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
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
- aggregation
- degradation
28
Q
Chaperone Proteins
A
- helps other proteins to fo;d
- binds to hydrophobic groups to stabilize
29
Q
Denaturation
A
- Chemical
- 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
- Native Albumen
- Denaturation
- expose hydrophobic groups
- hydrophobic groups stick together to avoid interactions with solvent - 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
- Chromatography
- Gel electrophoresis
- Mass spectometry
- 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
- gel filtiration
- ion exchange
- 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
