UNIT 1 NOTES
Biological Chemistry Review
Why study Chemistry in Biology?
• The understanding of the basic chemistry of life is vital to a full comprehension of biology.
• Important atoms include:
o Oxygen (O)
o Phosphorous (P)
o Carbon (C )
o Potassium (K)
o Hydrogen (H)
o Sulphur (S)
o Nitrogen (N)
Atoms:
Atom = smallest part of an element that displays the properties of that element
- Made up of 3 subatomic particles:
o Protons (positively charged)
Found in the nucleus o Neutrons (uncharged / neutral)
o Electrons (negatively charged) – found outside of the nucleus
Ions:
Ions = atoms that have gained or lost electrons
- Signified by either (+) or (-)
+
+
2+
- Ex. Na , K , Cl , Ca
Types of bonding:
1. Ionic bonds:
- Transfer of electrons from a metal (positive ion) to a non-metal (negative ion)
2. Covalent bonds:
- Atoms share electrons between 2 non-metals
- Can be single covalent bond (sharing 2 electrons), double covalent bond (sharing 4 electrons) or triple
covalent bond (sharing 6 electrons)
o
Nonpolar covalent bonds
- Electrons shared fairly equally between atoms
o
Polar covalent bonds
- Unequal sharing of electrons
3. Hydrogen bonds:
- When a covalently bonded H within a molecule (eg H2O) is also attracted to
another atom (usually O, N or F) of a different molecule.
- Always represented by dotted lines
Inorganic Compounds:
Inorganic Compounds
Usually metal + non-metal
Usually ionic bonding
Associated with non-living
Ex. Salts, water, acids, bases, buffers
Organic Compounds
Always contain carbon and hydrogen
Always covalent bonding
Associated with living things
Ex. Carbohydrates, lipids, proteins and nucleic acids
A. Salts:
- Needed for survival
- Too little → fatigue, exhaustion, cramps, nausea, thirst, decrease in blood pressure and even death
- Too much → dehydration of cells and hypertension; can lead to heart attack
B. Water:
Structure of water:
- Biological importance is due to its chemical structure
- Water is a polar molecule
o How does polarity of water produce H-bonding?
§ Oxygen is bigger & negatively charged
§ H is smaller & positively charged
§
Oxygen pulls the electrons toward it creating a dipole
• O is slightly more negative symbolized as - (electrons spend more time around the oxygen)
• H is slightly more positive symbolized as + (electrons spend less time around the hydrogen)
= polar compound
• In a H-bond:
o H (positive dipole) of one water attracted to O (negative dipole) of different water
molecules
o H-bonding can occur between the H and other polar compounds
4 Special Properties of Water:
1) Temperature regulator:
Ø Water has a high specific heat capacity
o Means takes a lot of energy to increase temperature of water and loses energy slowly
Ø Keeps our body temperature constant
o Water vaporization → much heat energy released (sweating)
Ø High melting & boiling points
2) Acts as a solvent:
Ø When polar substances (ie salts, sugars, some proteins) are added to water, oxygen ( -) attracts positive
end of solute & H (+) attracts negative of solute thus pulling the substances apart
o Water acts as a solvent
+
o Eg. NaCl dissolves into Na & Cl in water
3) Acts as a lubricant:
Ø In mouth, joints, lungs, etc.
o In lungs CO2 & O2 only diffuse across moist membranes
4) Water has a high surface tension:
Ø This allows some insects to walk on the surface of a pond or lake
C. Acids / bases/ buffers:
Acids and bases:
+
Ø When water ionizes, it releases an equal number of hydrogen ions (H ) and hydroxide ions (OH )
+
o H2O H + OH
+
Ø Acids release H ions into the solution
+
o HCl → H + Cl
+
Ø Bases remove H ions from the solution
+
o NaOH → Na + OH
Ø Neutral solutions:
+
o Equal amounts of H and OH
o Neutralization reaction: Acid + base → water + salt
§ Eg. HCl + NaOH → H2O + NaCl
pH scale: The pH scale (proportion of H ions)
Ø Measures acidity & alkalinity (basicity) of a solution
Ø Ranges from 0 – 14
+
o A pH below 7 is acidic [H ] > [OH ]
+
o A pH above 7 is alkaline [OH ] > [H ]
+
o A pH of 7 is neutral [H ] = [OH ]
+
pH is the concentration of [H ] expressed as a logarithm. Every change in the pH scale of one unit is a
+
change in 10 times the concentration of H
+
Ø To determine pH from a diagram, only pay attention to the OH and H
+
o If there are more H , solution is acidic
o If there are more OH , solution is basic
+
o If there is an equal number of OH and H , solution is neutral
Ø
Why is it important to maintain pH?
Ø The pH of most living systems is between pH 6-8. Maintaining the proper pH then is vital for living systems.
Ø Living organisms maintain a proper pH balance by using the homeostatic control of buffers.
Buffers:
Ø A buffer is a chemical(s) that can resist changes in pH
+
Ø Living organisms’ internal chemical processes are sensitive to changes in H and OH . Examples:
o Stomach pH = 2.5 – 3.0
o Blood pH = 7.4 or get sick (most important buffer is bicarbonate HCO3 )
o Small intestine pH ~8.3
Ø We have a built in system to maintain our internal pH (homeostasis) via natural buffers
+
Ø Buffers function by taking up excess H or OH to help keep pH constant
À In a strong acid solution, there are too many hydrogen ions
o if we add a strong acid to a buffered solution, the buffer is attracted to the hydrogen ions so that the pH
does of the solution does not change
+
§ In an acidic solution, the buffer will absorb the H
À In a strong base solution, there are too many hydroxide ions
+
o if we add a strong base to a buffered solution, the buffer will give up H in order to combine with OH
of the base to produce water (H2O).
+
§ H + OH
H 2O
Ø Therefore,the pH of the solution does not change
+
o In a basic solution, a buffer will donate / release H ions to neutralize the OH
Ø Buffers only work until all the ions are gone meaning they are not permanent
Important Organic Compounds: Biological Molecules
•
The most important biological compounds are polymers
POLYMERS (poly = many)
• The polymers are proteins, carbohydrates, lipids (fats), and nucleic acids (DNA / RNA)
• A polymer is made up of a chain of many monomers linked together
• Large polymers are also called macromolecules
MONOMERS (mono = one)
• Monomers are: amino acids, sugars, fatty acids, and nucleotides
• These are made or broken down over and over in living cells
MONOMER
POLYMER
(building block)
(Biological organic molecule)
Monosaccharide (glucose)
Carbohydrate
Glycerol and fatty acid
Lipid (fat)
Amino acid
Protein
Nucleotide
Nucleic acid
Examples:
Monomer èH - - OH (one block)
Polymer è H - - - - - - OH (many blocks)
Process to build polymers
• Dehydration synthesis: covalently bonding monomers together by removing water
o Chains of monomers are called polymers
•
Looks like….
H-
- OH
+
H-
(monomer)
H-
-
- OH →
H-
(monomer)
- OH
+
H-
(dimer)
-
- OH
+
H 2O
(dimer)
-
- OH
→
(water)
H-
(dimer)
-
-
-
- OH
(polymer)
•
-
-
-
- OH + 3 H20 →
4H-
H 20
(water)
To break apart polymers
• Hydrolysis: Add H2O for every covalent bond that needs to be broken
H-
+
- OH
1 H2O will be consumed for every 1 covalent bond to be broken
Organic Molecules:
1. Carbohydrates (simple and complex sugars)
2. Lipids (Fats)
3. Proteins
4. Nucleic Acids
**reminder: organic molecules always contains C & H & covalent bonds
1.
Carbohydrates (simple sugars and complex carbohydrates)
Where does the name come from?
Hydrated carbons: (CH2O)n
• C = carb ; H2O = hydrate
Carbohydrates have the empirical formula of (CH2O)n
o Where n = the number of times the chain is repeated
The carbons, hydrogens and oxygens are found in the ratio of 1:2:1 and are made up of a repeating chain of
sugars.
•
•
Ie. (CH2O)3 = C3H6O3
ie glucose = (CH2O)6 or C6 H12O6 in a ring shape
o sugars are also known as saccharides
o carbohydrates usually end in ‘ose’
a) Monosaccharides (simple sugars)
– basic sugar molecule is GLUCOSE - C6H12O6
– glucose has a ring structure
– other monosaccharides include fructose, ribose, deoxyribose
•
•
glucose b) Disaccharides (simple sugars)
– When two monosaccharides bind together via dehydration synthesis (water lost)
Examples:
–
–
–
glucose + glucose = maltose + water
glucose + galactose = lactose (milk sugar) + water
glucose + fructose = sucrose (table sugar) + water
C12H22011
maltose c) Polysaccharides (complex carbohydrates)
• Polymer of identical monosaccharides (typically glucose)
Examples:
i.
Starch
ii.
Glycogen
iii.
Cellulose
i.
Starch
• Function: Storage form of glucose in plants (long glucose chains)
• Structure: Few or no side chains branches
• Sugars produced by photosynthesis are stored as starch (in leaves, stems, roots) until needed
ii.
Glycogen
• Function: Animals store their energy (extra glucose) as glycogen in the liver and muscles
• Structure: Long chains of glucose with many side chains
iii.
Cellulose
• Function: Cell walls of plants are made of cellulose to give it strength
• Structure: Long chains of glucose with no side chains and have alternating position of linking oxygen
atoms
• No mammals can break the bond (indigestible) however, important for digestive system as it serves as
fibre
Carbohydrate review
Source
Animal
Plant
Monomer
Glucose
Glucose
Polymer
Glycogen
Starch
Cellulose
Characteristic
Highly branched
No (or few) branches
Alternating O bonds
Functions:
• Energy for cells
• Energy storage (starch, glycogen)
• Cell recognition role = glycoprotein or glycolipid
o For example: the basis for A, B, and O blood groups
2. Lipids
Characteristics:
– made up of C, H, O (sometimes P or N)
– large, insoluble (in water) molecules
• Ex. Water in oil
– 2 monomers:
• Glycerol
• Fatty acids (long hydrocarbon chains)
3 types of Lipids:
A. Triglycerides – aka neutral fats (nonpolar) or “fats and oils”
Structure:
– “E” shaped molecule made of one glycerol and 3 fatty acids
– synthesized by dehydration of 3 H2O molecules
–
–
glycerol Fatty acids are hydrocarbon chains with COOH end
3 main types of fatty acid
glycerol 1. Saturated – no C=C which means it is “full” of H, fairly straight,
solid at room temp, “fat” (from animals)
2. Unsaturated – at least one C=C bond, structurally bent, liquid at room temp., “oil” (from plants)
3. Polyunsaturated – many C=C bonds so few H’s (e.g veggie oils)
µImportant - hydrogenation adds H’s (margarine or shortening) but forms trans fats L
2 Types of triglycerides (due to different fatty acids):
a) Fats= animal based & solid (eg. butter, lard)
• functions:
1. Long term energy source
2. Cushions organs
3. Insulation
b) Oil = plant based & liquid (eg. olive, corn, etc)
• Main energy source for plants
nd
B. Phospholipids (2 type of lipid)
o Comprised of 1 glycerol, 1 phosphate group & 2 fatty acids
o think of a triglyceride except one fatty acid has been replace by a phosphate group
o Primary components of cellular membranes
Phospholipid bilayer
• when placed in H2O, phospholipids form 2 layers
– the polar heads (hydrophilic) face out and the non-polar tails (hydrophobic) face in
Diagram:
rd
C. Steroids (3 type of lipid)
Structure:
• 4 fused rings of carbon with “stuff” attached (called functional groups)
• all made of cholesterol (a steroid)
• eg. Testosterone, estrogen, cholesterol and vitamin D
• Non-polar so can easily pass through cell membranes
• Are water insoluble (it is a lipid)
Function:
• Used as sex hormone (e.g. estrogen & testosterone)
Emulsification
• Needed to mix fats/oils into water
• e.g. soap and bile (produced by gallbladder)
3. Proteins
Functions in cells.
– Structural – strength and support
– Enzymes- speed up chemical reactions
– Hormones – chemical messages in body
– Antibodies –provides immunity
– Transport – in blood and across cell membranes
– Contraction – muscle movement (eg. actin & myosin)
Protein Structure:
• Monomer = amino acid (symbolized by aa)
• Made up of C, H, O, and N (but not in a set ratio like carbs were)
R-groups / side chains: 20 different R-groups for 20 different AA’s
•
Peptides
o A peptide bond joins amino acids (a dipeptide) between C
and N and one water is lost
o A polypeptide is a chain of amino acids
o Another name for a polypeptide is protein
Protein Structure is due to folding and bonding:
4 types of structures:
i.
Primary (1°) protein
ii.
Secondary (2°) protein
iii.
Tertiary (3°) protein
iv.
Quaternary (4°) protein
i.
Primary (1°) Protein
• Single chain of aa’s in linear form
• Held together by peptide bonds only
ii.
Secondary (2°) Protein
• H-bonding within polypeptide pulls 1° into alpha-helix or pleated sheet
• Held together by Hydrogen & peptide bonds
o
iii. Tertiary (3°) Protein
• Covalent bonding between R-groups pulls coil into tertiary shape
• Held together by covalent, hydrogen & peptides bonds
iv. Quaternary (4°) Protein
• 2 or more peptides ionically bonded together (“blobs”)
• Held together by covalent, hydrogen, peptide& ionic bonds
Why is the shape of a protein so important?
•
•
The shape of each individual protein is specific to its function; therefore, without the proper shape, it will not
function
Eg. if folding does not occur correctly, it can cause diseases such as Parkinson’s or Alzheimer’s
Denaturation
• is the disruption of the shape of a protein & therefore, a loss of function
• is caused by exposure to high temp., pH, chemicals & heavy metals
4. Nucleic Acids
À Monomer = nucleotide which is composed of:
o Phosphate
o Pentose sugar (5 carbon)
o Nitrogen-containing base
À Polymers of Nucleic Acids
a) DNA (deoxyribonucleic acid)
– DNA nucleotide has: Sugar (deoxyribose), phosphate & one of 4 bases [adenine (A), thymine (T), cytosine
(C), & guanine (G)]
– DNA is double stranded: 2 linear strands held together by H-bonds between the bases
o A with T and C with G
– DNA twists into a double helix
– Always has phosphate-sugar backbone
–
*different number & arrangements of N-bases provides variety in genetic information
–
Function: Directs and controls all cell activities
b) RNA (ribonucleic acid)
– Single stranded (no helix)
– Ribose sugar (not deoxyribose)
– Has Uracil (U) instead of thymine (T)
– 3 types of RNA needed to make proteins (discussed later)
DNA Structure vs RNA structure comparison table
DNA
Sugar
Deoxyribose
Bases
RNA
Ribose
adenine, guanine, cytosine,
thymine
adenine, guanine, cytosine,
uracil
2 – double
1 - single
Yes
No
Strands
Helix
c) ATP (Adenosine Triphosphate)
Function:
– Provides energy for cells
– Produced during cellular respiration in the mitochondria (an organelle)
Structure:
– Adenosine & 3 phosphate groups
• Adenine (a base) + ribose (a sugar) = “adenosine”
nd
rd
• Energy-rich bond between the 2 & 3  which when broken releases a large amount of energy
• ATP ↔ ADP +  + energy
Functions of nucleic acid polymers summary:
•
•
•
DNA stores genetic information and codes for proteins.
RNA helps make proteins
ATP is the energy currency in cells
3 phosphates + ribose sugar + adenine = ATP!