1
Q
Proteins are the main…
A
building blocks of the cell
2
Q
what are 8 functions of protein?
A
- Enzymes
- Structural proteins (like keratin, hair, nails)
- Transport
- Motor proteins (move things across cell)
- Storage (storing AA for later use)
- Signalling
- Receptors
- Transcription regulators (allows for genes to turn on/off)
3
Q
what does alchohol dehydrogenase do?
A
Catalyzes chemical reaction to strip electrons off of alchohol
(taking e- from alcohol also takes H, so H- ion, dehydrogenating taking H, bc alcohol is being oxidized taking H getting O)
4
Q
wha type of protein is collagen?
A
Structural, they’re part of the extracellular matrix.
5
Q
amino acids are joined by…
A
peptide bonds
6
Q
What is the polypeptide backbone made up of?
A
Repeating core atoms -N-C-C (peptide bonds join each NCC group)
7
Q
N-terminus
A
End that carries an amino group
8
Q
C-terminus
A
End that carries a carboxyl group
9
Q
What does the side chain (R group, Variable group) do?
A
Gives the amino acid its identity and unique properties.
10
Q
what does charge of an amino acid determine?
A
If it has a charge (positive or negative) it’s chemically reactive, and polar (hydrophillic).
If no charge it’s neutral, not chemically reactive and nonpolar (hydrophobic).
11
Q
what are 3 amino acids that are chemically reactive
A
histadine, aspartic acid and tyrosine are all chemically active (as they have charges).
Henry Ate Trent or HAT
12
Q
Polypeptide chains are flexible due to…
and shape constrained by…
A
- flexible due to rotation around single covalent bonds
- shape constrained by weak interactions within the molecule
-between polypeptide backbones and amino acid side chains
13
Q
describe hydrophobic force for polypeptide chains
A
Nonpolar side chains (hydrocarbons just H and C , no charge) are forced together towards the inside of a folded protein
14
Q
Polar amino acids lay near the outside of the folded protein, what must happen for them to be buried inside a protein?
A
- They must be hydrogen bonded to other polar amino acids to be buried inside a protein.
15
Q
conformation
A
- Final folded 3D structure of a polypeptide chain
- energetically favorable to minimize free energy
16
Q
what are the 3 ways amino acids can bind?
A
backbone to backbone, backbone to side chain, side chain to side chain
17
Q
denaturation
A
protein loses its conformation due to the disruption of noncovalent bonds
18
Q
renaturation
A
Spontaneous refolding of the protein when the proper conditions are provided
(protein is always trying to get back into original conformation if conditions are correct
19
Q
what do chaperone proteins do?
A
assist a polypeptide to fold into its most energetically favorable conformation
chaperone proteins are added to partially folded protein to help them fold correctly
20
Q
is protein folding using chaperone proteins spontaneous or not?
A
still spontaneous, they just make folding more efficient and reliable.
21
Q
what do isolation chambers do?
A
Isolation chambers (formed by chaperone proteins) help polypeptide fold correctly and prevent the polypeptide from grouping with other polypeptides.
(still spontaneous)
22
Q
what’s the size range of proteins (how many AA) overall? what’s the average size?
A
- overall range: 30-10 000 AA
- average: 50-2000 AA
23
Q
describe the backbone protein model
A
most simple model, just N-C-C backbone repeating
24
Q
describe the wire model
A
the wire model shows all side chains, so we can see charges
25
describe the ribbon model
shows some folding patterns: alpha helices, and beta sheets
26
space-filling model
what protein will look like if another protein approaches
27
Primary structure
Amino acid sequence
28
Secondary structure
a-helices and B-sheets
29
Tertiary structure
full 3D conformation of the polypeptide chain
30
Quaternary structure
Multiple polypeptides interacting to form the complete protein
31
most proteins are what level of structure?
Most are quaternary structures, bc they have multiple subunits that have multiple polypeptides
32
describe alpha Helix structure, and where its found
* Many similar subunits next to each other in the same repeated relationship as the one before
* Hydrogen bonds between every 4th amino acid
* right handed helix with a complete turn every 3.6 AA
* found lots in proteins embedded in cell membranes
33
what's a coiled coil? what proteins form coiled coils?
* Two or three alpha-helices wrapped around each other (very stable structure)
* Elongated proteins such as alpha keratin, and myosin form coiled coils
34
describe the structure of beta sheets and the two types
* rigid structures at the core of proteins
* hydrogen bonds between neighboring segments of polypeptides
two types:
1. Parallel B-sheets: polypepetides run in the same direction
2. Antiparallel B-sheets: polypeptides run in opposite directions
35
what are amyloid structures and an example
* B sheets stacked together with side chains interlocked like the teeth of a zipper
ex: storage of peptide or protein hormones for efficient packaging
36
how can amyloid structures damage cells? what can they cause
If misfolded proteins form amyloid structures they can damage cells
* cause Alzheimer's, Parkinson's, Huntington's disease
* some amyloid proteins can move from cell to cell causing further misfolding
37
Prions
* Infectious misfolded proteins which contain amyloid structures.
38
what are the different names for prions in different animals: sheeps and goats, cows, humans, deer
* scrapie in sheeps and goats
* Bovine spongiform encephalopathy in cows
* Creutzfeldt-Jakob's disease in humans that eat infected cows
* chronic wasting disease in deer
39
Protein domain
any segment of a polypeptide that can fold independently into a compact, stable structure
* 40-350 amino acids
40
Unstructured sequences
short polypeptide chains that link domains together
41
what's an example of a protein that has protein domains?
* Bacterial transcription regulator
-small domain binds DNA
-large domain binds cAMP
-when the large domain binds, it causes a conformational change in the small domain so that it can bind DNA
42
what are protein families and an example?
Groups of protein that closely resemble each other
-but each has its own distinct enzymatic function
-ex: serine proteases, each has slightly different conformations, both break proteins just in different ways
43
Binding site
Region on a protein's surface that interacts noncovalently with another molecule
44
each polypeptide is called a _. Each one of these may have multiple _.
Each polypeptide is called a **subunit**.
Each subunit may have multiple domains
45
Dimer
Two identical polypeptide chains bound together
46
how are dimers and tetramers formed?
Each individual polypeptide (monomer) has a binding site, the binding sites bind to eachother
47
tetramer
Four identical subunits
* subunits can be non-identical (ex. Hemoglobin)
48
Chains of identical proteins are often in what shape? example?
* Often in a helix shape
* ex: actin filaments (repeating protein actin), microtubules
49
what's an example of cage-like spherical shell proteins?
Protein coats of viruses: capsids
50
what's an example of mixtures of various proteins and RNA/DNA?
Ribosomes, viruses
## Footnote
ribosomes are proteins and rRNA
51
what are 3 fibrous proteins
1. a-keratin
2. Intermediate filaments
3. Extracellular matrix
52
describe a-keratin
-dimer of two identical subunits wound into a coiled coil
-extremely stable and long-lived
-hair, horns, nails
53
describe intermediate filaments
* Rope-like components of the cytoskeleton
* give cells mechanical strength (in skin cells)
54
what do stable covalent cross-linkages do
* Tie together **amino acids** in the same polypeptide chain
* and join together **many polypeptide chains** in a larger complex
55
what do disulfide bridges do? what proteins do they form in
* Link together two -SH groups from cysteine side chains
* do not form in the cytosol, only in proteins that have been excreted from the cell
## Footnote
(excretion puts protein in a very diff. environment than in the cell, so disulfide bridges hold it together)
56
what do antibodies bind to
viruses, bacteria, white blood cells
57
what do enzymes bind to
substrates
58
what does actin bind
to other actin to form actin filaments
59
is actin binding weak and short-lived or strong and long-lived? what about enzymes?
* actin is strong and long-lived, stays together
* enzymes are weak and short lived, bind to substrate for a second then release product
60
describe extracellular matrix and 2 examples
* binds cells together to form tissues
* ex: collagen
-3 peptide chains in a helix with the nonpolar amino acid glycine at every third position at its core
-collagen fibrils: overlapping arrays of collagen
* ex: elastin
-loose unstructured polypeptide chains covalently linked into an elastic meshwork
-enable skin, arteries, lungs, etc to stretch without tearing
61
ligand
* substance that is bound by a protein (but not a protein itself)
* binding requires weak bonds between protein and ligand (noncovalent)
62
binding site
region of a protein that associates with a ligand
-cavity on the protein surface
-binding regulates protein activity
-can attach the protein to a particular location in the cell
63
substrate
ligands that bind enzymes
64
active site
binding site where a substrate binds
65
transition state
the conformation of the enzyme-substrate complex when it is distorted to lower the activation energy (induced-fit, when the enzyme binds it changes shape to hold onto the ligand better, makes it energetically favorable)
66
Metabolic pathway
Network of enzymatic reactions where the product of one reaction becomes the reactant for another.
## Footnote
each step is catalyzed by a different enzyme
67
Many drugs do what to enzymes
Inhibit enzymes
68
Many proteins need the help of small nonprotein molecules called: _ and _
cofactors and coenzymes
69
what's a cofactor and 2 examples
small **inorganic** molecule that aids enzymes
* heme groups use cofactor **iron**
* Carboxypeptidase cuts polypeptide chains with the help of cofactor **zinc**
70
what's a coenzyme and 3 examples
small **organic** molecuke that aids enzymes.
* biotin aids enzymes tranfer of carboxl groups
* retinal aids rhodopsin to absorb light in our eyes
* many coenzymes are vitamins we get from our diet
## Footnote
(you can remember its organic by thinking how enzymes are organic -protein, and enzyme is in the name)
71
what two things control the amount of protein?
* gene expression
* rate of protein degradation
72
protein activity can be controlled by what 3 things?
* Confine proteins to sub-cellular compartments (ex; a protein usually in the cytosol is kept in the golgi to prevent it from functioning)
* Adjust activity at the level of the protein itself (inhibit or turn on)
* Regulatory site: site where a molecule binds to alter the rate at which an enzyme functions
73
control of proteins by interactions with other molecules often results in changes in _
conformation
74
multiple _ can compete for the same substrate
enzymes
75
feedback inhibition
* an enzyme acting early in a reaction pathway is inhibited by a molecule produced later in that pathway.
* when product accumulates it slows down catalytic action on the original substrate
76
negative regulation
prevents an enzyme from acting
77
positive regulation
product in one branch of the metabolic maze stimulates the activity of an enzyme in another pathway
78
allosteric proteins
* proteins that have two different conformations based on what ligands are bound
* protein will spontaneously switch between active conformations
* ligand stabilizes the protein in the correct conformation
79
describe phosphorylation
* can control activation
* attaching a phosphate group to an amino acid side chain
* negatively charged phosphate interacts with positively charged side chains to cause conformational changes
* removal returns the protein to its original conformation
80
more than _ of the proteins in a mammalian cell are phosphorylated at any one time
1/3
81
explain an example of a pathway that uses phosphorylation
signal transduction pathways
* Protein kinase: transfers a phosphate from ATP to a the serine OH group
* protein phosphotase: removes the phosphate group
82
phosphorylation creates _ for other molecules
docking sites (bc negative charge attracts positive charge of other molecules)
83
what's an example of a pathway that creates a docking site for other molecules?
ex: receptor tyrosine kinases becomes phosphorylated to serve as docking sites for intracellular signalling proteins (when it receives signal on cell surface it causes phosphorylation and a conformation change
84
protein can be modified based on the addition of what 3 things?
1. acetyl groups to lysine side chains like in histones (DNA winds around histone proteins, adding acetyl groups causes it to bind looser to turn on gene expression)
2. fatty acids to cysteine side chains to associate a protein to the cell membrane (bc fatty acid must stay in membrane)
3. Ubiquitin to target a protein for degradation
85
many proteins can be modified at many different sites, whats an example of this
ex: p53 protein responds to DNA damage. It can be modified on at least 20 different sites
86
is the protein conformation active or inactive when GTP is bound? is it active or inactive when GTP is hydrolyzed to GDP?
* Active when bound
* Inactive when GTP is hydrolyzed to GDP
87
how is protein bound GDP reactivated to GTP?
stimulated by cell signals
88
Motor proteins do what?
Generate the forces responsible for muscle contractions and other cellular and intracellular movements
89
conformational changes are unidirectional, what does this mean?
* One step must be irreversible
* ATP molecule is bound to the protein
* hydrolysis of the ATP (removal of phosphate) releases a burst of free energy. -This step is irreversible because it would be energetically unfavorable to add the phosphate back on
90
Protein machines
* Highly coordinated linked sets of proteins.
* Hydrolysis of ATP or GTP drives an ordered series of conformational changes, enabling the ensemble of proteins to coordinate their movements
* successive reactions in a series (ex. Protein synthesis, DNA replication)
91
Scaffold proteins
* large molecules that contain binding sites recognized by multiple proteins
* enhances the rate of a cell process while confining it to a particular area of the cell
* can be rigid or elastic
* long molecules of RNA can also act as scaffolds
92
Biomolecular condensates and example
* Collections of proteins and RNA, held together by a continuously shifting set of weak interactions
-fluid membraneless subcompoartments that perform a function
-contain at least one type of RNA or protein scaffold
-remains separated from its surroundings
* ex: nucleolus -proteins and rRNA are assembled into ribosomes, separate from nucleus.
93
Clients
Molecules which become concentrated on the scaffold
* non-covalently bonded
94
Describe the steps of protein purification
1. Break open the cells (using chemical detergents or sonification -sound waves) to release the contents: **cell homogenate or extract**
2. Fractionation: separates out the class of molecules of interest (using centrifuge spins things fast gets rid of big chunks)
3. Chromatography: separates individual components into fractions based on the properties of the protein
95
affinity chromatography
form of chromatography that separates polypeptides based on ability to bind particular molecules
96
electrophoresis
polypeptides migrate through a gel at different speeds depending on size and net charge.
97
how do we determine protein structure?
direct analysis of amino acids by breaking the protein into smaller pieces using protease. Then we can figure out exactly what AA are present.
98
how do we determine the exact mass of every peptide fragment
Mass spectroscopy
99
describe how mass spectroscopy works
* allows for identification of amino acids from a database
* applies knowledge of the genetic code
* blast peptides with a laser so they become electrically charged and gaseous and fly towards a detector. The time it takes them to reach the detector is related to mass and charge (big things move slower).
100
what are 3 methods of determining 3D structure of protein
1. X-ray crystallography
2. Nuclear magnetic resonance (NMR) spectroscopy
3. Cryo-electron microscopy (cryoEM)
## Footnote
if we combine these pictures with knowledge of the amino acid sequence we can figure out the position of each atom in the molecule.
101
X-ray crystallography
We take folded protein in spontaneous conformation, and fix it, then blast it with x rays, and x rays bounce off based on density, so you can analyze the scattering patterns.
102
Nuclear magnetic resonance (NMR) spectroscopy
magnetic pull or push on different R groups, so you can identify hydroxyl groups etc, adds knowledge on structure.
103
Cryo-magnetic microscopy (cryoEM)
fixes protein in 3D shape in ice (not water ice ethanol ice), then using TEM take 2D pics of every face of protein from all angles, so you can piece together 3D shape
104
why do we care about protein structure?
* develops a basic understanding of how cells operate
* knowing the structures allow us to design new drugs to alter metabolic pathways or stop infection (like creating inhibitors)
* recognizing sequence patterns: most proteins belong to families, when we see the same domain over and over we can predict that it plays the same role no matter what cell it came from
105
how can AI help us learn about proteins?
* AI is used to learn how proteins fold by analyzing readily available data
* predicts the structures of approx. half of the proteins
* greatly accelerates the pace of biological research
106
how are proteins used in genetic engineering?
* bacteria, yeast, mammalian cells mass-produce a variety of therapeutic proteins: insulin, human growth hormone, fertility enhancing drugs
* New proteins and enzymes can perform unusual tasks like metabolizing toxic wastes, synthesizing life-saving drugs
* a synthetic protein that contains a cage that can swing open like a latch when exposed to the key compound was developed:
-this can allow delivery of drugs or specfic molecules to switch on a target gene, boost immune response (targeting the problem directly instead of medicine flowing through blood), and trigger cell death.
Cell bio
flashcards
Decks in class (9)
# Cards
-
Topic 1. Introduction to Cell biology54
-
Topic 2: Chemical Components of Cells94
-
Topic 3: Bioenergetics, Enzymes, and Metabolism51
-
Topic 4: Protein Structure and Function106
-
Topic 5: DNA and Chromosomes41
-
Topic 6: DNA replication62
-
Topic 7: From DNA to Protein89
-
Topic 8: Control of Gene Expression67
-
Topic 9: Genetic Evolution and the Study of Genes66
