2- Biochem basics

Question 1

what does hydrophobic mean?

Answer 1

non-polar substances that are insoluble in water

Question 2

what is hydrophobic effect?

Answer 2

oil & water don’t mix

Question 3

what does amphipathic mean?

Answer 3

both hydrophobic & hydrophilic

Question 4

what do amphipathic molecules do in water?

Answer 4

form micelles
-> hydrophillic head = interacts with water
-> hydrophobic tail = doesn’t interract with water

Question 5

what is a hydrogen bond?

Answer 5

• A covalent bond between hydrogen and a more electronegative atom (e.g. oxygen) creates a polarized bond, dipole
• hydrogen has partial positive charge
• This hydrogen can interact with unshared electrons from another electronegative atom

Question 6

what are the types of amino acid?

Answer 6

1. non-polar hydrophobic amino acid = in part of protein that interacts with lipid
2. polar, uncharged amino acid = charge difference across side group so uncharged. sitting zone between aqeous & non aqeous environment
3. acidic amino acid
4. basic amino acid

Question 7

what are peptide bonds?

Answer 7

CONH bond in connecting amino acid
- very strong & rigid

Question 8

what is Ka?

Answer 8

acid dissociation constant - shows strength of acid by how quickly it donates
(acids - donate, bases - accept)

Question 9

what is henderson hasselbach equation?

Answer 9

connects Ka of weak acid to find pH of a solution containing this acid (pKa + log… equation- don’t need to know equation)

• lets us calculate propertioes of buffer solutions

Question 10

what is pH?

Answer 10

measurment of amount of proteins in solution

Question 11

why are hydrogen bonds important in biochemical reactions?

Answer 11

they’re weak but they’re reversible which makes them important in biochemical reactions & transitional stabilisation of molecular interactions

Question 12

what is a buffer?

Answer 12

solution to control the pH of a reaction mixture
- At their pKa value buffers tend to resist a change of pH on addition of moderate amounts of acid or base

Question 13

what does zwitteroin mean?

Answer 13

amino acid can buffer at 2 pHs giving acid different dependant characteristics
= unique buffering properties to proteins that can affect their function

Question 14

how does protein buffering characteristics have important consequences for protein function?

Answer 14

because different pH can change ionisation of a protein and therefore changes in structure and thereby function
- changes in protein function impact ability to interact with other binding partners and distribution in cell

Question 15

what are the 3 types of secondary structure?

Answer 15

• alpha helix
• beta strands & sheets
• triple helix

Question 16

what is structure if alpha helix? what can break it?

Answer 16

• rod like
• peptide change
• CONH bonds throughout structure in 3D type bond so structure stable

proline residues breaks them - changes direction due to side chain on proline

Question 17

what is beta sheet structure?

Answer 17

• polypeptide backbone extended
• can involve multiple chains
• anti-parallel & parallel
• held stable by hydrogen bonds

Question 18

why is vitamin C needed collagen triple helix structure?

Answer 18

important in connective tissue, proline needs to be hydroxylated so it can twist and hold structure and vitamin C is needed for enzyme to hydroxylate

Question 19

what is collagen triple helix structure?

Answer 19

• most abundant protein in vertebrates
• water-insoluble fibres
• 3 helical chains twisted around each other to form right handed super helix
• repeating sequence of amino acid, proline, glycine
• also contains hydroxylysine

Question 20

why is collagen relevant in triple helix?

Answer 20

• influences strength of connective tissue
• weakened collagen results in bleeding gums

Question 21

what is involved in tertiary structure?

Answer 21

arrangement of atoms in polypeptide space

all the bonds added like:
- Covalent disulphide bonds
- Electrostatic interactions = salt bridges
- Hydrophobic interactions
- Hydrogen bonds (backbone + side chain)
- Complex formation with metal ions

Question 22

what are fibrous proteins?

Answer 22

• consist of long fibres/ large sheets
• mechanically strong
• insoluble in water
• play important structural roles in nature like keratin in hair and collagen in bones, teeth, skin

Question 23

what are globular proteins?

Answer 23

• soluble in water
• polar side chains mostly on outside & interact with aqeuous environment with non-polar chains buried inside

examples = myoglobin & haemoglobin

Question 24

what is strength of each hydrophobic interaction?

Answer 24

hydrogen to hydrogen = strongest
water to hydrocarbon
hydrocarbon to hydrocarbon (van der waals)

Question 25

what interrupts protein structure?

Answer 25

• heat
• pH
• detergents (interrupt hydrophobic interactions)
• thiol agents/reducing agents = reduce & disrupt disulphide bonds

Question 26

quaternary structure?

Answer 26

multi-subunit like haemoglobin

Question 27

what does D and L refer to?

Answer 27

D and L amino acids are stereo-isomers = non super imposable images of each other
(l- left moving, d - dextrious right hand)