BIOCHEMISTRY
IB SYLLABUS TOPIC 3
I. BASIC CHEMISTRY
A. Elements Found in Living Things
1. Carbon
A. found in carbohydrates, lipids, proteins, nucleic acids
2. Oxygen
A. found in carbohydrates, lipids, Proteins, nucleic acids
3. Hydrogen
A. found in carbohydrates, lipids, proteins, nucleic acids
4. Nitrogen
A. found in proteins and nucleic acids
5. Phosphorus
A. found in nucleic acids, phospholipids, bones and teeth
B. often found in the form of phosphate (PO43-)
6. Sulphur
A. found in proteins
7. Calcium
A. found in bones and teeth
B. essential for opening and closing of stomata, muscle contraction,
nerve transmission and blood clotting
8. Iron
A. found in hemoglobin
9. Sodium
A. essential for nerve transmission
B. Ways of Showing Chemical Structure
1. Molecular Formula
a. e.g. C6H12O6 (glucose)
b. only the atoms and their relative proportions
c. the spatial positions of the atoms is not shown
2. Empirical Formulae
a. the simplest whole number ratios of the elements are shown
b. many different compounds can have the same empirical formula
i. e.g. CH2O can be C6H12O6 (glucose) or C2H4O2 (vinegar) or even just
CH2O (formaldehyde)
ii. What's different is their total molar mass: glucose is 180.18 g/mol,
vinegar is 60.06 g/mol and formaldehyde is 30.03 g/mol
3. Structural Formulae
a. attempt to show (in two dimensions) the relative positions of the atoms
b. Molecules with the same molecular formula can have different structural
formulae
i. These molecules (called isomers) have different properties from one
another by virtue of a rearrangement of their constituent atoms
ii. An example is C4H10O which can be 1-butanol, 2-butanol, diethyl
ether, or methyl propyl ether.
1-Butanol
2-butanol
Diethyl ether methyl propyl ether
iii. Another example is C6H12O6 which can be a number of simple sugars
such as glucose, fructose and galactose
Glucose
Fructose
Galactose
3. Ball and Stick Models
A. use balls and sticks to show the spatial arrangement of atoms in a molecule
i. balls represent the atoms and sticks represent the bonds
ii. Sticks can be flexible or rigid depending on the type of bond represented
ii. Good models show the bonds at correct angles and the distances between
atomic nuclei are in proportion
B. can be inconvenient to draw on paper
4. Space-filling Models
A. use three-dimensional spheres where the radii are proportional to the atomic radii
and the center-to-center distances are proportional to the distances between the nuclei
all to the same scale
B. also inconvenient to draw on paper
For information purposes only:
http://en.wikipedia.org/wiki/CPK_coloring
C. Types of Bonds
1. Ionic
A. usually between a metallic element and a non-metallic element
B. the metallic atom(s) gives one or more electrons to the non-metallic
atom(s) so that the atoms become charged ions
C. metallic ions are positively charged and non-metallic ions are
negatively charged
D. because the ions are oppositely charged, they attract each other
negatively charged ions are attracted to nearby ions of the opposite
charge so that individual molecules do not exist
F. instead the ions form ionic crystals/solids that tend to dissociate in
water and other polar solvents, have high melting and boiling points
and conduct electricity when melted
A. usually between two non-metallic elements or between hydrogen
and one of the elements in Rows 2 and 3 of the Periodic Table
B. the atoms share electrons in such a way that each atom has a stable
electron arrangement
i. no ions are formed and the atoms do not gain a charge
C. the sharing of electrons results in bonding
D. individual molecules of solid, liquid or gas are formed
i. tend to dissolve in non-polar solvents but not in water (this
depends on how polar the molecules are and their size), have
low melting and boiling points and do not conduct electricity
when melted
E. carbon often forms covalent bonds
F. water has covalent bonds that are polar
i. but water will also form ions
ii. This illustrates the fact that covalent and ionic bonds are
merely two ends of a continuum
II. WATER
A. Chemical structure and Polarity
1. Chemical and Molecular Formulae
a. Molecular Formula: H2O
B. Structural Formula
http://www.gcsescience.com/a30-covalent-bond-water-molecule.htm
c. Ball and Stick Model
http://www.progressivegardens.com/growers_guide/waterstructure.jpg
d. Space-Filling Model
http://upload.wikimedia.org/wikipedia/commons/thumb/1/1c/Water_molecule_3D.svg/100pxWater_molecule_3D.svg.png
2. Polarity and Hydrogen Bonding
A. describes the uneven distribution of electrons or uneven electron density of
the water molecule hydrogen atom shares one pair of electrons with the oxygen
atom and the oxygen atom also has 2 more pairs of electrons that are not
shared with any other atom
B. the oxygen atom has a partialnegative charge and the hydrogen atoms each
have a partial positive charge
C. the partially positive hydrogen atoms are attracted to partially negative
oxygen atoms nearby resulting in a hydrogen bond
D. hydrogen bonding and polarity of water contribute to the properties of water
that are so important to life
1. Water is colorless and transparent
a. light is able to penetrate water and Tissues
2. Water has a high surface tension
a. some animals are able to “walk” on water
i. e.g. water strider (insects)
3. The solid is less dense than the liquid
a. ice insulates the liquid water underneath it which is important to the organisms that
live in the water
b. aquatic environments freeze from the top down, not bottom up
i. plants that are anchored to the substrate do not freeze and die
4. Water is liquid at the average temperatures in most parts of the world
a. water provides a liquid medium/habitat for living things and within living things (cells)
5. Water has a low viscosity
a. water flows easily
i. is the medium for blood, intracellular fluid, minerals and sugars in plants etc.
6. Water is the universal solvent
a. many compounds dissolve in water and are able to be used in chemical reactions that
are necessary for life
i. ionic bonds can be broken apart in water; the ions dissociate
ii. Compounds with covalent bonds can be slightly polar and therefore
also dissolve in water
Sugar dissolving in water
7. Water has a high specific heat capacity
a. it takes the addition of a lot of energy to increase/decrease the temperature of water
or make water evaporate/freeze
i. the evaporation of sweat removes a lot of energy from an organism
ii. Large bodies of water are relatively stable environments for organisms to live
in
iii. Land near large bodies of water do not experience as great a variability in
temperature because the water bodies can absorb heat
iv. Organisms' bodies are not likely to freeze
v. organisms can have relatively stable internal temperatures
C. Acids and Bases
1. pure water spontaneously dissociates into H+ ions and OH- ions
a. acids are substances that donate protons or H+ ions to bases
i. the greater the concentration of H+ ions, the more acidic the solution
b. bases are substances that accept protons or H+ ions from acids
i. often have OH- ions
ii. the greater the concentration of OH- ions, the more basic the solution
c. strong acids or bases dissociate more completely in solution
i. e.g. HCl and NaOH
d. weak acids or bases do not dissociate completely
i. e.g. carbonic acid H2CO3 and Ammonia NH3
ii. These compounds exist in equilibrium such that there is a fixed ratio of
dissociation products to reactants
iii. This equilibrium can be disturbed when either more product or more
reactant is added to the solution which results in the formation of the other
material
iv. e.g. carbonic acid dissociates as in the equation below:
H2CO3
=
H+ + HCO3-
v. If more H2CO3 is added more product will be formed
vi. If more H+ or HCO3- is added to the solution, more H2CO3 will be
formed
2. pH
a. is a measure of the concentration of H+ ion in the solution
b. is a logarithmic scale
i. a pH difference of 1 translates into a difference in H+ concentration
of 10X
c. a lower pH indicates a higher concentration of H+ and therefore
greater acidity
d. the scale has a range between 0 and 14
III. SYNTHESIS AND HYDROLYSIS OF POLYMERS
A. synthesis: a chemical reaction that results in large molecules being made from smaller ones
B. dehydration synthesis: water is one of the products
C. also known as a condensation reaction
D. hydrolysis: a chemical reaction that results in large molecules being broken down into smaller
molecules with water as one of the reactants
E. Dehydration synthesis and hydrolysis are opposite reactions.
F. polymer: a large molecule made from many smaller subunits joined together
G. monomer: a small molecule that can be a subunit of a polymer
1. e.g. glucose (and other simple sugars), amino acids, fatty acids, and nucleotides
http://www.yellowtang.org/images/dehydration_hydroly_c_la_784.jpg
A. Organic compounds are those that contain the element carbon, with the exception of: carbon oxides
and carbon monoxide (CO) and carbon dioxide (CO2), carbonates (CO32-), hydrogen carbonates (HCO3-),
cyanides, cyanates, carbides, and thiocyanates.
V. CARBOHYDRATES
A. composed of carbon, hydrogen and Oxygen
B. the empirical formula is (CH2O)n
C. Monosaccharides
1. all carbohydrates are made of one or more monomers called simple sugars or
monosaccharides
2. e.g. glucose, fructose and galactose which have the chemical formula C6H12O6
Glucose, fructose, galactose
3. e.g. deoxyribose which has the chemical formula C5H10O4
4. e.g. ribose which has the chemical formula C5H10O5
D. Disaccharides
1. two simple sugars joined together is called a disaccharide
2. a water molecule is produced in the process
3. e.g. 2 glucose molecules joined together produces a disaccharide
called maltose
4. e.g. 1 glucose joined to 1 galactose produces a disaccharide called lactose
http://www.chembook.co.uk/fig25-4.jpg
http://images.google.ca/imgres?imgurl=http://www.ncbi.nlm.nih.gov/bookshelf/picrender.fcgi%3Fbook
%3Dmcb%26part%3DA259%26blobname%3Dch2f10.jpg&imgrefurl=http://www.ncbi.nlm.nih.gov/books
helf/br.fcgi%3Fbook%3Dmcb%26part%3DA259%26rendertype%3Dfigure%26id%3DA278&usg=___63GG
tMVgzYxhap-D6C8qzwLn-w=&h=260&w=539&sz=53&hl=en&start=15&um=1&itbs=1&tbnid=HpaxlP8Pr74M:&tbnh=64&tbnw=132&prev=/images%3Fq%3Dsucrose%2Bformation%26um%3D1%26hl%3Den%26
client%3Dfirefox-a%26sa%3DG%26rls%3Dorg.mozilla:en-US:official%26tbs%3Disch:1
E. Polysaccharides
1. a long chain of simple sugars joined together is called a polysaccharide
a. a polymer of glucose with few side or branched chains
i. has amylose (unbranched) and amylopectin (branched) chains
b. the main form of carbohydrate storage in plants
c. a major source of energy for animals
2. glycogen
a. a polymer of glucose with many chains
b. the main form of carbohydrate storage in animals
c. glucoses are linked in the same way as in starch
d. synthesized and stored in liver and muscles
http://www.biotopics.co.uk/JmolApplet/glycogen2.html
http://www.emc.maricopa.edu/faculty/farabee/BIOBK/1glycogen.gif
4. cellulose
a. also a polymer of glucose
b. forms cell walls
c. glucoses are linked differently than in starch and glycogen
d. mammals cannot break down these bonds and therefore are
unable to digest cellulose
http://www.biotopics.co.uk/JmolApplet/cellulosejdisplay.html
http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookCHEM2.html
VI. LIPIDS
A. formed from carbon, hydrogen and oxygen
B. large molecules, usually insoluble in water
1. Neutral Fats
a. made of a molecule of glycerol with 3 fatty acids attached
http://science-tutor.com/images/Triglyceride%20block.gif
http://hyperphysics.phy-astr.gsu.edu/HBASE/organic/imgorg/lipid.gif
b. the different types of fatty acids account for the different properties
(such as taste, smoke point etc.) of different fats
c. non-polar and therefore insoluble in water
d. main function is long-term energy storage
i. more efficient than starch and glycogen in terms of
space occupied
e. can function as an insulator
f. can function as a cushion
g. found in adipose tissue (cells that contain many
molecules of neutral fats)
2. Phospholipids
a. structurally similar to a neutral fat except that one of the fatty acids is
replaced by a phosphorous group
i. this part of the molecule is polar and therefore soluble in water
ii. this makes the molecule amphiphilic/amphipathic, meaning that part of it
“likes” water and part of it doesn't
b. found in cell membranes the molecule accounts for the phopholipid bilayer
i. the phosphate group is oriented so that it is in contact with water and
protects the fatty acids from being in contact with water
http://bioweb.wku.edu/courses/biol115/wyatt/biochem/Lipid/Lipid_2.asp
3. Steroids
a. base structure is 4 fused carbon rings
http://www.elmhurst.edu/~chm/vchembook/556steroids.html
b. cholesterol
i. occurs in cell membranes
ii. Made in the bloodstream, nerve tissue and brain tissue
iii. is the basis for steroid hormones and Vitamin D
iv. The major compound found in bile and gallstones
v. contributes to deposits on the inner walls of arteries that
can harden and lead to atherosclerosis
a. results in various heart diseases, high blood
pressure and strokes
http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=cooper&part=A249
c. sex hormones
i. testosterone
ii. estrogens such as estradiol
http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=cooper&part=A249
VII. PROTEINS
http://publications.nigms.nih.gov/structlife/chapter1.html
A. made of carbon, hydrogen, oxygen, nitrogen, and sulphur
B. Functions of Proteins
1. structural components of muscle (actin, myosin), tendons (collagen), hair
(keratin), nails (keratin), etc.
2. enzymes to speed up chemical reactions in the body and therefore control
metabolism
3. hormones to carry messages from one part of the body to another
4. storage proteins such as the proteins in ovalbumin (in egg
whites) and casein (in milk)
5. contractile proteins in muscles
6. transport proteins in cell membranes
7. antibodies to defend the body against foreign organisms
a. can immobilize the invading organism for the white blood cells to phagocytize
them
C. Amino acids
1. the monomers that make up proteins
a. differ in their “R” groups
http://www.starsandseas.com/SAS%20OrgChem/SASProteins.htm
2. 20 different amino acids; 8 are essential
a. human body can’t synthesize them from the other amino acids
b. must get them in our diet
D. Peptides
1. two amino acids joined together is called a dipeptide
a. the bond is called a peptide bond
http://zebu.uoregon.edu/internet/images/peptide.gif
2. many amino acids joined together is called an polypeptide
3. breaking a peptide bond requires the addition of water
4. a functional protein is made of one or more polypeptides
E. Levels of Protein Structure
1. Primary structure: the order of amino acids in the peptide
a. determined by the DNA (to be studied in more detail soon)
2. Secondary structure: folding of the primary structure due to H-bonding
a. caused by H-bonding
b. alpha helix is a coiled chain of amino acids
i. keratin has mostly alpha helices
c. beta pleated sheet is formed by peptide chains that lie side
by side but in opposite directions
i. silk protein has mostly beta
pleated sheets
http://www.umass.edu/molvis/workshop/imgs/protein-structure2.png
3. Tertiary structure: various kinds of bonds between R groups causes the secondary structure to
fold into a specific shape
4. Quaternary structure: 2 or more tertiary structures clump together to form a functional
protein
a. e.g. insulin is composed of 2 polypeptides
b. hemoglobin is composed of 4 polypeptides
http://www.umass.edu/molvis/workshop/imgs/protein-structure2.png
F. Globular versus Fibrous Proteins
1. Fibrous Proteins
a. insoluble in water
b. physically tough, may be
supple or stretchy
c. parallel polypeptide chains in long fibres or sheets
d. e.g. collagen (structural), actin (contractile), myosin(contractile)
2. Globular Proteins
a. easily water soluble
b. structure very folded resulting in a more spherical shape
c. function as enzymes, hormones, transport proteins, and protective proteins
d. e.g. insulin
G. Denaturing of Proteins
http://highered.mcgrawhill.com/sites/0072943696/student_view0/chapter2/animation__protein_denaturation.html
1. occurs when secondary and tertiary structure is disrupted
2. changes the shape of the protein causing it to have different properties and lose
its function
a. heat and radiation: increase the amount of kinetic energy in the molecules
and causes them to vibrate so strongly that the H- bonds are broken
b. heavy metals such as lead and mercury generally cause precipitation of the
protein
i. can bind to the sulphur on cysteine breaking the disulphide bonds of the
tertiary structure
ii. can disrupt ionic bonds, form bonds with the carboxyl groups of the R
groups, and reduce protein charge
c. strong acids and bases
i. disrupt ionic bonds and cause coagulation
d. detergents (amphiphilic molecules) and non-polar solvents
i. disrupt protein structure by forming bonds with the nonpolar groups in the protein so non-polar parts of the protein no longer associate
with each other
3. Remove denaturing conditions and proteins will try to refold.
a. However, if you destroy the primary structure, protein is totally destroyed.
b. Denatured protein may have trouble refolding
i. Folding process for proteins is not straight-forward.
ii. Involves intermediate stages
iii. Final form may not give clues to intermediate steps in folding process.
iv. “Chaperone Proteins” proteins which form “temporary braces” in
complex folding process of a protein
4. abnormally folded proteins
a. in some diseases, these agents have the ability to subvert normal proteins to unfold and
refold abnormally
H. Prions
1. abnormally folded proteins
a. in some diseases, these agents have the ability to subvert normal proteins
to unfold and refold abnormally
b. see this in some forms of Alzheimer’s, Creutzfeld-Jakobs, bovine spongiform
encephalopathy (BSE/Mad cow disease),scrapie, etc.
I. Modification of Proteins
1. occurs in the ER or the Golgi
2. Modifications
a. addition of carbohydrate groups to form glycoproteins
i. may identify the protein so cell will know its destination
ii. may help orient or position the protein in the cell membrane
iii. may make the protein behave as a marker in the cell membrane
b. addition of fatty acids to form lipoproteins
i. protein can transport lipids in the blood
VIII. NUCLEIC ACIDS
A. made of carbon, hydrogen, oxygen, nitrogen, phosphorus
B. monomers are called nucleotides
1. Each nucleotide is made of a sugar (ribose or deoxyribose), one or more phosphate groups
and a nitrogenous base
2. The carbon the nitrogenous base bonds to is called the 1' (one-prime) carbon
3. The carbon that has the H in deoxyribose and the OH in ribose is called the 2' (two-prime)
carbon
4. The carbon that the phosphate group attaches to is known as the 5' (five-prime) carbon
5. When 2 nucleotides join, the 5'phosphate of one nucleotide bonds with the 3' carbon of
the next nucleotide
http://www.yellowtang.org/images/structure_of_nucleo_c_la_784.jpg
a. 5 types of nitrogenous bases belonging to 2 groups
i. purines (2 rings) are adenine and guanine
ii. pyrimidines (1 ring) are cytosine, thymine and uracil
http://www.yellowtang.org/images/structure_of_nucleo_c_la_784.jpg
C. nucleosides are made of a sugar and a nitrogenous base, no phosphate
1. named “___sine” or “___dine”
D. Adenosine Triphosphate (ATP)
1. Made of a ribose, adenine and three phosphate groups
http://www.uic.edu/classes/bios/bios100/lectf03am/ATP02a.jpg
2. used for very short term energy storage
a. the bond between the second and third phosphate groups releases a large amount of
useful energy when broken (~7.3kcal/mol)
http://www.accessexcellence.org/RC/VL/GG/ecb/ATP_ADP.php
http://www.britannica.com/EBchecked/topic-art/457374/2659/DNA-structure-showing-the-nucleotidebases-cytosine-thymine-adenine-and
3. in aerobic cellular respiration, ATP is produced in the mitochondria
4. also used for synthesis of RNA and DNA
5. also regulates many biochemical pathways
6. In mammals, ATP released
a. from damaged cells elicits pain
b. from carotid body signals lack of O2 in blood
c. from taste receptor cells triggers action potentials in the sensory nerves leading
back to the brain
d. from the stretched wall of the urinary bladder signals when the bladder needs
emptying
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/A/ATP.html
1. Structure
a. sugar is deoxyribose
b. chain of sugars and phosphates is known as the sugar-phosphate backbone
c. bases are adenine, guanine, cytosine and thymine
d. forms a double stranded helix (double helix)
i. strands held together by hydrogen bonding between the opposite
nitrogenous bases
ii. A always binds to T
iii. C always binds to G
iv. known as complementary base pairing and is vital to the functioning of DNA
and RNA
http://www.starsandseas.com/SAS%20OrgChem/SASNucleic.htm
e. a molecule of DNA can be almost any length and the bases can come in almost any
order so there is theoretically an infinite number of genes
For history of DNA structure discovery: http://www.mansfield.ohiostate.edu/~sabedon/campbl16.htm#antiparallel_strands
http://bcs.whfreeman.com/thelifewire/content/chp03/03010.html?v=&i=03010.01&s=03000&n=00010
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http://bcs.whfreeman.com/thelifewire/content/chp03/03010.html?v=&i=03010.01&s=03000&n=00010
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http://www.britannica.com/EBchecked/topic-art/457374/2659/DNA-structure-showing-the-nucleotidebases-cytosine-thymine-adenine-and
2. Location
a. only found in the nucleus
3. Function
a. the “blueprint of life”
b. stores genetic information
F. RNA
1. Structure
a. sugar is ribose
b. chain of sugars and phosphates is known as the sugar-phosphate backbone
c. bases are adenine, guanine, cytosine and URACIL
d. usually forms a single stranded molecule
i. complementary base pair bonding can cause nitrogenous bases to come together causing the
formation of 3- dimensional structures, most often hairpin loops
ii. This bonding is very important in synthesis and function of RNA
http://bcs.whfreeman.com/thelifewire/content/chp03/03010.html?v=&i=03010.01&s=03000&n=00010
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2. Types, Locations and functions of RNA
a. messenger RNA/mRNA
i. found in the cytoplasm
ii. used to translate the DNA code into the amino acid sequence that makes
polypeptides and therefore proteins
b. ribosomal RNA/rRNA
i. makes up ribosomes
ii. Used to hold amino acids in place while they are being joined into peptides
iii. Different in the prokaryotes and eukaryotes resulting in 70S ribosomes in
prokaryotes and 80S ribosomes in eukaryotes
c. transfer RNA/tRNA
i. found in the cytoplasm
ii. attach to amino acids and bring them to the ribosome for polypeptide formation
*Note that RNA is synthesized in the nucleus so it is also found there.
**Mitochondria and chloroplasts also have RNA.