Chapter 2: Biochemistry

Atomic structure

- 3 subatomic particles: protons, neutrons, and electrons

- Ground state: electrons in the atom are in lowest energy level

- Exited state: electrons move to higher energy level

- Isotopes: atoms of on element that vary only in the number of neutrons (i.e. carbon-12
and carbon-14)
- Half-life: time required for half of radioactive material to decay (radioactive decay)

Bonding

- Bond is formed between to atoms due to attraction

- Energy released when bond is formed (outer shell is filled)
- 2 types: ionic and covalent
1. Ionic bond
- Results from transfer of e-
- Anion (negative ion) and cation (positive ion) attract
2. Covalent bond
- Share e-
- Nonpolar molecule (balanced): e- shared equally
i.e. diatomic molecules like O2
- Polar bond (unbalanced): unequally
i.e. H2O and CO2

Hydrophobic and hydrophilic

- “like dissolves like”

- Hydrophobic (“water hating”)
 Nonpolar substances
 Dissolve in lipids (nonpolar)
 Does not in water (polar)

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 - Hydrophilic (“water loving”)
 Polar substances
 Dissolve in water
- Water known as universal solvent (many substances dissolve in water)

Properties of Water

- Water is very polar because O pulls the shared electrons more than H
 strong attraction between positive H and negative O of different water
molecules (hydrogen bonding)

1. high specific heat

-amount of heat needed to heat 1 gram of substance by 1 °C
-hard to change temperature
2. high heat of vaporization
-evaporation needs lot of heat (that’s why sweating cools the body well)
3. universal solvent
-dissolves all polar and ionic substances
4. strong cohesion tension
-surface tension allows for round water drops

pH

- measure of acidity/ alkalinity

- more H+= more acidic, more OH-= more basic

- increase of 1 in pH scale= 10 times more basic (pH 10= 1000 times more basic than pH 7)
- internal pH of most cells is close to 7
- buffer prevents harmful change in pH by absorbing excess H+ or OH-
- bicarbonate ion (HCO3-): most important buffer in blood

-isomers: compounds that have same molecular formula but different structures and properties

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Organic Compounds

- all organisms are made up of organic compounds, compounds that contain carbon
- monomer: smallest subunit
- polymer: monomers combine to form polymer through polymerization
- 4 classes: carbohydrates, lipids, proteins, and nucleic acids
1. Carbohydrates:
- Used as fuel (quick energy) and building materials
- Made of carbon, hydrogen, and oxygen
- 3 classes: monosaccharides, disaccharides, and polysaccharides
A) Monosaccharides (C6H12O6)
- Glucose, galactose, fructose (isomers)
- Monomer of carbohydates
B) Disaccharides (C12H22O11)
- Dehydration synthesis: Two monosaccharides joined with release of water
Glucose + glucose = maltose + water
Glucose + galactose = lactose + water
Glucose + fructose = sucrose + water
- Hydrolysis: breakdown of compound by adding water
C) Polysaccharides
- Many monosaccharides joined together
- Cellulose: plant wall
- Starch: energy storage in plants
- Chitin: exoskeleton in arthropods/ cell walls in mushrooms
- Glycogen: energy storage in animals

2. Lipids:
- Hydrophobic (fats, oils, waxes, steroids)
- Consist of 1 glycerol and 3 fatty acids (monomers)

- Saturated or unsaturated?

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- Saturated: only single bonds between carbons in fatty acid tail
 Comes from animals
 Solid at room temp.
 Bad for you in large quantities
- Unsaturated: at least one double bond
 Comes from plants
 Liquid at room temp.
 Much healthier
- Steroids: 4 fused rings
 Include cholesterol, sex hormones
- Lipid functions
1. Long term energy storage
2. Structural i.e. cell membrane
3. hormones
- Phospholipids
 Modified lipids: two fatty acids and a phosphate group attached to glycerol
 Phosphate is charged and thus hydrophillic
 Hydrophilic head (Phosphate + glycerol)
 Hydrophobic tails (fatty acids)
 Form phospholipid bilayer in the cell membrane

3. Proteins:
- Polymers (polypeptides) of amino acids (monomer)
joined by peptide bonds
- An amino acid consists of carboxyl group, an amine
group, and a variable (R) attached to central carbon
- 4 levels of structure: primary, secondary, tertiary,
and quaternary

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- Primary structure: linear sequence of amino acids
 Determines how protein will fold
- Secondary structure: hydrogen bonding within polypeptide
 alpha helix and beta pleated sheet
 fibrous proteins: proteins that exhibit alpha or beta i.e. wool, spide webs, keratin

- tertiary structure: 3D shape of protein superimposed on secondary structure

 determines protein’s function
- Quaternary structure: more than one peptide chain i.e. hemoglobin
- Protein-folding problem
 Structure can be affected by pH, temperature, etc.
 Denaturing: protein losing its shape (and thus its function)
 Chaperone proteins (or chaperonins) assist in folding proteins properly
 Misfolded proteins (prions) can cause diseases i.e. mad cow disease, Alzheimer’s
4. Nucleic Acids:
- Polymers (polynucleotides) of nucluotides (monomer)
- Ribonucleic acid (RNA) and deoxyribonucleic acid (DNA)
- A nucleotide consists of a phosphate, a 5-carbon sugar, and
a nitrogen base
- 5 types of nitrogen bases: adenine (A), cytosine (C), guanine
(G), and thymine (T) (in DNA) or Uracil (U) (in RNA)
- Sugar and phosphate form the sugar-phosphate backbone

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Energy, enzymes and metabolism

- living organisms need constant input of energy, and energy is transformed to carry out
different life functions
- 1st law of thermodynamics (conservation of energy): energy can’t be created or
destroyed (only transformed)
- 2nd law of thermodynamics: entropy increases during all energy conversions (more
disordered)
- Gibb’s free energy (G): free energy available to do work
- Exergonic/ exothermic: energy released in a reaction, ΔG <0
- Endergonic/ endothermic: energy absorbed, ΔG >0
- In cellular reactions, exergonic reactions often power endothermic ones
- Metabolism: all chemical reactions that take place in cells
 Catabolism: break down molecules
 Anabolism: build up molecules
- Pathways: series of metabolic reactions controlled by enzymes
- For all reactions, energy is needed to trigger it. This is called activation energy (EA)

Enzymes

- Enzymes: proteins that speed up a reaction by lowering EA

- Substrate: reactants that enzymes act on
- Induced fit model: when substrate enters the active site, the enzyme alters its shape
slightly so the substrate fits better. (old theory: lock-and-key is wrong!)

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- Enzymes are not used up during a reaction; they are reused
- Named after their substrate with ending “ase” i.e. Sucrase acts on sucrose
- Cofactors or coenzymes (vitamins) assist enzymes
- Efficiency of enzyme determined by temperature and pH (enzymes may denature too)

Control of enzyme activity

- What would have happen if enzyme activity is not controlled?
- Two types of inhibition: competitive and non-competitive
1. Competitive Inhibition
- Competitive inhibitors prevent substrate from binding to the enzyme by binding to active site
- increasing the concentration of substrate can overcome inhibition

2. Noncompetitive inhibition
- Noncompetitive or allosteric (“changing shape”) regulators bind to allosteric site to change
shape of enzyme; thus, substrate cannot bind anymore

Cooperativity
- type of allosteric activation
- binding of one substrate molecule to one active site of a subunit of
enzyme causes change in entire molecule and locks all subunits in
an active position, amplifying response of enzyme to substrates