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Flashcards in Ch 2 Deck (52):
1

How many essential amino acids are there and what are they?

9/20 are essential and must be obtained from food: histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine

2

What. Is a zwitterion?

Molecules containing both positive and negative charges. exist at neutral pH

3

aliphatic amino acids in increasing hydrophobicity

glycine, proline, alanine, valine, leucine, isoleucine

4

Aromatic amino acids:

All very hydrophobic, while tyrosine has an ionizeable hydroxyl, thus is less hydrophobic than Phe

5

UV absorption spectra of aromatic amino acids

trp: lambda max = 278 nm
tyr: lambda max = 275 nm
phe: lambda max = 260 nm

6

Sulfur containing amino acids

Methionine; starting amino acid for almost all proteins, very hydrophobic.
cysteine: contains a sulfhydryl go up which is very reactive; can form disulfide crossings; can function as a weak acid

7

What is important about cysteine?

2 cysteine can engage in an oxidation reaction to form a disulfide bond-stabilizes the structures of many proteins.

8

describe hydrophobicity of cysteine

cys is a polar amino acid, but the disulfide links are strongly hydrophobic

9

Acidic amino acids

contain carboxyl groups in the R sidechain: hydrophilic: aspartate, glutamate

10

What charge do acidic amino acids have at physiological pH

They are negatively charged at physiological pH and usually present as conjugate bases

11

How are acidic amino acids important for active sites?

Carboxyl groups coordinate catalytic metal ions in the active sites of many enzymes and act as nucleophiles in enzymatic reactions

12

Basic amino acids:

Contain nitrogenous R groups

13

What charge do basic amino acids have at physiological pH

positive

14

How do basic amino acids react in enzymatic reactions/

Act as nucelophiles

15

Histidine:

imidazole ring can be protonated and ionized at neutral pH; only amino acid that functions as buffer in physiological range

16

Lysine:

Diamond aid: protonated at pH 7

17

arginine

guanidinium ion always protonated, most basic amino acid

18

Polar uncharged amino acids

Have R groups containing nitrogen or oxygen; are uncharged at physiological pH

19

threonine:

Has 2 chiral carbons

20

asparagine

amide of aspartic acid

21

glutamine:

amide of glutamic acid

22

where do you find hydrophobic amino acids?

interior of proteins where they are. shielded fromd direct contact with water

23

where do you find hydrophilic amino acids?

on the solvent exposed exterior of proteins and active sites of enzymes

24

what does the imidazole group of histidine do?

accept or donate protons at physiological pH, found in the active sites of enzymes

25

What do hydroxyl and thiol groups do?

function as nucelophiles during catalysis. thiol groups also from disulfide bonds important for overall 3 dimensional folding of proteins

26

what is a peptide bond?

link between alpha carboxyl group of one amino acid to the alpha amino group of another amino acid

27

what are the 2 basic configurations of a peptide bond, and which is more common/why

cis and trans, trans more common. cis causes steric clashes:

28

when do cis linkages occur?

when proline is involved

29

what is the phi angle?

angle of rotation between the nitrogen and the alpha carbon

30

what is the psi angle?

angle of rotation between the alpha carbon and the carbonyl carbon

31

why are 75% of possible psi and phi combinations excluded?

steric clashes

32

how is an alpha helix stabilized?

intrachain hydrogen bonds; all the main chain CO and NH groups are H-bonded

33

are right handed or left handed alpha helices more stable?

right handed: less steric clashes.

34

how do the 2 types of beta sheets differ?

antiparallel B-sheet have adjacent beta strands running in opposite direction. each amino acid is hydrogen bonded to as ingle amino acid on the adjacent strand
parallel beta-sheets: adjacent b- sheets run in parallel each amino acid is hydrogen bonded to 2 free amino acids on opposite strand

35

beta sheets can be:

purely parallel, antiparallel, or mixed. also can be flat or twisted.

36

a protein rich in beta sheets:

fatty acid binding protein

37

how do polypeptide chains change directions?

making reverse turns and loops

38

how do reverse turns work?

the CO group of the first residue is hydrogen bonded to the 4th residue to stabilize the turn

39

where are loops found?

often found on the surface of proteins where they engage in contacts with other proteins

40

what is an alpha-helical coiled coil? and what is an example

2 alpha helices coiled together. alpha-keratin is the primary component of hair. 2 right handed helices are intertwined to form a larger left handed super helix

41

how do alpha helical coiled coils stay together?

primarily van der waals and ionic interactions bridging 2 alpha-helices

42

how does the tertiary structure of a porin differ from other proteins?

it is embedded within hydrophobic membranes and allows transport of water through membrane? outside of porin is hydrophobic, inside I hydrophilic

43

how does quaternary structure form/

hydrogen bonding, covalent bonding, hydrophobic packing and hydrophilic exposure

44

how do proteins fold?

it folds cooperatively: many amino acids need to cooperate to produce enough intramolecular interactions to cause protein to fold

45

why is protein folding seen as an all or none process? what does this tell you about a denaturation curve?

if you disrupt part of a protein structure, it may unravel the structure completely: middle of denaturation curve contains a mixture of full folded and fully unfolded proteins, not partially unfolded proteins

46

what are diseases caused by misfolded proteins?

prion diseases

47

how are prion diseases transmissible?

misfolded PrP protein binds to properly folded prP protein and induces misfolding

48

what are 2 examples of protein misfolding diseases

mad cow disease and Alzheimer's

49

what is protein primary structure

linear sequence of amino acids, polymer of amino acid residues, linked by peptide bonds: covalent amide linkages

50

what is secondary structure:

local regular conformations observed for parts of peptide backbone of a protein

51

what is tertiary structure?

3 dimensional conformation of whole folded polypeptide chain

52

what is quaternary structure?

3 dimensional relationship between different polypeptide chains