Brainscape's Knowledge GenomeTM

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


See full index

BIOC 212 > Protein Folding in the cell (L3-6) > Flashcards

Protein Folding in the cell (L3-6) Flashcards

1
Q

Which are the main functions of proteins?

A
  • Enzymes catalyze cell chemical reactions
  • Membrane proteins form communication channels
  • transport of cargo and mechanical forces
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Which molecules carries the main functional components in the cell?

A

Proteins

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

What is the importance of protein folding?

A
  • Gives its function to the protein
  • Provides physical stability
  • Provides functional surfaces for interaction with other molecules

*Sequence of amino acid and interactions between them determine structure, function, localization

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

Name 3 different polymers

A
  • DNA
  • RNA
  • Peptide chains / Proteins
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What is the standard structure for an amino acid?

A

H2N - alpha C - COOH
often in ionized form at pH 7

(+) H3N - alpha C - COO (-)

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

What are different characteristics of side chains?

A
  1. Hydrophobic, polar or charged (acidic/basic)
  2. Small or large
  3. Covalently linked into polypeptides (links are not between side chains, but between the core of AA)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Which are the polar amino acids?

A

*Not Quite Your Show Time
- Asparagine (NH2) (N)
- Glutamine (NH2) (Q)
- Serine (OH) (S)
- Threonine (OH) (T)
- Tyrosine (ring + OH) (Y)

*H2O = hydrogen bond donor (H linked)
NH3 = hydrogen bond acceptor (N linked)

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

Which are the acidic amino acids?

A
  • Aspartate
  • Glutamate

*Have COO (-)

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

Which are the basic amino acids?

A
  • Lysine
  • Arginine
  • Histidine

*Have NH3+ or HN2+

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

Which are the hydrophobic nonpolar amino acids?

A
  • GAVe LIFe With My Partner in Crime
  • Glycine (G)
  • Cysteine (C)
  • Methionine (M)
  • Alanine (A)
  • Phenylalanine (F)
  • Valine (V)
  • Leucine (L)
  • Isoleucine (I)
  • Proline (P)
  • Tryptophan (W)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Explain the peptide bond formation reaction (in the polypeptide backbone)?

A
  • Condensation (H2O released, joining of 2 molecules)
  • N - alpha C - C - BOND - N - alpha C

H2O release = OH from C-terminal and H from N-terminal

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

What part of polypeptides determine the charge and hydrophobicity?

A

Side chains

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

What are characteristics of the peptide bond?

A
  • Planar, can’t rotate (bc of hybrid/partial double bond from C=O)
  • Peptide bond is uncharged, but polar
  • Can form non-covalent contact with other AA
  • Only L-amino acids
  • Peptide bond always in trans configuration except P (proline), can be trans or cis bc of NH2 loop
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Why do we say the polypeptide backbone has limited freedom?

A
  • Peptide bond is planar and can’t rotate
  • Rotation around alpha C (both sides)

*Some rotation angles between amino acid residues in a polypeptides a prefered for better interaction

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

What interactions between residues of a polypeptide act to stabilize structure?

A
  1. Hydrogen bonds
  2. Van der Waals interaction (ALL)
  3. Ionic bonds
  4. Hydrophobic interactions (hydrophobic residues assemble ∆S < 0)
  5. Covalent interactions between cysteines (Disulfide Bonds)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Where can we find disulfide bonds?

A

Secretory proteins:
- In extracellular proteins
- Inside secretory organelles

NOT in cytosolic proteins (cytosol, nucleus, mitochondria)

Can be intrachain or interchain

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

What are the main characteristics of tertiary structure?

A
  • Secondary elements organized between each other
  • Hydrophobic contacts between 2ndary elements
  • Long-rang contacts between residues that are far in primary sequence
  • Confers its function to the polypeptide (or part of it)
  • Domains are tertiary structure
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What are intrinsically disorderd regions in proteins and why are they important?

A
  • Not involved in 2ndary structures
  • Provide flexibility to the protein
  • Receive post-translation modification (bc more exposed)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What level of structures are dimers, trimer, tetramer, 5-mer, 6-mer, …, oligomers?

A

Quaternary structures

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

What are the 4 ways to visualize proteins?

A
  1. Polypeptide backbone → only backbone, no 2ndary structure
  2. Ribbon diagram → backbone + 2ndary structure (not side chains)
  3. Stick diagram → backbone + side chains
  4. Space-filling model → filled with volume of atoms
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What is a domain? Give an example.

A

A domain is an independently folded unit within a protein
Different domains = different functions
ex: Hsp70 polypeptide

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

What are modular domains?

A

Conserved domains found in many different proteins

They form reversible, specific non-covalent contacts with other molecules
ex: contact with DNA, carbohydrates, lipids, other cofactors, etc.

23
Q

What is the normal/average length of a domain and the one of a polypeptide?

A

Most human polypeptides = 100-800 AA long = 12 kDa - 90 kDa MW

Domain = 50 - 200 AA long

24
Q

What are 4 characteristics of protein interactions

A
  • Non-covalent
  • Specific (molecular surface) → “lock and key”
  • Often transient → bc thermal motion → molecules constantly moving, colliding
  • Binding equilibrium → depends on concentrations of all proteins involved in interaction
25
Q

What is the difference between identical, similar and divergent amino acid sequences?

A

Identical = same AA
Similar = same properties, same group, similar structures, charges, both have a ring, etc.
Divergent = very different

*Similarity in sequences suggests evolutionnary conservation even if not identical, bc similar sequences have similar functions

26
Q

What are protein families?

A

A set of proteins or domains which have homologous sequences and structures
- related functions
- Can be found in different organisms

Important family = Hsp70

27
Q

Which polar amino gets involved in hydrophobic interactions?

A

Tyrosine

28
Q

Which hydrophobic nonpolar amino acid gets involved in hydrogen bonds?

A

Tryptophan (bc of N)

29
Q

When/Why does protein misfolding occur?

A

Occur before they are completely folded, in the folding process
- Immediatly after protein synthesis
- If a required ligand is not available
- Genetic mutation in AA sequence (ex: cystic fibrosis)
- harmeful environmental conditions (ex: heat)
- Aging → ledd efficient protein quality control mechanism

30
Q

How can aging be responsible for disease at a protein folding level?

A

Aging → Deacreased efficiency of protein quality control mechanism → lose of protein homeostasis → aggregates of misfolded proteins (ex: amyloid) → Neurodegeneration (Alzheimer, parkinson, ALS, dementia)

31
Q

Why can some mutations be non-pathogenic?

A

If an AA is substituted for a similar amino acid, it will interact in a similar manner with the rest of the sequence → similar folding → similar native state → similar function
ex: Asp → Asn

32
Q

What does protein homeostasis / proteostasis refer to?

A

Extensive NETWORK of components that act to maintain proteins in correct:
- Concentration
- Conformation
- Subcellular location
To cooperatively achieve stability and functional features of proteome

*Chaperones are at the center of the protein quality control network

33
Q

Are PTM permanent?

A

No, they act as On-Off switches for cells

34
Q

In what conditions are HSP upregulated?

A

In stress conditions
*Levels of HSP are tightly regulated in order to match the levels of unfolded/misfolded proteins depending on stress

35
Q

What are the 2 main categories of Heat Shock Proteins?

A
  1. Heat Shock Response (HSR)
    - Cytosolic and nuclear proteins
    - Protects against cell death
  2. Unfolded Protein Response (UPR)
    - ER proteins
    - Can promote cell death if stress is too severe
36
Q

Which amino acids get involved in van der Waals interactions?

A

ALL OF THEM

37
Q

What are different types of modification proteins can undergo post-translation? (not reaction names)

A
  • Cleaved into smaller proteins by peptidases (specifically transmembrane proteins get their cytoplasmic part cut to go and send a signal)
  • Covalent modification of N-terminus (co-translational)
  • Covalent modifications of side chains → introduce functional groups to proteins
38
Q

What are different roles of side chain PTM?

A
  • Can change surface of conformation of protein
  • Can create or block binding site for other proteins
  • Useful as switched bc fast
    *many modifications are regulated and reversible
39
Q

What molecules mediate ALL PTM?

A

Enzymes

40
Q

What are the main types of PTM?

A
  • Phosphorylation
  • Methylation
  • Acetylation
  • Glycosylation, Sumoylation, Ubiquitination
41
Q

What if the role/effect of phosphorylation? Which AA can be phosphorylated?

A
  • Major regulatory mechanism
  • Phosphorylation can be required for specialized binding of specific domains
  • Adding phosphoryl group changes the charge (neutral to negative) and size

Need hydroxyl groups → S, T, Y only

42
Q

Which enzymes are involved in phosphorylation?

A

Kinases tranfer phosphate from ATP
Phosphatases remove phosphate

43
Q

What are the different Kinase and Phosphatase families?

A

Kinase:
- Ser/Thr kinases
- Tyr kinases
- dual specificity (Ser/Thr and Tyr)
*Same for Phosphatase families

44
Q

What molecules are used to study the role of phosphorylation in protein function?

A

Phosphomimic (S by D) If you want your molecule to be permanently in the phosphorylated state
Change phospho-serine (PO4 2-) for Aspartic acid (COO-)

De-phosphorylated (S by A) If you want to study the effect of your molecule being never phosphorylated
Serine → Alanine (same structure but no OH on Alanine)

45
Q

Give an example of specialized binding to phosphorylated AA.

A

WD40 domain of Cdc4 interacts with Sic 1 CPD peptide which has been phosphorylated

p-Thr fits perfectly in pocket → negative p-Thr interacts with positive arginines (electrostatic intractions)

46
Q

Which amino acid can be acetylated?
How does it occur?

A

Lysine (K)
Lysine acetyltransferases (KATs) and deacetylases (KDACs) recognize specific sequences, also Histone acetyltransferases

NH3+ at bottom of the chain → H-N-Acetyl group (Given by Acetyl CoA)
Acetyl = −C(=O)−CH 3

47
Q

What is the effect of Acetylation of Lysine?

A
  • Increase in size of the side chain
  • Change in the charge (positive → neutral)

Regulates transcription:
Lys is positive → interacts with negative DNA → compact DNA → Heterochromatin (no transcription)

Acetylated Lysine → neutral → less interaction with DNA → Euchromatin

*ON-OFF activation and repression of gene expression

48
Q

Which amino acids can be methylated?

A

Lysine (K) (can’t be methylated and acetylated at the same time, they are competing reactions) → mono, di, trimethylation
Arginine (R) → mono, Asymmetric di-, Symmetric dimethylation
*NO change in charges (keep their positive charge compared to acetylation)

49
Q

Which enzymes are responsible for methylation?
What is the reaction?

A

Lysine methyltransferase (KMT) and Lysine demethylases (KDM) or RMT and RDM
Reaction changes the N-H into N-CH3

50
Q

How do PTM (specifically methylation an d acetylation) change the binding capacities of a protein?

A

Provides new binding sites

methylation and acetylation → Important role in DNA repair mechanisms and Transcription

51
Q

When in the process of protein synthesis can post-translational modification occur?

A

After the protein has been fully folded

52
Q

What is the native state of a protein?
What is it determined by?

A
  • Complete folded conformation
  • State of minimal energy of that AA sequence, Thermodynamically favoured
    Linear conformaiton → Native State → ∆G < 0 (Spontaneous)
  • Stabilized by hydrophobic contacts (exclusion of water)
  • Some domains require ligand factor to be stable

Determined by primary sequence of AA

53
Q

What is a folding intermediate?

A
  • Has some 2ndary structure, but tertiary structure is incomplete
  • Some hydrophobic side chains exposed instead of buried
  • More of the polypeptide is flexible and disordered
54
Q

Which side chain interactions are the strongest/more abundants?

A

Strength:
Disulfide > Ionic > Hydrophobic > Hydrogen > Van der Waals

Quantity:
Van der Waals / hydrogen / hydrophobic > ionic / disulfide

BIOC 212 (15 decks)

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