proteins

Question 1

structure of amino acid

Answer 1

carboxyl, carbon then amine

• all amino acids except glycine are chiral therefore optically active

Question 2

almost all amino acids are __ enantioners

Answer 2

L

Question 3

fisher projection for aino acids

Answer 3

Question 4

acid base characteristics of amino acids

Answer 4

• have acidic and basic functionality, amphoteric (act as acid or base depending on env)
• have 2 protons that can dissociate, 2 Ka/Kb values
• in sol can be zwitterionic (pos pos an neg charge)

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Question 5

what is the isoelectic point

Answer 5

• pH lies between pKa1 and pKa2
• aa is neutral and exists as a zwitterion

Question 6

explain the titration of amino acids

Answer 6

• amino acid acts as a buffer so pH changes slowly upon addition of base
• @pKa1 +NH3CH2COOH = +NH3CH2COO-
• when more base added all COOH deprot, mol is now electrically neutral (zwitterion) and pH =pI
• pKa2 reached when past pI
• after pKa2 mol mostly NH2CH2COO-

Question 7

___ moles of base are requires to deprotonate 1 mole of mot amino acids

Answer 7

2 mol

one for COOH and one for NH3+

Question 8

where is the buffering capacity of amino acids greatest?

Answer 8

near Ka1 and Ka2

• at isoelectric point bufferin capacity is minimal

Question 9

how to determine how much prot and deprot aa you have

Answer 9

pH = pKa + log (depot/prot)

ex: 3.3 = 2.3 + log (deprot/prot)

1 = log(deprot/prot)

10 = deprot/prot

*10x as many zwitterions as fully protonated form

Question 10

non polar amino acids

Answer 10

alanine, valine, leucine, isoleucine, proline, phenylalanine, glycine and tryptophan

Question 11

polar amino acids

Answer 11

methionine, serine, threonine, cysteine, tyrosine, asparagine, glutamine

Question 12

acidic amino acids

Answer 12

• aspartic acid, glutamic acid, aspartate, glutamate
• carry net eng charge at physiological pH

Question 13

basic amino acids

Answer 13

• carry net pos charge at physiological pH
• arginine, lysine and histidine

Question 14

study amino acid structures

Question 15

what are pepties

Answer 15

composed of amino acid subunits

• also called residues
• linked by peptide bonds

2 aa = dipeptide, 3= tripeptide, and many = polypeptide

Question 16

peptide reactions

Answer 16

• aa joined by peptide (amide) bonds formed via condensation rxn
• can hydrolyse by adding water w/ acid or base

Question 17

what does trypsin so to peptide linkages? what about chymotrypsin

Answer 17

• certain enzymes digest chain at specific linkage
• trypsin cleaves at COOH end of arg and lys
• chymotrypsin cleaves COOH end oh phenylalanine, tyrosine and tryptophan

Question 18

peptide properties

Answer 18

• terminal amino acid w/ a free alpha amino group = amino terminal (N terminal)
• other is carboxy (C-terminal)
• have 2 res structues so rotation along C-N bond is resticted

Question 19

what are proteins

Answer 19

• polypeptides that can range from only a few -> thousands of aa
• are enzymes, hormones, memrbane pores, receptors, elements of ell structure
• have primary, secondary, tertiary and quat structures

Question 20

describe the primary structure of an amino acid

Answer 20

• seq of amino acids listen from N term -> C term
• other levels depend on this sequence
• can determine primary strucute in lab vai sequencing

Question 21

what is secondary structure

Answer 21

• local structure of neighbouring amino acids governed mianly by H bond interactions within and between peptide chains
• A helix and B pleated sheet
• most complex prot contain both

Question 22

describe the alpha helix

Answer 22

• rod-like structure in whih peptide chain coils clockwise about central axis
• helix is stab by intramol h bonding between carbonyl oxygen atoms and amine hydrogen atoms 4 residues away

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Question 23

describe the beta pleated sheet

Answer 23

• peptide chains lie alongside eachother in rows
• intra mol h bondinh between carbonyl oxygen atoms on one chian and amine on another
• r groups point above and below

Question 24

describe tertiary structure

Answer 24

• 3D shapre of the protein determined by hydrophilic and hydrophobic interactions between R groupds and distribution of disulfide bonds
• aa with hydrophobic R groups tend to be found closer together, and face inwards
• hydrophilic aa arrange themselves with T groups interacting with aqueous env

Question 25

what is the effect of 2 cysteine mol

Answer 25

- can form a disulfide bond, created loop in tertiary structure

Question 26

what happens when proline is present in chain

Answer 26

- cannot fit into alpha helix, will cause a kink in the chain

Question 27

what are the 2 major classifications of proteins based on tertiary structure

Answer 27

- fibrous (ex collagen) found in long sheets or strands - globular (ex myoglobin) spherical in shape

Question 28

what is quaternary structure

Answer 28

- some proteins contain more than one polypeptide unit - quat structure refers to the way in which these subunits arrange themselves to yield a functional protien molecule ex: hemoglobin is composed of 4 polypeptide chains

Question 29

what are conjugated proteins

Answer 29

- derive part of function from ovaletly attached molecules called **prosthetic groups** \*at least one portion of thier structure is not made of protein (could be orgnic mol or metal ions) - many vit are prosthetic groups - playmajor role in determining the function of proteins ex: the heme group in myo and hemoglobin

Question 30

what are proteins that have lipid, carbohydrate and nuceltic acid prosthetic groups refered to as

Answer 30

lipoproteins, glycoproteins and nucleoproteins respectively

Question 31

what are albumins and globulines

Answer 31

- primry globular in nature and function as carriers or enzymes

Question 32

what are scleroproteins

Answer 32

- fibrous proteins that act as structural proteins

Question 33

whar are chromoproteins

Answer 33

proteins bound to pigmented molecules

Question 34

what are metalloproteins

Answer 34

proteins complexed around a metal ion

Question 35

explain denaturing proteins

Answer 35

- also called melting - protein loses 3 structure and revert to a random coil state - caused by detergent or changes in pH, temp or solute cnoc - weak intermolecular forced keeping the proteins table and functional are disrupted - damage usually permanent \*some gentle denaturing agents do not permanently disrupt the protein and remocal may allow protein to renature and therefore regain function