Brainscape's Knowledge GenomeTM

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


See full index

Biochem 2280 > Topic 3 > Flashcards

Topic 3 Flashcards

1
Q

Proteins

A
  • linear polymers of amino acids
  • not static
  • molecule made of 1+ polypeptide chains
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Dipeptide

A
  • peptide chain of 2 AA
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Tripeptide

A
  • peptide chain of 3 AA
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Ogliopeptide

A
  • peptode chain of 3-20 AA
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Polypeptide

A
  • peptide cgain of many AA
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Peptide Bonds

A
  • a series of planar peptide groups
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Double Bonds

A
  • restricted rotation
  • can’t rotate
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Bonds that Can’t Rotate

A

Calpha - C
N- Calpha

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

Levels of Protein Stricture

A
  1. Primary Structure
  2. Secondary Structure
  3. Tertiary Structure
  4. Quanternary Structure
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Primary Structure

A
  • sequence of AA residues
  • protein sequence
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Secondary Structure

A
  • spatial arrangement of backbone atoms (anything that is not a side chain)
  • stabilized by H bonds- between backbone N-H and C–O groups
  • proline can’t be apart of secondary because it doesn’t H bond
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Majot Types of Secondary Structure

A
  1. alpha helix
  2. beta sheets
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Hydrogen Bonds

A
  • bond between H atom and an electronegative atom (acceptor); such asN/O
  • H is covalently bonded to another electronegative atom (donor)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Alpha Helix

A
  • carbonyl O of each residue forms an H bond with the backbone NH groups
  • proline causes a “kink” - will change the sequence - destabilize some of the H bonds due to its structure
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Why is the Alpha Helix Destablilized by Glycine

A
  • too flexible
  • no side chain
  • not usually found in apla helices
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Beta Sheet

A
  • H bonds formed between neighbouring strands ( not within the same strand)
  • only involves backbone atoms
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Classes of Protein Structure

A
  • depends on side chains and the functions of the protein
  • stabillized by H-bonding between backbone atoms not side chains
    1. all alpha protein
    2. all beta protein
    3. alpha/beta protein
    4. intristically disordered protein
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Tertiary Structure of Proteins

A
  • 3D structure of single-chain polypeptide
  • conformations of its side chains
  • stabillized by interactions between side chains + backbone atoms
  • interactions between residues distant in sequence
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

Ionic Interaction

A
  • charge charge interaction
  • very strong
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Disulfide Bonds

A
  • a type of covalent bond
  • formed by 2 cystines
  • only under oxidizing conditions
  • is reversible
  • important to stabilize protein structure
21
Q

Representations of Protein Structures

A
  • backbond model
  • ribbon model
  • wire model
  • space filling model
  • electrostatic potential map
22
Q

Electrostatic Potential Map

A
  • tells us the charge on the surface of the protein
  • red: negative charge
  • blue: positive charge
23
Q

Quanternary Structure

A
  • 3D arrangements if multiple polypeptide chains
  • stabilized by same bonds as for tertiary structure
  • strong implications for protein function
24
Q

Non covalent

A
  • H bonds
    (backbone-backbone, backbone - sidechain, sidechain-sidechain)
  • ionic bonds
  • vanderwaals interactions
25
Q

Covalent

A
  • disulfide bonds
  • others
26
Q

The Hydrophpbic Effect

A
  • protein core is hydrophobic
  • polar side chains can be found on the outside of the protein
27
Q

What Happens when A Protein Can’t Refold?

A
  1. aggregation
  2. degradation
28
Q

Chaperone Proteins

A
  • helps other proteins to fo;d
  • binds to hydrophobic groups to stabilize
29
Q

Denaturation

A
  1. Chemical
  2. Thermal
30
Q

Chemical Denaturation

A
  • high concentratuon of urea= protein denatures
  • remove urea = protein can refold to original conformation
31
Q

Thermal Denaturation

A
  • denature proteins by adding heat
32
Q

Protein Thermal Irreversible Denaturation

A
  1. Native Albumen
  2. Denaturation
    - expose hydrophobic groups
    - hydrophobic groups stick together to avoid interactions with solvent
  3. Crosslinking
33
Q

Protein Domains

A
  • critical for larger proteins
  • distinct region of a protein
  • many proteins= made up of connected domains
  • related domains found in different proteins
  • ecolution has ‘mixed + matched’ domains
34
Q

Protein Families

A
  • during evolution, new proteins come from old ones
  • related by evolution (similar primary sequence, structures, functions, and domains)
  • residues that are critical for function do not change on an evolutionary timescale (conserved residues)
35
Q

Analysis of Proteins

A
  1. Chromatography
  2. Gel electrophoresis
  3. Mass spectometry
  4. Structural Analysis
36
Q

Chromatography

A
  • indispensible for purification of proteins from complex mixtures
  • purification procedure requires multiple steps
  • different types of chromatography exploits differences in ciochemical + functional properties
37
Q

Types of Chromatography

A
  1. gel filtiration
  2. ion exchange
  3. affinity chromatography
38
Q

Size Exclusion Chromatography

A
  • each gel bead has pores which small proteins enter through
  • if a protein can get into a bead, it is slowed down
  • if a protein is excluded, it will come out of the column early
  • protein shape also affects evolution speed
39
Q

Ion Exchange Chromatography

A
  • ion exchange relies on attraction of opposite charges
  • binds anions ( negative)
  • exchanging with ions previously bound
  • to get protein off, increase salt concentration
  • usually done as a gradient of increasing concentration
    (-) charge proteins: bind to column
    (+) charge proteins: go right through
40
Q

Isoelectric Point (pI)

A
  • pH= pI : charge on protein is 0
  • pH < pI : charge on protein is (+)
  • pH > pI : charge on protein is (-)
41
Q

Affinity Chromatography

A
  • relies on specific interactions between protein + ligand
  • if a ligand is attatched to column matrix, certain proteins will bind to it, others won’t
  • powerful method but requires knowledge of what ligand to use
42
Q

Ligand

A
  • a compound that binds to a protin
43
Q

What is SDS- PAGE

A
  • analytical method
  • denatures proteins
  • ionic detergent
  • binds to proteins and gives them a (-) charge
  • negatively charged
44
Q

SDS PAGE

A
  • seperates basis of polypeptise chain size
  • charged molecules migrate in an electric field
  • a gel acts as a molecular sieve
  • smaller molecules go faster
45
Q

Mass Spectrometry

A
  • characterize proteins in complex mixtures (proteoms)
  • provide info on identity, abundance, and modifications
46
Q

X-ray Crystallography

A
  • determine 3D structures of proteins
  • the protein must first be crystallized
47
Q

NMR Definition

A
  • nuclear magnetic reasonance
48
Q

NMR For Protein Structure Determination

A
  • determines structures of small proteins
  • crystallization of protein is not required
  • an ensemble of structures is obtained

Biochem 2280 (8 decks)

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