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BIOL 2020 > Amino Acids & Proteins > Flashcards

Amino Acids & Proteins Flashcards

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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

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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

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3
Q

What amino acids have a pkR?

A

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

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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)

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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

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6
Q

What value does pK1 and pK2 tend to be around?

A

9 and 2

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7
Q

What are amino acids?

A

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

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8
Q

What are zwitterions?

A

molecule/ion that has seperate negative and positively charged groups

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9
Q

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

A

alpha carbon

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10
Q

What is chiral? Are all amino acids chiral?

A

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

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11
Q

Why are the active sites of enzymes stereospecific?

A

they are chiral, this is because amino acids are chiral

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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

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13
Q

Why does every protein have at least one sulphur?

A

methionine has a sulfur and it is the start codon

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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

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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

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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

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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)

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18
Q

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

A

aspartate, glutamate

very hydrophilic (have pKr)

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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

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20
Q

Which amino acid has an ionizable group at physiologica pH?

A

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

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21
Q

How are amino acids joined together?

A

peptide bonds

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22
Q

Why type of reaction makes peptide bonds?

A

condensation reaction, loss of a water molecule to make bond

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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

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24
Q

What are the amino acids in a protein called?

A

residues

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25
What direction are proteins written?
n terminus to c terminus
26
Why is the peptide bond rigid and resistant to rotation? What does this cause?
has a partial double bond due to resonance with the carbonyl carbon two conformations, cis and trans
27
Which conformation is favoured in peptides?
trans, less steric clash
28
What is a prosthetic group?
an extra chemical group not coded for in protein (iron in hemoglobin), called conjugated proteins
29
If a protein is made up of 1 polypeptide chain its called? What about multiple chains?
monomeric, oligomeric
30
What are the two classes of proteins? Examples?
globular (water soluble), fibrous (water insoluble) all enzymes, keratin/collagen
31
What is the primary structure of the protein?
sequence of amino acids
32
How can you determine the primary strcture of a protein?
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
33
What is the secondary structure of protein? What does it depend on?
alpha helices and beta pleated sheets (depends on permissible bond angles)
34
What is a ramachandran plot?
shows permissible f/y angle pairs for proteins
35
What has the fewest bond angle combinations? What about the most?
proline, glycine
36
What is the formation of alpha helices driven by?
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
37
What directions are the R groups pointing in alpha helices?
out, exposed
38
What directions do the R groups face in beta sheets?
alternate between up and down
39
What are the two ways beta pleated sheets arranged? Which is more common? Why?
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
What are beta bends stabilized by? How do the two types vary?
by hydrogen bond between the 1st and 4th amino acid the orientation of the second carbonyl in carbon 2
41
Where are left handed alpha helices vs right handed alpha helices located on ramachandran plot?
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
Where are parallel vs antiparallel beta sheets located on ramachandran plot?
both in top left chunk, anti parallel are higher up and further to the left
43
How can the proportion of protein that have a specfic secondary structure be found?
estmiated through the absorption circularly polarized light
44
What do the graphs for alpha helices vs beta sheets look like when using circular dichroism spectroscopy?
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
What determines the native fold of the protein?
all info is in primary sequence
46
What is the tertiary strcuture?
3D shape of protein
47
What guides a protein to fold into its native shape?
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
What is the correct folding proteins assisted by?
chaperones and chaperonins
49
What is the structure of collagen?
repeating PGX amino acids that form a tight triple helix held together by covalent and hydrogen bonds
50
What are protein domains?
stable unit of protein structure that can fold on its own includes discreet elements of function/evolution, folding, compact structure
51
How are proteins typically purified?
charge, size, interactions with other proteins/ligands
52
What are some methods to separate proteins using size?
centrifugation, electrophoresis, size-exclusion chromatography (gel filtration)
53
During centrifugation which particles end up at the bottom of the tube?
ones with greater mass
54
What are some advantages of electrophoresis?
low cost, simple, good resolution, easy to reproduce, useful for preparation and analysis
55
What is the equation that describes electrophoresis?
electrophoretic mobility=charge/friction
56
What can electrophoresis only distinguish size?
SDS is used which denatures the proteins so they don't work, gives all proteins uniform negative charge
57
How does size-exclusive chromatography work? (gel filtration)
columns filled with porous resin, let through smaller substnces and exclude large ones, b/c of this the alrger ones exit first
58
How does affinity chromatography work?
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
How can you find the specific activity of an enzyme when purifying?
divide the total activity by the amount of protein specific activity is measure of purity
60
Why do we need heme group to have iron in RBC?
free iron is really reactive, heme prevents iron from reacting
61
What is hemoglobin made up of?
2 alpha helixes and 2 beta sheets, each one of this has a heme group
62
How many bonds is iron capable of? What are they used for in heme?
6, 4 are in plane of heme and binded to nitrogen, 5 bond is used by histidine side chain, 6th is for oxygen
63
Why is the oxygen binding site buried in hemoglobin?
prevents other gases from binding to site, small channel means mostly onyl oxygen can get in
64
What is myoglobin?
found in muscles, made of 1 polypeptide and one heme
65
Why do we have hemoglobin and myoglobin?
hemoglobin transports and myoglobin stores in muscles
66
What pressure does hemoglobin pick up/release oxygen? What about myoglobin?
picks up in lungs (high pressure) releases in muslces (low pressure) has high affinity for oxygen at low partial pressures
67
What is cooperative binding in hemoglobin?
binding one oxygen makes the affinity increase for the other three heme groups easier time binding oxygen after the first binds
68
What are the two states of hemoglobin?
tense state (low affinity), relaxed state (high affinity)
69
How does the binding of oxygen cause a conformational change in hemoglobin?
shifts plane of polyphorin ring, pulling histidine and the associated helix with it
70
At what pH is hemoglobins binding capability with oxygen inhibited? Why?
low pH (more H+) protonating histidines imidazole ring stabilizes the tense state
71
How does BPG affect homeglobin binding?
lowers the binding capability binds to center of tense state, locks it in place (relaxed state hole is too small for BPG)
72
What amino acid does A stand for?
alanine
73
What amino acid does R stand for?
arginine
74
What amino acid does N stand for?
asparagine
75
What amino acid does D stand for?
aspartate (aspartic acid)
76
What amino acid does C stand for?
cysteine
77
What amino acid does E stand for?
glutamate (glutamic acid)
78
What amino acid does Q stand for?
glutamine
79
What amino acid does G stand for?
glycine
80
What amino acid does H stand for?
histidine
81
What amino acid does I stand for?
isoleucine
82
What amino acid does L stand for?
leucine
83
What amino acid does K stand for?
lysine
84
What amino acid does M stand for?
methionine
85
What amino acid does F stand for?
phenylalanine
86
What amino acid does P stand for?
proline
87
What amino acid does S stand for?
serine
88
What amino acid does T stand for?
threonine
89
What amino acid does W stand for?
tryptophan
90
What amino acid does Y stand for?
tyrosine
91
What amino acid does V stand for?
valine
92
What are some common post translational modifications of proteins?
proteolytic cleavage, amino acid modification, attaching carbs, attaching prosthetic groups
93
What is the most common posttranslation amino acid modification?
phosphorylation of serine, theornine, and tyrosine
94
How are proteins targetted to the ER?
involves the recognition and cleavage of a peptide signal sequence by SRP
95
What is 35S?
Isotope used to radioactively label proteins

BIOL 2020 (8 decks)

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