CH 4 Flashcards

1
Q

Maintaining pH and salt concentrations is critical to keeping proteins functional. What is the molecular mechanism by which pH affects protein function?

A

A few of the polar R-groups can change charge, and the new attraction or repulsion can alter the shape of the protein

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

To study how proteins fold, scientists must be able to purify the protein of interest, use solvents to denature the folded protein, and observe the process of refolding at successive time points. What is the effect of the solvents used in the denaturation process?

A

The solvents break some to most of the noncovalent interactions, resulting in a misfolded protein.

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

what amino acids form disulfide bonds

A

cysteine amino acids

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

makeup of an amino acid

A

central carbon, amine group, carboxylic acid, and side chain R group

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

Molecular chaperones can work by creating an “isolation chamber.” What is the purpose of this chamber?

A

This chamber serves to protect unfolded proteins from interacting with other proteins in the cytosol, until protein folding is completed.

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

Why is it necessary to fully denature polypeptides (including breaking disulfide bonds) to accurately separate proteins on the basis of size in an SDS-PAGE gel?

A

disulfide bonds and protein folds would alter the migration of polypeptides.

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

Michaelis-Menton curve

A

point where enzyme rate is maximized with high substrate conditions

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

Which of the following best describes the molecular mechanisms in which lysozyme lowers the energy required for its substrate to reach its transition-state conformation?

A

by altering the shape of the substrate to mimic the conformation of the transition state

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

Studies conducted with a lysozyme mutant that contains an Asp→Asn change at position 52 and a Glu→Gln change at position 35 exhibited almost a complete loss in enzymatic activity. What is the most likely explanation for the decrease in enzyme activity in the mutant?

A

These amino acid substitutions will change the shape of the protein in the active-site scaffold.

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

In some cases, small molecules are integral to the function of enzymes and are dubbed “coenzymes.” Which of the following is a coenzyme for the enzyme carboxypeptidase?

A

zinc

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

The phosphorylation of a protein is typically associated with a change in activity, the assembly of a protein complex, or the triggering of a downstream signaling cascade. The addition of ubiquitin, a small polypeptide, is another type of covalent modification that can affect the protein function. Ubiquitylation often results in. …

A

protein degradation

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

Energy required by the cell is generated in the form of ATP. ATP is hydrolyzed to power many of the cellular processes, increasing the pool of ADP. As the relative amount of ADP molecules increases, ADP can bind to glycolytic enzymes, which will lead to the production of more ATP. The best way to describe this mechanism of regulation is …

A

allosteric activation

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

Elastin molecules

A

help bendy-flexible properties for structure

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

Disulfide bonds are stronger than…

A

hydrogen

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

Acidic

A

O-, lost a proton

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

Basic

A

O+, gained a proton

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

How antibodies defend

A

Form aggregates and then are ingested by phagocytic cells

18
Q

Lysozyme

A

antibiotic enzyme
attacks polysaccharide chains of bacterial cell wall

19
Q

Allosteric enzymes

A

have two or more binding sites that influence eachother

20
Q

GTP binding proteins on/off

A

turned on and off by gain and loss of phosphate group

21
Q

What drives motor protein movement

A

ATP hydroylsis

22
Q

many interacting proteins are brought together by…

23
Q

Many amino acids are made from…

A

other amino acids

24
Q

Orthosteric inhibitation

A

Inhibitor binds to active site

25
Q

Allosteric inhibitation

A

inhibitor binds to regulatory site (not active site) that changes shape of active site

26
Q

Kinase vs Phosphatase

A

Kinase adds Phosphate group
Phosphatase removes

27
Q

Scaffolds

A

Similar to enzymes, bring many proteins together to make a protein complex

28
Q

Homogenization

A

methods to rupture plasma membrane to empty contents

29
Q

Homogenate

A

soup or extract left over from homogenization that contains small molecules and organelles from the cytosol

30
Q

Supernatant

A

less dense portion of molecules and liquid from centrifuge above denser parts

31
Q

Column chromatography

A

method to filter proteins, can be separated by
-charge
-hydrophobicity
-size
-ability to bond to certain groups

32
Q

3 types of chromatography

A

-ion exchange
-gel-filtration chromatography
-affinity chromatography

33
Q

Ion exchange Chromatography

A

column packed with small beads carrying either positive or negative charges to retard opposite charge proteins. Matrix depends on PH and ionic strength of solution

34
Q

Gel filtration Chromatography

A

columns separate based on size, hollow beads allow smaller proteins to envelope and allow larger proteins to pass through

35
Q

Affinity Chromatography

A

Matrix has molecules that bind to protein of interest, they can be released by pH change or conc. salt solutions

-highly pure

36
Q

Electrophoresis

A

electric field in a protein solution causes proteins to move based on their size and charge

37
Q

Isoelectric focusing

A

electric field gradient applied to filter proteins based on their isoelectric points

38
Q

Isoelectric point

A

pH point where protein has no charge and wont move in an electric gradient

39
Q

two-dimensional polyacrylamide-gel electrophoresis

A

can resolve more than 1000 proteins in a 2d map
-separated top to bottom by atomic weight
-separated left to right by pH

40
Q

X-Ray crystallography

A

first 3d images of proteins, protein is coaxed to from crystals

41
Q

Storage proteins

A

store ions or amino acids

42
Q

Transport proteins

A

transport small molecules or ions