Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

BIOL 2020 > Amino Acids & Proteins > Flashcards

Amino Acids & Proteins Flashcards

1
Q

Can amino acids be titrated? What is different about them compared to an acid?

A

yes they can, they have multiple pK’s and their r group might also have a pkR

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What is the pK1 associated with?What about pK2 and pKR?

A

pk1 is associated with the carboxyl group

pk2 is associated with the amino group

pKR is associated with the R group

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What amino acids have a pkR?

A

tyrosine (Y), Cysteine (C), Lysine (K), histidine (H), Arginine (R), Aspartate (D), Glutamate (E)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What is the isoelectric point? What’s another name?

A

the pH where the amino acid or protein has no net charge (isoelectric pH)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

How do you calculate the isoelectric point?

A

determine the pKa that defines the neutral species and avaergae that number with the pKR

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What value does pK1 and pK2 tend to be around?

A

9 and 2

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What are amino acids?

A

building blocks of proteins, the monomers that make up the polymer that is a polypeptide

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What are zwitterions?

A

molecule/ion that has seperate negative and positively charged groups

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What is the carbon bonded to the carboxylic acid and amino group called?

A

alpha carbon

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What is chiral? Are all amino acids chiral?

A

4 bonds on carbon that are all different, all amino acids except glycine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Why are the active sites of enzymes stereospecific?

A

they are chiral, this is because amino acids are chiral

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What amino acids are in the non polar, aliphatic R group? How are they in water?

A

glycine, alanine, proline, valine, leucine, isoleucine, methionine

not happy in water, but not too unhappy, tend to be in center of proteins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Why does every protein have at least one sulphur?

A

methionine has a sulfur and it is the start codon

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What amino acids are in the aromatic R group? How are they in water?

A

phenylalanine, tyrosine, tryptophan

most hydrophobic group, will be buried in center of protein, will drive how proteins fold

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What amino acids are in the polar, uncharged R group? How are they in water?

A

serine, threonine, cysteine, asparagine, glutamine

happy in water, good at making hydrogen bonds but not ionized

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Which of the amino acids in the aromatic R group is happiest in water?

A

tyrosine (because OH group), still not happy in water though

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What amino acids are in the positively charged R groups? How are they in water?

A

lysine, arginine, histidine

very hydrophillic (have pKr)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What amino acids are in the negatively charged R groups? How are they in water?

A

aspartate, glutamate

very hydrophilic (have pKr)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What is a covalent disulfide bond?

A

R group of cysteine can join its sulfur atom with another cysteine in an oxidation reaction, very important for protein structure

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Which amino acid has an ionizable group at physiologica pH?

A

histidine, r group is an imidazole ring that can be ionzied

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

How are amino acids joined together?

A

peptide bonds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

Why type of reaction makes peptide bonds?

A

condensation reaction, loss of a water molecule to make bond

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

What are two amino acids joined by a peptide bond called? What about 3? What about more than 3? More than 100?

A

dipeptide, tripeptide, polypeptide, protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

What are the amino acids in a protein called?

A

residues

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

What direction are proteins written?

A

n terminus to c terminus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

Why is the peptide bond rigid and resistant to rotation? What does this cause?

A

has a partial double bond due to resonance with the carbonyl carbon

two conformations, cis and trans

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

Which conformation is favoured in peptides?

A

trans, less steric clash

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

What is a prosthetic group?

A

an extra chemical group not coded for in protein (iron in hemoglobin), called conjugated proteins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

If a protein is made up of 1 polypeptide chain its called? What about multiple chains?

A

monomeric, oligomeric

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

What are the two classes of proteins? Examples?

A

globular (water soluble), fibrous (water insoluble)

all enzymes, keratin/collagen

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

What is the primary structure of the protein?

A

sequence of amino acids

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

How can you determine the primary strcture of a protein?

A

directly (digested via a procedure called Edman degradation, amino acids are removed one at a time and identified by high-performance liquid chromatography)

if dna sequence is known it can be inferred

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

What is the secondary structure of protein? What does it depend on?

A

alpha helices and beta pleated sheets (depends on permissible bond angles)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

What is a ramachandran plot?

A

shows permissible f/y angle pairs for proteins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

What has the fewest bond angle combinations? What about the most?

A

proline, glycine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

What is the formation of alpha helices driven by?

A

the hydrogen bonds between the NH group of one amino acids and the carbon double bonded to oxygen group of the amino acid 4 residues ahead

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

What directions are the R groups pointing in alpha helices?

A

out, exposed

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

What directions do the R groups face in beta sheets?

A

alternate between up and down

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

What are the two ways beta pleated sheets arranged? Which is more common? Why?

A

parallel/anti parallel

anti parallel is more comon

because the distance travelled to fold back on itself is shorter than if all facing the same direction like in parallel

40
Q

What are beta bends stabilized by? How do the two types vary?

A

by hydrogen bond between the 1st and 4th amino acid

the orientation of the second carbonyl in carbon 2

41
Q

Where are left handed alpha helices vs right handed alpha helices located on ramachandran plot?

A

left handed are in the seperate vertical chunk located in top right chunk

right handed are in the horizontal chunk in the bottom left square

42
Q

Where are parallel vs antiparallel beta sheets located on ramachandran plot?

A

both in top left chunk, anti parallel are higher up and further to the left

43
Q

How can the proportion of protein that have a specfic secondary structure be found?

A

estmiated through the absorption circularly polarized light

44
Q

What do the graphs for alpha helices vs beta sheets look like when using circular dichroism spectroscopy?

A

alpha starts very high and drops quickly before making a small bump and returning to 0

beta starts medium and drops less steep and not as far before gradually returning to 0

45
Q

What determines the native fold of the protein?

A

all info is in primary sequence

46
Q

What is the tertiary strcuture?

A

3D shape of protein

47
Q

What guides a protein to fold into its native shape?

A

try to get lowest gibbs free energy

  1. ordering amino acids w/respect to water
  2. hydrogen bonds/salt bridges provide enthalpic push to fold
    3.
48
Q

What is the correct folding proteins assisted by?

A

chaperones and chaperonins

49
Q

What is the structure of collagen?

A

repeating PGX amino acids that form a tight triple helix held together by covalent and hydrogen bonds

50
Q

What are protein domains?

A

stable unit of protein structure that can fold on its own

includes discreet elements of function/evolution, folding, compact structure

51
Q

How are proteins typically purified?

A

charge, size, interactions with other proteins/ligands

52
Q

What are some methods to separate proteins using size?

A

centrifugation, electrophoresis, size-exclusion chromatography (gel filtration)

53
Q

During centrifugation which particles end up at the bottom of the tube?

A

ones with greater mass

54
Q

What are some advantages of electrophoresis?

A

low cost, simple, good resolution, easy to reproduce, useful for preparation and analysis

55
Q

What is the equation that describes electrophoresis?

A

electrophoretic mobility=charge/friction

56
Q

What can electrophoresis only distinguish size?

A

SDS is used which denatures the proteins so they don’t work, gives all proteins uniform negative charge

57
Q

How does size-exclusive chromatography work? (gel filtration)

A

columns filled with porous resin, let through smaller substnces and exclude large ones, b/c of this the alrger ones exit first

58
Q

How does affinity chromatography work?

A

similar to gel filtration, but resin contains a substance that the protein has an affinity for, so protein binds and all other molecules flow out, then a solution used to release the binding allows the protein to flow out

59
Q

How can you find the specific activity of an enzyme when purifying?

A

divide the total activity by the amount of protein

specific activity is measure of purity

60
Q

Why do we need heme group to have iron in RBC?

A

free iron is really reactive, heme prevents iron from reacting

61
Q

What is hemoglobin made up of?

A

2 alpha helixes and 2 beta sheets, each one of this has a heme group

62
Q

How many bonds is iron capable of? What are they used for in heme?

A

6, 4 are in plane of heme and binded to nitrogen, 5 bond is used by histidine side chain, 6th is for oxygen

63
Q

Why is the oxygen binding site buried in hemoglobin?

A

prevents other gases from binding to site, small channel means mostly onyl oxygen can get in

64
Q

What is myoglobin?

A

found in muscles, made of 1 polypeptide and one heme

65
Q

Why do we have hemoglobin and myoglobin?

A

hemoglobin transports and myoglobin stores in muscles

66
Q

What pressure does hemoglobin pick up/release oxygen? What about myoglobin?

A

picks up in lungs (high pressure) releases in muslces (low pressure)

has high affinity for oxygen at low partial pressures

67
Q

What is cooperative binding in hemoglobin?

A

binding one oxygen makes the affinity increase for the other three heme groups

easier time binding oxygen after the first binds

68
Q

What are the two states of hemoglobin?

A

tense state (low affinity), relaxed state (high affinity)

69
Q

How does the binding of oxygen cause a conformational change in hemoglobin?

A

shifts plane of polyphorin ring, pulling histidine and the associated helix with it

70
Q

At what pH is hemoglobins binding capability with oxygen inhibited? Why?

A

low pH (more H+)

protonating histidines imidazole ring stabilizes the tense state

71
Q

How does BPG affect homeglobin binding?

A

lowers the binding capability

binds to center of tense state, locks it in place (relaxed state hole is too small for BPG)

72
Q

What amino acid does A stand for?

A

alanine

73
Q

What amino acid does R stand for?

A

arginine

74
Q

What amino acid does N stand for?

A

asparagine

75
Q

What amino acid does D stand for?

A

aspartate (aspartic acid)

76
Q

What amino acid does C stand for?

A

cysteine

77
Q

What amino acid does E stand for?

A

glutamate (glutamic acid)

78
Q

What amino acid does Q stand for?

A

glutamine

79
Q

What amino acid does G stand for?

A

glycine

80
Q

What amino acid does H stand for?

A

histidine

81
Q

What amino acid does I stand for?

A

isoleucine

82
Q

What amino acid does L stand for?

A

leucine

83
Q

What amino acid does K stand for?

A

lysine

84
Q

What amino acid does M stand for?

A

methionine

85
Q

What amino acid does F stand for?

A

phenylalanine

86
Q

What amino acid does P stand for?

A

proline

87
Q

What amino acid does S stand for?

A

serine

88
Q

What amino acid does T stand for?

A

threonine

89
Q

What amino acid does W stand for?

A

tryptophan

90
Q

What amino acid does Y stand for?

A

tyrosine

91
Q

What amino acid does V stand for?

A

valine

92
Q

What are some common post translational modifications of proteins?

A

proteolytic cleavage, amino acid modification, attaching carbs, attaching prosthetic groups

93
Q

What is the most common posttranslation amino acid modification?

A

phosphorylation of serine, theornine, and tyrosine

94
Q

How are proteins targetted to the ER?

A

involves the recognition and cleavage of a peptide signal sequence by SRP

95
Q

What is 35S?

A

Isotope used to radioactively label proteins

BIOL 2020 (8 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions