Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Biochem > Lecture 4 Information > Flashcards

Lecture 4 Information Flashcards

1
Q

What are proteins used for in neurons?

A

involved in the movement of ions across a membrane

involved in the formation of membrane potential

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

Tertiary structure

A

the total geometric rearrangement of all atoms in a polypeptide

includes the 1º and 2ºstructure

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

What stabilizes the tertiary structure?

A

1) Hydrogen bonds
2) Hydrophobic interactions
3) Disulfide bonds
4) Ionic bonds
5) Van der Waals interactions

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

When do we see disulfide bonds in the 3º structure?

A

places that are very hot use Van der Waals interactions to help stabilize

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

Quaternary structure

A

Two protein units come together

Protein units can have independent functions

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

Protomers

A

quaternary structures with the same peptide subunits

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

Example of a protomer

A

hemoglobin has 4 similar groups

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

Prosthetic groups

A

a covalently bonded group to the peptide that is not an amino acid

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

Cofactors

A

interact with enzymes/proteins through NONCOVALENT means

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

Example of a prosthetic group

A

Vitamin K is found in enzyme that modifies thrombin

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

Fibrous proteins

A

long, extended rope-like proteins

mainly used to give structure

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

Globular proteins

A

compact – blobby proteins

used for “action” (enzymes, regulators, movers)

Huge diversity of globular proteins

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

Alpha keratin

A

An example of a fibrous protein

Has a repeating alpha helix structure

Can be strengthened through a disulfide bond

Has hydrophobic regions that point towards each other and stabilize each other

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

Collagen

A

An example of a fibrous protein

Found in tendons, cartilage, bone, cornea

Left-handed helix

Chains of collagen are cross-linked by modified lysines

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

Collagen tripeptide repeat

A

Gly-X-Y

Glycine is used because it has no R-group. Can be very tightly packed

X is normally proline. This forms a kink which leads to helical structure. Proline can also contribute to a left-handed helix

Y is often times hydroxyproline

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

What are 2 main uses for glycine?

A

it allows proteins to be tightly packed or it allows for flexibility/turns

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

Silk

A

fibrous protein

Gly and Ala are used because small R-groups can pack tightly with each other in B-sheets

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

Myoglobin

A

globular protein

an oxygen storing protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What is the red section on the inside of myoglobin?

A

A prosthetic “heme” group

Heme group is found in hemoglobin and myoglobin to bind oxygen because of the presence of the ion atom

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Motif

A

a recognizable folding pattern involving 2 or more 2ºstructures and the connections between them

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

a+B motif

A

structures tend to have alpha and beta regions as almost separate subunits of the protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

a/B motif

A

structures have alpha and beta subunits very close together

hard to separate

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Domains

A

separate units of protein structure

physically part of the same polypeptide

an independently stable and functional part of a protein that can undergo movement as a single entity

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

Example of types of domains within a protein

A

Some domains may be used to: bind ligands, enzymatic activity, etc

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

Three types of post-translational modification of proteins discussed

A

1) Phosphorylation
2) Glycosylation
3) Add lipids

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

Phosphorylation of a protein

A

can accept a phosphate group on amino acids that have a hydroxyl group (T, S, Y)

if you make one of these amino acids have a negatively charged phosphate group, you could lead to repulsion from nearby amino acids

or, you could make the protein more functional

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

Glycosylation

A

can attach sugars to a protein

sugar tags allow for better identifcation of a protein

can also increase functionality

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

Attaching lipids to a protein

A

creates lipid-anchored proteins

these proteins can embed themselves within the phospholipid membrane

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

What is the functional state of a protein?

A

It’s folded state!

30
Q

Which conformation of a protein will prevail?

A

the one with the lowest energy

31
Q

How do polypeptides fold?

A

they fold in stages

first, independent secondary structures arise

then, these secondary structures collapse into a 3D conformation

32
Q

Native state of a protein

A

the fully folded, functional state of a protein

33
Q

What 4 things will cause a protein to denature?

A

1) Addition of urea
2) Changes in temperature
3) Addition of organic solvents
4) Changes in pH

34
Q

What does the addition of urea and mercapoethanol tell us about protein structure? Why?

A

the primary structure encodes the tertiary structure

disulfide bonds break and the proteins unfold. then, when the urea and mercapoethanol is removed, the protein returns to the same 3D shape

35
Q

Why does heat denature a protein?

A

heat breaks the weak Hydrogen Bonds

36
Q

Why does the addition of organic solvents denature a protein?

A

organic solvents make the surrounding environment much more hydrophobic

hydrophobic groups of the protein will face outwards now

37
Q

Why can changes in pH denature a protein?

A

the R-group ionization states will change

this might cause repulsion or destabilization

38
Q

What drives protein folding?

A

the increase in entropy of the aqueous environment by placing hydrophobic groups together in middle of protein

39
Q

Do proteins have a final 3D structure?

A

No! They are constantly moving about and changing

40
Q

What is a problem with unfolded proteins?

A

If unfolded proteins are floating in the cytoplasm, they can interact with other unfolded proteins and form a precipitate

41
Q

Molecular chaperones

A

helper proteins that help proteins fold in order to keep proteins from floating around unfolded

42
Q

HSP

A

heat shock proteins

type of molecular chaperone

when there is an increase in temperature, more HSPs are found

more proteins unfold at higher temperatures, so need more HSPs

43
Q

Chaperonins

A

will bind to unfolded proteins

protein is put inside of complex in order to refold into correct conformation

large percentage of hydrophobic groups within the complex

hydrophobic groups are forced to interact with each other and refold

44
Q

Do chaperonins require a lot of atp?

A

yes!

45
Q

Ubiquitin ligase

A

marks proteins that are targeted for destruction with a ubitiquin mark

proteasomes will break down proteins with the ubiquitin tag

this allows proteins parts to be recycled

46
Q

Amyloid diseases

A

occur due to a misfolding mechanism in proteins

proteins become unfolded and congregate within the cell

47
Q

Alzheimers and proteins

A

Alzheimers is an amyloid disease

a large complex of unfolded proteins will congregate outside of the cell and cause surrounding cells to die

this is the “holes” in the brain we see in Alzheimers patients

48
Q

Prions

A

misfolded proteins with the ability to transmit their misfolded shape onto normal variants of the same protein

seen in mad cow disease

49
Q

Mad cow disease

A

neural protein becomes unfolded and takes on a different shape

unfolded shape exposes phenylalanine and other aromatic amino acids

aromatic amino acids congregate through hydrophobic interactions (amyloid disease)

50
Q

How does mad cow disease get into human brain?

A

through lesions digestive tract

prions can get to the brain

51
Q

Why is mad cow disease hard to treat?

A

you are trying to breakdown proteins not cells

would have to use something like sodium hydroxide which is very unsafe

52
Q

Why does mad cow disease have such a high latency period?

A

unfolded proteins accumulate slowly

there are more normally folded proteins than unfolded proteins

53
Q

Is myoglobin a motif, domain, or 3D protein?

A

Myoglobin is all 3

the folded structure is a motif found in all globin proteins and it folds into a single domain which this single domain is also the 3D structure for myoglobin

54
Q

“Well” energy diagram of protein folding

A

around the top of the ring is an unfolded protein

secondary structures sample each other at the bottom of the well

when the correct low energy conformation is found, the protein collapses into the well

55
Q

What happens at the bottom of the energy well for proteins?

A

even at the bottom there is not one conformation

protein is not static

will move between a couple similarly stable conformations

56
Q

Parasite Schistosoma mansoni

A

uses an enzyme to break the collagen sequence in the skin

Gly-Pro-X-Y sequence is cut between X and Y

57
Q

Parasite Schistosoma mansoni

A

uses an enzyme to break the collagen sequence in the skin

Gly-Pro-X-Y sequence is cut between X and Y

58
Q

Structures of proteins in terms of increasing complexity

A

secondary structure < folding motif < protein domain < tertiary structure < quaternary structures

59
Q

Structures of proteins in terms of increasing complexity

A

secondary structure < folding motif < protein domain < tertiary structure < quaternary structures

60
Q

3 types of motifs

A

B-a-B, helix-turn-(loop)-helix, B-barrel

61
Q

Where is the helix-loop-helix motif used?

A

in the binding of DNA/gene expression

62
Q

Where is the B-barrel motif used? And give a specific example

A

a pore in membranes

ex: bacteria will insert a B-barrel into a red blood cell and this will lyse the blood cell

63
Q

Is myoglobin a single polypetide?

A

yes!

64
Q

Where is the helix-loop-helix motif used?

A

in the binding of DNA/gene expression

65
Q

Where is the B-barrel motif used? And give a specific example

A

a pore in membranes

ex: bacteria will insert a B-barrel into a red blood cell and this will lyse the blood cell

66
Q

What is myoglobin mostly made up of?

A

alpha helices

67
Q

Is myoglobin a single polypetide?

A

yes!

68
Q

Do heat shock proteins require energy?

A

yes, it is an endergonic process

69
Q

What happens if a heat shock protein can’t get a protein to fold?

A

the protein goes to a chaperonin

70
Q

Do heat shock proteins require energy?

A

yes, it is an endergonic process

71
Q

What happens if a heat shock protein can’t get a protein to fold?

A

the protein goes to a chaperonin

Biochem (20 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions