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MCP Unit 2 > Lecture 10: Protein building blocks > Flashcards

Lecture 10: Protein building blocks Flashcards

1
Q

What two factors determine the 3D structure, which dictates function of proteins?

A

polymer length

amino acid composition

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2
Q

Which is more complex - proteome or genome?

A

proteome

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3
Q

What residue is key in HIV-1 protease - Tipranivir interaction?

A

Asp26

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4
Q

What is the cause of Alzheimer’s?

A

42-residue fragment from Alzheimer precursor protein (SPP) is not cleaved to its normal 40-residue length
forms amyloid plaque

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5
Q

How many amino acids are deleted in cystic fibrosis?

A

one

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6
Q

What are three characteristics of each piece of a peptide and the order of connectivity which determine final shape?

A
  1. atomic bumping, backbone dihedral angles, secondary structure
  2. polar vs nonpolar
  3. charges, pKa
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7
Q

Why can’t a peptide bond be rotated?

A

partial double bond formed by N and C

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8
Q

What two things must happen for a protein to fold?

A
  1. rotate plates (atoms attached to C and N) to minimize clashing
  2. satisfy H-bond requirements of N and O on backbone
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9
Q

What angles determine final 3D structure of a protein?

A

phi

psi

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10
Q

What are the phi-psi angles of alpha helices and beta sheets?

A

alpha - ~0

beta - ~180

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11
Q

What does a ramachandran map show?

A

allowed phi-psi angles
grey regions are allowed
different AA favor different angles

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12
Q

Which amino acid has the largest grey area on a Rmacgandran map?

A

glycine (two H’s)

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13
Q

What is the pKa of Asp?

A

4.0

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14
Q

What is the pKa of Glu?

A

4.0

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15
Q

What is the pKa of His?

A

6.5

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16
Q

What is the pKa of Cys?

A

8.5

17
Q

What is the pKa of Lys?

A

10.0

18
Q

What is the pKa of Arg?

A

12.0

19
Q

What is the pKa of the carboxy terminus?

A

4.0 (+ in cell conditions)

20
Q

What is the pKa of the amino terminus?

A

8.0 (- in cell conditions)

21
Q

What is an imino acid? Which molecule fits this description?

A

backbone N is not bonded to H
backbone N is bonded to its own side chain
Proline

22
Q

What does Proline cause?

A

cis peptide bond

–> kink

23
Q

Does a molecule with a high/low pKa bind H+ tightly/weakly?

A

high pKa - binds H+ tightly (basic)

low pKa - binds H+ weakly (acidic)

24
Q

What is pKa?

A

pH at which 1/2 ionizing groups are protonated, half are deprotonated

25
Q

What happens when pH < pKa?

A

ionizing group takes up h+ from solution

26
Q

What happens when pH > pKa?

A

ionizing group gives off H+

27
Q

What is special about histidine?

A

ionizes near pH 7

can both accept and donate protons at physiological conditions

28
Q

What can be used to change pKa?

A

structure, environment

29
Q

Under what conditions does Cys form the tiolate anon (–S-)

A

moderately alkaline (pKa 8.5)

30
Q

Is the structure of a protein static or dynamic? Why?

A

dynamic

doesn’t get that much stability from folding

31
Q

Do covalent interactions have a role in protein folding?

A

No

32
Q

What four interactions have a role in protein folding?

A

electrostatics
H-bonds
van der Waals
hydrophobic effect

33
Q

Where are charged groups usually found on a peptide? Give an example of a molecule

A

outside - interacting with water

ubiquitin

34
Q

What is an example of a protein with a buried charge?

A

F0 proton channel of the F0F1 ATP Synthase

35
Q

What two residues are essential for proton trasnport in the F0 proton channel of the F0F1 ATP Synthase?

A

Glu - proton binds

Pro - kink

36
Q

Which - alpha helix or beta sheet - aligns peptide dipoles in parallel conformations? Is this favorable?

A

Alpha

Not favorable

37
Q

How are polypeptides written?

A

N term –> C term

38
Q

How is the peptide bond characterized? Why does it have this formation?

A 
planar
trans (except Pro) - avoid clashing between C=O groups

MCP Unit 2 (17 decks)

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