IB: Proteins Flashcards
1
Q
made of long unbranched chain of these amino acids
A
Protein
2
Q
a linear chain of amino acids
A
polypeptides
3
Q
repeating sequence of atoms along the core of the polypeptide chains
A
Polypeptide backbone
4
Q
give amino acids its unique properties
A
side chains
5
Q
involved in protein folding
A
weak covalent bonds
6
Q
Types if if weak noncovalent bonds on protein folding
A
-Hydrogen bonds
-electrostatic attrations
- Van der Waals
7
Q
contains all the information needed for specifying the three-dimensional shape of a protein
A
amino acid sequence
8
Q
assist in protein folding
A
Molecular chaperones
9
Q
Common folding patterns
A
- α helix
- β-sheet
10
Q
Types of folding that leads to α-helix and β-sheet folding patterns?
A
Hydrogen bonding between N-H and C=O groups
11
Q
Types of β-sheet structures
A
- Parallel chains
- antiparallel chains
12
Q
form from neighboring segments of the polypeptide backbone that run in the same orientation
A
parallel chains
13
Q
-from a
polypeptide backbone that folds
back and forth upon itself
-each section of the chain running in the direction opposite of that of its immediate neighbors
A
Antiparallel chains
14
Q
Formation of α-helix
A
- when single polypeptide chain twist around on it self to form rigid cylinder
-Hydrogen bonds between every 4th peptide
-coiled-coil form
15
Q
4 levels of protein structure
A
- Primary structure
- secondary structure
- tertiary structure
- Quaternary structure
16
Q
amino acid sequence
A
primary structure
17
Q
hydrogen
bonding of the peptide
backbone; α helices and β sheets
A
Secondary structure
18
Q
full 3D
organization of a polypeptide chain
A
tertiary structure
19
Q
protein
molecule formed as a complex of more than one polypeptide chain
A
Quaternary structure
20
Q
How are protein classified?
A
Based on their tertiary structure
21
Q
used to see structure of protein
A
X-ray crystallography
22
Q
the basic units of proteins that can fold,
function, and evolve independently
A
Protein domains
23
Q
process of
creating new combination of gene functional domains
A
domain shuffling
24
Q
subset of protein domains, mobile during evolution
A
protein modules
25
only in humans, the reason why humans cant receive blood from other organisms
MHC (Major Histocompatibility Complex)
26
allow proteins to bind to each other to produce
structures in the cell
Weak noncovalent bonds
27
any region of a protein’s surface that can interact with another molecule
binding site
28
forming a symmetric complex of two protein subunits (dimer)
"Head-to-head" arrangement
29
two identical α-globin
subunits and two identical β-globin subunits, symmetrically arranged
Hemoglobin
30
long helical structure produced from many molecules of the protein actin
actin filament
31
a long chain comprised of identical protein molecule
Filaments
32
Why is alpha helix common?
All subunits are identical
- can only fit together in one way
33
Types of protein molecule shapes
-Fibrous protein
-Elongated protein
34
elongated three-dimensional structure
fibrous protein
35
example of fibrous protein
- keratin filaments
- a(alpha) keratin
36
ropelike structures;
important component of the cytoskeleton
intermediate filaments
37
consists of three long polypeptide chains
- each containing that nonpolar amino acid glycine at every 3rd position
collagen
38
Another abundant protein in ECM
- highly disordered polypeptide
Elastin
39
causes of disordered polypeptide chain
- To form specific binding sites for other protein
- Trigger cell signaling
- Restrict diffusion
- Serves as tether to hold two domains
40
act as atomic staple
stabilize monomeric and multisubunit proteins
S-S bonds (Disulfide bonds)
41
Advantages of subunits
-requires only small amount of genetic information
- assembly and disassembly
- error in synthesis can be avoided easily
42
example of subunit
capsid of viruses
43
made of identical protein subunits that enclose and protect viral nucleic acid
Capsid of viruses
44
Guide construction but take no part in the final assembled structure
Assembly factors
45
self propagating, stable β-sheet aggregates
amyloid fibrils
46
What dangers does amyloid cause?
- Alzheimers disease and other neurodegenerative illness
47
may be released from dead cells and accumulate as amyloid
Protein aggregates
48
caused by a misfolded, aggregate form of a particular protein called PrP (prion protein)
Prion diseases
49
What does misfolded protein do?
convert normal PrP into abnormal conformation
50
acts like a vesicle containing peptide and hormones
specialized “secretory granules” that consist of amyloid fibrils
51
Protein functions
- Contractile
- Hormonal
- Protection
- Transport
- Enzyme
- Storage
- Structural
- Receptor
52
each protein molecule can usually bind just one or a few molecules out of many thousands
Specificity
53
the substance that is bound by the protein
Ligand
54
Noncovalent bonds in proteins
- Hydrogen bonds
- Electrostatic attractions
- Van der Waals
55
the region of protein that associates with a ligand
Binding site
56
Determines the chemistry of protein
Surface Conformation
57
Types of Surface conformation
1. Interaction of neighboring parts of polypeptide chain
2. Clustering of neighboring polar amino acid chains
58
Types of Interfaces (Protein binding)
1. Surface string interaction
2. Helix-helix
3. Surface-surface
59
Most common interface
Surface-surface
60
binds tightly to a particular target molecule (antigen), inactivating directly or making it for destruction
antibody or immunoglobulins
61
Shape of antibody molecules
Y-shaped
62
cause the chemical transformations that make and break covalent bonds in cells
Enzymes
63
speed up reactions, act as catalysts
Enzymes
64
the maximum rate of reaction divided by the enzyme concentration
Turnover number
65
unstable intermediate state
Transition state
66
the free energy required to attain the transition state
Activation energy
67
adds a molecule of water to a single bond between two adjacent sugar groups in the polysaccharide chain, thereby causing the bond to break
Hydrolysis
68
Add Extra Functions to Proteins
Tightly Bound Small Molecules
69
key light-sensitive protein expressed exclusively in rod photoreceptor cells of the retina
Rhodopsin
70
tightly related to rhodopsin, helps it to carry reaction
Retinal
71
Gives red color in blood
heme group
72
- a large protein assembly
- allows the product of enzyme A to be passed directly to enzyme B, and so on
multienzyme complex
73
the factor that limits the reaction rate is the frequency wuth which the enzymes collides with its substrate
Diffusion-limited
74
a product produced late in a reaction pathways inhibits an enzyme that acts earlier in the pathway
feedback inhibition
75
prevent an enzyme from
acting
Negative regulation
76
regulatory molecule stimulates the enzyme’s activity rather than shutting the enzyme down
Positive regulation
77
have at least two binding sites on their surface
Allosteric enzymes
78
Two binding site of allosteric enzymes
- Active site
- Regulatory site
79
that recognizes the
substrates
Active site
80
that recognizes a regulatory molecule
Regulatory site
81
interaction between separated sites on a protein
conformational change
82
can occur in multimeric proteins, where each subunit of the protein has its own ligand binding site
cooperative allosteric
transition
83
Contains a Large Collection of Protein Kinases and Protein Phosphatases
Eukaryotic cell
84
transfer of the terminal phosphate group of an ATP molecule to the hydroxyl group
Protein phosphorylation
85
phosphorylates
Protein kinase
86
phosphate removal,
dephosphorylate
Protein phosphates
87
- phosphate is part of guanine nucleotide GTP
- addition and removal of phosphate
GTP-binding proteins
88
generate forces responsible for muscle contraction and the crawling and swimming of cells
Motor proteins
89
major function of motor proteins
Move other molecules, reversible
90
coupling one of the conformational changes to the hydrolysis of an ATP molecule that is tightly bound to the protein
unidirectional conformation changes
91
function to export
hydrophobic molecules from the cytoplasm
ABC transporters
92
are made up of individual proteins that collaborate to perform specific task
Protein machines
93
proteins binding sites for multiple other proteins
Scaffold proteins
94
What does scaffold proteins serve?
- both to link together specific sets of interacting proteins
- Position them at specific locations (inside a cell)
95
Computer based bioinformatics tools
Proteomics
96
protein is represented by a box or dot in two-dimensional network
Protein interaction map
