Structure and function of proteins and their constituent amino acids Flashcards

You may prefer our related Brainscape-certified flashcards:
1
Q

absolute configuration at the alpha position

A

All chiral amino acids in eukaryotes are L, and have their amino acid therefor drawn at left in Fischer Projections.
All chiral amino acids are S except cysteine.
All amino acids are chiral but glycine.
The alpha carbon is adjacent to the carbonyl.

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

Amino acids as dipolar ions

A

pKa of group is the pH at which, on average, half are protonated and half are not.
Above that pKa, the majority of the species is deprotonated.
pKa1 is the -COOH, pKa2 is the -NH2, pKa3 is the R group.
A whole amino acid is a zwitterion at its pI.
Titration curve is flat at the pKa’s and vertical at the pI.
Like Icharus, amino acids lose protons as they ascend.

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

Acidic amino acids

A

Glutamatic acid, Glu, E
Aspartatic acid, Asp, D
Negatively charged at phys pH (7.4)

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

Basic amino acids

A

Histidine, H, His
Arginine, R, Arg
Lysine, Lys, K
Positive at physiological pH

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

Hydrophobic

A

LIMPVAG (as well as W and F)

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

Hydrophilic

A

GSTAC (and Y)

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

oligopeptides

A

up to 20

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

resonance between amino nitrogen and carbonyl provides

A

rigidity

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

hydrolysis of amino acids

A

enzyme adds H to N and OH to C

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

secondary structure

A

alpha helix or beta sheet

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

helix breakers

A

glycine and proline

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

turns of beta sheets

A

glycine and proline

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

Denaturing

A

reduced to primary structure.
heat adds energy which overcomes hydrophobic interactions.
solutes can overcome cistine, H-bonds, and other side chain interactions.

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

Isoelectric point

A

average the two pKa’s flanking the pI.
No charged side chain, pI around 6.
positive side chain (basic), pI above 6.

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

Non-enzymatic protein function: binding

A

ex: hemoglobin, tscription factors, ca-binding.
transport or sequester.
transport affinity varies much with environment.
sequester affinity high across large range of conc.

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

Non-enzymatic protein function: cell adhesion

A

integral membrane proteins. surface of most cells. bind ECM and or other cells. three families: cadherins, integrins, selectins.

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

cadherins

A

group of glycoproteins. mediate ca-dependent cell adhesion. often hold similar cell types together: E-cadherin for epithelial, etc.

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

integrins

A

binding/communicating with ECM. Cellular signalling. Influence cellular function such as division. Ex: platelets use them to stick to fibrinogen, which triggers platelets to stabilize clot.

19
Q

selectins

A

unique in that they bind to carbs projecting from other cells. weakest bond of CAMs. white blood cells and endothelial cells lining blood vessel. role in host defense including white blood cell migration and inflammation.

20
Q

immunoglobulins

A

made by B-cells. can neutralize antigen(pathogen), mark pathogen for destruction for other WBC right away, or agglutination of antibody and antigen into large insoluble complex that can be phagocytized by macrophages. heavy chains together by disulfide. each light chain with each heavy disulfide.

21
Q

Non-enzymatic protein function

A

some structural proteins, such as motile cilia and flagella, and sarcomeres, have motor function in the presence of motor proteins. motor proteins also display enzymatic function, acting as ATPases that power conformation changes necessary for motor function. motor proteins have transient interactions with either actin or microtubules.

22
Q

myosin

A

primary motor protein that interacts with actin. thick filament in myofibrils. can be involved in cellular transport.

23
Q

kinesins and dyneins

A

assoc with microtubules. vesicle transport. kinesin to positive end, such as to synapse of neuron.

24
Q

kinesin

A

aligning xsomes during metaphase. depolymerizing microtubules during anaphase.

25
Q

dynein

A

sliding movement of cilia and flagella. toward negative end of MT. Ex: waste and recycled NT toward soma.

26
Q

function of enzymes in catalyzing biological reactions

A

lower activation energy. increase reaction rate. do not alter equilibrium constant. not changed or consumed in reaction and so appear in product and reactant side. pH and temp sensitive with optimal activity at specific pH and temp ranges. do not affect overall deltaG. specific for particular reaction or class of reactions.

27
Q

oxidoreductase

A

catalyze oxidation-reduction reactions. often have cofactor that acts as electron carrier.

28
Q

transferase

A

catalyze movement of functional group from one molecule to another. often called transferases, but also include kinase.

29
Q

hydrolase

A

breaking down of compound into two with addition of water. commonly named after substrate. examples are phosphatases, peptidases, nucleases, lipases.

30
Q

lyase

A

cleavage of one into two without water. reversible. often called synthetase in reverse.

31
Q

isomerase

A

rearrangement of bonds within a molecule. might also be classified as oxidoreductases, transferases, lyases. catalyze reations between constitutional AND stereoisomers

32
Q

LI’L HOT

A

ligase, isomerase, lyase, hydrolase, oxidoreductase, transferase

33
Q

ligase

A

addition or synthesis generally between large similar molecules. often require ATP. synthesis with smaller molecules generally accomplished by lases. examples of ligase are nucleic acid synthesis and repair.

34
Q

active site model

A

no alteration of secondary or tertiary structure necessary upon binding of substrate

35
Q

induced fit

A

endergonic binding. exergonic letting go.

36
Q

cofactors

A

don’t carry, but participate in reaction. inorganic.

37
Q

coenzyme

A

organic. often carrier. NAD+.

38
Q

prosthetic group

A

tightly bound coenzyme or cofactor

39
Q

apoenzyme

A

does not include cofactor

40
Q

vitamin

A

organic cofactors and coenzymes

41
Q

mineral

A

inorganic cofactors

42
Q

charge of DNA

A

negative

43
Q

temperature change, effect on enzyme

A

wrong geometry, misfolding