................ 89
Outline ........................................................................................................................................................................... 89
Xenobiotics ................................................................................................................................................................... 90
Responding to Xenobiotics ........................................................................................................................................ 91
Review Questions ............................................................................................................................................................. 92
Key Terms .......................................................................................................................................................................... 95
Review Question Answers ............................................................................................................................................ 107
References ....................................................................................................................................................................... 111
Table of Figures
Figure 1 Linear Form of Fructose ..................................................................................................................................... 2
Figure 2 Glucose vs. Galactose ....................................................................................................................................... 3
Figure 3 Alpha Glucose vs. Beta Glucose ..................................................................................................................... 4
Figure 4 Chirality of Alpha Glucose ............................................................................................................................... 4
Figure 5 Chirality of Beta Glucose ................................................................................................................................. 4
Figure 6 Hemiacetal Carbon ............................................................................................................................................ 5
Figure 7 Equilibrium Mixture of D-glucose in Aqueous Solution ................................................................................ 5
Figure 8 Axial and Equatorial Bonds in Glucose ......................................................................................................... 6
Figure 9 Fischer Projection of L and D sugars............................................................................................................... 6
Figure 10 Converting from Fischer to Haworth Projection ......................................................................................... 8
Figure 11 Furan and Pyran .............................................................................................................................................. 8
Figure 12 Epimerization with D-glucose and D-mannose ........................................................................................... 9
Figure 13 Enediol Rearrangement: D-glucose into D-fructose................................................................................... 9
Figure 14 Oxidizing Glucose to Glucaric Acid using Nitric Acid ........................................................................... 10
Figure 15 Formation of Ester and Ether Derivatives of Monosaccharides ........................................................... 10
Figure 16 Reaction Mechanism for Williamson Ether Synthesis ............................................................................. 10
Figure 17 Glycoside Formation from D-Glucopyranose ......................................................................................... 11
Figure 18 Kiliani-Fischer Synthesis ............................................................................................................................... 12
Figure 19 Formation of D-Arabinose from D-Glucose through Wohl Degradation .......................................... 13
Figure 20 Glycosidic Link in Maltose ........................................................................................................................... 14
Figure 21 Diastereomers and Enantiomers................................................................................................................. 14
Figure 22 Erythro and Threo Compounds ................................................................................................................... 15
Figure 23 Amylose and Amylopectin .......................................................................................................................... 15
Figure 24 Glycogen ........................................................................................................................................................ 16
Figure 25 Hydrogen Bonding in Cellulose.................................................................................................................. 16
iii | P a g e
Biochemistry – Nature17
Figure 26 Chitin Monomer ............................................................................................................................................. 17
Figure 27 Glycosaminoglycan Examples.................................................................................................................... 17
Figure 28 Aggrecan Impact Shock Absorption.......................................................................................................... 18
Figure 29 Bomb Calorimeter......................................................................................................................................... 20
Figure 30 Halogenation of Alkenes in Lipids ............................................................................................................. 21
Figure 31 Fatty Acids and Triglycerides .................................................................................................................... 21
Figure 32 Oleic Acid, Elaidic Acid, Stearic Acid ....................................................................................................... 22
Figure 33 Phospholipid (Phosphatidylcholine) ........................................................................................................... 23
Figure 34 Liposome ......................................................................................................................................................... 24
Figure 35 Micelle............................................................................................................................................................. 24
Figure 36 Sphingosine and Sphingomyelin ................................................................................................................ 25
Figure 37 Phospholipids in the Cell Membrane......................................................................................................... 25
Figure 38 Archaeal Phospholipid vs. Eukaryotic and Bacterial Phospholipid ..................................................... 26
Figure 39 Cerebroside ................................................................................................................................................... 26
Figure 40 Steroid Carbon Skeleton ............................................................................................................................. 27
Figure 41 Cholesterol ..................................................................................................................................................... 27
Figure 42 Soap Chemical Structure ............................................................................................................................. 28
Figure 43 Saponification................................................................................................................................................ 28
Figure 44 Soap Micelle .................................................................................................................................................. 28
Figure 45 Component of Beeswax .............................................................................................................................. 29
Figure 46 Eicosanoids ..................................................................................................................................................... 30
Figure 47 Natural Rubber and Gutta-percha ........................................................................................................... 31
Figure 48 Production of Cholesterol from Squalene ................................................................................................ 31
Figure 49 Major Types of Lipoproteins ...................................................................................................................... 32
Figure 50 Amino Acid Structure .................................................................................................................................... 34
Figure 51 Isoelectric Point .............................................................................................................................................. 35
Figure 52 Zwitterion........................................................................................................................................................ 35
Figure 53 pKa Values of Amino Acids ......................................................................................................................... 36
Figure 54 D-alanine and L-alanine.............................................................................................................................. 37
Figure 55 Reaction Mechanism of Alanine Racemase (from Bacillus stearothermophilus) ................................ 37
Figure 56 Peptide Bond ................................................................................................................................................. 38
Figure 57 Peptide Bond Resonance Structure............................................................................................................ 38
Figure 58 Resonance of Glycine .................................................................................................................................. 39
Figure 59 Steric Hindrance of Cis Configured Peptide Bond ................................................................................ 39
Figure 60 Nonstandard Amino Acids........................................................................................................................... 42
Figure 61 Production of Aspartic Acid by Transamination ..................................................................................... 43
Figure 62 Chaperonin Action ........................................................................................................................................ 43
Figure 63 Primary Structure of a Protein ................................................................................................................... 44
Figure 64 α-helix Structure............................................................................................................................................ 45
Figure 65 Formation of a Coiled Coil ......................................................................................................................... 45
Figure 66 β-pleated Sheet Structure ......................................................................................................................... 46
Figure 67 Parallel β-pleated Sheets ........................................................................................................................... 47
Figure 68 Antiparallel β-pleated Sheets .................................................................................................................... 47
Figure 69 Tertiary Structure .......................................................................................................................................... 48
Figure 70 Protein Models .............................................................................................................................................. 49
Figure 71 Activation Energy of Exergonic Reaction ................................................................................................. 52
Figure 72 Orders of Reactions and Effects on Rate Law ........................................................................................ 53
Figure 73 Michaelis-Menten Plot Graph..................................................................................................................... 54
Figure 74 Lineweaver-Burk Plot Graph ...................................................................................................................... 54
iv | P a g e
Biochemistry – Nature17
Figure 75 Competitive and Noncompetitive Inhibition ............................................................................................. 55
Figure 76 Michaelis-Menten Plot (with chemical inhibitors) ..................................................................................... 56
Figure 77 Lineweaver-Burk Plot (with chemical inhibitors) ...................................................................................... 56
Figure 78 Paper Chromatography .............................................................................................................................. 57
Figure 79 Ninhydrin Reacting with an Amino Acid ................................................................................................... 58
Figure 80 An Allosteric Motor Protein "Walking" ..................................................................................................... 59
Figure 81 Porphyrin ........................................................................................................................................................ 60
Figure 82 Chlorophyll ..................................................................................................................................................... 61
Figure 83 Heme Group .................................................................................................................................................. 61
Figure 84 Hemoglobin .................................................................................................................................................... 62
Figure 85 Myoglobin ...................................................................................................................................................... 62
Figure 86 Partial Pressure of O2 vs. Hemoglobin Percent Saturation .................................................................. 62
Figure 87 Alpha and Beta Carotene........................................................................................................................... 63
Figure 88 Anthocyanin.................................................................................................................................................... 65
Figure 89 Thin-layer Chromatography ....................................................................................................................... 65
Figure 90 Structure of Different Forms of Cobalamin ............................................................................................. 67
Figure 91 Vitamin B6 ....................................................................................................................................................... 68
Figure 92 Thiamine's Involvement with Citric Cycle .................................................................................................. 68
Figure 93 Biotin Attached to Lysine Residue .............................................................................................................. 68
Figure 94 Vitamin K's Role in Blood Clotting ............................................................................................................. 70
Figure 95 Vitamins .......................................................................................................................................................... 71
Figure 96 Gene to Protein ............................................................................................................................................. 73
Figure 97 Deoxyribose and Ribose ............................................................................................................................. 74
Figure 98 The Pyrimidines ............................................................................................................................................. 74
Figure 99 The Purines ..................................................................................................................................................... 75
Figure 100 Nucleotide.................................................................................................................................................... 75
Figure 101 Nucleotide Connectivity ............................................................................................................................ 76
Figure 102 Addition of Nucleoside Triphosphates ................................................................................................... 77
Figure 103 Phosphate Ionization State in a Ribonucleotide ................................................................................... 77
Figure 104 DNA Double Helix ...................................................................................................................................... 78
Figure 105 Antiparallelism in DNA .............................................................................................................................. 79
Figure 106 RNA Double Stranded Structures ............................................................................................................ 79
Figure 107 A, B, and Z DNA ......................................................................................................................................... 80
Figure 108 Triplex DNA Base Pairing ........................................................................................................................ 81
Figure 109 ATP Serves as Short-term Energy Carriers in the Cell ........................................................................ 82
Figure 110 Formation of Carbamoyl Phosphate ...................................................................................................... 82
Figure 111 Formation of Carbamoyl Aspartate ....................................................................................................... 83
Figure 112 Forming the Ring in the Pyrimidine Nitrogenous Base ........................................................................ 83
Figure 113 Formation of UMP ...................................................................................................................................... 84
Figure 114 Forming TMP and CTP ............................................................................................................................... 85
Figure 115 Formation of IMP ........................................................................................................................................ 86
Figure 116 Converting IMP to AMP............................................................................................................................. 87
Figure 117 Converting IMP to GMP ............................................................................................................................ 87
Figure 118 Hypoxanthine and Inosinate .................................................................................................................... 88
Figure 119 Semi-conservative Model of Replication ............................................................................................... 89
Figure 120 Bioaccumulation of DDT ............................................................................................................................ 90
Figure 121 Chemical Structure of DDT........................................................................................................................ 91
Figure 122 BOBCalix6 Forming a Supermolecule with Radioactive Cesium Ion ................................................ 91
v|Page
Biochemistry – Nature17
Objectives
I.
II.
III.
IV.
V.
VI.
VII.
VIII.
IX.
X.
XI.
XII.
XIII.
XIV.
XV.
XVI.
XVII.
XVIII.
XIX.
XX.
XXI.
XXII.
XXIII.
XXIV.
XXV.
XXVI.
XXVII.
XXVIII.
XXIX.
XXX.
XXXI.
XXXII.
XXXIII.
XXXIV.
XXXV.
XXXVI.
XXXVII.
XXXVIII.
XXXIX.
XL.
XLI.
XLII.
XLIII.
XLIV.
XLV.
XLVI.
Compare polysaccharides, disaccharides, and monosaccharides
Describe monomers and polymers.
Define ketose and aldose.
Compare α-glucose and β-glucose.
Define anomers and epimers.
Explain what makes alpha glucose less stable than beta-glucose.
Compare the Fischer Projection, Haworth projection and chair conformation.
Compare furanoses and pyranoses.
Describe the epimerization and enediol rearrangement reactions monosaccharides can undergo.
Understand the reactions where monosaccharides are converted to either their ester or ether
derivatives.
Describe the formation of glycosides.
Explain how monosaccharide chains can be lengthened and shortened.
Describe why are all monosaccharides are reducing sugars.
Describe how glycosidic links form.
Sugars can be differentiated from one another based on whether they are diastereomers or
enantiomers of each other.
Explain the purposes of the polysaccharides starch, cellulose and chitin.
Define what characteristics make a glycosaminoglycan.
Define what proteoglycans.
Describe lipids.
Distinguish between simple and complex lipids.
Describe how to identify the amount of energy and unsaturated level of lipids.
Describe fats and their structure.
Distinguish between saturated fatty acids, trans fats and cis fats.
Describe rancidity.
Define phospholipids and compare them to fats.
Compare micelles and liposomes.
Describe the differences between the cell membrane of Archaea and Eukaryotes.
Describe glycolipids.
Describe steroids.
Explain how steroids can be used as performance-enhancing drugs.
Explain how soaps and detergents formation.
Describe emulsion.
Define waxes.
Compare the eicosanoids.
Distinguish between terpenes and terpenoids.
Describe the important of lipoproteins in lipid transport.
Describe the chemical properties of amino acids.
Explain how D-amino acids and L-amino acids can be interconverted by bacteria.
Explain peptide bonds.
List the standard amino acids and their chemical properties.
Identify the ketogenic and glucogenic amino acids.
Define essential amino acids and complete proteins.
Define nonstandard amino acids.
Describe the process of synthesizing amino acids.
List the functions of proteins.
Compare fibrous proteins with globular proteins.
vi | P a g e
Biochemistry – Nature17
XLVII.
XLVIII.
XLIX.
L.
LI.
LII.
LIII.
LIV.
LV.
LVI.
LVII.
LVIII.
LIX.
LX.
LXI.
LXII.
LXIII.
LXIV.
LXV.
LXVI.
LXVII.
LXVIII.
LXIX.
LXX.
LXXI.
LXXII.
LXXIII.
LXXIV.
LXXV.
LXXVI.
LXXVII.
LXXVIII.
LXXIX.
LXXX.
LXXXI.
LXXXII.
LXXXIII.
LXXXIV.
Compare primary, secondary, tertiary, and quaternary structures.
Explain the different protein models.
Define prions.
Distinguish between types of enzymes.
Describe the kinetics and thermodynamic qualities of enzymes.
Identify how to calculate the maximum rate of a reaction with an enzyme by using the MichaelisMenten equation or Lineweaver-Burk equation.
Distinguish between competitive and non-competitive inhibitors.
Identify the type of inhibitor affecting an enzyme through Michaelis-Menten or Lineweaver-Burk
equation.
Describe how proteins can be analyzed through chromatography and electrophoresis.
Summarize protein assays.
Define motor proteins.
Define proteomes.
Discuss the significance of biological pigments.
Compare porphyrins, carotenoids, and anthocyanins.
Explain the importance of chlorophyll.
Compare and discuss the functions of myoglobin and hemoglobin.
Describe the process of analyzing pigments through thin-layer chromatography.
Describe vitamins.
Distinguish between water-soluble and lipid-soluble vitamins.
Describe the functions and structure of each of the vitamins.
Compare the different B-complex vitamins.
Describe malnutrition and health effects caused by lack of proper vitamins supply.
Describe the function and structure of nucleotides.
Compare pyrimidines and purines.
Explain the process of forming a nucleic acid bond.
Describe complementary base pairing.
Compare DNA and RNA.
Compare A, B, and Z DNA.
Explain triplex DNA.
Explain the structure and importance of ATP.
Describe the process of nucleotide synthesis through the de novo pathway and the salvage
pathway.
Summarize transcription, translation, and DNA replication.
Summarize the benefits and concerns surrounding GM food.
Define xenobiotics.
Explain what pharmaceutically active compounds are.
Explain the process of biomagnification.
Describe the effects of DDT.
Describe the responses to xenobiotics using bioremediation, host-guest chemistry, and utilizing
biodegradable substances.
vii | P a g e
Biochemistry – Nature17
Carbohydrates
Outline
I.
II.
III.
Monosaccharides
A. Monosaccharides are monomers of polysaccharides.
i. They can be differentiated as ketoses and aldoses based on whether they contain an
aldehyde or ketone.
B. Important monosaccharides include glucose, galactose, ribose, and fructose.
C. Monosaccharides can be epimers to each other.
i. α-glucose and β-glucose differ at carbon 1.
a. α-glucose is less stable than β-glucose due to steric hindrance.
D. Monosaccharides can be expressed in their linear form using the Fischer projection.
i. This distinguishes between L and D sugars.
E. Monosaccharides and be expressed in their cyclic forms using the chair conformation or the
Haworth projection.
i. Shows α and β variants.
F. Monosaccharides can undergo epimerization and enediol rearrangement.
G. All monosaccharides can act as reducing agents, making them reducing sugars.
i. Can be detected using Fehling’s solution and Benedict’s solution.
Disaccharides
A. Disaccharides form from monosaccharides making glycosidic links between each other.
i. Maltose and cellobiose are formed from a 1-4 linkage between glucoses.
B. Glucose and fructose make sucrose.
C. Lactose is the result of glucose and galactose.
D. Disaccharides can be differentiated by chirality.
i. Some can be diastereomers of each other and some can be enantiomers.
Polysaccharides
A. Polysaccharides are polymers made up of monosaccharides.
B. Starch is essential for energy storage.
i. Amylose lacks branching
ii. Amylopectin contains some branching.
iii. Glycogen contains a lot of branching.
C. Cellulose is a polysaccharide of beta-glucose and is used for structure.
i. Forms straight, non-branching structures.
ii. Hydrogen bonds increase the structural capabilities of cellulose.
D. Chitin is another polysaccharide essential for the exoskeleton of insects and cell wall of some
fungi.
E. Glycosaminoglycans are polysaccharides made up of repeating disaccharides containing an
amine group and a negatively charged group.
i. One important example is heparin sulfate, serving as an anticoagulant.
ii. When connected to a protein, they become proteoglycans.
a. One proteoglycan that acts as a lubricant joint and absorb impact shocks is
aggrecan.
Monosaccharides
•
Carbohydrates are monosaccharides, and any polymer made up of monosaccharides, like
disaccharides and polysaccharides
o Monomers are structural and repeating units that form a larger molecule: polymers.
1|Page
Biochemistry – Nature17
▪
o
An example of a monomer and polymer is glucose and maltose. Starch is a polymer
made up of the repeating units: glucose (a monomer).
• Glucose (an important compound for metabolic processes) is also involved with
the production of ethanol (which is used in biofuels).
o Glucose is converted to ethanol through a process known as alcoholic
fermentation. Every mole of glucose produces 2 moles of ethanol and
2 moles of carbon dioxide.
Monosaccharides are sugars; molecules that typically has an empirical formula of CH2O
▪
1 and a
Some characteristics of sugars is that they have a carbonyl group
2
hydroxyl group (R-OH)
• Depending on where the carbonyl group and hydroxyl group determines what
type of sugar it is: a ketose or an aldose.
o A ketose is a ketone sugar (where the carbonyl group is internal) and
an aldose is an aldehyde sugar (where the carbonyl group is on a
terminal carbon)
o This is what differentiates a glucose and galactose (who has a
carbonyl group in their linear form on carbon 1) from fructose (who
has a carbonyl group in their linear form on carbon 2)3
Figure 1 Linear Form of Fructose
•
•
Another way to define sugars is by the number of carbons.
o Having 3 carbons (C3H6O3) makes a triose, 4 (C4H8O4) makes a
tetrose, 5 (C5H10O5) makes a pentose, and 6 (C6H12O6) makes a
hexose.
Often, sugars only differ by the stereochemistry of carbon atom.
o These sugars are epimers of each other. Glucose and galactose for
example are C4 epimers (differing only at carbon 4).
The value ‘R’ stands for any other group, a variable group.
The carbonyl group can only be seen when the sugar is in its linear form but not in the ring form.
3 When labelling carbons in their linear form, you go top to bottom (or left to right if drawn that way). In ring form, you
label it going clockwise starting with the left and topmost carbon in the ring.
1
2
2|Page
Biochemistry – Nature17
▪
The most common and important monosaccharide is glucose (C6H12O6), which is a
hexose and an aldose sugar.
• Sugars can also be differentiated by spatial arrangement of asymmetric
carbons, which is what differentiates glucose from galactose
i
Figure 2 Glucose vs. Galactose
•
•
Galactose and glucose differ on carbon 4, with glucose and galactose having
their hydrogen and hydroxyl group inverted from one another.
Another important monosaccharide is ribose, which is one of the 3 major components that makes up a
nucleotide.
o Ribose is a pentose aldose (the ketose equivalent to ribose is known as ribulose).
Types of Glucose
•
Glucose appears in two forms that differ at carbon 1 (in ring form)
o α glucose (alpha glucose) is a glucose represented by having a hydrogen pointing upwards in
carbon 1, and the hydroxyl group pointing down.
▪ Alpha glucose has the IUPAC name of (2S,3R,4S,5S,6R)-6-(hydroxymethyl)oxane2,3,4,5-tetrol.
o β glucose (beta glucose) is a glucose represented by having a hydrogen pointing downwards in
carbon 1, and the hydroxyl group pointing up.
▪ The IUPAC name of beta glucose is (2R,3R,4S,5S,6R)-6-(hydroxymethyl)oxane-2,3,4,5tetrol
o The two are isomers to one another
3|Page
Biochemistry – Nature17
ii
Figure 3 Alpha Glucose vs. Beta Glucose
•
The reason they are drawn differently is due to chirality.
o Carbon 1 and carbon 2 in alpha glucose travel in the same direction
iii
Figure 4 Chirality of Alpha Glucose
▪
o
Look back to figure 1-3. Note how the hydroxyl groups pointing upwards are
represented as wedges (by convention), and the hydroxyl groups pointing downwards
are represented by dashed lines.
Carbon 1 and Carbon 2 in beta glucose travel opposite directions from one another (allowing
for structural uses)
iii
Figure 5 Chirality of Beta Glucose
•
Alpha and beta glucose are types of epimers known as anomers.
o Anomers are epimers that differ at the hemiacetal carbon in the ring configuration.
▪ In the case of glucose, it is at carbon 1.
▪ In the case of anomers, the hemiacetal carbon is known as the anomeric carbon.
4|Page
Biochemistry – Nature17
Figure 6 Hemiacetal Carbon
•
•
Despite the two looking very similar, they are vastly different compounds.
o Alpha glucose is typically used to store energy/glucose, while beta glucose is typically for
structural uses.
o Alpha-D-glucose has a melting point of 146°C, while beta-D-glucose has a melting point of
150°C.
When glucose is in aqueous solution, the two variations will form an equilibrium mixing between the two,
with the open chain being an intermediate.
o To isolate one anomer, the glucose must be crystallized. Crystallization above 98°C produces a
pure sample of the beta anomer, while crystallization below 98°C produces a pure sample of
the alpha anomer.
iv
Figure 7 Equilibrium Mixture of D-glucose in Aqueous Solution
•
When glucose is alternating between the beta anomer and the alpha anomer (with the open chain
conformation as an unstable intermediate), we find that 66% of the glucose molecules are beta
anomers, while 33% are alpha.
o This is because in the alpha glucose, the OH group of carbon 1 is closer in space to the OH
group of carbon 2.
▪ This is due to the OH group of carbon 1 in the alpha glucose having a axial bond,
which is less favorable for larger groups than equatorial bonds.4
▪ This causes electrostatic repulsion of these two negatively charged groups creates steric
hindrance between each other, increasing the energy of the glucose.
▪ This is also why beta-glucose is more structurally stable, and used as a monomer of
structural compounds, while alpha glucose, being high in energy, is used for energy
purposes.
Note: Equatorial bonds are nearly parallel to the plane of the ring while axial bonds are nearly perpendicular to the
plane of the ring.
4
5|Page
Biochemistry – Nature17
v
Figure 8 Axial and Equatorial Bonds in Glucose
Shape of Carbohydrates
•
Monosaccharides can be in both the ring form and the linear form; however, the chemical equilibrium in
solution between the two typically greatly favors the ring form.
o The linear form is drawn using the Fischer Projection
▪ In the Fischer Projection, atoms bonded horizontally are supposed to pointed to the
viewer while the atoms bonded vertically are pointed away.
Mnemonic: You can remember atoms bonded Horizontally are coming forward as the molecule is
trying to Hug you.
o
The Fischer Projection can be used to determine the type of sugar, and whether it is a D sugar
or an L sugar.
▪ When looking at the last chiral center (reading top to bottom), if the OH group is
drawn on the right side, it’s a D Sugar. If the OH is drawn on the left side, it’s an L
sugar.
• This carbon atom is typically the last atom before the terminal one.
▪ D sugars are more commonly found in nature.
vi
Figure 9 Fischer Projection of L and D sugars
6|Page
Biochemistry – Nature17
Mnemonic: You can remember L sugars have pointing Left because the L in L sugar indicates the
direction.
•
When in ring form, the sugar is either drawn using the Haworth projection or the chair conformation.
o The Haworth projection draws the sugar in the normal (pent/hex/hept/oct)agonal shape, with
the bottom of the ring (the part closest to the reader) being bold.
▪ This is due to the perspective of drawing, as the Haworth projection shows the sugar
coming 3D (out of place).
▪ The Haworth projection is the most commonly used form to show sugars.
o The chair conformation shows the actual shape of the sugar.
▪ In nature, glucose (for example) is not a perfect hexagon, but instead, a distorted
hexagon
Table 1 Projections of Glucose
α-D-glucose
β-D-glucose
Fischer Projection
Haworth Projection
Chair Conformation
7|Page
Biochemistry – Nature17
Things to note from Table 1
•
The Fischer projection (and in general, the linear form of a sugar) does not determine whether the sugar
is alpha or beta. The sugar being alpha or beta is determined by the way carbon number one and the
OH group on carbon 5 bind to each other.
• The chair conformation looks the same for both alpha and beta carbon; however, carbon #1 has the
OH group pointed down in the alpha glucose, and up for the beta glucose. This is similar to the Haworth
Projection (and is also due to chirality).
vii
Figure 10 Converting from Fischer to Haworth Projection
•
Cyclic forms of carbohydrates are called furanoses (5-membered rings) and pyranoses (6-membered
rings).5
Figure 11 Furan and Pyran
Monosaccharide Reactions
•
•
While sugars most commonly exist in their cyclic form, they are in equilibrium with their open-chain
forms when in solution.
o While in their open chain form, the sugar can do the usual reactions involving
ketones/aldehydes6 and alcohols.
o One issue with sugar chemistry is the fact that it can lead to many unwanted side reactions.
There are two main base-catalyzed reactions with sugars: epimerization and enediol rearrangement.
o Epimerization is the chemical conversion of one epimer to another.
▪ For example, D-glucose undergoing epimerization at C2 can form D-mannose with
enolate as an intermediate.
▪ D-glucose can also undergo epimerization at C4 and become D-galactose
5
Note: One of the “members” of the ring is oxygen, while the rest is carbon.
6
Depending if the sugar is a ketose or an aldose.
8|Page
Biochemistry – Nature17
viii
Figure 12 Epimerization with D-glucose and D-mannose
o
Enediol rearrangement in base catalyst is the shifting of C=O.
▪ Acidic or neutral solutions of the sugar can preserve the identity of the sugar.
▪ One type of enediol rearrangement is known as Lobry de Bruyn-van Ekenstein
transformation.
• This is a transformation reaction where an aldose transforms into a ketose or a
ketose into an aldose.
▪ A typical intermediate of enediol rearrangement is enediol.
ix
Figure 13 Enediol Rearrangement: D-glucose into D-fructose
•
Sugars can also be made into an acid.
o Nitric acid can also oxidize aldehydes and alcohols into carboxylic acids.
▪ When reacting with glucose it forms glucaric acid.
9|Page
Biochemistry – Nature17
Figure 14 Oxidizing Glucose to Glucaric Acid using Nitric Acid
•
•
Monosaccharides are highly soluble in water and generally insoluble in most organic solvents.
o However, the ester derivatives of monosaccharides are often soluble in most organic solvents.
▪ Converting to their ester derivatives can be done by treating the monosaccharides with
excess acid chloride or acid anhydride in the presence of a base.7
Monosaccharides can also be converted into ether derivatives by the Williamson ether synthesis, which
generally involves treating an alcohol (like the ones on the monosaccharides) with a strong base.
o This forms a alkoxide ion which is treated with an alkyl halide.
x
Figure 15 Formation of Ester and Ether Derivatives of Monosaccharides
xi
Figure 16 Reaction Mechanism for Williamson Ether Synthesis
•
Monosaccharides are cyclic hemiacetals.8
o When converted into acetal products through the addition of alcohol under acid-catalyzed
conditions, the product produced is called glycosides.
▪ When naming glycosides, you name it by placing the alkyl group as a prefix and use
‘-oside’ as a suffix.
When dealing with monosaccharides, a strong base should not be used.
Remember: Hemiacetal carbons are carbons connected to two other carbons, an alcohol and an oxygen which is
connected to an ‘R’ group. Acetal carbons are carbons connected to two carbons and two oxygens with their R groups.
7
8
10 | P a g e
Biochemistry – Nature17
o
During glycoside formation, the process begins with the anomeric hydroxyl accepting a
hydrogen from an acid
▪ After the anomeric hydroxyl becomes water, it is released, leaving a resonancestabled carbocation.
▪ The carbocation Is then attacked by an alcohol, before ending with the loss of a
proton.
▪ Depending on the plane of attack by the alcohol, a beta or alpha anomer can be
formed.
xii
Figure 17 Glycoside Formation from D-Glucopyranose
•
9
Monosaccharides can also experience chain lengthening and chain degradation.
o The Kiliani-Fischer synthesis is a common mechanism for lengthening monosaccharide chains.
▪ This means that, for example, an aldopentose can form into an aldohexose.
▪ The monosaccharide begins as its acyclic form.
• This allows there to be a free aldehyde, which is attacked by a protonated
cyanide.
• The cyanide acts as an acid, protonating onto the oxygen which gains a
positive charge.9
▪ Cyanide will then attack the carbon either from the top side or bottom side, producing
two stereoisomers.
▪ The next step is hydrogenation, which is catalyzed by palladium.
• Palladium will bind to the C≡N group through van der Waals forces.
▪ Afterwards, hydronium attacks the NH group, which forms NH2+.
• This positive charge is delocalized with the carbon through resonance.
▪ Water then attacks the carbon attached to the nitrogen group.
• The water, once attached to the carbon, will then protonate.
o Water will do this either with a base or with the NH2 group, that is in
close proximity to it.
The positive charge is delocalized by resonance with the charge travelling between oxygen and the carbon.
11 | P a g e
Biochemistry – Nature17
•
▪
▪
Oxygen will then form a pi bond with the carbon10, with NH3 (a good leaving
group), leaving.
The final step involves ammonia or water deprotonating the hydrogen found on the
oxygen of the carbonyl.
This process produces two products that are isomers of each other.
xiii
Figure 18 Kiliani-Fischer Synthesis
o
10
Wohl degradation involves the removal of a carbon atom from an aldose.
▪ The aldehyde group is first converted to a cyanohydrin followed by loss of HCN in
presence of base.
• This is done through oxime formation followed by dehydration.
▪ The carbohydrate when treated with base, loses HCN.
▪ Note: Unlike Kiliani-Fischer synthesis, only one product is produced.
Note: This carbon was not found in the original monosaccharide but is instead from the cyanide.
12 | P a g e
Biochemistry – Nature17
xiv
Figure 19 Formation of D-Arabinose from D-Glucose through Wohl Degradation
Detecting Reducing Sugars
•
•
•
Glucose is known as a reducing sugar as its terminal carbonyl group is readily oxidized (making them
reducing agents).
o All monosaccharides as well as some disaccharides and some polysaccharides are reducing
sugars.
Reducing sugars can be detected with Fehling’s solution.
o Fehling’s solution is prepared from copper(II), sulfate, sodium, potassium tartrate, and sodium
hydroxide
o Caused a shift in color from blue to red as a precipitate of copper(I) oxide is formed
Reducing sugars can also be detected with Benedict’s reagent
o Mixture of aqueous copper(II) sulfate, sodium citrate, and sodium carbonate.
Disaccharides
•
•
•
•
Disaccharides are the combination of two monosaccharides joined together by a glycosidic link
o A glycosidic link is a covalent bond between monosaccharides, formed via a dehydration
synthesis (a reaction that forms a bond between two molecules and produces a water molecule)
▪ Another name for dehydration synthesis is condensation reaction.
One of the most common disaccharide is the combination of glucose and fructose, known as sucrose.
o Table sugar is an example of sucrose
o Plants, when transporting carbohydrates, usually transport carbohydrates in the form of sucrose
o Sucrose cannot further polymerize
The glycosidic link is between the hydroxyl group in carbon 1, and the hydroxyl group in carbon 4. This
linkage is known as 1-4 linkage.
o This is an important linkage for forming glucose disaccharides.
Maltose is the combination of two alpha-glucose units
o Maltose is an important ingredient for brewing beer
o Formed by 1-4 bonds known as α—1,4’ glycosidic linkage.
13 | P a g e
Biochemistry – Nature17
Figure 20 Glycosidic Link in Maltose
•
•
Cellobiose is a more structural disaccharide and is made up of two beta-glucose units.
o Formed by a β-1,4’ glycosidic linkage.
Lactose, the sugar present in milk, is the disaccharide of glucose and galactose.
o Linked by a 1-4 linkage.
Erythro and Threo Sugars
•
One way chemists differentiate between sugars, like disaccharides, is by chirality.
o If the asymmetric disaccharides are diastereomers of each other, they are either erythro or
threo.
▪ Diastereomers is a stereoisomer compound where some, but not all, of the stereocenters
are mirror images of each-other.
• Enantiomers on the other hand, have all of their stereocenters mirror images of
each other.
xv
Figure 21 Diastereomers and Enantiomers
•
•
Erythro diastereomer sugars are those with the similar groups being on the same side of each other (as
seen in the Fisher projection).
o Derived from cis alkene
Threo diastereomer sugars are sugars with the similar groups on the opposite sides of each other (as
seen in Fisher projection).
o Derived from trans alkene.
14 | P a g e
Biochemistry – Nature17
•
If the compounds are symmetric at their terminal ends, the terms erythro and threo are replaced with
meso and (d,l) respectively.11
xvi
Figure 22 Erythro and Threo Compounds
Polysaccharides
•
Polysaccharides are macromolecules that are polymers of multiple (can be up to the hundreds if not the
thousands) monosaccharides.
o One important polysaccharide is starch, which is a storage polysaccharide made up of maltose.
▪ Photosynthesis in plants produces glucose. In order to store the glucose (which is used
for cellular respiration), the glucose units are joined via α 1-4 linkages to other
glucoses to form starch
▪ Plants store starch in the form as granules, within cellular structures in one of two forms
• Amylose – Simplest form of starch that does not have any branching
• Amylopectin – Complex form of starch that experiences branching12.
xvii
Figure 23 Amylose and Amylopectin
11
12
Sometimes (±) rather than (d,l).
Branching occurs with 1-6 linkages
15 | P a g e
Biochemistry – Nature17
▪
o
When a glucose needs to be withdrawn, hydrolysis is used to release an individual
glucose
Animals store glucose as glycogen, a polysaccharide similar to amylopectin but, has a lot more
branching
▪ Glycogen is mostly stored in liver and muscle cells of the body
xviii
Figure 24 Glycogen
Structural Polysaccharides
•
Cellulose is another polysaccharide of glucose; however, it is a polysaccharide of beta glucose and
used for structural purposes.
o Made of cellobiose.
o While starch is typically helical and can branch off, cellulose is straight and never branched.
▪ This causes enzymes that can hydrolyze α 1-4 linkages but not be able to hydrolyze β
1-4 linkages. In most organisms, like humans, cellulose travels through the digestive
system, and is eliminated with feces
• Only certain organisms (like the microbes that live in the digestive systems of
cows and termites) can digest cellulose
o Hydroxyl groups of each beta glucose are freely able to hydrogen bond with other hydroxyl
groups.
▪ Allows cellulose to be tougher.
▪ This allows cellulose chains to link with other chains to form microfibril
xix
Figure 25 Hydrogen Bonding in Cellulose
•
Another structural polysaccharide is chitin, a polysaccharide made up of monomers known as 2(acetylamino)-2-deoxy-D-glucose, a derivative of glucose.
16 | P a g e
Biochemistry – Nature17
o
o
Chitin makes up the exoskeleton of many arthropods and the cell wall of many fungi
▪ Pure chitin is leathery but it becomes hardened when calcium carbonate is added.
While technically known as an amino sugar, it actually contains an amide and not an amine.
xx
Figure 26 Chitin Monomer
Glycosaminoglycans and Proteoglycans
•
Glycosaminoglycans are a special type of polysaccharide that consists of repeating disaccharides units
which contain an amino group and some sort of negatively charged group.
o One example is heparin sulfate, which acts as an anticoagulant, being released from mast cells.
▪ Heparin sulfate contains two carboxylate groups and two sulfate groups in the
disaccharide unit (one of the sulfate groups is attached to the amino group).
o Other examples include chondroitin-6-sulfate, keratan sulfate, dermatan sulfate, and
hyaluronate.
xxi
Figure 27 Glycosaminoglycan Examples
17 | P a g e
Biochemistry – Nature17
•
Proteoglycans are structures that consists of a protein that are attached to glycosaminoglycan(s).
o Typically, 95% of the proteoglycan (by mass) is made up by the glycosaminoglycan.
o Proteoglycans have four important functions: acting as joint lubricants, acts as a structural
component of tissue (ex: connective), to bind cells to extracellular matrix, and to regulate the
movement of molecules through the extracellular matrix.
o One well-studied proteoglycan is aggrecan, which is a proteoglycan found in the extracellular
matrix of connective tissue.
▪ Aggrecan acts as a lubricant joint and serves to absorb impact shocks.
▪ Aggrecan has three protein domains: G1, G2, and G3. Between G2 and G3, there is
a long sequence of amino acids, with the glycosaminoglycans keratan sulfate and
chondroitin sulfate attached to them.
• G1 protein domain is attached to a hyaluronate backbone.
▪ The glycosaminoglycan groups being negatively charged have water attracted to
them.
• This is due to water being polar, having a partially positive charge on the
hydrogen ions.
• When a force is applied to the aggrecan, the water molecules that are noncovalently attached to the aggrecan leave, and the aggrecan becomes slightly
deformed (absorbing some of the force).
o Once the force is released, the water is then attracted back to
aggrecan, bringing aggrecan back to its original shape.
xxii
Figure 28 Aggrecan Impact Shock Absorption
Lipids
Outline
I.
Lipids are a class of biomolecules that are hydrophobic.
A. Can be classed as complex lipids (can be hydrolyzed into simpler units) and simple lipids (not
easily hydrolyzed into simpler units).
18 | P a g e
Biochemistry – Nature17
II.
III.
IV.
V.
VI.
VII.
VIII.
IX.
X.
B. Serves as long-term energy storage.
i. Energy of a lipid can be determined using bomb calorimetry
C. The unsaturation level of a lipid can be determined through the iodine number.
Fats are lipids containing a glycerol and a fatty acid.
A. Fatty acids are long hydrocarbon chains.
B. Glycerol can hold three fatty acids (making it a triglyceride)
C. Saturated fatty acids contain no carbon-carbon double bonds
D. Unsaturated fatty acids contain one or more double bonds.
i. Trans fats have a trans alkene (hydrogens are opposite of each other in space)
ii. Cis fats have a cis alkene (hydrogens are next to each other in space)
a. Contains a kink.
E. Fats can become rancid due to the hydrolysis of the fatty acid chains.
Phospholipids are a glycerol attached to a phosphate group and two fatty acids.
A. Have a polar and non-polar region.
i. Causes phospholipids to form liposomes and micelles in aqueous solution.
B. Forms cell membranes
Glycolipids are sugar-containing lipids.
Steroids are simple lipids with a tetracyclic skeleton.
A. Cholesterol is an important one found in the cell membranes of animals.
i. Also serves as a precursor for other steroids.
B. Often used as performance enhancing drugs by athletes to enhance strength and endurance.
Soaps and detergents are amphiphilic fats which can act as surfactants.
A. Formed through saponification where glycerides are hydrolyzed by heating it with NaOH.
B. Can form micelles with grease and other hydrophobic materials in the center.
i. Emulsion
Waxes are esters of long-chain fatty acids.
Eicosanoids are simple lipids derived from arachadonic acid.
A. Leukotrienes are formed from the action of lipoxygenase
i. Serve as cell-to-cell communication and mediate immune and inflammatory response.
B. Prostaglandins and thromboxane are formed from the action of cyclooxygenase.
i. Thromboxane serves as an important molecule involved with blood clotting.
ii. Prostaglandins are involved with the sensation of pain at the site of pain
a. Aspirin provides pain relief by blocking the action of cyclooxygenase.
Terpenes are a large class of biomolecules that have 5n carbon units (isoprene rule).
A. These units are known as isoprene units
B. Natural rubber is an example of a terpene
C. Terpenoids, like cholesterol, are derivatives of terpenes.
i. Do not follow the isoprene rule
Lipoproteins are lipid-protein complexes.
A. Used to transport fats around the body.
i. Chylomicrons carry gats to the liver, skeletal muscles and adipose tissue.
ii. LDLs carry fats around the entire body within the bloodstream
iii. HDLs collect fats from cells and return it to the liver.
Lipids
•
Lipids are a class of biomolecules that have little-to-no affinity for water but are soluble in organic
solvents like chloroform
o This is a broad group of biomolecules that does not consist of polymers. They are defined by
their properties (instead of their chemical structure).
19 | P a g e
Biochemistry – Nature17
▪
•
There are two main types: complex lipids which are easily hydrolyzed into simpler
constituents, and simple lipids which are lipids not easily hydrolyzed by aqueous base
or acid.
• Two main groups of complex lipids: waxes and glycerides.
o Serve as long-term energy storage, signal molecules, and to make up membranes
▪ While lipids are easier to store and store more energy (per gram) than carbohydrates,
they are harder to access (cannot be easily digested).
• Excessive consumption of lipids (typically known as fats and oils) has been
linked to heart disease, obesity, and diabetes.
o Fat and oil should only provide 30-40% of a human’s daily energy
intake.
▪ Animal fat stores are known as adipose tissue or blubber.
The energy of a lipid can be determined via a tool known as bomb calorimeter.
o The bomb calorimeter works by igniting a reaction in the bomb chamber (also known as bomb
cell). In this case, a lipid will be burned. The released thermal energy will be absorbed by the
surrounding water.
▪ The energy change is measured at a constant volume.
xxiii
Figure 29 Bomb Calorimeter
•
The number of double bonds per unit mass of a lipid substance can be determined through the iodine
number.
o The iodine number is determined by finding the max number of iodine that 100 grams of lipid
substance consumes.
o This reaction occurs due to the alkenes being halogenated.
20 | P a g e
Biochemistry – Nature17
xxiv
Figure 30 Halogenation of Alkenes in Lipids
Fats
•
•
A fat is a molecule that consists of a glycerol and a fatty acid
o Fatty acids are long chains of carbons that consist, at one end, a carboxylic acid group,
followed by a long non-polar hydrocarbon chain.
o Due to water, not being able to hydrogen bond to fatty acids, it makes it hydrophobic
In order to attach a glycerol to a fatty acid, a dehydration synthesis needs to occur, resulting in an ester
linkage between glycerol and fatty acid
o Since glycerol has three hydroxyl groups, it can form three ester linkages with fatty acids
▪ The resultant is known as a triacylglycerol or simply triglyceride
Figure 31 Fatty Acids and Triglycerides
•
Based on the hydrocarbon chain, the chain can have different structures
o A saturated fatty acid contains NO carbon-carbon double bonds in the hydrocarbon chain (like
the C16:0 and C18:0 fatty acids in Figure 25)
▪ An example of a saturated fatty acid is stearic acid.
21 | P a g e
Biochemistry – Nature17
▪ Due to this, they are often packed together and are usually solid at room temperature
An unsaturated fatty acid has one or more double bonds.
▪ Tends to have a lower melting point than saturated fats
▪ An elaidic acid is a fatty acid with a carbon-carbon double bond with the resulting
hydrogens being opposite to one another (contains trans alkene)
• Because of this, this fatty acid would not be bent.
• This fatty acid is rare in nature and has been linked to heart disease
▪ An oleic acid has a cis double bond (where the hydrogens are on the same side of
each other). This forms a kink in the molecule
• Contains a cis alkene
• This means, the oleic acids are not as tightly packed together. This causes them
to be liquid at room temperature.
o Due to this, many companies will make saturated fats through
hydrogenation of lipids.
▪ However, partial hydrogenation can occur, breaking only
some of the C=C. The remaining double bonds with then shift
from cis to trans geometry
Animals tend to store triglycerides as fats (solid) while plants tend to store triglycerides as oils (liquid)
o
•
xxv
Figure 32 Oleic Acid, Elaidic Acid, Stearic Acid
Rancidity of Triglycerides
•
Triglycerides can be hydrolyzed by strong acids and strong bases.
o Hydrolysis by strong acids produces the original alcohol and fatty acid
o Hydrolysis by strong bases produces the original alcohol and the salt of the fatty acid
o A triglyceride can develop a bad smell and taste (rancidity) due to the hydrolysis of the short
fatty acid chains.
22 | P a g e
Biochemistry – Nature17
▪
•
Accelerated in high levels of moisture, acidic conditions, hot conditions, and the
presence of certain enzymes known as lipase
Oxidative rancidity (rancidity caused by oxidation) is caused by the reaction of C=C bonds with free
radicals of oxygen.
o Produce aldehydes and ketones
o Accelerated by the presence of oxygen and sunlight
Phospholipids
•
Phospholipids are similar to triglycerides, however, instead of three fatty acids, phospholipids have two,
with the third hydroxyl group being joined to a phosphate group.13
o One type of phospholipid has a group known as choline attached to the phosphate.
o The phosphate heads of phospholipids are hydrophilic, unlike the hydrocarbon tails which are
hydrophobic.
o When put in water, phospholipids will form a bilayer, with the hydrophobic heads pointing
outwards and the hydrophobic tails collecting inwards
▪ This is what makes up the cellular membrane.
Figure 33 Phospholipid (Phosphatidylcholine)
•
13
If the phospholipids are vigorously mixed with water, a liposome can form, which is a spherical structure
made up of phospholipids (with an aqueous interior and exterior)
o The cell is an example of a complex liposome.
Note: There are some phospholipids that do not have a glycerol, but they typically do.
23 | P a g e
Biochemistry – Nature17
xxvi
Figure 34 Liposome
•
Phospholipids can also form a micelle (which do not have an aqueous interior), however, micelle
formation from phospholipids are not as common as the formation of a liposome
Figure 35 Micelle
•
There is a lot of different phospholipids, each differing in the fatty acid chains and the groups attached
to the phosphate group.
o Phospholipids can have a glycerol attached between the phosphate and fatty acids (as
described above), or a sphingosine (making a sphingolipid also known as a sphingomyelin)
▪ In sphingomyelin, the amino group of sphingosine links (via an amide bond) to a fatty
acid. The primary alcohol is esterified to a phosphoryl choline.
▪ Sphingomyelins are membrane lipids that make up a major component of the myelin
sheath surrounding nerve fibers.
24 | P a g e
Biochemistry – Nature17
xxvii
Figure 36 Sphingosine and Sphingomyelin
•
The cell membrane is made up of a composition of phospholipids including sphingomyelin,
phosphatidylcholine, phosphatidylserine, phosphatidylinositol, as well as other biomolecules, such as
proteins and cholesterol.
xxviii
Figure 37 Phospholipids in the Cell Membrane
Phospholipids in Archaeal Membranes
•
The kingdom of organisms known as Archaea have different membrane lipids that differ from that of
bacteria and eukaryotes.
o Most of these differences are due to the hostile environments the organisms live in. Their
modified membranes allow for them to live at high temperatures, high concentrations of salt,
and low pH.
▪ This allows the Archaea to resist oxidation and hydrolysis
o One major difference between Archaeal phospholipids and other organisms is that their tails
bind to the glycerol backbone using ether linkages (instead of ester linkages)
o Another major difference is that Archaeal phospholipids have branched alkyl chains and not
just linear chains.
o Finally, Archaeal phospholipids are of L configuration, unlike that of bacteria and eukaryotes
which are of D configuration.
25 | P a g e
Biochemistry – Nature17
xxix
Figure 38 Archaeal Phospholipid vs. Eukaryotic and Bacterial Phospholipid
Glycolipids
•
Glycolipids are sugar containing lipids.
o In animals, they are made of sphingosine (similar to sphingomyelin). Unlike sphingomyelin
though, glycolipids have a sugar unit (instead of a phosphate group and choline).
o The simplest glycolipid is known as cerebroside, which is a fatty acid unit, sphingosine, and a
single sugar unit (either glucose or galactose).
xxx
Figure 39 Cerebroside
•
Glycolipids can serve as membrane lipids like phospholipids
o The sugar monomer(s) are always on the extracellular side of the membrane.
Steroids
•
Steroids are simple lipids consisting of a steroidal backbone (also known as a tetracyclic skeleton),
made of three fused six-member rings and one five-member ring. They are one of the two major
classes of nonsaponifiable lipids (along with terpenes).
o They also contain various R groups attached to the rings which vary in functionality and
structure
o The 17-carbon skeleton is counted 1-17 (and does not follow IUPAC rules), with four rings (A, B,
C, and D).
26 | P a g e
Biochemistry – Nature17
▪
▪
The most common locations for functional group substituents (other than methyl and
hydrogen) is at carbon 3, 4, 7, 11, 12, and 17.
Ring A can is often an aromatic group
xxxi
Figure 40 Steroid Carbon Skeleton
•
•
Steroids can be natural (like testosterone and progesterone) or it can be synthetic (like norethindrone).
Cholesterol is an important steroid, found on animal cell membranes14, and serves as a precursor for
other steroids.
o Makes up almost 25% of the membrane lipids in certain nerve cells
o In membranes, cholesterol is oriented parallel to the fatty acid chains of the phospholipids.
▪ The hydroxyl group of cholesterol is able interacts with the nearby phospholipid heads.
xxxii
Figure 41 Cholesterol
•
Performance enhancing drugs are steroids used by athletes to enhance strength and endurance.
o Performance enhancing drug use is banned in most organized sports
Soaps and Detergents
•
•
14
Carboxylic acids made up of alkyl chains exhibit both hydrophilic characteristics (CO2) and
hydrophobic characteristics (alkyl chain) in the same molecule
o These molecules are considered amphiphilic
o Fatty acids with alkyl chains that are made up of 10 or more carbons, are nearly insoluble in
water. The alkyl chains will spread evenly over the water surface (while the carboxylic acid
forms hydrogen bonds with the water).
▪ These can then form a monomolecular layer, and change the surface properties.
▪ Substances that accumulate at water surfaces, changing the surface properties are
known as surfactants.
Alkali metal salts of fatty acids are strong surfactants.
o A common example of these are soaps and detergents, each consisting of a nonpolar
hydrocarbon tail and a polar head group.
Cholesterol is completely absent from the membranes of prokaryotes.
27 | P a g e
Biochemistry – Nature17
xxxiii
Figure 42 Soap Chemical Structure
▪
The formation of soaps is done through a process known as saponification, where
glycerides are hydrolyzed by heating it with sodium hydroxide.
• Fatty acids separate from the triglyceride and fuse with the hydroxide ions.
xxxiv
Figure 43 Saponification
•
Soap’s use as a cleaning material is due to its ability to do two things: decreasing the surface tension of
water, and it binds to various materials like bacteria, dirt, and oils.
o The hydrophobic tails of the soap binds to the oils and phospholipids in the bacteria, with the
hydrophilic heads of soap following the water.
▪ This is done by the formation of micelles around the oil molecules.
▪ The negative charge around the exterior of micelles prevent other micelles from
bunching together.
o This process of forming a stable mixture between two or more liquids that normally cannot be
mixed (oils and water) is known as emulsion
xxxv
Figure 44 Soap Micelle
28 | P a g e
Biochemistry – Nature17
Wax
•
•
Waxes are esters of long-chain fatty acids with long-chain alcohols.
o Complex lipids
o Serve a multitude of purposes, such as regulating buoyancy of the sperm whale, to preventing
excess loss of water by evaporation in many desert plants.
Beeswaxes, for example, is a mixture of waxes, alcohols, and hydrocarbons used to form the
honeycomb for bees.
xxxvi
Figure 45 Component of Beeswax
Prostaglandins, Thromboxanes, and Leukotrienes
•
•
•
These biomolecules are all derived from one fatty acid known as arachadonic acid.
o Because of this, they are known as eicosanoids.
o Simple lipids
Leukotrienes are formed from arachadonic acid through the action of the enzyme lipoxygenase.
o Leukotrienes are used to convey information from cell-to-cell, or within a cell to mediate immune
and inflammatory responses
o Leukotrienes are also involved with allergic and asthmatic reactions.
▪ Leukotriene receptor antagonists have been used to treat asthma.
Prostaglandins and thromboxane are formed from the catalytic enzymes known as cyclooxygenases
o Thromboxane is an important molecule involved with blood clotting.
▪ The production of thromboxane is done to set off a cascade of reactions that will allow
clotting to work
o Prostaglandins are involved with the sensation of pain, and are released at the site of pain.
▪ Aspirin and other non-steroidal anti-inflammation drugs (NSAIDs) blocks the synthesis of
prostaglandins by stopping the activity of cyclooxygenase, and is used for pain relief.
• However, since cyclooxygenase is involved with thromboxane production,
aspirin has the side effect of preventing clotting and preventing heart disease.
29 | P a g e
Biochemistry – Nature17
xxxvii
Figure 46 Eicosanoids
Terpenes and Terpenoids
•
Terpenes are large diverse class of biomolecules made up of isopentane (also known as isoprene). They
are one of the two major classes of nonsaponifiable lipids (along with steroids).
o Simple lipids.
o Most terpenes are produced by plants but some of the more complex ones are produced by
animals
o Terpenes thus follow the empirical feature known as the isoprene rule with terpenes having 5n
carbon atoms. Each terpene is divided into its isopentane units.
Table 2 Isoprene Rule
•
•
Classification
Isopentane Units
Number of Carbon Atoms
Monoterpenes
2
C10
Sesquiterpenes
3
C15
Diterpenes
4
Sesterterpenes
5
C20
C25
Triterpenes
6
C30
Many terpene compounds are highly volatile and many monoterpenes are responsible for specific
odors and flavors in plants
o Examples: Menthol from mint and limonene from lemons
Natural rubber is an example of a terpene. Natural rubber is typically soft elastic; however, its isomer
gutta-percha produces a more rigid and tough substance.
30 | P a g e
Biochemistry – Nature17
xxxviii
Figure 47 Natural Rubber and Gutta-percha
•
Terpenoids are a broad group of compounds that is a derivative of terpenes but not contain the
isoprene units.
o Cholesterol is an example of a terpenoid, as it was derived from the terpene known as
squalene.
xxxix
Figure 48 Production of Cholesterol from Squalene
Lipoproteins
•
Due to lipids being insoluble in water, lipids form complexes with proteins known as lipoproteins, in
order to be transported in the blood. Different types of lipoproteins carry different amounts of fats.
o Chylomicrons carry fats to the liver, skeletal muscles, and adipose tissue.
▪ They are produced in the intestine
o Low density lipoproteins (LDLs) carry fats around to the entire body within the bloodstream
▪ Diets rich in saturated fats or trans fats raise the cholesterol levels in the blood due to
their being a raised amount of LDLs
o High density lipoproteins (HDLs) collects fats from cells and returns it to the liver.
▪ Diets rich in cis unsaturated fats or trans fats lower the cholesterol levels in the blood
due to their being a raised amount of HDLs
31 | P a g e
Biochemistry – Nature17
xl
Figure 49 Major Types of Lipoproteins
Proteins
Outline
I.
II.
III.
Amino acids are monomers of polypeptides.
A. Proteins are made up of polypeptides
Amino acids are carbon atoms bonded to a hydrogen, amine group, carboxylic acid group and an R
group
A. The R group is what differentiates between different amino acids.
B. Contains L and D forms
i. L isomer is more common
ii. Racemases can aid interconverting between the two
C. Amphiprotic and amphoteric
D. Electrically neutral at the isoelectric point.
i. At the isoelectric point, amino acids are zwitterions.
E. Polyprotic acids
F. Can act as pH buffers.
G. Standard Amino acids: 20 amino acids are the most common ones, and are added to growing
polypeptides through translation
i. Of those, 10 are essential (humans can’t synthesize them).
ii. There are non-standard amino acids found in many proteins.
H. Polypeptides form when amino acids form peptide bonds.
i. Polypeptide chain has a C-terminus and a N-terminus.
I. Has double bond character due to resonance
J. Synthesized through the reductive amination of α-ketoglutaric acid.
Proteins are essential for transport, communication, sensor, movement, immune defense, chaperonin
behavior and acting as catalysts.
A. Globular proteins are protein tool used to drive reactions of metabolism.
i. Soluble in water
B. Fibrous proteins are structural proteins.
32 | P a g e
Biochemistry – Nature17
IV.
V.
VI.
VII.
VIII.
IX.
i. Insoluble in water
Proteins are an accumulation of different structures
A. Primary structure is the polypeptide sequence
B. Secondary structure is the folding of the primary structure
i. Can be helical, forming an α helix.
a. Elastic and flexible
b. Can wrap around another α helix to form a coiled coil.
c. Direction of rotation is known as screw sense
ii. Beta pleated sheets are side-by-side polypeptide chains with cross-linking caused by
hydrogen bonds.
a. Can run parallel and anti-parallel
C. Tertiary structures are the polypeptide chain twisting.
i. Lots of noncovalent interactions
a. Hydrophobic interactions
b. Hydrogen bonding
c. Ionic bonding
d. Disulfide bridges
a. Formed by two cysteine units linked, forming a cystine.
e. Hydrophilic interactions
D. Quaternary structures are the interactions of multiple polypeptide chains
i. Can form a conjugated protein when a prosthetic group is added.
Proteins can be modeled using the backbone model, ribbon model, wire model, and space-filling model.
A. Backbone model is used for overall organization.
B. Ribbon model is to show organization and shows secondary structures.
C. Wire model shows side chain interactions and determining amino acid sequence.
D. Space-filling model provides protein shape.
Proteins can misfold becoming infectious agents known as prions.
A. Example: Mad Cow Disease
Enzymes are biological (protein catalysts)
A. Highly specific to a specific substrate
B. Globular proteins
C. Induced fit model and lock and key model
i. Describes the enzyme’s active site and the interactions with the substrate.
D. Might need to be activated by a cofactor.
Enzymes are put into 6 classes
A. Oxidoreductases: Involved with redox reactions.
B. Transferases: Transfer of a functional group from molecule to another.
C. Hydrolases: Enzymes involved with hydrolysis
D. Lyases: Enzymes involved with removing atoms or breaking bonds in order to form a new
double bond or ring structure
E. Isomerase: Involved with transferring a chemical group intramolecularly.
F. Ligase: Separating substrates at the expense of ATP hydrolysis
The amount of energy that can used in a reaction is known as Gibbs free energy.
A. If negative: Spontaneous and exergonic reaction.
B. If positive: Nonspontaneous and endergonic reaction.
C. If zero: Reaction is at equilibrium
D. Can be calculated using the following reaction:
E. Activation energy is the minimum amount of energy that must be supplied to get a reaction
start.
33 | P a g e
Biochemistry – Nature17
X.
XI.
XII.
XIII.
XIV.
i. Catalysts, like enzymes, lower this.
The rate of a reaction can be described as how quickly reactants are consumed or how fast products
are produced.
A. Controlled by frequency of collisions, temperature, activation energy, and concentration of
reactants.
i. Zeroth order reactions are reactions where the rate is independent of the reactant’s
concentration.
ii. First order reactions are reactions where the reaction’s rate is directly proportional to
the concentration of the reaction.
iii. Second order reactions are where the rate is proportional to the square of the
reactant’s concentration.
B. Michaelis-Menten Equation: Calculates the saturation effect in respect to substrate concentration
i. Depends on max velocity of a reaction and Km.
C. Enzymes work at an optimum temperature and optimum pH.
i. Can be deactivated and denatured.
D. Chemical inhibitors can decrease catalytic activity
i. Competitive inhibitors and allosteric inhibitors are reversible
ii. Non-competitive inhibitors are not reversible
Proteins can be analyzed by chromatography and electrophoresis
A. Paper chromatography involves a solvent traveling up a piece of paper, separating amino
acids
i. Ninhydrin reacts with amino acids to produce a color.
B. Electrophoresis separates amino acids (and mixtures) by the movement of charged particles in
an electric field.
Protein assays are procedures used to measure protein concentration of a sample
A. UV-vis is a protein assay seeing how proteins interact with UV light and visible light
Motor proteins are proteins that generate forces that allow movement of a cell or a certain
biomolecule.
A. Done by conformational changes to a protein.
Proteomes are the totality of proteins expressed within a cell, tissue, or organism.
Amino Acids
•
•
Proteins are made up of a group of biomolecules known as polypeptides.
o Polypeptides are made up of the monomers known as amino acids.
Amino acids consist of a central carbon, which is bonded to a hydrogen, an amine group (NH2), an acid
group (COOH), and an ‘R’ group
o The R group is known as the variable group, as it is different between the different types of
amino acids.
▪ Within a polypeptide, this ‘R’ group is known as a side chain.
o There are about 20 different naturally occurring amino acids, each given a three-letter
abbreviation
Figure 50 Amino Acid Structure
34 | P a g e
Biochemistry – Nature17
•
•
•
Similar to carbohydrates, amino acids can be found in both L and D forms.
o However, unlike carbohydrates, living organisms use L isomers more than D.
Amino acids are crystalline compounds with a high melting point (above 200°C).
Amino acids can move in an electric field, which suggests amino acids contain charged groups, which are
a result of internal acid-base behavior.
o Amphiprotic (can donate and accept hydrogen ions) and amphoteric (able to act as Lewis base
and Lewis acid)
▪ Amino acids are less acidic than most carboxylic acids but less basic than most amines.
o Charge comes from the transfer of a proton from the acid group to the basic amine group in
the same acid. (Brønsted-Lowry behavior)
▪ Acids preferred at high pH
▪ Base preferred at low pH
o The isoelectric point is the pH where the amino acid is electrically neutral (not able to move in
an electric field)
xli
Figure 51 Isoelectric Point
•
In aqueous solution and crystalline form, amino acids have positive and negative charges within the
molecule, making them zwitterions.
o Also known as dipolar ion.
o This makes most amino acids have a neutral charge, as the negative charge of the COO
cancels out with the positive charge of the NH3.
xlii
Figure 52 Zwitterion
•
Amino acids are weak polyprotic acids.
o Of the common amino acids, all but 5 have 2 pKa values.
35 | P a g e
Biochemistry – Nature17
▪
▪
pKa1 is associated with the alpha-carboxyl group, pKa2 is associated with the alphaammonium ion.
• pKa1 is around 2 for all amino acids, and around 9 for pKa2.
Aspartic acid, glutamic acid, lysine, arginine, and histidine have a pKa3, which is caused
by the side chain group.
• The R group is what makes these amino acids have a positive or negative
charge.
o Aspartic acid and glutamic acid are deprotonated (lost a proton) at
the physiological pH, making them have an overall negative charge.
o Histidine, lysine, and arginine are protonated (gained a proton) at the
physiological pH, making them have an overall positive charge.
xliii
Figure 53 pKa Values of Amino Acids
•
•
Amino acids can act as pH buffers.
o This means, that by reacting with both H+ ions and OH- ions, they can make the pH more
resistant to change.
o Helps keep a constant pH in cells which allows the different cell organelles and enzymes to
work properly.
o If the blood pH is between 7.0 and 7.35, a person can experience acidosis, and if the blood
pH is between 7.45 and 7.8, a person can experience alkalosis
▪ A blood pH above 7.8 or below 7.0 will result in death in humans
Except for glycine, all the standard amino acids have chirality.
o The standard amino acids are the 20 α-amino acids found in nearly every naturally occurring
protein.15
o Due to this chirality, there are two types of amino acids: L-amino acids and D-amino acids.
▪ L-amino acids are amino acids with S chirality, and are the most common in nature.
Note: Not all proteins have all 20 standard amino acids, but most naturally occurring proteins have a majority of the 20
standard amino acids
15
36 | P a g e
Biochemistry – Nature17
▪
D-amino acids are amino acids with R chirality, and are rarely found in nature.
xliv
Figure 54 D-alanine and L-alanine
•
Bacteria can interconvert between the D and L amino acids by using specific
enzymes known as racemases.
o Because mammals lack racemases and cannot interconvert between D
and L amino acids, compounds that block racemases are a potential
source for future antibiotics.
xlv
Figure 55 Reaction Mechanism of Alanine Racemase (from Bacillus stearothermophilus)
•
Amino acids can form a substituted amide link between the carboxylic acid of one amino acid, and the
amine from the other.
o This bond is known as a peptide bond and results from a condensation reaction
o 2 amino acids are known as a dipeptide.
▪ 3 amino acids make a tripeptide, 12-20 makes an oligopeptide, and 21+ make a
polypeptide.
o When amino acids link, they can form different peptides based on the order.
▪ Example: Val-Asn-Cys ≠ Asn-Cys-Val
o Amino acids linked together makes a polypeptide (which forms a protein)
▪ The polypeptide chain has two ends, the amino end (known as the N-terminus) and a
carboxyl end (known as the C-terminus)
37 | P a g e
Biochemistry – Nature17
▪
Proteins are usually made up of at least 50 amino acids (1.1 x 1065 variations of
proteins).
xlvi
Figure 56 Peptide Bond
•
One thing to note about the peptide bonds is that they are stabilized by resonance.
o That means the peptide bond in between two amino acids flip between single and double
bond.
▪ This is done by the electrons of nitrogen forming a π bond, kicking out the electrons in
the pi bond in the carbonyl.
o Because of this, peptide bonds are technically not single bonds, but instead have double bond
character.
▪ This makes the bond length between the carbon and nitrogen of the peptide bond
longer than a typical single bond but shorter than a typical double bond.
▪ This also makes the peptide bond planar and prevents any rotation of the peptide
bond.
xlvii
Figure 57 Peptide Bond Resonance Structure
▪
The carboxyl group in an individual amino acid can also have double bond character
IF the carboxyl group is already protonated.
• This is because, if the carboxyl group is COOH instead of COO-, resonance
(movement of electrons by their own action) does not occur but instead, the
proton will move causing the electrons to move. This is a case of structural
isomerization (movement of atoms) and not resonance.
38 | P a g e
Biochemistry – Nature17
Figure 58 Resonance of Glycine
o
Note that when a polypeptide is drawn, it typically is drawn with trans configuration instead of
cis configuration.
▪ This is because the trans configuration is more stable and thermodynamically favored
over the cis configuration (which is high in energy).
• This is because there is no steric hindrance between atoms in trans configuration
due to the atoms being pointed away from each other. But in cis configuration,
the atoms will be pointed to each other, causing electrostatic repulsion.
xlviii
Figure 59 Steric Hindrance of Cis Configured Peptide Bond
•
Amino acids are also important for production of glucose and ketone bodies.
o Many amino acids are said to be glucogenic meaning they can be converted to glucose through
gluconeogenesis.
▪ This process occurs in the liver when starvation is a risk.
o Amino acids can also be ketogenic meaning they can be converted to ketone bodies.
39 | P a g e
Biochemistry – Nature17
Table 3 The Standard Amino Acids
Amino Acid
3-Letter
Symbol
1-Letter
Symbol
Alanine
Ala
Arginine
Structural Formula
pH of
isoelectric
point
Side
Chain
Polarity16
Side
Chain
Charge
(at pH
7.2)17
Ketogenic
or
Glucogenic
A
6.0
Nonpolar
Neutral
Gluco
Arg
R
10.8
Polar
Positive
Gluco
Asparagine
Asn
N
5.4
Polar
Neutral
Gluco
Aspartic Acid
Asp
D
2.8
Polar
Negative
Gluco
Cysteine
Cys
C
5.1
Nonpolar
Neutral
Gluco
Glutamic Acid
Glu
E
3.2
Polar
Negative
Gluco
Glutamine
Gln
Q
5.7
Polar
Neutral
Gluco
Glycine
Gly
G
6.0
Nonpolar
Neutral
Gluco
Histidine
His
H
7.6
Polar
Positive
Gluco
Isoleucine
Ile
I
6.0
Nonpolar
Neutral
Both
Leucine
Leu
L
6.0
Nonpolar
Neutral
Keto
Lysine
Lys
K
9.7
Polar
Positive
Keto
Methionine
Met
M
5.7
Nonpolar
Neutral
Gluco
16
17
Remember: Polar side chains are hydrophilic and nonpolar side chains are hydrophobic
A typical cell’s pH is about 7.2
40 | P a g e
Biochemistry – Nature17
Table 4 The Standard Amino Acids cont.
Amino Acid
3-Letter
Symbol
1-Letter
Symbol
Phenylalanine
Phe
Proline
Structural Formula
pH of
isoelectric
point
Side
Chain
Polarity18
Side
Chain
Charge
(at pH
7.2)19
Ketogenic
or
Glucogenic
F
5.5
Nonpolar
Neutral
Both
Pro
P
6.3
Nonpolar
Neutral
Gluco
Serine
Ser
S
5.7
Polar
Neutral
Gluco
Threonine
Thr
T
5.6
Polar
Neutral
Both
Tryptophan
Trp
W
5.9
Nonpolar
Neutral
Both
Tyrosine
Tyr
Y
5.7
Polar
Neutral
Both
Valine
Val
V
6.0
Nonpolar
Neutral
Gluco
•
•
•
18
19
Not all the standard amino acids can be synthesized by the human body.
o Ten amino acids are known as essential amino acids, and can only be obtained from the diet.
▪ The ten essential amino acids are arginine, histidine, isoleucine, leucine, lysine,
methionine, phenylalanine, threonine, tryptophan, and valine.
• Proteins that provide all of the essential amino acids for humans are known as
complete proteins. Examples include proteins found in fish, meat, and eggs.
While the 20 standard amino acids make up most of the proteins seen in the natural world, there are
many uncommon amino acids.
o For example: hydroxylysine and hydroxyproline are found in collagen.
o Carboxyglutamate is involved in blood-clotting proteins.
o Many phosphorylated amino acids are used for signaling.
Some of these uncommon amino acids are just isomers of standard amino acids.
o D-serine for example is found in earthworms, and D-glutamic acid is found in the cell walls of
many bacteria.
Remember: Polar side chains are hydrophilic and nonpolar side chains are hydrophobic
A typical cell’s pH is about 7.2
41 | P a g e
Biochemistry – Nature17
Figure 60 Nonstandard Amino Acids
Mnemonic: A way to remember the non-polar standard amino acids (based on their 1-character symbol) is to
use the following phrase: “Would ya’ Give Friendly Vampires Intimate Love After Marriage”
Synthesis of Amino Acids
•
•
While many amino acids can be obtained from hydrolyzing proteins, it is often less expensive to
synthesize the amino acids if possible.
One way to produce amino acids is through a process known as reductive amination.
o It begins with an a α-ketoacid which forms an imine when treated to excess ammonia.
▪ The imine is then reduced by H2 into an α-amino acid.
o Note: reductive amination is a biomimetic synthesis, and does not occur fully in nature.
▪ The biosynthesis of amino acids begins with something similar to ketoacid, αketoglutaric acid, which is treated with excess ammonium, followed by NADH acting as
the reducing agent.
• This produces glutamic acid, and through the process known as transamination,
the amino group can be transferred to a different compound to produce a
different amino acid.
42 | P a g e
Biochemistry – Nature17
▪
Unlike reductive amination, which produces a racemic mixture of D and L amino acids,
biosynthesis produces a pure mixture of L amino acids.
xlix
Figure 61 Production of Aspartic Acid by Transamination
Protein Function
•
Proteins are polymers of one or more polypeptides put together
o They are synthesized at a ribosome
o There are 10 main functions for proteins: structure, amino acid storage, transport,
communication, acting as a receptor, acting as a sensor, movement, defense, acting as a
catalyst, and chaperonins
▪ Chaperonins are protein chambers used to sequester other proteins during folding.
l
Figure 62 Chaperonin Action
•
There are two main types of proteins: fibrous proteins and globular proteins
o Fibrous proteins are structural proteins responsible for structure, support, and movement.
▪ Insoluble in water
▪ Less sensitive to changes in pH and temperature
▪ Typically made up of a repetitive amino acid sequence
o Globular proteins are protein tools that drive the reactions of metabolism
▪ Usually soluble in water
▪ More sensitive to changes in pH and temperature
▪ Made up of irregular amino acid sequence
Protein Structure
•
The primary structure of a protein is the unique sequence of amino acids in its polypeptide chain
o Different amino acid sequences will fold into different configurations due to the chemical
properties of the variable side chains.
43 | P a g e
Biochemistry – Nature17
o
o
o
o
The amino acid sequence is a determinant of the protein’s final structure.
▪ Each amino acid in a polypeptide chain is known as residues.
▪ The polypeptide chain consists of residue units that makes up the backbone.
• Follows a pattern of atoms: nitrogen, carbon, carbon, nitrogen, carbon, carbon,
etc.
Under normal conditions, primary structures have polarity due to the N terminus having a
positive charge and the C terminus having a negative charge.
The nitrogen in a residue is electronegative, and will take some electron density from the
hydrogen.
▪ This gives the hydrogen a partially positive charge, making a N-H group of the
polypeptide backbone a hydrogen-bond donor.
The oxygen in a residue’s carbonyl group (C=O) is more electronegative than the carbon it’s
bonded to, so it takes some electron density from the carbon.
▪ This makes the oxygen develop a negative charge, making a carbonyl group of the
polypeptide backbone a hydrogen-bond acceptor.
li
Figure 63 Primary Structure of a Protein
•
The secondary structure refers to the folding of primary structures. The folding is usually caused by
hydrogen bonds
o The alpha helix or α helix is a coiled configuration of the primary structure, with hydrogen
bonds forming between every fourth amino acid.
▪ Elastic and flexible. Hydrogen bonds can easily break and re-form if the coil is
stretched or compressed.
• Hydrogen bonds link C=O of one peptide to the N-H of another.
▪ Example: Keratin
▪ An alpha helix is generated when a single polypeptide chain twists around itself.
• The polypeptide backbone is usually hydrophilic. The backbone is protected
against the lipid environment of the cell membrane from the nonpolar side
chains of most of the amino acids
▪ Proline and glycine are helix breakers, and can only appear in an alpha helix at the
turns.
• This makes them the least likely amino acids to appear in the helix overall (with
proline being less likely to appear than glycine).
44 | P a g e
Biochemistry – Nature17
lii
Figure 64 α-helix Structure
▪
In some proteins, the alpha helices can form more stable structures by wrapping around
another alpha helix, forming a structure known as a coiled-coil.
• Forms when the two alpha helices have their nonpolar side chains on one side,
causing the two to twist around one-another with the side chains facing
inwards.
liii
Figure 65 Formation of a Coiled Coil
45 | P a g e
Biochemistry – Nature17
▪
o
Alpha helices direction in relation to the direction it rotates is known as the screw sense.
• Left-handed helices rotate counterclockwise, while right-handed helices rotate
clockwise.
o Right-handed helices are more common because the side chains
experience less steric hindrance.
The beta-pleated sheets or β-pleated sheets is a structure with side-by-side polypeptides. They
are cross linked by inter-chain hydrogen bonds
▪ Flexible but inelastic
▪ Example: Fibroin
liv
Figure 66 β-pleated Sheet Structure
▪
There are two types of beta-pleated sheets and they are determined by the
orientation of the polypeptide chains.
• Parallel β sheets have polypeptide chains that run the same direction, while
antiparallel β sheets fold back and forth upon itself, with each section of the
chain running in the opposite direction of itself.
46 | P a g e
Biochemistry – Nature17
lv
Figure 67 Parallel β-pleated Sheets
lvi
Figure 68 Antiparallel β-pleated Sheets
•
Tertiary structures involve the polypeptide chain twisting, resulting in R group interactions known as side
chains.
o Conformation is the resulting structure, a 3D compact protein with the most stable arrangement
of the protein. Stabilized by four interactions.
▪ Hydrophobic interactions (London dispersion forces and induced dipoles) between nonpolar side chains.
• Hydrophobic interactions is the most essential interactions for a tertiary
structure.
• Nonpolar side chains will aggregate together towards the center in aqueous
solution, with residues containing hydrophilic side chains being towards the
outside (surface) of a protein.
o This is due to this structure being thermodynamically favored.
• Once aggregated together, the inner core of hydrophobic amino acids can
interact with one-another via instantaneous dipole moments.
o While relatively weak, these van der Waal interactions can create a
binding effect.
▪ Hydrogen bonding between polar side chains
▪ Ionic bonding between side chains that carry a charge.
• The amino acid residues must contain side chains that are opposite in charge.
o Example: Arginine and aspartic acid.
▪ Disulfide bridge found between two cysteines (sulfur-containing amino acid).
• Forms between two cysteine molecules near each other after an oxidation
reaction occurs.
47 | P a g e
Biochemistry – Nature17
o
o
• These cross-linked units are known as cystines.20
Hydrophilic side is towards the exterior of the protein and all hydrophobic interactions are
interior to the protein.
Presence of metal ions, temperature changes, and pH changes can cause denaturation
lvii
Figure 69 Tertiary Structure
•
Quaternary structures contain multiple interacting polypeptide chains.
o Most proteins do not have a quaternary structure.
o Unlike the other structures (which only rely on intramolecular forces), quaternary structures
involve intermolecular forces.
o Can contain a non-protein (like iron in hemoglobin), known as a prosthetic group, which makes a
conjugated protein.
o Globular and fibrous proteins are two main classes of protein quaternary structure.
o The simplest quaternary structure is known as a dimer which is made up of two polypeptide
chains.
Protein Models
•
•
•
•
•
20
There are four different models for depicting a protein.
o These models are most ideal for smaller proteins.
The backbone model shows the overall organization of the polypeptide.
o Clean and easy to understand way to see the structure and compare it to other structures
The ribbon model is similar to the backbone model; however, the ribbon model shows the secondary
structures of proteins like alpha helices and beta sheets
The wire model contains the polypeptide chain and the side chains.
o Useful way for determining the amino acids involved in a protein and the protein’s activity.
o Shows relative proximity of side chains to one another
The space-filling model provides the shape of the protein.
Do not confuse this with the spelling of “cysteine” which are the amino acids that form the cross-linked units.
48 | P a g e
Biochemistry – Nature17
o
Also shows the amino acids exterior to the protein, allowing scientists to know the possible
function of the protein.
lviii
Figure 70 Protein Models
Protein Misfolding
•
•
•
Protein folding is essential in the fact it is a protein’s 3-dimensional shape.
o Determined by the polypeptide chain(s) involved in the folding.
o The 3D shape of the protein determines the protein’s function.
Due to how intricate the process is, there are bound to be errors to occur.
o If a protein folds incorrectly, it can (rarely) form an infectious agent known as prions.
Prions are normal proteins that become infectious agents caused by protein misfolding.
o Examples of prion diseases include mad cow disease and CJD in humans.
o Insoluble.
▪ No way the cell in the body can take in the prion and denature the protein.
o Can cause other normal proteins to be misfolded.
Enzymes
•
Enzymes are biological (protein) catalysts that control all biochemical reactions in and around a cell.
o Globular Proteins
o Highly specific for each reaction, and thus can be individually controlled.
▪ Specificity does vary between enzymes. For example, take the two proteolytic
enzymes known as subtilisin and trypsin.
49 | P a g e
Biochemistry – Nature17
•
•
Subtilisin can act as an enzyme aiding in the cleavage of any peptide bond,
regardless of the amino acids.
• Trypsin on the other hand, can only catalyze the splitting of peptide bonds on
the carboxyl side of lysine and arginine residues.
o Enzymes increase the rate of a reaction without undergoing any chemical change
▪ Lowers activation energy
o Substrate: Reactant of the reaction that the enzyme catalyzes.
▪ Enzyme-substrate Complex: When an enzyme (temporarily) binds to the substrate
• The place where this occurs (on the enzyme) is known as the active site.
• Substrates are bound by multiple weak attractions.
▪ Note: Not all substrates will fit with a specific enzyme. Enzymes are highly specific (can
differentiate between isomers).
• Can target simple things like a specific peptide bond between amino acid.
• This is known as enzyme-substrate specificity
o When the substrate enters the active site of an enzyme, stress is put on the molecule which
lowers the activation energy, making it easier to break bonds.
▪ Induced-fit model of enzyme action
▪ The other model for enzyme action is lock and key model where the substrate fits
perfectly into the active site of the enzyme.
Sometimes the catalytic ability of enzymes depends on the presence of molecules known as cofactors.
o The precise role of the cofactor varies between enzymes.
▪ If the cofactor is organic, its known as a coenzyme. If its inorganic, it’s probably a
metal ion.
o The enzyme without its cofactor is known as an apoenzyme, while a catalytically active enzyme
is known as a holoenzyme.
Types of Enzymes
•
•
In 1964, the International Union of Biochemistry developed a nomenclature for enzymes.
There are 6 major classes of enzymes, each give their own enzyme commission (EC) numbers.
o Oxidoreductases are enzymes involved with redox reactions.
▪ EC Number: 1
o Transferases are enzymes involved with the transfer of a specific functional group from one
molecule (donor) to another (acceptor).
▪ EC Number: 2
o Hydrolases are enzymes involved with hydrolysis reactions.
▪ EC Number: 3
o Lyases are enzymes involved with the breaking of chemical bonds and removal of a group of
atoms (other than hydrolysis and oxidation reactions), forming a new double bond or ring
structure.
▪ Includes aldolases and decarboxylases.
▪ EC Number: 4
o Isomerases are enzymes involved with isomerization.
▪ Isomerization is the transfer of a chemical group intramolecularly.
▪ EC Number: 5
o Ligases are enzymes involved with the ligation of two substrates at the expense of the
hydrolysis of ATP.
▪ Includes synthetase.
▪ EC Number: 6
50 | P a g e
Biochemistry – Nature17
•
Every enzyme-catalyzed reaction has their own EC number.
o So, if two enzymes are involved in the same reaction, they have the same EC number.
▪ Even non-homologous isofunctional enzymes (NISE) have the same EC number.
• NISE are a group of enzymes that are unrelated to each other but catalyze the
same chemical reaction, evolving in different organisms through convergent
evolution. NISE are examples of analogous reactions.
o Format: Starts with EC, followed by four numbers separated by periods, with each number
showing the progressively finer classification of the enzyme.
▪ Example: Tripeptide aminopeptidase has the code: “EC 3.4.11.4”
Gibbs Free Energy and Activation Energy
•
•
•
Gibbs free energy (ΔG) is the amount of the energy that can be used in a reaction.
In the reaction reactants ⇌ products, if the reaction has yet to reach equilibrium, it can have a positive
or negative value of ΔG.
o ΔG can be calculated by subtracting the free energy of products minus free energy of
reactants.
▪ If ΔG is negative (products have less free energy than reactants), then the reaction is
exergonic and spontaneous.
• This means energy is released from the reaction.
▪ If ΔG is positive (reactants have less free energy than products), then the reaction is
endergonic and non-spontaneous.
• That means an energy input is required for the reaction to take place.
▪ ΔG = ΔG° + 2.303RT × log Q
• ΔG° is the difference in free energy between products and reactants in their
standard state.
• R is the gas constant of a reaction.
• T is the temperature of a reaction (in kelvins)
• Q is the reaction quotient (quotient of concentration of products over
concentration of reactants).
o Note: ΔG only depends on the free energy of the products and reactants.
▪ So ΔG is not affected on whether the reaction is catalyzed or not.
o If ΔG is zero, the reaction is said to have reached equilibrium with the rate of the forward
reaction being equal to the rate of the reverse reaction.
Activation energy (ΔEa) is the minimum amount of energy that must be supplied to any reaction to get it
to start.
o Found from the difference between the transition state and the reactants of a reaction.
▪ The transition state, since it has the highest energy, is very unstable and does not exist
for a long time.
o Describes how quickly a reaction can take place or how quickly a reaction takes until it reaches
equilibrium.21
▪ A reaction can be spontaneous but if it has a high activation energy, it may not be
able to occur.
o Catalysts (like enzymes) lower the activation energy required for a reaction to occur.
Remember: Catalysts do not change the equilibrium of a reaction and they do not change the energy of either the
products or reactants.
21
51 | P a g e
Biochemistry – Nature17
lix
Figure 71 Activation Energy of Exergonic Reaction
Enzyme Kinetics and Activity
•
The rate of a reaction can be described by determining how quickly reactants are consumed or how
quickly products are formed.
o Take for example the reaction: A + 2B → C + 3D
∆[A]
∆[B]
∆[C]
∆[D]
▪ The rate of the reaction = − ∆t = −(1⁄2)( ∆t ) = ∆t = (1⁄3)( ∆t )
• Remember [A] is the concentration of the reactant A, and Δt is the change in
time.
o The rate of a total reaction (rate law) involves the concentrations of molecules involved with the
reaction (like the equation above) as well as the rate constant (k).
▪ Rate constant is the effect on activation energy, temperature, and frequency of a
reaction based on its rate.
▪ Rate constant can be calculated through the Arrhenius equation.
•
22
Ea
k = Ae−RT
o A is the frequency of collisions.
o Note how the rate constant is independent of the concentrations of the
reactants and products.
o Since we got to keep our body at a constant temperature (37°C), the
only way the body can physically speed up reactions without
increasing concentration is by decreasing the activation energy).22
The order of a reaction is how the rate of a reaction depends on concentration.
o Zeroth order reactions are reactions where the rate is independent of the reactant’s
concentration.
o First order reactions are reactions where the reaction’s rate is directly proportional to the
concentration of the reaction.
▪ Most single-substrate enzyme-catalyzed reactions are first order that occurs in two
steps.
• The first is the formation of the enzyme-substrate complex, and the second is
the release of the product from enzyme.
•
Enzymes can also affect the frequency of collisions occurring.
52 | P a g e
Biochemistry – Nature17
𝑘3
o
• This means that E + S
ES → E + P23
Second order reactions are where the rate is proportional to the square of the reactant’s
concentration.
lx
Figure 72 Orders of Reactions and Effects on Rate Law
•
•
•
When graphed (substrate concentration vs. rate of reaction), the slope shows the saturation
o At low substrate concentration - The rate of the reaction is proportional to substrate
concentration
o Increasing substrate concentration – Reaction rate decreases due to many enzymes already
being occupied by other substrates
o High substrate concentration – Enzyme is saturated with substrate. Rate is constant and
independent of substrate concentration.
If the second step is the rate-determining step of the reaction, then rate = k3 × [ES]
o So, the rateformation = k1× [E] × [S] and ratedecomposition = (k2 × [ES]) + (k3[ES]).
Michaelis-Menten Equation: Calculating the saturation effect in respect to substrate concentration. Two
key components.
o Max Velocity of Reaction – Varies between enzymes and environmental conditions.
• Rate of enzyme reactions sometimes expressed as turnover number (number of
molecules of substrate that can be turned into products per enzyme molecule per time
unit)
o Michaelis Constant (Km) – Substrate concentration at half the max velocity.
(k2 + k3 )
• KM = k
1
23
E: Enzyme; S: Substrate; ES: Enzyme-substrate complex; P: Product
53 | P a g e
Biochemistry – Nature17
•
•
•
o
•
Gives info about affinity of the enzyme.
Low value – Reaction is going quickly
High Value – Enzyme has a low affinity to the substrate.
[S]
The Michaelis-Menten equation is V0 = Vmax × K +[S]
M
Lineweaver-Burk Equation provides an alternative way to find the Vmax
o
1
v
=
Km
[S] × Vmax
+
1
Vmax
lxi
Figure 73 Michaelis-Menten Plot Graph
lxii
Figure 74 Lineweaver-Burk Plot Graph
•
Enzymes work in an optimum temperature and optimum pH where the rate of the reaction is highest.
o In the human body, most enzymes have an optimum temperature of 37°C
o Higher temperature causes the enzyme to break down (denaturation)
▪ Irreversible
o Digestion – Loss of covalent backbone of protein molecules
54 | P a g e
Biochemistry – Nature17
Deactivation: At a lower temperature, the enzyme does not function properly, but since it does
not change the tertiary structure it is reversible
Heavy metal ions also influence enzyme activity. Positive metal ions react with sulfhydryl group in
cysteine. Replaces hydrogen forming a covalent bond
o Causes irregular folding of proteins.
Chemical Inhibitors can decrease catalytic activity.
o Competitive inhibitors bind at the activation site, blocking the substrate from binding
▪ Reversible
o Non-competitive inhibitors bind at a different location on the enzyme (allosteric site), causing
the protein structure to change, which includes the active site.
▪ This inhibits the substrate’s ability to bind to the enzyme.
▪ Generally irreversible
o
•
•
lxiii
Figure 75 Competitive and Noncompetitive Inhibition
•
•
Like non-competitive inhibitors, allosteric inhibition is reversible noncompetitive inhibition and is a part of
normal metabolic regulation
o An allosteric inhibitor binds to the allosteric site when an excess of products is present.
▪ When there are little-to-no products available, the allosteric inhibitor has a low affinity
to the enzyme
o Can result in feedback inhibition, also known as end-product inhibition.
Allosteric activation, involves having an allosteric activator binding to an allosteric site, allowing the
substrate to bind to the enzyme
55 | P a g e
Biochemistry – Nature17
lxiv
Figure 76 Michaelis-Menten Plot (with chemical inhibitors)
lxv
Figure 77 Lineweaver-Burk Plot (with chemical inhibitors)
•
Note: Enzymes only affect the reaction rate of a reaction but does NOT affect the reaction equilibrium.
o Enzymes must accelerate the forward and reverse reaction by the same factor.
o Enzymes can accelerate the attainment of equilibria.
Analysis of Proteins
•
It is important to break the peptide bonds to see the amino acid composition. Two ways this can be
done
o Chromatography
▪ Different amino acids have different affinities to a stationary phase and a mobile
phase
56 | P a g e
Biochemistry – Nature17
▪
▪
Locating reagent added to make colorless amino acids visible.
Paper chromatography – Has paper with 10% water, with a solvent at the bottom
acting as the mobile phase.
• Sample of amino acid mixture spotted at bottom (origin). The paper is placed
in a flask with solvent at bottom. Through capillary action, the solvent will rise,
and the amino acids will separate themselves. Once the solvent reaches near
the top of the paper (solvent front), it is treated with ninhydrin, a locating
reagent.
o The final result is known as a chromatogram
o The position of the amino acid (retention factor or Rf) can be
calculated using 𝑅𝑓 =
▪
𝐷𝑖𝑠𝑡𝑎𝑛𝑐𝑒 𝑚𝑜𝑣𝑒𝑑 𝑏𝑦 𝑎𝑚𝑖𝑛𝑜 𝑎𝑐𝑖𝑑
𝐷𝑖𝑠𝑡𝑎𝑛𝑐𝑒 𝑚𝑜𝑣𝑒𝑑 𝑏𝑦 𝑠𝑜𝑙𝑣𝑒𝑛𝑡
Different amino acids have different Rf values
lxvi
Figure 78 Paper Chromatography
o
Electrophoresis
▪ Technique for the analysis and separation of a mixture based on the movement
charged particles have in an electric field.
▪ Mixture of amino acids separated by being placed in a buffered solution at a set pH
(since amino acids carry different charges at different pH)
• pH = isoelectric point – Amino acids do not move
• pH > isoelectric point – Amino acids move to the anode as they exist as anions
• pH < isoelectric point – Amino acids move to the cathode as they exist as
cations
• Rate of movement changes based on molecular mass and number of charges
on ion
o Slower ions are bigger and have less highly charged ions
Reaction with Ninhydrin
•
The reagent known as ninhydrin can be used to identify the presence of amino acids (on a sample or
from chromatography).
o When ninhydrin reacts with an amino acid, the nitrogen atom is surrounded by 2 ninhydrin
molecules making a molecule known as Ruhemann’s purple.
o The side chain of the amino acid is lost as an aldehyde.
o Pyridine is used as a catalyst for this reaction.
57 | P a g e
Biochemistry – Nature17
•
•
Because Ruhemann’s purple produces a deep violet coloration, ninhydrin is used as a reagent used to
detect amino acids on a wide variety of substrate.
o For example: If a suspect had touched an item, ninhydrin can react with the amino acids from
the suspect’s skin secretions to show a fingerprint.
Ninhydrin is important as it produces Ruhemann’s purple for all of the standard amino acids.
lxvii
Figure 79 Ninhydrin Reacting with an Amino Acid
Protein Assays
•
Protein assays are procedure used to measure protein concentration of a sample.
o UV-visible spectroscopy (UV-vis): Commonly used protein assay involved with how proteins
interact with UV and visible light.
▪ After the different wavelengths pass through the sample, an absorption spectrum is
obtained with each absorption corresponding to an electronic transition
▪ Obtained via spectrophotometer
▪ In order to find the amount of light absorbed at maximum wavelength, Beer-Lambert
law is applied: log(I0/I) = ε x l x c
• I0 = Intensity of light before passing through sample
• I = Intensity of light after passing through sample
• ε = Molar absorbance of a 1.00 mol dm-3 solution in a 1.00 cm cell
• c = concentration of solution
• l = path length
▪ May require a reagent to generate a color change to promote color absorption
▪ Standard curve based on standard solutions (those with a known concentration of
protein) which are prepared to cover a range of concentrations
• Absorbance of the solution is then measured at the same wave length as the
standard solution to find the protein concentration (when compared to
standard curve)
Motor Proteins
•
Motor proteins are proteins that generate forces that allow movement of cell or certain biomolecules.
o This includes muscle contraction, and the crawling of cells.
o This is done by the conformational changes of proteins which allows the protein to move from
one location to another.
▪ However, the protein must use energy in order to change shape and move.
▪ Protein “walking” is done by the hydrolysis of ATP, which causes 3 conformation shapes
of the protein.
• After ATP is hydrolyzed into phosphate and ADP, the two molecules are
released until another ATP molecule is added.
58 | P a g e
Biochemistry – Nature17
lxviii
Figure 80 An Allosteric Motor Protein "Walking"
Proteomes
•
•
The proteome is the totality of proteins expressed within a cell, tissue, or organism at a certain time.
o Each individual’s proteome is unique as protein expression patterns are determined by an
individual’s genes.
The proteome is always significantly larger than the number of genes in an individual for multiple
reasons
o One set of gene sequence after being transcribed can be spliced in different ways to generate
multiple protein variants
o Proteins may be modified following translation (glycosylated, phosphorylated).
Pigments
Outline
I.
II.
Biological pigments are molecules that absorb light due to their chemical bonds.
A. Produced by metabolism
Porphyrins are compounds with four heterocyclic rings linked by carbon atoms.
A. Chlorophyll is a pigment involved with photosynthesis
i. Absorbs a lot of red and blue light
ii. Contains Mg
B. Hemoglobin is an oxygen-carrying molecule
i. Contains four polypeptides and four heme groups
a. Each heme group contains Fe
ii. Myoglobin is involving with storing oxygen in muscles
a. Both form temporary bonds with oxygen.
59 | P a g e
Biochemistry – Nature17
III.
IV.
V.
b. Oxygen is outcompeted by carbon monoxide
C. Cytochromes are a group of enzymes involved in the reduction of oxygen to water in the
mitochondria.
i. Inhibited by cyanide
Carotenoids are a group of pigments containing long hydrocarbon chains with many double bonds.
A. Absorbs light in blue region.
i. Color depends on structure and number of delocalized electrons.
Anthocyanins are responsible for many blue, red, and pink colors in plants.
A. Tricyclic polyphenols, containing substituents.
B. Color can change based on temperature and pH.
Pigments can be analyzed using thin-layer chromatography.
A. Similar to paper chromatography, bur TLC plastic sheets are used (after being coated with a
silica and alumina layer).
Pigments
•
Biological pigments are molecules that absorb visible light (due to their chemical bonds) which are
produced by metabolism.
o They all have intense absorption bands.
o Usually highly conjugated structures (electrons in p orbitals are delocalized through alternating
between single and double bonds.
o The part of the pigment responsible for light absorption is known as the chromatophore
Porphyrins
•
Porphyrins are compounds that are made up of four heterocyclic rings (made up of carbon and
nitrogen), linked by carbon atoms.
lxix
Figure 81 Porphyrin
Chlorophyll
•
•
Chlorophyll is the primary pigment in photosynthesis, absorbing a lot of light in the blue and red
spectrum
o Contains a Magnesium atom in the center of the porphyrin.
Chlorophyll is the most stable in alkaline conditions
o In acidic conditions, the magnesium atom is lost from the porphyrin ring and then replaced by
two hydrogen atoms
▪ This makes the color brownish.
▪ Cooking food breaks down the cell wall, releasing acids that lower the pH.
60 | P a g e
Biochemistry – Nature17
•
Accessory pigments harvest light in different parts of the spectrum and pass the energy to the
chlorophyll, causing a redox reaction, allowing the passing of electrons through the electron transport
chain.
o Chlorophyll is reduced back by reabsorbing electrons from water.
o Chlorophyll stores ‘reducing energy’ to be used for the reduction of carbon dioxide in light
independent reactions
Figure 82 Chlorophyll
Hemoglobin and Myoglobin
•
•
Hemoglobin is an oxygen carrying molecule in the blood
o Contains four heme groups and 4 polypeptide chains
▪ Heme group is a prosthetic group which, unlike chlorophyll, the heme group’s central
metal is iron (usually in +2 oxidation state).
Myoglobin is a molecule that stores oxygen in muscles
o Myoglobin is made up of one heme group and one polypeptide chain.
lxx
Figure 83 Heme Group
61 | P a g e
Biochemistry – Nature17
lxxi
Figure 84 Hemoglobin
Figure 85 Myoglobin
•
•
When hemoglobin and myoglobin bind to oxygen, it is done (weakly) by the iron in the heme group.
o Due to this, hemoglobin can bind to four oxygen atoms, while myoglobin can only do so to one.
o Since the iron’s oxidation state does not change, myoglobin and hemoglobin are said to be
oxygenated.
▪ The products of myoglobin and hemoglobin oxygenation are known as oxymyoglobin
and oxyhemoglobin.
For each oxygen atom that is bonded to the hemoglobin, the ability for the next oxygen to bind is
easier.
o The binding process between hemoglobin and oxygen is said to be cooperative.
o This is due to the changes that occur in the quaternary structure
lxxii
Figure 86 Partial Pressure of O 2 vs. Hemoglobin Percent Saturation
62 | P a g e
Biochemistry – Nature17
•
An equilibrium exists between hemoglobin and oxygen
o Hb + 4O2 ⇌ Hb-(O2)4
▪ Equilibrium shifts right in the lungs and left in respiring cells
o
o
Equilibrium can be affected by temperature, pH, and CO2 concentration.
▪ Increasing the temperature reduces hemoglobin’s affinity to oxygen
▪ Decreasing the pH reduces hemoglobin’s affinity to oxygen
▪ High concentrations of CO2 reduce hemoglobin’s affinity to oxygen.
• Carbon monoxide (CO) has 200x the affinity to hemoglobin (making
carboxyhemoglobin). This means the blood can’t be oxygenated properly, and
oxygen can’t make it to respiring cells.
Fetal hemoglobin has a higher affinity to oxygen than adults do.
Cytochromes
•
•
Cytochromes are a group of enzymes involved in the reduction of oxygen to water in the mitochondria.
o Responsible for electron transport during the redox reactions of aerobic respiration and
photosynthesis
▪ Final cytochrome involved in aerobic respiration passes the electron to the terminal
acceptor oxygen (becoming water).
o Unlike the iron in hemoglobin, the iron in cytochromes oxidation state alternates between +2
and +3
Cytochromes are inhibited by cyanide.
o Cyanide preventing aerobic respiration is what causes cyanide to be so deadly.
Carotenoids
•
•
•
Carotenoids are a group of pigments containing long hydrocarbon chains with many double bonds
o Absorb light in blue region so color appearance ranges from yellow to red
▪ Color depends on structure and number of delocalized electrons
• Larger systems absorb wavelengths of lower frequency and longer wave
length
o Fat-soluble (and thus, water-insoluble)
o They are accessory pigments in plants
α-carotene and β-carotene are precursors to vitamin A
Multiple conjugated carbon-carbon double bonds make carotenoids susceptible to oxidation
o Able to act as antioxidants
▪ Sensitive to photooxidation
lxxiii
Figure 87 Alpha and Beta Carotene
63 | P a g e
Biochemistry – Nature17
Table 5 Carotenoids and the Characteristic Color
Name of Compound
Characteristic Color Observed
Alpha-carotene
Yellow
Beta-carotene
Orange
Gamma-carotene
Red-orange
Lutein
Yellow
Violoxathin
Yellow
Beta-cryptoxanthin
Orange
Zeaxanthin
Yellow-orange
Astaxanthin
Red
Lycopene
Red
Anthocyanins
•
•
•
Anthocyanins are responsible for many of the pink, blue, and red coloration in plants
o Tricyclic polyphenols with an aromatic backbone, containing substituents.
▪ Example: A residue of alpha-glucose
o Absorb strongly in the blue and green parts of the spectrum
o Polar hydroxyl groups allow the formation of hydrogen bonds – increases solubility in water
▪ Concentrate in vacuoles of plant cells
Formed by a light-dependent reaction between sugars and proteins.
o This is why fruit changes color as it ripens
Anthocyanins coloration is sensitive to pH.
o This allows anthocyanins to serve as pH indicators
▪ Example: Red cabbage extract
o Acidic conditions – Red to pink
o Neutral conditions – Blue to purple
o Basic conditions – Greenish-yellow
64 | P a g e
Biochemistry – Nature17
lxxiv
Figure 88 Anthocyanin
Analysis of Pigments
•
Pigment extracts from plants are typically mixtures of multiple pigments.
o Thin-layer chromatography (TLC) allows to observe and analyze pigments
▪ TLC plastic sheets are coated with silica or alumina layer of particles of about 0.2 mm
thick. This layer is known as the stationary phase
▪ The solvent mixture (known as the mobile phase) is applied.
▪ Small spots of pigment extract are then put at the origin. Capillary action draws the
pigments up, but due to different pigments having different polarities, the compounds
begin to separate.
lxxv
Figure 89 Thin-layer Chromatography
Vitamins
Outline
I.
Vitamins are organic micronutrients needed for the body.
65 | P a g e
Biochemistry – Nature17
II.
III.
IV.
V.
VI.
VII.
VIII.
a. Two types: water-soluble (B and C), and fat-soluble (A, D, E, K).
Vitamin B-complex are all non-vitamin C water-soluble vitamins.
a. B9: Essential for amino acid, nucleotide synthesis
i. Hematopoietic vitamin
b. B12: Important for methylation of homocysteine and isomerization of methylmalonyl.
i. Hematopoietic vitamin
c. B6: Used for condensation, decarboxylation, deamination, and transamination.
d. B1: Important coenzyme for the citric cycle.
e. B3: Important component of NAD
f. B2: Important component of FAD
g. Biotin: Coenzyme serving as a carrier of CO2.
h. Pantothenic Acid: Component of coenzyme A.
Vitamin C: Coenzyme essential for acting as a reducing agent
a. Important for maintenance of connective tissue and wound healing
Vitamin A consists of the retinoids
a. Includes retinol, retinal, retinoic acid, and 11-cis-retinal.
b. Important for vision, growth, and reproduction.
Vitamin D: Group of sterols with hormone-like function
a. One important one is 1,25-diOH-D3.
i. Involved with regulating phosphorus and calcium levels in the plasma.
Vitamin K: A coenzyme that serves in the carboxylation of glutamic acid residues
Vitamin A: Important antioxidant
Malnutrition is the absence of a regular and balanced supply of nutrients, including vitamins.
a. Malnutrition of vitamins can lead to beriberi, scurvy, and rickets.
b. Can be combatted with vitamin fortification.
Vitamins
•
•
Nutrients are an array of molecules that maintain the health of the organism
o Micronutrients: Any nutrient that is needed only in a small amount (less than 0.00005% body
mass).
▪ Without these nutrients, a person can suffer from deficiency diseases
▪ Includes trace minerals and vitamins (organic micronutrients)
There are two main types of vitamins
o Water-soluble: Polar bonds, can form hydrogen bonds with water.
▪ Excess water-soluble vitamins are filtered out by the kidneys, and are transported by
blood.
▪ Examples include vitamins B and C, biotin, folic acid, pantothenic acid, and niacin.
• Vitamin C is easily oxidized, and thus usually destroyed in manufactured food
▪ More sensitive to heat
o Lipid-soluble: Mostly non-polar molecules, contains long hydrocarbon rings or chains
▪ Slower to absorb. Stored in fat tissues. Excess amount can cause serious side effects
• Examples include vitamins A, D, E, and K.
Vitamin B-complex
•
•
Vitamin B-complex refers to all known essential water-soluble vitamins with the exception of vitamin C.
o The reason for this grouping is due to “vitamin B” was once thought to be a single nutrient.
o The B-complex vitamins also contains a few nonessential vitamins such as choline and paraaminobenzoic acid (PABA).
Folic acid (also known as folate or vitamin B9) is essential for the biosynthesis of many compounds.
66 | P a g e
Biochemistry – Nature17
Reduced folate, known as tetrahydrofolate is a recievor of one-carbon fragments, holding onto
the atoms until needed for nucleotide or amino acid synthesis.
o Known as a hematopoietic vitamin, as it is important for the production of blood cells.
Cobalamin (vitamin B12) is another hematopoietic vitamin, and is essential for two enzymatic reactions.
o The first reaction is the methylation of homocysteine to methionine.
o The second reaction is to isomerize methylmalonyl coenzyme A, producing succinyl coenzyme A.
o Colobamin contains a corrin ring with cobalt at the center making 6 coordinated covalent
bonds.
▪ This is held together by four nitrogens each apart of a pyrrole group, one from the
nitrogen of 5,6-dimethylbenzimidazole, and one a carbon atom.
• Depending on the type of colobamin causes different atoms to be attached to
the cobalt.
o Synthesized only by microorganisms. Animals obtain it from their gut flora and/or from food
like pork, shrimp, chicken, liver, or dairy.
o
•
lxxvi
Figure 90 Structure of Different Forms of Cobalamin
•
Vitamin B6 is a collective term containing the vitamins pyridoxine, pyridoxal, and pyridoamine.
o All three serve as precursors for the coenzyme pyrioxal phosphate which can be used for
condensation, decarboxylation, transamination, and deamination reactions.
o Pyridoxine is found mainly in plants while pyridoxal and pyridoamine is found mainly in
animals.
▪ Pyridoxal is the only water-soluble vitamin which can be easily be taken in excess
causing toxic symptoms.
67 | P a g e
Biochemistry – Nature17
lxxvii
Figure 91 Vitamin B 6
•
Thiamine (Vitamin B1) is an important coenzyme for the ctiric cycle.
o Involved with oxidative decarboxylation of α-ketoacid and degradation of α-ketol.
lxxviii
Figure 92 Thiamine's Involvement with Citric Cycle
•
•
•
Vitamin B3 contains the compouns niacin and nicotinamide which are both important components of
NAD+
Riboflavin (Vitamin B2) is an important component of FAD, which is formed from the addition of a
phosphate from ATP, and the addition of AMP from ATP.
Biotin is a coenzyme serving as a carrier of CO2.
o Attaches itself to a lysine residue for many biotin-dependent enzymes.
lxxix
Figure 93 Biotin Attached to Lysine Residue
•
Pantothenic acid is a component of coenzyme A (CoA), which functions in the transfer of acyl groups.
68 | P a g e
Biochemistry – Nature17
Vitamin C
•
Ascorbic acid (vitamin C) is a coenzyme important for acting as a reducing agent in many reactions.
o Important for maintenance of normal connective tissue and wound healing.
o Facilitates the absorption of dietary iron from the intestine.
Vitamin A
•
•
•
Vitamin A is a collective term for several biomolecules that are structurally related to one-another.
o Also known as retinoids.
o Includes retinol, retinal, retinoic acid, and 11-cis-retinal.
Retinyl esters found in food is hydrolyzed by the intestinal mucosa which releases retinol and fatty
acids.
Vitamin A has a lot of functions, including vision, growth, and reproduction.
o Vitamin A is a component of the visual pigments found in rod and cone cells.
▪ Rhodopsin, for example, consists of 11-cis retinal and is the visual pigment of the
retina’s rod cells.
o Vitamin A is important for the differentiation and maintenance of epithelial tissue.
o Retinol and retinal are essential for spermatogenesis and prevention of fetal resorption.
Vitamin D
•
Vitamin D is a group of sterols with hormone-like function.
o One of the most important molecules is 1,25-dihydroxycholecalciferol (1,25-diOH-D3).
▪ 1,25-diOH-D3 is important as it regulates the plasma’s level of calcium and phosphorus.
• This is done in a multitude of manners.
o For one, 1,25-diOH-D3 can increase the intestine’s uptake of calcium.
o Another way is by having the kidney minimize calcium loss.
o The third way is to stimulate resorption of bone.
▪ 1,25-diOH-D3 is produced through two reactions. First UV light converts 7dehydrocholesterol into cholecalciferol on the skin. Then cholecalciferol is converted into
1,25-diOH-D3 in the liver.
• Vitamin D can also be obtained from fatty fish, liver, and yolk.
Vitamin K
•
•
Vitamin K is a coenzyme that serves in the carboxylation of certain glutamic acid residues.
o Vitamin K is also important in its interaction with prothrombin.
o Vitamin K1 exists in plants as phylloquinone, while vitamin K2 (menaquinone) is synthesized by
intestinal bacterial flora.
Vitamin K is essential for the carboxylation of glutamic acid residues.
o This causes blood clotting factors II, VII, IX, and X to be matured and be ready for activation.
o
•
The γ-carboxyglutamate residues of prothrombin, once having undergone carboxylation by
vitamin K, has two negatively charged carboxylate group, which can then readily bind to
phospholipids on platelets.
Vitamin K is found in liver, cabbage, kale, spinach, and egg yolk, but can be synthesized by the gut
flora.
69 | P a g e
Biochemistry – Nature17
lxxx
Figure 94 Vitamin K's Role in Blood Clotting
Vitamin E
•
•
Vitamin E is an important antioxidant, preventing non-enzymatic oxidation of various cellular
components.
o This is essential for plants as they live in sunlight and with the constant exposure to free radicals
which can cause disruption in the cell.
▪ This is why many of the photosynthetic regions of plants are high in antioxidants.
o Also, essential for animals to, as they can have to deal with molecular oxygen and other free
radicals.
E vitamins consist of eight naturally occurring tocopherols with the most active one being α-tocopherol.
Mnemonic: The following phrase can be used to identify fat-soluble vitamins: “A DEK in their fat ass.”
Malnutrition
•
•
The absence of a regular and balanced supply of the diverse set of needed nutrients is known as
malnutrition.
o Major issue in poorly-developed countries despite freedom from malnutrition being a human
right
o Other causes include soil/water nutrition depletion, lack of education on diet, and overprocessing foods
There are a multitude of health effects and possible ways to combat malnutrition
o A – Promotes good eyesight
▪ Solution to malnutrition of A: Vitamin fortification, the adding of fat soluble vitamin A to
margarine, and eventually in rice
o B – Deficiencies of B can cause mental health issues, anemia, and beriberi
▪ Major issue in vegans and vegetarians, as B contains Cobalt (something commonly
obtained from animals).
▪ Lack of thiamine can cause beriberi.
• Beriberi in adults can cause irritability, disordered thinking, dry skin, and
progressive paralysis.
▪ Solution to malnutrition of B: Fortification of cereals
o C – Deficiencies of C can cause scurvy and increased chances of scurvy
▪ Solution to malnutrition of C: Fresh fruits and vegetables
70 | P a g e
Biochemistry – Nature17
D – Promotes healthy bones. Obtained from action of sunlight. Deficiencies of D can cause
rickets (where the bones do not harden and become malformed).
▪ High doses of vitamin D can be toxic and can cause nausea, loss of appetite, thirst, and
stupor.
o K – Deficiencies are rare in adults, but seen in many newborns with symptoms of excessive
bleeding.
o E – Deficiencies is rare but some symptoms include red blood cell fragility which can lead to
hemolytic anemia.
Vitamin supplements are another way to combat malnutrition.
Note: While people who have diets rich in fruits and vegetables are shown to have decreased
occurrences of chronic diseases, clinical trials that contain people receiving vitamin supplements show no
evidence for vitamins like A, C, E, B, etc. preventing cancer or cardiovascular disease.
o
•
•
lxxxi
Figure 95 Vitamins
Nucleic Acids
Outline
I.
Nucleic acids are important for storing genetic information and expressing it.
A. DNA is involved with the storage of information.
B. RNA is involved with the expression of information.
71 | P a g e
Biochemistry – Nature17
II.
III.
IV.
V.
VI.
VII.
VIII.
IX.
Nucleic Acids are polymers made up of nucleotides.
A. Nucleotides have three components: pentose sugar, nitrogenous base and phosphate group
i. Two types of pentose sugar: ribose (found in RNA) and deoxyribose (found in DNA).
ii. Two types of nitrogenous bases: pyrimidines and purines.
a. Purines are larger and consist of adenine and guanine
b. Pyrimidines are smaller and consist of thymine (found only in DNA), cytosine,
and uracil (found only in RNA).
iii. The pentose sugar and nitrogenous base (without the phosphate group) is known as a
nucleoside.
a. Connected at carbon 1’ of pentose sugar.
b. Phosphate group of a nucleotide is connected to carbon 5’ of pentose sugar
iv. Nucleotides are added to existing RNA and DNA molecules as nucleoside
triphosphates.
a. The leaving of the pyrophosphate fuels the synthesis reaction.
DNA is typically double stranded while RNA is typically double stranded.
A. DNA forms a double helix.
i. Runs antiparallel
ii. Can be wrapped around histones to make chromosomes.
a. Makes DNA more packaged.
iii. Can sometimes form a triple helix.
a. Third strand only contains thymine and C+.
B. Both follow base pairing rules (hydrogen bonding)
i. A goes to T and U. G goes to C.
Three types of DNA
A. B: Most common (10 pairs per turn)
B. A: Found in low humidity (11 pairs per turn)
C. Z: Appears in conditions with high salt concentrations (12 pairs per turn).
ATP is an important energy carrier, used to fuel energy for many reactions.
Nucleotides can be synthesized using the de novo pathway and the salvage pathway
A. De novo synthesis of pyrimidines
i. Bicarbonate → Carboxyphosphate → Carbamic acid → Carbamoyl phosphate →
Carbamoyl aspartate → Dihydro orotate → Orotate → Orotidine 5-monophosphate
→ Uridine 5-monophosphate → UDP → dTTP or dCTP.
B. De novo synthesis of purines
i. Ribose-5-phosphate → PRPP → Phosphoribosyl-beta-amine → Glycinamide
ribonucleotide → FGAR → FGAM → AIR → CAIR → SAICAR → AICAR → FAICAR →
Inosine monophosphate → AMP or GMP.
C. The salvage pathway is the pathway used to produce nucleotides when a nucleic acid source is
already present.
The genetic code is made up of four letters. Codes for a specific amino acid
A. Transcription: Producing a strand of RNA (either pre-mRNA or mRNA) from DNA.
B. Translation: Producing a polypeptide chain from an mRNA sequence
i. Occurs at the ribosomes
DNA replication follows a semi-conservative pathway.
Genetic engineering is the artificial manipulation of an organism’s genes to produce traits.
A. Leads to GM crops.
Nucleic Acid Function
•
Nucleic acids are important acidic molecule found in the nucleus of many eukaryotic cells
72 | P a g e
Biochemistry – Nature17
Includes deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)
▪ DNA stores information that controls the genetic information of organisms.
• To function, DNA must be a stable molecule, be able to replicate itself,
and store a code of genetic information (which it does)
• Found in the nucleus of eukaryotic cells24
▪ RNA expresses the information stored in DNA, promoting the assembly of certain
primary structures of proteins to form
• Each gene along a DNA molecule directs the synthesis of a certain RNA
molecule, known as messenger RNA (mRNA)
Since DNA, which controls the production of proteins, it kept inside the nucleus25, and protein
production occurs in the cell’s cytoplasm (in an organelle known as a ribosome), an intermediate is
needed. mRNA, conveys the information from the DNA to the ribosome (serving as an
intermediate).26
o
•
Figure 96 Gene to Protein
Nucleotides
•
Nucleic acids are polymers of the monomer, nucleotides
o This is why nucleic acids are also known as polynucleotides
o Nucleotides are made up of three major components
▪ Pentose sugar
▪ Nitrogenous Bases
▪ Phosphate Group
Pentose Sugar
•
One of the differences between DNA and RNA is their pentose sugar.
o DNA has the pentose sugar, deoxyribose, while RNA has the pentose sugar, ribose.
Note: Mitochondria and chloroplasts also contain their own DNA. However, according to endosymbiont theory, these
organelles were once prokaryotic organisms.
25 DNA is kept in the nucleus, so to lessen its chance of suffering any damage to it (which can be caused by the various
metabolic processes occurring in the cell.
26 Even prokaryotic cells, which lack a nucleus, use RNA as an intermediate between DNA and protein.
24
73 | P a g e
Biochemistry – Nature17
Figure 97 Deoxyribose and Ribose
▪
•
Note how the ribose and deoxyribose are nearly identical, with the exception of
carbon 2’. On ribose, the carbon contains one hydrogen and one hydroxide.
Deoxyribose on the other hand, has two hydrogens.
▪ Note: When labelling carbons, the first carbon is the carbon on the far right. This is
carbon 1’ or carbon one-prime.
The pentose sugar is what causes the DNA and RNA to be known as deoxyribose and ribose.
o Deoxyribonucleic acid is missing on oxygen from the ribose structure (at 2’), hence its name
‘deoxy”.
▪ De means missing
▪ Oxy means oxygen
o The type of pentose sugar determines if you have a ribonucleotide or a deoxyribonucleotide.
Nitrogenous Base
•
There are five different nitrogenous bases, separated into two main categories
o Pyrimidines – Smaller, 6-membered rings.
Figure 98 The Pyrimidines
▪
o
Note: Uracil is only found in RNA (and not DNA), and thymine is only found in DNA
(and not RNA)
Purines – Larger, fused rings, containing a five-member and a six-member ring.
74 | P a g e
Biochemistry – Nature17
Figure 99 The Purines
Mnemonic: The purines (adenine and guanine), make up Ag, which is the chemical symbol for silver,
something commonly associated with pureness
Nucleosides and Nucleotides
•
•
Connectivity:
o The nitrogenous base binds to the pentose sugar at carbon 1’.
o The phosphate group binds to the pentose sugar at carbon 5’.
o When the nucleotides need to connect (to form a nucleic acid), they connect via the phosphate
group and through carbon 3’.
Nucleoside: The nitrogenous base and pentose sugar component of the nucleotide.
o Depending on the pentose sugar, it can be referred to as a deoxyribonucleoside or a
ribonucleoside.
Figure 100 Nucleotide
• Pentose Sugar: Red
• Nitrogenous Base: Blue
• Phosphate Group: Green
•
Note how in DNA there is a 5’ end and a 3’ end, as seen in the pentose sugar.
o The 3’ end of one nucleotide bonds the phosphate group on the next nucleotide
75 | P a g e
Biochemistry – Nature17
o
When describing the direction of DNA, you read it describing the end where the chain starts to
the opposite end.
▪ So, in the picture below, if you read top to bottom, you are reading the DNA molecule
in the 5’ → 3’ direction. If you were reading the picture above from bottom to top, you
are reading the DNA molecule in the 3’ → 5’ direction.
Figure 101 Nucleotide Connectivity
Nucleic Acid Bond Formation
The carbon and phosphate group links together via covalent bond known as a phosphodiester
linkage.
o When the nucleic acid is forming, the nucleotides don’t attach themselves as nucleotides. Instead
they come as a nucleoside triphosphate. One example is deoxynucleoside triphosphates.
▪ The bonds between the other two phosphate groups are broken, and the energy from
the bond breaking is used to form the phosphodiester linkage.
This bond is formed via condensation reaction27. One of the oxygens and two hydrogens leave the
phosphate group and the 3’ carbon of the pentose sugar to form the phosphodiester linkage. This also
forms some water.
o The reason DNA elongates from nucleoside triphosphates instead of nucleoside diphosphates is
because pyrophosphate is a better leaving group than phosphate.
o
•
27
Also known as a dehydration synthesis
76 | P a g e
Biochemistry – Nature17
Figure 102 Addition of Nucleoside Triphosphates
•
Depending on the pH of the solution, the phosphate can be in three different ionization states.
o In acidic solution, the phosphate is not ionized and contains two OH groups.
o In neutral conditions, like when pH is 7.6 (the typical pH of the cell), only one hydrogen remains
on the phosphate.
o In basic conditions, the group is completely ionized.28
lxxxii
Figure 103 Phosphate Ionization State in a Ribonucleotide
DNA and RNA
•
•
Unlike RNA, which has a single strand of itself, DNA is double-stranded forming a double helix.29
The backbone of the double helix is the sugar-phosphate group. The two sides are connected via the
nitrogenous bases, which, unlike the sugar and phosphate, are connected via hydrogen bonds
o Although hydrogen bonds are strong, they are not as strong as covalent bonds. This allows them
to be easily split for events like replication and transcription
▪ Adenine (which can only pair with thymine in DNA, and uracil in RNA) forms 2
hydrogen bonds thymine/uracil
▪ Cytosine can only base pair with guanine, forming three hydrogen bonds between
itself and guanine.
Unless the pH is important to identify, by convention, the phosphate groups are written as if they were completely
ionized.
29 There are certain types of viruses that break this convention. Some viruses have double-stranded RNA and some viruses
have single-stranded DNA.
28
77 | P a g e
Biochemistry – Nature17
•
Each nitrogenous base can only bind to one other nitrogenous base. This is known as complementary
base pairing.
o Note: Even though RNA is usually single stranded, it still follows complementary base pairing
rules.
Table 6 Complementary Base Pairing
•
DNA
RNA
A-T
A-U
T-A
U-A
G-C
G-C
C-G
C-G
Note how even though DNA and RNA have a difference with uracil and thymine, they still follow similar
base-pairing rules.
lxxxiii
Figure 104 DNA Double Helix
•
•
Ten nucleotides make up one complete turn (3.4 nm)
Note how one strand of DNA is going (from top to bottom) in the 5’ → 3’ direction while the other
strand is going in the 3’ → 5’ direction. This means that DNA strands run parallel to each other but in
opposite directions. The strands are said to run antiparallel.
o Allows the molecule to be stable
78 | P a g e
Biochemistry – Nature17
lxxxiv
Figure 105 Antiparallelism in DNA
•
•
•
DNA fragments are attached to proteins known as histones
o DNA (being negatively charged due the phosphate group) coils itself around the positively
charged histones, making DNA super compact
▪ Stabilizes DNA to create chromosomes. This super-condensed form is important for
mitotic division.
RNA is usually a single-stranded nucleic acid.
o Contains A, U, C, and G for its nitrogenous bases.
o Used for transcription and translation.
o Ribose is the sugar used instead of deoxyribose (found in DNA).
Due to RNA’s intermolecular interactions, like hydrogen bonding, when RNA forms a double helix it can
take multiple structures.
o These include the multibranched junction, stem-loop, internal loop, and bulge loop.
lxxxv
Figure 106 RNA Double Stranded Structures
Types of DNA
•
30
While DNA does typically follow a similar structure, there are various different types of DNA that have
slightly different structures.
o The most common type of DNA found in cells is known as B DNA.
▪ B DNA has a “right-handed” helix, with about 10 base pairings per 360-degree turn,
with base pairs located centrally and H-bonds being perpendicular to the central axis.
o A DNA is a similar structure to B DNA, occurring in conditions of low humidity.30
This is under experimental conditions in X-ray diffraction studies.
79 | P a g e
Biochemistry – Nature17
▪
▪
▪
o
The number of base pairs per 360-degree turn is 11.
Bases are tilted relative to central axis.
Function is currently unknown, but it is thought to be a way to protect the DNA from
damage during dehydration.
Z DNA appears under conditions with high salt concentrations or when cytosine is methylated at
lower ionic strength.
▪ Left handed helix.
▪ The number of base pairs per 360-degree turn is 12.
▪ Bases are tilted relative to central axis.
▪ Z DNA plays a role in transcription of certain genes and affecting the level of
compaction in chromosomal structure.
• Certain protein that regulate transcription specifically recognize Z DNA.
• Z DNA also is thought to relieve stress during transcription.
lxxxvi
Figure 107 A, B, and Z DNA
•
DNA can also form triple helical structures known as triplex DNA.
o Consists of only thymine and a protonated cytosine
▪ Follows similar base pairing rules. T interacts with AT pairings and C+ interacts with CG
pairings.
o Formed via a B DNA double helix structure interacting with a synthetic single-strand of DNA.
▪ Can be used for inhibition of specific genes and to cause mutations.
▪ Has also been found in E. coli, and is the result of the action of the recombination
enzyme RecA.
80 | P a g e
Biochemistry – Nature17
lxxxvii
Figure 108 Triplex DNA Base Pairing
ATP
•
•
31
One example of nucleotides is ATP (adenosine triphosphate), which is a ribonucleoside triphosphate.
o ATP serves as short-term energy carriers of chemical energy.
o This chemical energy can then be used to power various other reactions that are important in
maintaining a cell.
ATP contains three phosphate groups, one of then connected to carbon 5’ on the ribose, and the other
two connected in a linear string to the other phosphates.
o While the phosphate connected to the carbon atom is connected through a phosphodiester
linkage, the phosphates bonded to another phosphate is connected through phosphoanhydride
bonds.
▪ A common misconception is that the breaking of the bond between the second and third
phosphate group releases energy for the cell. In reality it requires an input of energy
to break the bond31.
• What causes energy to be released is the formation of bonds between H+ and
OH- ions (or any other group, though it is typically OH- and H+) binding to the
phosphate groups.
• Note: There is also a net energy release from the breaking of the bond
between the first and second phosphate group, but it is much greater between
the second and third phosphate groups.
This bond is relatively weak and easy to break due to the structure of ATP.
81 | P a g e
Biochemistry – Nature17
lxxxviii
Figure 109 ATP Serves as Short-term Energy Carriers in the Cell
Nucleotide Synthesis
•
•
Purines and pyrimidines can be synthesized in two ways: the de novo pathway and the salvage
pathway.
o The de novo pathway is the process of producing nucleotides from scratch, while the salvage
pathway is the process of obtaining nucleotides from other sources.
o The salvage pathway is the process of producing nucleotides from intermediates, often
obtained through the degradation of RNA and DNA.
Pyrimidine de novo synthesis begins with the building of the pyrimidine nitrogenous base and then
attaching it to a sugar molecule.
o Occurs in the cytoplasm of the cell.
o The process starts with a bicarbonate ion, and then ATP is added to the molecule.
▪ This is because bicarbonate is a stable molecule, and so adding ATP to it will make it
more reactive.
▪ Adding ATP phosphorylates the bicarbonate ion into carboxyphosphate.
• This process is catalyzed by the enzyme carbamoyl phosphate synthetase type
II.
o This will be simplified as CPS 2 for the rest of these notes.
o CPS 2 then hydrolyzes glutamine into glutamate and ammonia.
▪ The ammonia molecule is then attached onto the carboxy phosphate making carbamic
acid.
o Carbamic acid is then phosphorylated by ATP (using the enzyme CPS 2) to form carbamoyl
phosphate.
lxxxix
Figure 110 Formation of Carbamoyl Phosphate
o
After carbamoyl phosphate is formed, it leaves the active site of CPS 2 and moves to the active
site of aspartate transcarbamoylase (ATCase).
82 | P a g e
Biochemistry – Nature17
▪
Aspartate is then attached to the carbon atom in carbamoyl phosphate, kicking out the
phosphate group. This forms carbamoyl aspartate.
• This reaction is catalyzed by ATCase.
xc
Figure 111 Formation of Carbamoyl Aspartate
o
A dehydration synthesis occurs, which kicks off one hydrogen from the ammonia (attached
directly to the carbon that was from the original bicarbonate ion) and an oxygen from
aspartate.
▪ This forms a sigma bond between the nitrogen of ammonia and the carbon from
aspartate (that was deoxygenated). This forms the ring.
xci
Figure 112 Forming the Ring in the Pyrimidine Nitrogenous Base
o
o
o
Next, NAD+ takes electrons from the ring from two carbon atoms. This forms a π bond between
the two atoms, making NADH + H+ and orotate.
Then, orotate can be attached to the sugar molecule known as phosphoribosyl pyrophosphate
(PRPP).
▪ The addition of orotate to the sugar is catalyzed by the enzyme pyrimidine
phosphoribosyl transferase.
The final step is where a carbon dioxide molecule is kicked off the pyrimidine ring, using the
enzyme orotidylate decarboxylase, which forms a uridine monophosphate (UMP).
83 | P a g e
Biochemistry – Nature17
xcii
Figure 113 Formation of UMP
▪
UMP is then transformed into UDP and then goes into one of two the reaction series
depending on the pyrimidine needed:
• UDP → dUDP → dUMP → dTMP → dTDP → dTTP.32
• UDP → UTP → CTP 33 → CDP → dCDP 34 → dCTP.
The step going from dUMP to dTMP involves the enzyme thymidylate synthetase which is targeted by many drugs
CTP and UTP are often involved with RNA synthesis.
34 dCDP can also be converted into dUMP.
32
33
84 | P a g e
Biochemistry – Nature17
xciii
Figure 114 Forming TMP and CTP
•
The purine de novo pathway begins with 5-phosphoribosyl pyrophosphate (PRPP).
o Unlike the pyrimidine de novo pathway, the de novo pathway for purines initially begins with
the sugar molecule, with atoms being attached to it.
o The first step involves the enzyme glutamine phosphoribosyl amidotransferase, which has two
active sites.
▪ The first one is for PRPP, the second one is for glutamine.
• Glutamine is needed to replace the pyrophosphate of PRPP with ammonia
(which is formed from hydrolyzing glutamine).
▪ Once both PRPP and glutamine are in their appropriate active sites, glutamine is
hydrolyzed into glutamate and ammonia. Ammonia travels through a special channel in
the enzyme to the other active site where is nucleophilically attacks the carbon
containing pyrophosphate, so pyrophosphate is removed.
o Next, a series of intermediate reactions, requiring glycine, aspartate, folic acid, and a lot of
ATP.
▪ This produces inosinate (IMP).
85 | P a g e
Biochemistry – Nature17
xciv
Figure 115 Formation of IMP
o
o
Inosinate can then follow one of two pathways, to produce either adenylate (AMP) or
guanylate (GMP).
▪ The concentrations of AMP and GMP in the cell determines which pathway that
inosinate will follow.
The pathway that produces AMP beings with the enzyme adenylosuccinate synthetase adding
aspartate (after removing an oxygen atom).
▪ The energy from this reaction is done from the hydrolysis of GTP to GDP.
▪ This forms the intermediate adenylosuccinate.
▪ Finally, adenylosuccinate synthetase kicks off most of the aspartate (except for
ammonia), leaving just AMP and fumarate.
▪ This reaction can be reversed back into IMP, by the enzyme AMP deaminase.
86 | P a g e
Biochemistry – Nature17
xcv
Figure 116 Converting IMP to AMP
o
The pathway that produces GMP starts with NAD+, with the enzyme IMP dehydrogenase taking
electrons from the IMP and placing it on the NAD+ molecule forming NADH.
▪ Oxygen from water is attached to the electron deficient carbon, producing xanthosine
monophosphate (XMP).
▪ The oxygen is then replaced with an ammonia group.
• Energy provided by ATP.
• This process begins with AMP being removed from ATP, which is then attached
onto the oxygen atom, increases its energy.
• Ammonia then nucleophilically attacks the carbon, removing the AMP and
oxygen, producing GMP.
xcvi
Figure 117 Converting IMP to GMP
•
The purine salvage pathway begins with a type of phosphoribosyltransferases enzyme adding
activated PRPP onto the nitrogenous bases, creating nucleoside monophosphates.
o For the reaction of adenine + PRPP → adenylate + PPi , adenine phosphoribosyltransferases
(APRT) catalyzes the reaction.
o For the formation of guanylate from guanine or inosinate from hypoxanthine, hypoxanthineguanine phosphoribosyltransferase (HGPRT) is used.
▪ Inosinate can then be used in the de novo pathway to produce either GMP and AMP
(whichever is necessary).
87 | P a g e
Biochemistry – Nature17
xcvii
Figure 118 Hypoxanthine and Inosinate
•
•
For the pyrimidine salvage pathway, cytosine and thymine are obtained from degrading DNA.
o Cytosine is then converted into uracil through deamination.
▪ Uracil is then combined with ribose-1-phosphate (with uridine phosphorylase as the
enzyme) to form uridine.
▪ Nucleoside kinase then acts as a catalyst with the conversion of uridine into UMP.
o Thymine combines with deoxy-1-phosphate (with thymine phosphorylase as the enzymatic
catalyst) producing thymidine.
▪ Nucleoside kinase will convert thymidine into dTMP.
The reason the salvage pathway is not the primary way cells obtain DNA is because many of the
enzymes involved in the salvage pathway (like ribose-1-phosphate and deoxyribose-1-phosphate) are
rare in the cell.
DNA Expression (An Overview)
•
•
35
The genetic code of DNA is made up of four letters (A, C, T, G, (AKA the nitrogenous bases)). Each
grouping of three letters will make an amino acid and each grouping (of a random amount) of amino
acids makes a protein. This occurs in two main steps
o Transcription: The DNA begins unzipping (breaking of the hydrogen bonding between
nitrogenous bases). Each DNA acts as a template for a complementary strand of RNA that
forms. Due to base-pairing, the RNA formed becomes a clone of the DNA’s genetic code.
▪ Afterwards, the RNA leaves the nucleus, and the DNA reforms the double helix
o Translation: The RNA enters the ribosome, and gets changed into a different form.35 At one
end, a specific molecule identifies a specific triplet of nitrogenous bases (codon).
▪ At the other end, the codon is translated into a specific amino acid
o Genetic Code: A triplet code, (a sequence of three bases in RNA codes) for one amino acid.
o Central Dogma – A summarized idea that genetic information flows in one direction in cells:
DNA → RNA → Protein
DNA Replication is the process which DNA makes an exact copy of itself. Occurs before cellular division
in all cells except those used for sexual reproduction.
o DNA unzips itself, serving as a template for new DNA strips to form. Considered semiconservative replication as there is only one newly synthesized DNA strand.
Still represents the same code.
88 | P a g e
Biochemistry – Nature17
xcviii
Figure 119 Semi-conservative Model of Replication
•
Through genetic engineering, we are able to produce genetically modified organisms (GMOs).
o By transferring DNA from one species to another, we are able to produce GM crops, crops with
altered DNA patterns (compared to what they usually are).
▪ This can be used for stuff like creating natural pesticides in plants, increasing crop
yield, or keeping tomatoes fresh for longer
Table 7 Benefits and Concerns over GM Food
Benefits
Concerns
Longer shelf life
Lack of information about long-term effects
Improved flavor, texture, nutritional value
Changes to the ecosystem through cross pollination
Increased disease and pest resistance
Possible risks to increased allergies
Ability to produce a supply of substances like
vitamins
Increased crop yields
Risk of altering natural composition of food
Tolerance to a wider range of growing
conditions
Concerns of breeding species until they can’t be
controlled
Lack of proper food labelling
Xenobiotics
Outline
I.
II.
III.
Xenobiotics are foreign compounds found in an organism
A. One serious example is pharmaceutically active compounds.
i. Enter ecosystem due to them not being properly metabolized or from hospitals
ii. Some act like xenoestrogens, feminizing many male fish.
Xenobiotics can accumulate in an organism causing bioaccumulation.
A. Can accumulate up a food chain, due to them not being destroyed by enzymes.
i. This is biomagnification. One famous example of biomagnification is with DDT in marsh
environments.
There are many ways we respond to xenobiotics.
A. Host-guest chemistry: Host traps a xenobiotic, so it can’t react with environment.
i. Forms a supermolecule.
B. Bioremediation: Using microorganisms to break down xenobiotics
89 | P a g e
Biochemistry – Nature17
C. Using biodegradable substances can also limit the xenobiotic output into the environment.
Xenobiotics
•
•
•
Xenobiotics are compounds that may be found within a living organism, but are foreign to that
organism.
o Examples include pollutants, food additives, plastics, drugs, and insecticides.
▪ One xenobiotic that is concerning scientists is pharmaceutically active compounds, which
are released into the environment from hospitals, or pass through the human body not
fully metabolized.
• One effect is that xenobiotics like xenoestrogens are that it has feminized
many male fish, which is reducing many fish populations.
o Can have multitudes of effects on an organism.
Depending on the structure and properties of the molecule, different effects can be experienced by the
organism.
o Non-polar molecules easily pass through the cell membranes of cells and can be detoxified by
enzymes.
o If the xenobiotic cannot be modified by the organism’s cells, it can build up in the cells.
▪ The increasing concentration of this xenobiotic in the organism is known as
bioaccumulation.
Another issue with synthesized xenobiotics is that they are not broken down by enzymes.
o This means that the xenobiotics can persist in the environment and stay within the environment
for a long time.
o Biomagnification is the increase in concentration of a xenobiotic as it moves through a food
chain.
▪ Since the xenobiotic can’t be metabolized, when the prey item with the xenobiotic in its
system gets eaten, they predator gets all the xenobiotic in its system. Since the
predator will eat multiple organisms, the organisms towards the top of the food chain
will have more of the xenobiotic.
xcix
Figure 120 Bioaccumulation of DDT
90 | P a g e
Biochemistry – Nature17
▪
One well studied case of bioaccumulation was with the xenobiotic
dichlorodiphenyltrichloroethane (DDT).
• DDT was initially an insecticide used to control mosquito populations. However,
with DDT being fat-soluble (due to the two benzene rings), it is easily stored in
fat.
o The way DDT attacked insects was by not having insects have calcium
deposits in their exoskeletons.
• One issue with DDT, is that it accumulated in many fish populations. Those fish,
were eaten by birds like ospreys and bald eagles. DDT would cause the
eggshells of the birds of prey to not get enough calcium and then, have thin
eggshells.
o This would cause the eggs to be crushed under the weight of the
parents. This caused a reduction of many bald eagle and osprey
populations, until the ban of DDT in the 1970s.36
Figure 121 Chemical Structure of DDT
Responding to Xenobiotics
•
There are multiple attempts occurring that are trying to combat different xenobiotics so that they do not
have a major effect on the environment.
o One way is by using host-guest chemistry, which involves the synthesis of a host molecule to
bind, non-covalently37, around a guest molecule (in this case, the xenobiotic).
▪ This would form a supermolecule (also known as a host-guest complex), with the guest
(xenobiotic) being trapped within another molecule (host).
c
Figure 122 BOBCalix6 Forming a Supermolecule with Radioactive Cesium Ion
o
36
37
Another attempt at responding to xenobiotics is reducing their output into the environment.
▪ By using biodegradable substances, the synthesized compounds can be degraded
easily by bacteria or other natural processes, producing a non-harmful compound
found in nature.
• Two main biodegradable plastics exist: plant-based hydro-degradable
plastic, and petroleum-based oxo-biodegradable plastic.
Many developing countries still use DDT to combat the effects of malaria.
This can involve van der Waal interactions, hydrogen bonding, and ionic bonds.
91 | P a g e
Biochemistry – Nature17
o
Another way is by using microorganisms break down the xenobiotics. This process is known as
bioremediation.
▪ Often used to reduce the impact of oil spills. Many microorganisms will break down the
oil easily, using it as a food source.
Review Questions
1. Of the amino acids lysine, glutamic acid, leucine, threonine, and serine, which one is most likely to be
found in the interior of a globular protein?
2. List all the non-essential basic amino acids.
3. Under neutral conditions, anthocyanins become what color?
4. Draw the structure of β-D-glucose using the Fischer projection.
5. What are some symptoms of beriberi in adults?
6. While a glycosidic link between the disaccharide maltose is a 1-4 linkage, in amylopectin and
glycogen, there is also ____ linkages.
7. List the differences in the phospholipids in the cell membrane of Archaea, and of Bacteria.
8. An erythro diastereomer is derived from what functional group?
9. How does aggrecan absorb impact shocks?
10. What are the effects of peptide bonds because they contain double bond character?
11. Identify the following molecule:
12. Draw tryptophan.
13. Which of the following is true?
Cytosine: Amino Acid
a.
14.
15.
16.
17.
18.
19.
Cysteine: Linked Amino
Acids in Disulfide Bridge
Cystine: Nitrogenous Base
b.
Cytosine: Nitrogenous
Base
Cysteine: Linked Amino
Acids in Disulfide Bridge
Cystine: Amino Acid
c.
Cytosine: Linked Amino
Acids in Disulfide Bridge
Cysteine: Amino Acid
Cystine: Nitrogenous Base
d.
Cytosine: Nitrogenous
Base
Cysteine: Amino Acid
Cystine: Linked Amino
Acids in Disulfide Bridge
No amino acid has a pKa3 value except which five?
Define coiled coil.
What’s the difference between a simple lipid and a complex lipid?
The equilibrium, Hb + 4O2 ⇌ Hb-(O2)4, shifts to favor the ___ in the lungs.
Pyridoxine, pyridoxal, and pyridoxamine are all classified under what group?
How many hydrogen bonds form between guanine and cytosine in a DNA molecule?
92 | P a g e
Biochemistry – Nature17
20. Which of the following vitamins is fat-insoluble?
a. A
b. B
c. E
d. K
21. What was the original purpose for DDT?
22. Ruhemann’s purple is the result of two ninhydrin molecules surrounding what atom from amino acids?
23. Which of the following is the primary interaction that is the predominant determinant of a polypeptide
chain’s shape in aqueous solution?
a. Salt Bridge
b. Hydrophobic Interactions
c. Dipole-induced Dipole
d. Disulfide Bonds
e. Hydrogen Bonding
24. Xanthosine monophosphate (XMP), produced from de novo synthesis of nucleotides, is an intermediate
between IMP and what?
a. GMP
b. AMP
c. UMP
d. dTTP
25. Draw a peptide bond between the amino acids lysine and glycine. Make glycine have the N-terminus
and lysine have the C-terminus.
26. Thiamine is an important coenzyme for what biological process?
a. Gluconeogenesis
b. Alcoholic Fermentation
c. Krebs Cycle
d. Transamination
27. What is the function of myoglobin?
28. What is the difference between isomerase and a transferase?
29. Draw proline.
93 | P a g e
Biochemistry – Nature17
30. Which of the following is not a terpene?
a.
b.
c.
d.
31.
32.
33.
34.
35.
36.
37.
38.
39.
40.
41.
42.
43.
44.
What are some of the possible benefits with GM food?
What does having a low Km value mean?
During de novo synthesis of pyrimidines, what are the steps to go from UDP to dCTP?
What is the importance of vitamin E?
Which of the following least accurately describes cholesterol?
a. Terpenoid
b. Type of Steroid
c. Simple Lipid
d. Found in the cell membranes of prokaryotes.
The third strand of DNA in triplex DNA only contains two nitrogenous bases? What are those
nitrogenous bases?
Draw α-d-glucose using chair conformation.
What’s the difference between the ribbon model and backbone model for depicting proteins?
What chemical inhibits cytochromes?
a. CO
b. CNc. CO2
d. O2
What are oxidoreductases?
What is the role of LDLs and HDLs?
What’s the difference between amylopectin and glycogen?
____ and _____, both falling under the class known as vitamin ___ is essential for spermatogenesis and
prevention of fetal reabsorption.
When in acid, the phosphate group of a nucleotide contains how many OH groups?
94 | P a g e
Biochemistry – Nature17
45. Which of the following most accurately describes cells?
a. Liposomes
b. Micelles
c. Emulsions
d. None of the above
46. What enzyme is essential for transforming arachadonic acid into prostaglandins and thromboxane?
47. Define NISE.
48. What is chitin used for in arthropods?
49. Why is beta-glucose more structurally stable than alpha-glucose?
50. In B DNA how many nucleotides make up one 360-degree turn?
a. 9
b. 10
c. 11
d. 12
Key Terms
1-4 linkage: A glycosidic link common for many
disaccharides. Formed from the hydroxyl group of
carbon 1 of one monosaccharide, and the hydroxyl
group on carbon 4 of another monosaccharide
undergoing a dehydration synthesis.
Adenylosuccinate: An intermediate in production of
AMP from inosinate.
1,25-dihydroxycholecalciferol (1,25-diOH-D3): An
important type of vitamin D serving to regulate the
plasma’s level of calcium and phosphorus.
A DNA: DNA molecule with 11 base pairings per
360-degree turn. Bases are slightly tilted to the
central axis. Found in conditions of low humidity.
Absorption Spectrum: A spectrum of the
electromagnetic radiation that was transmitted
through a substance that shows the substance’s
absorption of specific wavelengths.
α Helix: A type of secondary protein structure where
the polypeptide follows a coiled configuration with
hydrogen bonds between every fourth amino acid.
Accessory Pigment: Pigments in plants that harvest
light in different spectrum and pass the energy to the
chlorophyll.
Activation Energy (ΔEa): The minimum amount of
energy that must be supplied to any reaction, to get
it to start.
Active Site: The site of an enzyme where the enzyme
temporarily binds to the substrate.
Adenine: A purine found in DNA and RNA that base
pairs to both thymine and uracil.
Adenosine Triphosphate (ATP): A nucleoside
triphosphate that contains adenine, and is used for
energy-storage purposes.
Adenylate (AMP): A nucleotide containing adenine
as its nitrogenous base.
Adipose Tissue: Connective tissue in which fat is
stored as droplets
Aggrecan: An important proteoglycan that is found
in the extracellular matrix of connective tissue. Acts
as a lubricant joint and serves to
α Glucose: A glucose that has the hydrogen on
carbon 1 represented by pointing upwards. The
chirality of this carbon is S.
α Ketoglutaric Acid: A biomolecule that serves as a
precursor to amino acids. When treated by excess
ammonium followed by being reduced by NADH, it
forms an amino acid.
Alanine: A non-polar amino acid, that contains a
methyl (CH3) group as its ‘R’ group.
Alcoholic Fermentation: The biological process of
converting sugars like fructose and glucose into
cellular energy, while also producing ethanol and
CO2 as byproducts.
95 | P a g e
Biochemistry – Nature17
Aldehyde: An organic functional group,
characterized by a carbon that is double bonded to
an oxygen and bonded to a hydrogen
Aldose: A sugar that contains an aldehyde when in
its linear form.
Allosteric Activation: The process of an activator
molecule binding to an allosteric site, allowing the
substrate to bind to the enzyme.
Allosteric Inhibition: Reversible noncompetitive
inhibition.
Allosteric Site: A site where a non-competitive
inhibitor or an allosteric activator binds to on an
enzyme.
Amino Acid: A monomer that consists of a central
carbon bonded to an amine group, carboxylic acid
group, a hydrogen, and an ‘R’ group.
Amino Sugar: A sugar that contains an amine group.
Amphiphilic: A molecule that contains both
hydrophilic and hydrophobic parts
Amphiprotic: A compound or molecule that can
donate and accept a proton.
Apoenzyme: An enzyme that is not catalytically
active and is missing its cofactor.
Arginine: A positively charged, essential and basic
amino acid. ‘R’ group is CH2-CH2-CH2-NH(C=NH2+)-NH2.
Arrhenius Equation: An equation that can be used
to find the rate constant.
Ascorbic Acid: A coenzyme important for acting as
a reducing agent in many reactions. Also known as
vitamin C.
Asparagine: A polar and neutral amino acid. ‘R’
group is CH2-(C=O)-NH2.
Aspartate Transcarbamoylase (ACTase): An
enzyme that catalyzes the addition of aspartate to
carbamoyl phosphate in nucleotide de novo
synthesis.
Aspartic Acid: A negatively charged and acidic
amino acid. ‘R’ group is CH2-(C=O)-O-.
Aspirin: A non-steroidal anti-inflammatory drug that
blocks the synthesis of prostaglandins by stopping
the activity of cyclooxygenase.
Amphoteric: A compound or molecule that can react
as both an acid and as a base.
Backbone Model: A model used for showing
polypeptide organization but does not depict the
secondary structures of proteins.
Amylopectin: A complex form of starch where some
(but not a lot) branching occurs. Branching occurs with
1-6 linkages.
B DNA: DNA molecule with a right-handed helix,
with 10 base pairings per 360-degree turn. Bases
are perpendicular to the central axis.
Amylose: The simplest form of starch where no
branching is observed.
Benedict’s Reagent: A solution that can detect
reducing sugars, consisting of copper (II) sulfate,
sodium citrate, and sodium carbonate.
Anomer: Epimers where the carbons that differ on
at the hemiacetal carbon in the ring configuration.
Anomeric Carbon: The carbon of a hemiacetal
carbon that is an anomer.
Anthocyanin: Tricyclic polyphenol pigments that are
responsible for many of the pink, blue, and red
coloration in plants.
Antiparallel: Structures that are parallel to one
another but are oriented in opposite directions.
Antiparallel β Sheets: A type of secondary structure
where beta-sheets run in opposite directions of one
another.
Beriberi: A disease that is characterized in adults by
irritability, dry skin, disordered thinking, and
progressive paralysis. Caused by a deficiency in
thiamine.
β Glucose: A glucose that has the hydrogen on
carbon 1 represented by pointing downwards. The
chirality of this carbon is R.
Bioaccumulation: The increased concentration of a
xenobiotic in an organism.
96 | P a g e
Biochemistry – Nature17
Biodegradable: A substance that can be degraded
by natural processes, like being degraded by
bacteria.
Biological Pigment: Molecules produced by
metabolism that absorb light (due to their chemical
bonds).
Biomagnification: The increase in concentration of a
xenobiotic as it moves up a food chain.
Biomimetic Synthesis: The process of trying to
synthesize a target molecule through a series of
reactions, that are closely related to those that occur
during biosynthesis in its natural source.
β-pleated Sheets: A secondary-structure of amino
acids, with side-by-side polypeptides that are crosslinked by inter-chain hydrogen bonds.
Bioremediation: The process of using microorganism
to break down xenobiotics.
Biotin: An important coenzyme serving as a carrier
of CO2.
Blubber: The fat of marine mammals used to insulate
the animal from heat loss and serving as a food
reserve.
Bomb Calorimeter: A tool that can be used to test to
see the amount of energy a sample based on the
released thermal energy from the burning sample.
Carbamoyl Phosphate Synthetase Type II (CPS II):
An enzyme that catalyzes many reactions in
nucleotide de novo synthesis like the addition of ATP
added to a bicarbonate ion and the hydrolysis of
glutamine to glutamate and ammonia.
Carbohydrate: Any monosaccharide (sugar
molecule) or a polymer made up of
monosaccharides.
Carboxyglutamate: A nonstandard amino acid that
is involved in blood-clotting proteins.
Carboxyhemoglobin: The complex which contains
hemoglobin and carbon monoxide.
Carotenoid: A group of pigments containing long
hydrocarbon chains with lots of double bonds.
Cellulose: A structural polysaccharide made up of
cellobiose. Forms a straight and tough polymer.
Central Dogma: The summarized idea that genetic
information flows in one direction in cells (DNA to
RNA to protein).
Cerebroside: A simple glycolipid consisting of a fatty
acid unit and a simple carbohydrate.
Chair Conformation: A common representation used
to draw cyclic molecules (usually carbohydrates) in
their most stable and accurate form.
Chaperonin: Protein chambers used to sequester
other proteins during folding.
Chemical Inhibitor: A molecule or compound that
decrease the catalytic activity of an enzyme.
Chirality: Being asymmetric on a structure so that its
mirror image is not superimposable on itself.
Chitin: A structural polysaccharide used to make up
exoskeleton of many arthropods and the cell wall of
many fungi.
Chlorophyll: The primary pigment in plant
photosynthesis, absorbing a lot if light the red and
blue spectrum.
Cholesterol: An essential steroid found on the cell
membranes of animals and serves as an essential
precursor for other steroids.
Choline: A quaternary ammonium that is attached to
three methyl groups and a hydroxyethyl group
(CH2OH). Found in the phospholipid known as
phosphatidylcholine.
Chromatogram: The final result of a sample in
chromatography.
Chromatophore: The part of a pigment that is
responsible for light absorption.
Chromosome: A super-condensed and packaged
form of DNA, that is essential for mitotic division.
Chylomicron: A large lipid-protein complex that
carries fats to the liver, skeletal muscles and adipose
tissue.
Cellobiose: A disaccharide made from two betaglucose units.
97 | P a g e
Biochemistry – Nature17
Cobalamin: A hematopoietic vitamin essential for
certain enzymatic reactions, like the methylation of
homocysteine
and
the
isomerization
of
methylmalonyl coenzyme A. Also known as vitamin
B12.
Codon: A three-nucleotide long sequence that
represents a code for a specific amino acid.
Coenzyme: An organic cofactor
Cofactor: A molecule that is essential for the catalytic
activity of enzymes.
Coiled Coil: A stable structure formed by two alpha
helices wrapping around one another.
Competitive Inhibitor: A molecule that binds to the
active site of an enzyme, blocking the substrate from
binding.
Complementary Base Pairing: The concept that only
a certain type of nitrogenous base can form
hydrogen bonds with another type of nitrogenous
base.
Complete Protein: A protein that contains all of the
essential amino acids for humans.
Complex Lipid: A lipid that can easily hydrolyzed
into simpler constituents.
Condensation Reaction: The process of joining
together to compounds and/or molecules through the
removal of water. Also known as dehydration
synthesis.
Conformation: A shape of a macromolecule that
was induced by environmental factors.
Conjugated Protein: A protein that contains any
non-protein group in it (like metal ions).
C-terminus: The end of a polypeptide that ends with
the carboxyl group.
Cyclooxygenase: An enzyme essential for the
formation of prostaglandins and thromboxane from
arachadonic acid.
Cysteine: A polar and neutral amino acid. ‘R’ group
is CH2-SH.
Cystine: A cross-linked unit found in the disulfide
bridges of tertiary structures, that is the oxidized
dimer form of cysteine.
Cytochrome: A group of enzymes involved with the
reduction of oxygen to water in the mitochondria.
Cytosine: A pyrimidine found in DNA and RNA that
base pairs to guanine.
Deactivation: The loss of an enzyme’s catalytic
activity due to the enzyme being below its optimum
temperature.
Dehydration Synthesis: The process of joining
together to compounds and/or molecules through the
removal of water. Also known as condensation
reaction.
Denaturation: The breakdown of a macromolecule.
De Novo Synthesis: The process of producing
nitrogenous bases essential for nucleic acids, from
scratch.
Deoxynucleoside Triphosphate: A nucleoside that
contains deoxyribose as the pentose sugar, and has
three phosphate groups attached to it. Essential for
DNA elongation.
Deoxynucleotide: A nucleotide
deoxyribose as the pentose sugar.
that
contains
Deoxyribonucleic Acid (DNA): A nucleic acid that
serves to store information of a cell and organism.
Pentose sugar does not contain a hydroxyl group at
carbon 2’.
Diastereomer: A type of stereoisomer where some,
but not all, of the stereocenters (chiral carbons) are
mirror images of each other.
Dichlorodiphenyltrichloroethane
(DDT):
A
xenobiotic used as a pesticide that ended up causing
egg shells of eagles and ospreys to have thin egg
shells, due to lack of proper calcium.
Digestion: The loss of a covalent backbone of
protein molecules.
Dimer: A quaternary structure made up of two
polypeptide chains
Dipeptide: Two amino acids linked together via a
peptide bond.
98 | P a g e
Biochemistry – Nature17
Dipolar Ion: A molecule that has a positive and a
negative charge in the molecule. Also known as
zwitterion.
Disaccharide:
Two
simple
sugar
(monosaccharides) bonded together.
units
Disulfide Bridge: A linking of two cysteines in a
tertiary structure.
DNA Replication: The process of which DNA is
duplicated in the cell. Essential for cells that will soon
undergo mitosis or meiosis.
Double Bond Character: The ability for a molecule
to act similar to a double bond through resonance
but not be a full double bond.
End-product Inhibition: A cellular control mechanism
in where an enzyme that catalyzes the production of
a substance in the cell is then inhibited by that
substance when it has accumulated to a certain level.
Also known as feedback inhibition.
Enediol Rearrangement: The shifting of the carbonyl
group (C=O) in base catalyst.
Enzyme: A polypeptide that serves as a biological
catalyst for many reactions occurring in the
body/cells of an organism.
Enzyme Commission (EC) Number: The number
that is used to identify enzymes. Classed by the
reactions the enzymes catalyze.
Double Helix: A shape characterized by two twisted
structures twisting around each other. Shape of DNA.
Enzyme-substrate Complex: The structure of the
substrate and enzyme when they are (temporarily)
bonded to each other.
D Sugar: A sugar molecule where the last chiral
center (reading top to bottom) has hydroxide group
drawn on the right side of the molecule. Common in
nature.
Enzyme-substrate Specificity: The idea that
enzymes have a high specificity of what substrates
they can have.
Eicosanoid: A simple lipid that is derived from the
fatty acid known as arachadonic acid.
Elaidic Acid: A fatty acid with a carbon-carbon
double bond, resulting in the hydrogens attached to
the carbons being opposite (in space) to one another.
Contains a trans alkene.
Electron Transport Chain: A group of compounds
that pass electrons from one another via redox
reactions. Drives ATP synthesis.
Electrophoresis: A technique for the analysis and
separation of a mixture based on the movement of
charged particles in an electric field.
Emulsion: The process of forming a stable mixture
between two or more liquids that normally cannot be
mixed together (like oil and water).
Enantiomer: A pair of molecules that are mirror
images of each other.
Endergonic: A reaction where reactants have less
free energy than products.
Epimer: Two isomers that differ around of several
asymmetric carbon atoms.
Epimerization: The chemical conversion from one
epimer to another.
Essential Amino Acid: The amino acids that are
important for humans as the human body cannot
properly synthesize them, and so must acquire them
from their diet.
Ester Linkage: A bond between a typical fatty acid
and glycerol, where the resulting fat contains a
specific organic functional group: carbonyl (C=O)
bonded to an oxygen.
Ether Linkage: A bond between the fatty acid and
glycerol of the phospholipids found in the cell
membrane of archaebacteria. Contains a functional
group where a carbon from the fatty acid is
connected to an oxygen from the glycerol.
Exergonic: A reaction where the products have less
free energy than reactants.
Fat: A molecule that consists of both a glycerol and
a fatty acid.
Fatty Acid: Long chains of hydrocarbons with at one
end, a carboxylic acid group.
99 | P a g e
Biochemistry – Nature17
Feedback Inhibition: A cellular control mechanism in
where an enzyme that catalyzes the production of a
substance in the cell is then inhibited by that
substance when it has accumulated to a certain level.
Also known as end-product inhibition.
Fehling’s Solution: A solution that can detect
reducing sugars, where the color shifts from blue to
red. Consists of copper (II) sulfate, sodium, potassium
tartrate, and sodium hydroxide.
Fibrous Protein: A type of protein that is typically
insoluble in water, made of up a repetitive amino
acid sequence and is used for structure, support and
movement.
First Order Reaction: A reaction where the rate is
directly proportional to the concentration of the
reactant.
Fischer
Projection:
A
two-dimensional
representation of a three-dimensional molecule (that
is not in ring conformation). Atoms bonded
horizontally to the core atom are coming towards the
viewer while atoms bonded vertically to the central
core, are pointing away from the viewer.
Folic Acid: A vitamin involved with the biosynthesis
of many compounds. Essential for nucleotide, amino
acid, and red blood cell synthesis. Also known as
vitamin B9.
Furanose: A carbohydrate that, in its cyclic form, is
a 5-membered ring consisting of 4 carbons and 1
oxygen atom.
Galactose: An aldose and hexose monosaccharide
with the molecular formula of C6H12O6. Differs from
glucose by on carbon 4, with the hydroxyl group and
hydrogen being inverted of one another.
Genetically Modified Organism (GMO): An
organism that has had its DNA artificially
manipulated.
Genetic Engineering: The process of genetically
modifying the genetic code of an organism.
Gibbs Free Energy (ΔG): The amount of energy that
can be used in a reaction.
Globular Protein: A type of protein that is typically
soluble in water, made up of an irregular amino acid
sequence, and is typically used to drive the reactions
of metabolism.
Glucogenic Amino Acid: An amino acid that can be
converted to glucose via gluconeogenesis.
Gluconeogenesis: The process of generating
glucose from non-carbohydrate carbon sources,
usually through glycerol and amino acids.
Glucose: An aldose, and hexose monosaccharide
with the molecular formula of C6H12O6. Produced by
plants during photosynthesis.
Glutamic Acid: A negatively charged, and acidic
amino acid. ‘R’ group is CH2-CH2-(C=O)-O-.
Glutamine: A polar and neutral amino acid. ‘R’
group is CH2-CH2-(C=O)-NH2.
Glycerol: A molecule with three carbons attached to
each other (C-C-C), with each carbon being attached
to a hydroxide (OH).
Glycine: A nonpolar amino acid. ‘R’ group is
hydrogen.
Glycogen: A complex form of glucose where there is
a lot of branching. Utilized by animals to store
glucose.
Glycolipid: A sugar-containing lipid.
Glycosaminoglycan: A polysaccharide that consists
of repeating disaccharide units which contain an
amino group and some sort of negatively charged
group.
Glycoside: A compound formed from a simple sugar
(like a monosaccharide) and another compound by
replacement of a hydroxyl group in the sugar
molecule.
Glycosidic Link: A covalent bond that joins a
carbohydrate to another group, which is typically,
but not always, another carbohydrate,
GM Crop: Crops with artificially altered DNA
patterns. Used for things like having crops produce
natural pesticides to increasing crop yields.
Guanine: A purine found in DNA and RNA that base
pairs to cytosine.
100 | P a g e
Biochemistry – Nature17
Guanylate (GMP): A nucleotide that contains
guanine as its nitrogenous base.
Hydroxyproline: A nonstandard amino acid found in
collagen. Similar in structure to proline.
Haworth Projection: A common representation of
drawing the cyclic structure of monosaccharides. The
bottom three lines are drawn as wedges, so to
represent that the atoms are coming to the viewer.
Hypoxanthine: A precursor to guanine and inosinate
in the salvage pathway.
Hematopoietic Vitamin: Any vitamin essential for
the production of red blood cells.
Heme Group: A prosthetic group found in
hemoglobin that contains iron as its central atom.
Hemoglobin: A ligand-carrying molecule that
carries oxygen in the blood.
Heparin Sulfate: A glycosaminoglycan used as an
anticoagulant. Disaccharide units are glucuronic acid
and N-acetyl-glucosamine.
High Density Lipoprotein: A lipid-protein complex
that collects fat from the cells of the body and carries
it to the liver.
Histidine: A positively charged and basic essential
amino acid. ‘R’ group is a functional group known as
an imidazole ring (five member ring containing an
alkene and nitrogen).
Histone: A protein used, which DNA wraps itself
around, to so package DNA more tightly.
Holoenzyme: A catalytically active enzyme.
Induced Fit: A model of enzyme action stating that
the active site of enzymes and the substrate are not
a perfect fit, but the changing of the active site’s
shape (by the substrate) can allow the enzyme and
substrate to bind.
Inosinate (IMP): An important intermediate in purine
de novo synthesis that can form AMP or GMP.
Iodine Number: The maximum amount of iodine
absorbed by a 100-gram sample (like a lipid
substance).
Isoelectric Point: The pH where an amino acid,
excluding the R group, is electrically neutral (with a
positive charge from the amine and a negative
charge from the acid group).
Isoleucine: A nonpolar essential amino acid. R group
is (CH-CH3)-CH2-CH3.
Isomerase: An enzyme involving the transfer of a
chemical group intramolecularly.
Isoprene Rule: A rule stating that terpenes will
always have 5n units, with each terpene being able
to be divided into isopentane units.
Host-guest Chemistry: The synthesis of a host
molecule to bind non-covalently around a xenobiotic.
Ketogenic Amino Acid: An amino acid that can be
degraded into acetyl coenzyme A, which is a
precursor to ketone bodies.
Host-guest Complex: The structure of a guest
molecule (xenobiotic) being trapped within another
molecule (host). Also known as a supermolecule.
Ketone: An organic functional group that contains a
carbon that is double bonded to an oxygen and is
bonded to two carbons.
Hydrogen-bond Acceptor: Molecules involved with
hydrogen bonding, that have a lone pair of electrons
located on an electronegative atom.
Ketose: A sugar that contains a ketone when in its
linear form.
Hydrogen-bond Donor: Molecules involved with
hydrogen bonding, that contain a hydrogen
attached to an electronegative atom.
Kiliani-Fischer Synthesis: The process in which
monosaccharides can have a new chiral carbon
added onto the monosaccharide, producing two
epimers.
Hydrolase:
reactions.
with hydrolysis
Lactose: A disaccharide of glucose and galactose
that is present in milk.
Hydroxylysine: A nonstandard amino acid found in
collagen. Similar in structure to lysine.
Leucine: A nonpolar essential amino acid. R group is
CH2-(CH-CH3)-CH3.
Enzymes
involved
101 | P a g e
Biochemistry – Nature17
Leukotriene: A eicosanoid formed from the action of
the enzyme lipoxygenase. Used within a cell to
mediate immunity and convey information cell-tocell.
Malnutrition: The absence of a regular and
balanced supply of the needed nutrients.
Maltose: A disaccharide made from two alphaglucose units.
Ligase: An enzyme involved with the joining of two
large molecules, via the formation of a new chemical
bond, but at the expense of the hydrolysis of ATP.
Messenger RNA (mRNA): An essential RNA
molecule that is used for translation.
Lineweaver-Burk Equation: An equation that can be
used to calculate the rate of a reaction.
Methionine: A nonpolar essential amino acid. R
group is CH2-CH2-S-CH3.
Lipase: An enzyme involved in the breakdown of
lipids.
Micelle: A spherical structure made of phospholipids
where the exterior is aqueous but the interior is not.
Lipid: A class of biomolecules that have little-to-no
affinity for water but are soluble in organic solvents.
Michaelis
Constant
(Km):
The
substrate
concentration at half the max velocity of a reaction.
Lipoprotein: A complex consisting of lipid and
proteins that allow fats to be transported through the
bloodstream.
Michaelis-Menten Equation: An equation used to
calculate the saturation effect in respect to substrate
concentration.
Liposome: A spherical structure made of
phospholipids, containing an aqueous interior and
aqueous exterior.
Microfibril: A fiber-like strand consisting of cellulose
and glycoproteins.
Lobry de Bruyn-van Ekenstein transformation: A
type of enediol rearrangement where an aldose
transforms into a ketose or a ketose transforms into
an aldose.
Micronutrient: A molecule that is essential for an
organism to survive and be healthy, but need only in
small amounts.
Mobile Phase: The group, in chromatography,
separated from the initial point.
Locating Reagent: A chemical compound that makes
colorless amino acids visible and colorful.
Monomer: A small repeating unit that makes up a
larger molecule (polymer).
Lock and Key Model: A model that states that
enzymes and substrates are a perfect fit for each
other.
Monosaccharide: The simplest unit of a
carbohydrate (sugar). Can no longer be hydrolyzed
to give a simpler sugar unit.
Low Density Lipoprotein (LDL): A lipid-protein
complex that carries fats to the entire body.
Motor Protein: A protein that generate forces to
allow movement of cell or certain biomolecules.
L Sugar: A sugar molecule where the last chiral
center (reading top to bottom) has hydroxide group
drawn on the left side of the molecule. Rare in
nature.
Myoglobin: A molecule that stores oxygen in the
muscles.
Lyase: An enzyme involved with the breaking of
chemical bonds or removal of a group of atoms,
forming a new double bond or ring structure.
Lysine: A basic and positively charged essential
amino acid. R group is CH2-CH2-CH2-CH2-NH3+.
Ninhydrin: A locating reagent, where the reagent
bonds to the nitrogen of the amino acid’s amine
group.
Non-competitive Inhibitor: Irreversible inhibition
where the inhibitor molecule binds to a site different
from the active site of an enzyme, but changes the
shape of the active site.
Macromolecule: A molecule that contains a large
number of atoms.
102 | P a g e
Biochemistry – Nature17
Non-homologous Isofunctional Enzyme (NISE):
Enzymes that are unrelated to each other but
catalyze the same chemical reaction. Evolved in
different organisms through convergent evolution.
N-terminus: The end of a polypeptide that ends with
the amine group.
Nucleic Acid: An organic substance consisting of
repeating units known as nucleotides. Also known as
polynucleotide.
Nucleoside: A nitrogenous base connected to a
pentose sugar.
Nucleoside Kinase: An enzyme involved with the
conversion of uridine into UMP.
Nucleoside Triphosphate: Any nucleoside that
contains three phosphate groups attached to it.
Nucleotide: A pentose sugar, nitrogenous base and
phosphate group attached one-another. The
monomer that makes up a nucleic acid.
Nutrient: Any molecule that is used to maintain the
health of an organism.
Oleic Acid: A fatty acid with a carbon-carbon
double bond, resulting in the hydrogens attached to
the carbons being next to one another (in space).
Contains a cis alkene.
Oligopeptide: A biomolecule made up of 12-20
amino acids.
Optimum Temperature: The temperature which the
enzyme’s catalytic ability works its best.
Origin: The starting point in chromatography, where
the amino acid mixture is placed.
Oxidoreductase: An enzyme involved with a redox
reaction.
Oxyhemoglobin: The product of hemoglobin being
oxygenated in all of its heme groups.
Oxymyoglobin: The product of myoglobin being
oxygenated in all of its heme groups.
Pantothenic Acid: A vitamin B-complex that is a
component of coenzyme A (CoA), which functions in
the transfer of acyl groups.
Paper Chromatography: A technique which involves
a solvent travelling up a paper, separating the
amino acids in an amino acid mixture.
Parallel β Sheets: A type of secondary structure
where beta-sheets run in the same directions of one
another.
Partial Hydrogenation: A situation where some, but
not all, of the carbon-carbon double bonds are
hydrogenated (replacing the role of the electrons
used in a double bond, with them being shared with
another hydrogen group).
Peptide Bond: A bond between the amine group of
one amino acid and the carboxylic acid of another
amino acid. Forms from a condensation reaction.
Performance Enhancing Drug: Steroids used by
people, typically athletes, to enhance strength and
endurance.
Pharmaceutically Active Compound: Xenobiotic
compounds that are human drugs that released from
hospitals or the human body (if not properly
metabolized) into the environment.
Phenylalanine: A nonpolar essential amino acid. R
group is CH2 connected to a benzene ring.
Phosphoanhydride Bond: The bond between two
phosphate groups in nucleoside triphosphate.
Phosphodiester Linkage: The covalent bond
between the phosphate group and a carbon from
the pentose sugar.
Phospholipid: A lipid that typically contains a
glycerol (but not always) bonded to fatty acids and
one phosphate group.
Phosphoribosyl Pyrophosphate (PRPP): A sugar
molecule that is an intermediate in the pyrimidine de
novo pathway.
Polymer: A molecule that has a molecular structure
made primarily up of a large number of simple
repeating units.
Polynucleotide: An organic substance consisting of
repeating units known as nucleotides. Also known as
nucleic acid.
Polypeptide: A polymer biomolecule made up of
monomers known as amino acids
103 | P a g e
Biochemistry – Nature17
Polysaccharide: A carbohydrate polymer made up
of multiple simple sugar (monosaccharide) units.
Racemase: Enzymes that can interconvert between
D and L amino acids.
Porphyrin: Pigment compounds made up of four
heterocyclic rings linked by carbon atoms.
Rancidity: An unpleasant odor and flavor resulting
in lipids that are the result of the deterioration of the
lipid portion of food.
Primary Structure: The unique sequence of amino
acids in the polypeptide chain.
Prion: A misfolded protein that has become an
infectious agent.
Proline: A nonpolar amino acid. R group is CH2-CH2CH2 and it is connected in a cycle to the central
carbon and amino group.
Prostaglandin: A eicosanoid involved with
producing the sensation of pain. Produced at the site
of pain.
Prosthetic Group: Any non-protein group found in a
quaternary structure.
Protein: A biomolecules made up of polypeptide(s).
Protein Assay: A procedure used to measure the
protein concentration of a sample.
Proteoglycan: A structure that consists of a protein
that are attached to a glycosaminoglycan.
Proteolytic Enzyme: An enzyme involved with the
splitting of a peptide bond.
Proteome: The totality of proteins expressed within
a cell, tissue, or organism.
Purine: A large nitrogenous base found in
nucleotides that is a 6-membered ring fused to a 5member ring.
Pyranose: A carbohydrate that, in its cyclic form, is
a 6-membered ring consisting of 5 carbons and 1
oxygen atom.
Pyrimidine: A small nitrogenous base found in
nucleotides that is a 6-membered ring
Pyrimidine Phosphoribosyl Transferase: An
important enzyme that is essential for the production
of PRPP.
Quaternary Structure: A polypeptide structure that
contains multiple, interacting polypeptide chains.
Rate Constant (k): The effect on activation energy,
temperature and the frequency of the reaction
based on the rate of the reaction.
Reducing Sugar: Any sugar that is capable of acting
as a reducing agent (being readily oxidized) due to
a free aldehyde of free ketone group.
Reductive Amination: A biomimetic synthesis
involving the synthesis of amino acids from alphaketoacid.
Residue: The amino acids of a polypeptide chain.
Resonance: The movement of delocalized electrons
through a molecule, while still maintaining the same
connectivity. This causes the bonding of atoms in the
molecule to not be able to be described by one
Lewis diagram.
Retinoid: A group of fat-soluble vitamins essential
for vision, growth, and reproduction. Also known as
vitamin A.
Ribbon Model: A model used for showing
polypeptide organization that depicts the secondary
structures of proteins.
Riboflavin: A vitamin that is an essential component
of FAD. Also known as vitamin B2.
Ribonucleic Acid (RNA): A nucleic acid essential for
expressing the stored genetic information. Pentose
sugar has a hydroxyl carbon at carbon 2’.
Ribonucleotide: A nucleotide that contains ribose as
its pentose sugar.
Ribose: A pentose aldose monosaccharide that is
one of the 3 major components required to make a
nucleotide.
Ribulose: The ketose monosaccharide equivalent of
the aldose ribose.
104 | P a g e
Biochemistry – Nature17
Rickets: A disease where bones do not harden and
become malformed, causing the legs to be
abnormally bent. Caused by a deficiency in vitamin
D.
Ruhemann’s Purple: A molecule that is 2 ninhydrin
molecules surrounding a nitrogen atom.
Salvage Pathway: Producing nitrogenous bases
from a nucleic acid source.
Saponification: The process which glycerides are
hydrolyzed by heating them with sodium hydroxide.
Forms soaps.
Saturated Fatty Acid: A fatty acid that contains no
carbon-carbon double bonds in the hydrocarbon
chain.
Screw Sense: The direction of alpha helices in
relation to the direction it rotates.
Scurvy: A disease where people have swollen
bleeding gums and the opening of many healed
wounds. Caused by a deficiency of vitamin C.
Secondary Structure: The folding of primary
structures, which is usually caused by hydrogen
bonding.
Second Order Reaction: A reaction where the rate
of the reaction is proportional to the square of the
reactant’s concentration.
Semi-conservative Replication: The model of DNA
replication, where the daughter strands will contain
one parent strand of DNA, and one new strand of
DNA.
Serine: A polar, but neutrally charged amino acid. R
group is CH2-OH.
Spectrophotometer: A tool used to find the amount
of light absorbed at maximum wavelength.
Sphingomyelin: A type of phospholipid that
contains a sphingosine.
Sphingosine: A group containing an unsaturated
18-carbon long fatty acid connected to an amino
alcohol.
Spontaneous: A reaction that is thermodynamically
favorable, due to the Gibbs free energy being
negative.
Squalene: A terpene that is used to produce
cholesterol.
Standard Amino Acid: The 20 α-amino acids found
in nearly every naturally occurring protein.
Standard Curve: In a protein assay, the curve
produced from the known protein concentrations
measured against the assay measurement on Y axis.
Standard Solution: A solution of proteins of known
concentration.
Starch: A polysaccharide made up of maltose.
Utilized for long-term energy storage.
Stationary Phase: The group, in chromatography,
that has not moved from the initial point.
Stearic Acid: A fatty acid that contains no carboncarbon double bonds in the 18-carbon long
hydrocarbon chain.
Steric Hindrance: The slowing of a chemical reaction
or reactivity of a molecule due to the size of the
groups within a molecule.
Side Chain: The R groups of an amino acid in a
polypeptide.
Steroid: A simple lipid made up of a tetracyclic
skeleton, made of four fused rings (one that is sixmembered and one that is five-membered).
Simple Lipid: Lipids which are not easily hydrolyzed
by aqueous base or acid.
Steroidal Backbone: The tetracyclic skeleton that
makes up a steroid.
Solvent Front: In paper chromatography, the top
line which the solvent has reached on the piece of
paper
Substrate: The reactant of a reaction that is
catalyzed by an enzyme.
Space-filling Model: A protein model that shows the
shape of a protein.
Sucrose: A disaccharide made up of glucose and
fructose.
105 | P a g e
Biochemistry – Nature17
Super Molecule: The structure of a guest molecule
(xenobiotic) being trapped within another molecule
(host). Also known as a host-guest complex.
Surfactant: A substance that accumulate at water
surfaces, changing the surface properties.
Template Strand: A strand of DNA which will be
used by a polymerase enzyme for either DNA
replication or transcription.
Terpene: A large group of nonsaponifiable simple
lipids made up of isopentane, that does not contain
a tetracyclic skeleton.
Terpenoid: A broad group of compounds that are a
derivative of terpenes but do not contain the
isoprene units.
Tertiary Structure: A polypeptide structure involving
the chain twisting resulting in R group interactions.
Thiamine: A type of vitamin B involved with the
oxidative decarboxylation of alpha ketoacid and
the degradation of alpha-ketol in the citric cycle.
Also known as vitamin B1.
Thin-layer
Chromatography
(TLC):
Chromatography using the process of separating
pigments with the use of small plastic sheets coated
with silica or alumina.
Triacylglycerol: A glycerol that is attached to three
fatty acid groups. Also known as triglyceride.
Triglyceride: A glycerol that is attached to three
fatty acid groups. Also known as triacylglyceride.
Tripeptide: Three amino acids linked together
through peptide bonds.
Triplet Code: The concept that three nucleotide
nitrogenous base sequences are used to code for a
specific amino acid (with the exceptions of UGA,
UAG, and UAA, which code for the stopping of
translation).
Triplex DNA: A DNA helical structure that contains
three strands of DNA wrapped around each other.
Tryptophan: A nonpolar essential amino acid. R
group is an indole (five-member ring containing an
alkene and NH, fused to a benzene ring).
Tyrosine: A polar and neutrally charged amino acid.
R group is a benzene group attached to an OH.
Unsaturated Fatty Acid: A fatty acid that contains
one or more carbon-carbon double bonds in the
hydrocarbon chain.
Unzipping: The breaking of hydrogen bonds
between nitrogenous bases in DNA.
Threonine: A polar and neutrally charged essential
amino acid. R group is (CH-CH3)-OH.
Uracil: A pyrimidine found in RNA that base-pairs to
adenine.
Thromboxane: An important eicosanoid that is
involved with blood clotting.
Uridine Monophosphate (UMP): A nucleotide that
contains uracil as its nitrogenous base.
Thymine: A pyrimidine found in DNA that base pairs
to adenine.
UV-visible Spectroscopy (UV-vis): A commonly
used protein assay that shows how proteins interact
with UV and visible light.
Transamination: The process of transferring the
amine group from biomolecule to another.
Valine: A nonpolar essential amino acid. R group is
(CH-CH3)-CH3.
Transcription: The process that occurs in the cell’s
nucleus, involving the production of RNA from DNA.
Vitamin: Organic micronutrients.
Transferase: An enzyme involves with the transfer of
a specific functional group from one molecule to
another.
Vitamin A: A group of fat-soluble vitamins essential
for vision, growth, and reproduction. Also known as
retinoid.
Translation: The process that occurs in the cytoplasm
of a cell, involving the production of a polypeptide
chain from a mRNA sequence
Vitamin B3: Vitamins, like niacin and nicotinamide,
serving as important components of NAD+
Vitamin B6: A collective term containing the vitamins
pyridoxine, pyridoxal, and pyridoxamine.
106 | P a g e
Biochemistry – Nature17
Vitamin B-complex: All essential water-soluble
vitamins, with the except of vitamin C.
Wire Model: A model used for depicting proteins,
showing the polypeptide chain and the side chains.
Vitamin C: A coenzyme important for acting as a
reducing agent in many reactions. Also known as
ascorbic acid.
Wohl Degradation: The process in which a chiral
carbon atom is removed from an aldose, producing
one product.
Vitamin D: A group of fat-soluble vitamins that are
sterols with hormone-like function
Xanthosine Monophosphate: An important
intermediate for producing GMP from IMP.
Vitamin E: A fat-soluble vitamin that serves as an
important antioxidant.
Xenobiotic: A compound that may be found within a
living organism but are foreign to that organism.
Vitamin Fortification: The process of adding
vitamins into food items they were originally not in.
Xenoestrogen: A xenobiotic that mimics the effects
of estrogen.
Vitamin K: A fat-soluble vitamin that serves as a
coenzyme in the carboxylation of certain glutamic
acid residues.
Z DNA: DNA molecule that is a left-handed helix
with 12 base pairs per 360-degree turn. Based are
tilted relative to the central axis.
Wax: Complex lipids that are esters of long-chain
fatty acids with long-chain alcohols.
Zeroth Order Reaction: A reaction where the rate if
a reaction is independent of a reactant’s
concentration.
Williamson Ether Synthesis: An organic reaction
that forms an ether from an organohalide and an
alkoxide.
Zwitterion: A molecule that has a positive and a
negative charge in the molecule. Also known as
dipolar ion.
Review Question Answers
1. Of the amino acids lysine, glutamic acid, leucine, threonine, and serine, which one is most likely to be
found in the interior of a globular protein?
Leucine, because leucine’s R group is non-polar and globular proteins are typically soluble in water. This
means if you have leucine in a globular protein, it must be interior of the protein (away from the water),
or else the globular protein might not be soluble. Glutamic acid, lysine, threonine, and serine all have
polar R groups and so can be on the exterior and still keep the protein’s water-solubility.
2. List all the non-essential basic amino acids.
None. All the basic amino acids are essential
3. Under neutral conditions, anthocyanins become what color?
Blue to purple
4. Draw the structure of β-D-glucose using the Fischer projection.
5. What are some symptoms of beriberi?
Irritability, dry skin, disordered thinking, and progressive paralysis
6. While a glycosidic link between the disaccharide maltose is a 1-4 linkage, in amylopectin and
glycogen, there is also _1-6_ linkages.
107 | P a g e
Biochemistry – Nature17
7. List the differences in the phospholipids in the cell membrane of Archaea, and of Bacteria.
• Archaea have ether linkages instead of ester linkages
• Archaeal phospholipids are of L configuration while bacteria have D configuration
• Archaeal fatty acid tails contain branched alkyl chains, while bacteria have unbranching tails.
8. An erythro diastereomer is derived from what functional group?
Cis alkene
9. How does aggrecan absorb impact shocks?
By having water molecules that are attracted to the glycosaminoglycans be shaken off when a force is
applied. This causes the aggrecan to easily deform.
10. What are the effects of peptide bonds because they contain double bond character?
Peptide bond is planar. Bond is longer than a typical single bond but not as long as a typical double
bond.
11. Identify the following molecule:
Thymine
12. Draw tryptophan as a zwitterion.
13. Which of the following is true?
d.
Cytosine: Nitrogenous
Base
Cysteine: Amino Acid
Cystine: Linked Amino
Acids in Disulfide Bridge
14. No amino acid has a pKa3 value except which five?
Histidine, Arginine, Lysine, Aspartic Acid, and Glutamic Acid
15. Define coiled coil.
A stable structure formed by two alpha helices wrapping around one another.
16. What’s the difference between a simple lipid and a complex lipid?
Simple lipids can no longer be hydrolyzed into smaller units while complex lipids can.
17. The equilibrium, Hb + 4O2 ⇌ Hb-(O2)4, shifts to favor the __products_ in the lungs.
18. Pyridoxine, pyridoxal, and pyridoxamine are all classified under what group?
Vitamin B6
19. How many hydrogen bonds form between guanine and cytosine in a DNA molecule?
3
20. Which of the following vitamins is fat-insoluble?
b. B
21. What was the original purpose for DDT?
Pesticide to control mosquito populations
22. Ruhemann’s purple is the result of two ninhydrin molecules surrounding what atom from amino acids?
N
108 | P a g e
Biochemistry – Nature17
23. Which of the following is the primary interaction that is the predominant determinant of a polypeptide
chain’s shape in aqueous solution?
24. Xanthosine monophosphate (XMP), produced from de novo synthesis of nucleotides, is an intermediate
between IMP and what?
a. GMP
25. Draw a peptide bond between the amino acids lysine and glycine. Make glycine have the N-terminus
and lysine have the C-terminus.
26. Thiamine is an important coenzyme for what biological process?
c. Krebs Cycle
27. What is the function of myoglobin?
Store oxygen in muscles
28. What is the difference between isomerase and a transferase?
Transferase is an enzyme involved with the transfer of a functional group from one molecule to another.
Isomerase involves the transfer of a functional group intramolecularly.
29. Draw proline.
30. Which of the following is not a terpene?
d.
31. What are some of the possibly benefits with GM food?
• Longer shelf life
• Improved flavor, texture, and nutritional value
• Increased pest and disease resistance
• Ability to produce a supply of important nutrients like vitamins
• Tolerance to a wider range of growing conditions
• Increased crop yields
32. What does having a low Km value mean?
Reaction is going quickly. Enzyme has a high affinity to the substrate.
33. During de novo synthesis of pyrimidines, what are the steps to go from UDP to dCTP?
UDP → UTP → CTP → CDP → dCDP → dCTP
34. What is the importance of vitamin E?
Antioxidant. Essential to prevent non-enzymatic oxidation, especially those caused by free radicals.
109 | P a g e
Biochemistry – Nature17
35. Which of the following least accurately describes cholesterol?
d. Found in the cell membranes of prokaryotes.
36. The third strand of DNA in triplex DNA only contains two nitrogenous bases? What are those
nitrogenous bases?
Protonated cytosine and thymine.
37. Draw α-d-glucose using chair conformation.
38. What’s the difference between the ribbon model and backbone model for depicting proteins?
The ribbon model shows secondary structures like alpha helices and beta-pleated sheets.
39. What chemical inhibits cytochromes?
40. What are oxidoreductases?
An enzyme involved in any redox reaction.
41. What is the role of LDLs and HDLs?
HDLs collect fats from cells and brings it to the liver. LDLs carry fats around the body.
42. What’s the difference between amylopectin and glycogen?
Amylopectin has a lot less branching than glycogen.
43. _Retinol__ and __retinal__, both falling under the class known as vitamin _A_ is essential for
spermatogenesis and prevention of fetal reabsorption.
44. When in acid, the phosphate group of a nucleotide contains how many OH groups?
2
45. Which of the following most accurately describes cells?
a. Liposomes
46. What enzyme is essential for transforming arachadonic acid into prostaglandins and thromboxane?
Cyclooxygenase
47. Define NISE.
Enzymes that are unrelated to each other but catalyze the same chemical reaction. Evolved in different
organisms through convergent evolution.
48. What is chitin used for in arthropods?
Important component of their exoskeleton
49. Why is beta-glucose more structurally stable than alpha-glucose?
The OH on carbon 1 is close to the OH on carbon 2 in alpha glucose causing steric hindrance.
50. In B DNA how many nucleotides make up one 360-degree turn?
110 | P a g e
Biochemistry – Nature17
References
i
Image from http://www.nutrientsreview.com/carbs/monosaccharides-galactose.html
Image from https://www.meritnation.com/ask-answer/question/what-is-essentially-the-difference-between-form-ofgluco/chemistry/3831938
ii
iii
Images from http://www.chem.ucalgary.ca/courses/350/Carey5th/Ch25/ch25-3-1.html
iv
Image from Organic Chemistry 6th Edition, by L. G. Wade Jr
v
Image from https://socratic.org/questions/how-can-i-draw-axial-and-equatorial-bonds-in-glucose
Image from https://www.meritnation.com/ask-answer/question/what-is-the-difference-between-d-sugar-and-lsugar/biomolecules/9593113
vi
vii
Image from Organic Chemistry 6th Edition, by L. G. Wade Jr
viii
Image from http://wps.prenhall.com/wps/media/objects/340/348272/wade_ch23.html
ix
Image from Organic Chemistry 6th Edition, by L. G. Wade Jr
x
Image from Organic Chemistry 3rd Edition, by David R. Klein
xi
Image from https://www.name-reaction.com/williamson-ether-synthesis
xii
Image from Organic Chemistry 3rd Edition, by David R. Klein
xiii
Image from AK Lectures: https://www.youtube.com/watch?v=hMHs6NRRVcA
xiv
Image from Organic Chemistry 3rd Edition, by David R. Klein
Image from https://www.quora.com/What-type-of-isomerism-is-shown-by-the-compound-CH3CH-OH-CH-CH3CH2CH2CH2OH-and-how-many-are-there
xv
xvi
Image from Organic Chemistry 6th Edition, by L. G. Wade Jr
xvii
Image from Biology 9th edition, by Campbell and Reece
xviii
Image from Biology 9th edition, by Campbell and Reece
xix
Image from http://pubs.rsc.org/-/content/articlelanding/2009/cs/b808639g/unauth
Image from
https://bio.libretexts.org/Under_Construction/BioStuff/BIO_101/Reading_and_Lecture_Notes/Organic_Chemistry_and_B
iochemistry
xx
xxi
Image from https://mmegias.webs.uvigo.es/02-english/5-celulas/2-componentes_glucidos.php
Image from AK Lectures:
https://www.youtube.com/watch?v=l3W60xr9ac4&index=8&list=PL9jo2wQj1WCM3YIHEhlBVOY2JZyGGQssn
xxii
Image from
https://www.learner.org/courses/chemistry/text/text.html?dis=U&num=Ym5WdElUQS9PQ289&sec=YzJWaklUQS9OeW
89
xxiii
xxiv
Image from https://www.education.com/science-fair/article/lipid-testing/
111 | P a g e
Biochemistry – Nature17
xxv
Image from http://en.wikipedia.org/wiki/Trans_fat
xxvi
Image from https://www2.chemistry.msu.edu/faculty/reusch/virttxtjml/lipids.htm#phoslpd
xxvii
Image from Biochemistry 5th edition by Jeremy M. Berg, John L Tymoczko and Lubert Stryer
xxviii
Image from Principles of Virology 4th edition by Jane Flint, Vincent Racaniello, Glenn Rall, and Anna Skalka
Image from https://www.khanacademy.org/science/biology/bacteria-archaea/prokaryote-structure/a/prokaryotestructure
xxix
xxx
Image from Biochemistry 5th edition by Jeremy M. Berg, John L Tymoczko and Lubert Stryer
xxxi
Image from https://www2.chemistry.msu.edu/faculty/reusch/virttxtjml/lipids.htm
xxxii
Image from Biochemistry 5th edition by Jeremy M. Berg, John L Tymoczko and Lubert Stryer
xxxiii
Image from https://www2.chemistry.msu.edu/faculty/reusch/virttxtjml/lipids.htm#steroid2
xxxiv
Image from http://www.essentialchemicalindustry.org/materials-and-applications/surfactants.html
xxxv
Image from Organic Chemistry by William Brown
xxxvi
Image from Organic Chemistry 6th Edition, by L. G. Wade Jr
xxxvii
Image from Biochemistry 5th edition by Jeremy M. Berg, John L Tymoczko and Lubert Stryer
xxxviii
Image from https://www2.chemistry.msu.edu/faculty/reusch/virttxtjml/lipids.htm#steroid2
xxxix
Image from Organic Chemistry 6th Edition, by L. G. Wade Jr
Image from http://www.ib.bioninja.com.au/standard-level/topic-2-molecular-biology/23-carbohydrates-andlipids/lipoproteins.html
xl
xli
Image from Pearson Baccalaureate Higher Level Chemistry 2nd Edition by Catrin Brown and Mike Ford
xlii
Image from https://glossary.periodni.com/glossary.php?en=zwitterion
xliii
Image from http://www.chem.ucalgary.ca/courses/351/Carey5th/Ch27/ch27-1-4-2.html
xliv
Image from http://www.phschool.com/science/biology_place/biocoach/bioprop/landd.html
Watanabe, A., Yoshimura, T., Mikami, B., Hayashi, H., Kagamiyama, H., & Esaki, N. (2002). Reaction Mechanism of
Alanine Racemase from Bacillus stearothermophilus X-RAY CRYSTALLOGRAPHIC STUDIES OF THE ENZYME BOUND
WITHN-(5′-PHOSPHOPYRIDOXYL) ALANINE. Journal of Biological Chemistry, 277(21), 19166-19172.
xlv
xlvi
Image from http://www.web-books.com/MoBio/Free/Ch2B.htm
xlvii
Image from http://research.cm.utexas.edu/nbauld/peptides.htm
xlviii
Image from http://cbc.chem.arizona.edu/classes/bioc460/spring/460web/lectures/LEC4_Peptides/LEC4_Peptides
xlix
Image from Organic Chemistry 6th Edition, by L. G. Wade Jr
l
Image from Biology 9th edition, by Campbell and Reece
li
Image from http://slideplayer.com/slide/8459582/
lii
Image from Pearson Baccalaureate Higher Level Chemistry 2nd Edition by Catrin Brown and Mike Ford
112 | P a g e
Biochemistry – Nature17
Image from Molecular Biology of the Cell 5th Edition by Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith
Roberts, and Peter Walter
liii
liv
Image from Pearson Baccalaureate Higher Level Chemistry 2nd Edition by Catrin Brown and Mike Ford
Image from Molecular Biology of the Cell 5th Edition by Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith
Roberts, and Peter Walter
lv
Image from Molecular Biology of the Cell 5th Edition by Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith
Roberts, and Peter Walter
lvi
Image from Pearson Baccalaureate Higher Level Chemistry 2nd Edition by Catrin Brown and Mike Ford
lvii
Image from Molecular Biology of the Cell 5th Edition by Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff,
Keith Roberts, and Peter Walter
lviii
Image from https://www.khanacademy.org/science/biology/energy-and-enzymes/introduction-toenzymes/a/activation-energy
lix
Image from
https://chem.libretexts.org/Core/Physical_and_Theoretical_Chemistry/Kinetics/Experimental_Methods/Using_Graphs_to_
Determine_Integrated_Rate_Laws
lx
lxi
Image from Pearson Baccalaureate Higher Level Chemistry 2nd Edition by Catrin Brown and Mike Ford
lxii
Image from https://chelseaharripersad.wordpress.com/tag/lineweaver-burk-plot/
lxiii
Image from http://slideplayer.com/slide/9550040/
lxiv
Image from Image from Pearson Baccalaureate Higher Level Chemistry 2nd Edition by Catrin Brown and Mike Ford
lxv
Image from http://www.biology-pages.info/E/EnzymeKinetics.html
lxvi
Image from Pearson Baccalaureate Higher Level Chemistry 2nd Edition by Catrin Brown and Mike Ford
lxvii
Image from Organic Chemistry 6th Edition, by L. G. Wade Jr
Image from Molecular Biology of the Cell 5th Edition by Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff,
Keith Roberts, and Peter Walter
lxviii
lxix
Image from Pearson Baccalaureate Higher Level Chemistry 2nd Edition by Catrin Brown and Mike Ford
lxx
Image from Pearson Baccalaureate Higher Level Chemistry 2nd Edition by Catrin Brown and Mike Ford
lxxi
Image from https://medical-dictionary.thefreedictionary.com/hemoglobin+A
lxxii
Image from Pearson Baccalaureate Higher Level Chemistry 2nd Edition by Catrin Brown and Mike Ford
lxxiii
Image from http://en.citizendium.org/wiki/Carotenoid
lxxiv
Image from http://www.sciencedirect.com/science/article/pii/S0963996911006454
Image from https://www.khanacademy.org/test-prep/mcat/chemical-processes/separations-purifications/v/thin-layerchromatography
lxxv
lxxvi
Image from Biochemistry 5th edition by Richard Harvey and Denise Ferrier
lxxvii
Image from http://www.sparsen.com/biochemistry/vitamin-b6-pyridoxine-sources/
113 | P a g e
Biochemistry – Nature17
Image from Biochemistry 5th edition by Richard Harvey and Denise Ferrier
lxxviii
lxxix
Image from Biochemistry 5th edition by Richard Harvey and Denise Ferrier
lxxx
Image from Biochemistry 5th edition by Richard Harvey and Denise Ferrier
lxxxi
Image from http://www.compoundchem.com/2015/01/13/vitamins/
lxxxii
Image from Organic Chemistry 6th Edition, by L. G. Wade Jr
lxxxiii
Image from https://mrrittner.weebly.com/unit-4-cell-cycle.html
lxxxiv
Image from https://www.quora.com/Why-is-DNA-anti-parallel-in-nature
lxxxv
Image from Genetics Analysis and Principles 3rd edition by Robert J. Brooker
lxxxvi
Image from Genetics Analysis and Principles 3rd edition by Robert J. Brooker
lxxxvii
Image from http://www.madsci.org/posts/archives/1997-12/874439835.Ge.r.html
Image from Molecular Biology of the Cell 5th Edition by Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff,
Keith Roberts, and Peter Walter
lxxxviii
Image from
http://www.columbia.edu/cu/biology/courses/w3034/Larry/readings/PurineChapter/PurineChapter.html
lxxxix
xc
Image from http://www.columbia.edu/cu/biology/courses/w3034/Larry/readings/PurineChapter/PurineChapter.html
xci
Image from http://www.plantphysiol.org/content/138/4/1926
xcii
Image from http://www.plantphysiol.org/content/138/4/1926
Image from http://www.namrata.co/orotic-aciduria-causes-clinical-manifestations-diagnosis-and-treatment/steps-ofde-novo-pyrimidine-biosynthesis/
xciii
xciv
Image from http://www.bioinfo.org.cn/book/biochemistry/chapt21/bio6.htm
xcv
Image from http://watcut.uwaterloo.ca/webnotes/Metabolism/Nucleotides.html
xcvi
Image from https://seqcore.brcf.med.umich.edu/sites/default/files/html/mcb500/na/ampgmp.html
xcvii
Image from Biochemistry 5th edition by Jeremy M. Berg, John L Tymoczko and Lubert Stryer
xcviii
Image from Biology 9th edition, by Campbell and Reece
xcix
c
Image from Pearson Baccalaureate Higher Level Chemistry 2nd Edition by Catrin Brown and Mike Ford
Image from http://globalnewsconnect.com/improved-method-to-clean-up-legacy-radioactive-waste/
114 | P a g e