Topic 3 Flashcards
1
Q
Proteins
A
- linear polymers of amino acids
- not static
- molecule made of 1+ polypeptide chains
2
Q
Dipeptide
A
- peptide chain of 2 AA
3
Q
Tripeptide
A
- peptide chain of 3 AA
4
Q
Ogliopeptide
A
- peptode chain of 3-20 AA
5
Q
Polypeptide
A
- peptide cgain of many AA
6
Q
Peptide Bonds
A
- a series of planar peptide groups
7
Q
Double Bonds
A
- restricted rotation
- can’t rotate
8
Q
Bonds that Can’t Rotate
A
Calpha - C
N- Calpha
9
Q
Levels of Protein Stricture
A
- Primary Structure
- Secondary Structure
- Tertiary Structure
- Quanternary Structure
10
Q
Primary Structure
A
- sequence of AA residues
- protein sequence
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
12
Q
Majot Types of Secondary Structure
A
- alpha helix
- beta sheets
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)
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
15
Q
Why is the Alpha Helix Destablilized by Glycine
A
- too flexible
- no side chain
- not usually found in apla helices
16
Q
Beta Sheet
A
- H bonds formed between neighbouring strands ( not within the same strand)
- only involves backbone atoms
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
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
19
Q
Ionic Interaction
A
- charge charge interaction
- very strong
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
Covalent
- disulfide bonds
- others
26
The Hydrophpbic Effect
- protein core is hydrophobic
- polar side chains can be found on the outside of the protein
27
What Happens when A Protein Can't Refold?
1. aggregation
2. degradation
28
Chaperone Proteins
- helps other proteins to fo;d
- binds to hydrophobic groups to stabilize
29
Denaturation
1. Chemical
2. Thermal
30
Chemical Denaturation
- high concentratuon of urea= protein denatures
- remove urea = protein can refold to original conformation
31
Thermal Denaturation
- denature proteins by adding heat
32
Protein Thermal Irreversible Denaturation
1. Native Albumen
2. Denaturation
- expose hydrophobic groups
- hydrophobic groups stick together to avoid interactions with solvent
3. Crosslinking
33
Protein Domains
- 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
Protein Families
- 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
Analysis of Proteins
1. Chromatography
2. Gel electrophoresis
3. Mass spectometry
4. Structural Analysis
36
Chromatography
- indispensible for purification of proteins from complex mixtures
- purification procedure requires multiple steps
- different types of chromatography exploits differences in ciochemical + functional properties
37
Types of Chromatography
1. gel filtiration
2. ion exchange
3. affinity chromatography
38
Size Exclusion Chromatography
- 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
Ion Exchange Chromatography
- 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
Isoelectric Point (pI)
- pH= pI : charge on protein is 0
- pH < pI : charge on protein is (+)
- pH > pI : charge on protein is (-)
41
Affinity Chromatography
- 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
Ligand
- a compound that binds to a protin
43
What is SDS- PAGE
- analytical method
- denatures proteins
- ionic detergent
- binds to proteins and gives them a (-) charge
- negatively charged
44
SDS PAGE
- 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
Mass Spectrometry
- characterize proteins in complex mixtures (proteoms)
- provide info on identity, abundance, and modifications
46
X-ray Crystallography
- determine 3D structures of proteins
- the protein must first be crystallized
47
NMR Definition
- nuclear magnetic reasonance
48
NMR For Protein Structure Determination
- determines structures of small proteins
- crystallization of protein is not required
- an ensemble of structures is obtained
