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Adv Cell Bio - Quiz 01 > Lecture 3-4 > Flashcards

Lecture 3-4 Flashcards

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1
Q

General amino acid formula

A 
R group (amino acid side chain)
Carboxyl group (- charge)
Amino group (+ charge)
C (a-carbon atom)
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2
Q

What happens to amino and carboxyl groups at pH 7?

A

They get ionized

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3
Q

Optical isomers

A

Optical isomers occur because the a-carbon is asymmetric, which creates 2 mirror images (stereoisomers L and D)

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4
Q

What is the optical isomers of proteins?

A

L-isomer

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5
Q

Peptide bond

A

amide linkage that joins 2 amino acids (C-N bond)

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6
Q

Why is there no rotation around the C-N bond?

A

peptide bonds form a rigid planar unit

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7
Q

How can amino acids be more flexible?

A

single bonds allow rotation

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8
Q

How are amino acid side chain properties grouped?

A

size, charge, polarity

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9
Q

Protein shape is determined by?

A

amino acid sequence

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10
Q

amino acid sequence referred to as?

A

primary structure

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11
Q

Name 3 noncovalent bonds that help proteins fold?

A

Electrostatic attractions, van der Waals attraction, hydrogen bonds

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12
Q

Common folding patterns of proteins

A

a helix b sheet

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13
Q

Secondary structure

A

regular local structure of protein backbone stabilized by intramolecular bonding

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14
Q

B-sheets can occur in what configurations?

A

Antiparallel vs parallel

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15
Q

alpha helices can form what superstructure?

A

coiled coil

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16
Q

Coiled-coil

A

In the helix, there are amino acids from a-g. The amino acids in a and d are often nonpolar. Proline breaks the helix.

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17
Q

How does coiled-coil superstructure minimize exposure of hydrophobic amino acid side chains to aqueous environment?

A

alpha helices wrap around each other. Specifically, the hydrophobic amino acids in the a and d position of the alpha helices are wrapping around each other

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18
Q

What is the structure of the Scr kinase?

A

SH2 and SH3 domains, ATP

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19
Q

tertiary structure

A

full 3D organization of polypetide chain

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20
Q

What stabilizes extracellular proteins?

A

covalent cross-linkage (disulfide bonds SH)

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21
Q

What do intrinsically disordered regions often contain?

A

few hydrophobic amino acids and are relatively highly charged

22
Q

What are some functions of intrinsically disordered regions?

A

1) binding
2) signaling
3) tethering
4) diffusion barrier

23
Q

What determines protein chemistry?

A

Surface Conformation

24
Q

What are the 2 mechanisms to increase reactivity of active site?

A

Keep water out or cluster functional residues together

25
Q

What are 3 ways that proteins can bind to other proteins?

A

1) Surface-string
2) helix-helix
3) surface-surface

26
Q

equilibrium constant

A

measures binding strength (dissociation)

27
Q

How do enzymes speed up reactions?

A

By selectively stabilizing transition states

28
Q

Transition rate

A

Transition rate determines the activation energy, and is the most unstable intermediate in catalysis reactions.

29
Q

Why do enzymes selectively stabilize transition states during catalysis?

A

When they are stable, enzymes have a higher affinity for transition states than substrates

30
Q

Enzymes use acid and base catalysis simultaneously example

A

A) no catalysis

31
Q

Enzyme mechanisms

A

1) precise substrate orientation
2) distortions of electron clouds
3) forcing substrate into transition state

32
Q

Coenzymes are?

A

tightly bound small non-amino acid molecules that are often:

1) metal ions
2) small organic molecules
3) both in one molecule

ex retinal heme

33
Q

Since enzymes are effective, many reactions in the cell are ____?

A

diffusion limited

34
Q

3 Cellular mechanism for increasing metabolism?

A

1) use membranes to compartmentalize
2) enzymes are localized into the cell and group with enzymes that share the same pathway
3) form multi enzyme complex

35
Q

Multi enzyme complexes increase?

A

metabolism rate

36
Q

multi-enzyme complexes increase?

A

metabolism rate (fatty acid synthase)

37
Q

Explain how fatty acid synthase works?

A

It has 5 enzyme domains, and the acyl carrier domain passes it off to each enzyme domain

38
Q

Pathway nodes?

A

Enzymes compete for the same substrate

39
Q

Enzyme regulation is achieved by?

A

1) expression regulation
2) regulation of subcellular distribution
3) PTM
4) enzyme degradation
5) small molecule binding

40
Q

Feedback regulation

A

allostery, sometimes competition

41
Q

Feedback inhibition

A

?

42
Q

Example of feedback activation?

A

ADP activates enzymes for sugar catabolism

43
Q

Allosteric enzymes have how many binding sites?

A

Allosteric enzymes have two or more interacting binding sites

44
Q

symmetric protein assemblies produce?

A

cooperative allosteric transitions (ligand stabilizes the protein conformation it binds to)

45
Q

phosphorylation can affect?

A

1) protein conformation 2) allow protein binding 3) mask binding site on protein

46
Q

Which amino acid side chains can be phosphorylated?

A

Serine (S), Threonine (T), Tyrosine (Y)

47
Q

PTMS and allosteric shape changes enable protein to function as?

A

microprocessor, assembly factor/scaffold/mechanic motor/ ion pump

48
Q

Protein that functions like a microprocessor

A

Src protein

49
Q

Src kinase mechanism

A

1) phosphate removal loosens structure
2) activating ligand binds to SH3 domain
3) kinase can now phosphorylate tyrosine to self-activate

50
Q

molecular input-output device of Src kinase (micropressor)

A

inputs= has this phosphate been removed, has this binding been disrupted? has this phosphate been added

If yes to all three

Src-type protein kinase activity turns on

51
Q

Proteins can be regulated by?

A

covalent addition of other proteins: Ubiquitin, SUMO (small ubiquitin-related modifier)

52
Q

Covalent modification of proteins can direct proteins to?

A

Covalent modifications can direct proteins to specific cell sites

Adv Cell Bio - Quiz 01 (6 decks)

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