test 1 ch 4 Flashcards
Functions of proteins
Enzyme
structural ex: intermediate filaments
-transport ex: hemoglobin
-movement ex: actin, myosin and intermediate filaments
storage ex: farotin
protein signaling ex: insulin
receptor ex: cells that have insulin receptors
gene regulation: transcription factors
side chains: R group
20 total amino acids differ by R-group
3 types of R groups
- charged (acidic or basic) which depends on pH
- charge dependent on pH of environment
- polar
- non-polar
Type of R group effects solubility and non-covalent interactions that protein can participate in
proteins are made up of
amino acids linked together by peptide bonds
Asp
Aspartic acid, D, Negatively charged, Polar, acidic
Glu
Glutamic acid, E, Negatively charged, Polar, acidic
Arg
Arginine, R, positively charged, basic, polar
Lys
Lysine, K, positively charged, basic, polar
His
Histidine, H, positively charged, basic, polar
Asn
Asparagine, Asn, N, Uncharged polar
Gln
Glutamine, Q, Uncharged polar
Ser
Serine, S, Uncharged polar
Thr
Threonine, T, uncharged polar
Tyr
Tyrosine, Y, uncharged polar
2 special amino acids:
Glycine (nonpolar)
Cysteine (nonpolar)
Glycine
Smallest amino acid found in folds
Rgroup= -H
-Small, tends to be in bends of proteins
Cysteine
Has 2 sulfur grops
R groups= H2C-SH
-Two cysteines can form covalent disulfide bond by oxidation in ER
-Stabilizes extracellular proteins
disulfide bonds
Any R group to R group interaction that forms covalent bonds
Levels of protein structure
Primary structure:
-Order of the amino acids along polypeptide backbone
-Held together by peptide bonds
-Order determined by DNA
Folded structures of the polypeptide chain determined by non-covalent interactions:
-Electrostatic
-Hydrogen bonds
-Van Der Waals
-Hydrophobic
Folded structure can sometimes involve covalent disulfide bonds
Primary structure
the amino acid sequence of a protein
Draw this
Noncovalent bonds determine
Protein folding which involve electrostatic interactions and hydrophobic, disulfide bonds
Proteins fold into their conformation of lowest energy aided by
Chaperone proteins (look back at slide 11)
Secondary structure
H bonds between carboxyl and amide groups of peptide bonds. Held together by Hydrogen bonds between polar peptide bonds.
Also has two different forms that it can shape: Alpha and Beta sheet
Alpha helix
every fourth aa of the backbone are linked in H-bonds
Beta sheet
distinct linear regions are H-bonded together
When amino acids fold back between themselves
Tertiary structure
Folded structure of lowest free energy
-Noncovalent interactions between R groups
-H bonds between peptide bonds and R groups
-Disulfide bonds can stabilize
Factors that influence where amino acids end up in folded protein
Charge of R group
Polar vs. non-polar
Size of R group
Bonds R group can form with other R groups
Protein domains
independently foldedparts of the protein
Many domains are conserved in amino acid sequence and folded structure for multiple proteins= protein family
PROTEIN DOMAINS
Quaternary structure
two or more polypeptide chains held together by non-covalent Bonds between R groups;
sometimes disulfide bonds
Each polypeptide chain
is a subunit
- Some structures that can occur for tertiary structures can occur for quaternary structures
look on page 20 for examples of folded proteins
order of protein structures
Primary:
-Order of amino acids joined by covalent (peptide) bonds
between amino acids. Order determined by DNA
Secondary:
- Hydrogen bonding involving groups in peptide bonds:-helix
and ß-sheets
Tertiary:
- Non-covalent interactions between R groups
- H-bonds between R groups and peptide bonds
- Disulfide bonds between cysteines
- Domains: independently folded region of protein
Quaternary:
- two or more polypeptide chains interact to form functional
unit.
- Non-covalent interactions between R groups.
- Disulfide bonds between cysteines
mutations can affect protein folding and function
Sickle Cell Anemia due to single
mutation in DNA sequence leads
to single amino acid change
Normal β-Hemoglobin
- Glutamic acid
Sickle Cell β-Hemoglobin
-Valine
sickle cell changes one betahemoglobin from glutamic acid to valine
prions
are misfolded proteins
that cause additional
proteins to misfold
and aggregate
ex: mad cows’ disease, and Alzheimer’s
Disrupting protein structure
- Native folded functional protein
Denature: Disrupt all folding by disrupting all non-covalent bonds
ways to denature a protein:
Heat: H-bonding; secondary, tertiary and quaternary
pH change: Ionic interactions; tertiary and quaternary
High salt: Electrostatic interactions and H-bonds; secondary, tertiary
and quaternary
Organic solvent or detergent: Hydrophobic interactions; tertiary and quaternary
Reducing agent: Disulfide bonds; tertiary and quaternary
Degradation: Break peptide bonds between amino acids
Mechanical
Proteases 24
How proteins work
Proteins work by binding to other
molecules
Characteristics of protein binding:
- Specificity: Limited type of molecule protein can bind
Ligand: Molecule protein binds, eg chemical, protein, hormone, DNA…..
Binding Site: Region of protein that associates with ligand
- Distinct 3D shape and non-covalent interactions creates specificity
Ligand Bi
Specificity of ligand
binding to binding
site determined by
shape and non-
covalent interactions
Binding site specifity
Binding sites in folded protein create specific shape with distinct
amino acids exposed to the ligand
example protein: antibodies
Produced by immune system
- Highly folded,
multi- subunit
proteins - Binds to “foreign”
molecule =
antigen
example protein enzymes:
Catalyze energetically favorable chemical reactions in the cell
Bind to substrates at active site
Enzyme + Substrate(s) to Enzyme/Substrate(s) complex to
Product(s) + Enzyme
how enzymes lower the activation energy
- enzymes bind to two substrate molecules and orients them precisely to encourage a reaction to occur between them
- Binding of substrate to enzyme rearranges electrons in the substrate, creating partial negative and positive charged that favor a reaction
- enzyme strains the bound substrate molecule, forcing it toward a transition state that favors a reaction
overral enzymes alter bond geometry and electron distribution= transition state
Regulation of protein activity
*Protein activity is regulated by binding to various molecules
*Protein regulation can be inhibitory or stimulatory
feedback inhibition
in biosynthesis used to
regulate enzyme activity
and thus what products
are made (product inhibits an earlier enzyme forcing it to go another way) also an enzyme can’t inhibit the same protein
reversible inhibition
Feedback inhibition always reversible
*Other molecules can also inhibit reversibly
*Competitive inhibition: Inhibitor binds to enzyme at active site
*Non-competitive Inhibition (feedback usually this): Inhibitor binds outside active site (allosteric site) which prevents enzyme from working
*Other proteins can also be inhibited
*Proteins, including enzymes, can also be
positively regulated
allosteric regulation
protein regulation in which a molecule binds outside the protein’s active site/binding site and changes the proteins shape and activity.
Example of allosteric regulation of an enzyme: An allosteric effector binds to the enzyme, changing the shape of the active site, thereby changing its activity
Protein regulation by phosphorylation
Kinase adds phosphate
* Phosphatase removes phosphate
* Adds or subtracts a charged
phosphate which causes a
conformational change
Protein regulation by: GTP/GDP binding
3 Conformations:
1. GTP binds = active
2. GTP hydrolysis and
release of Pi = inactive
3. Release of GDP =
inactive
1. Bind GTP = active
again
protein regulation by ATP
ATP binding and hydrolysis can lead to directional protein movement
proteasome activity
Located in nucleus and
cytoplasm
*Complex of proteins that
breaks down misfolded,
damaged or no longer
needed proteins
*Proteins to be degraded
tagged with ubiquitin
chain
*Tagged protein enters
central cylinder of
proteasome lined with
proteases which hydrolyze
protein into amino acids
Other modifications that regulate proteins
Acetyl group – added to lysine side chain
*Palmitate – fatty acid added to cysteine side chain, causes proteins to associate with cell membrane
*Ubiquitin – a 76 amino acid polypeptide, tags proteins for
degradation in proteasomes
*All modifications are covalent and added by specific enzymes
The three dimensional structure of proteins is a result of
interactions at many levels
These interactions can be interrupted
chemically
__ can also disrupt protein structure by altering these interactions
Mutations
Proteins function by binding specifically to
ligand
enzymes and antibodies as proteins are subjected to all
the rules of protein structure weve discussed
regulation of protein and enzyme activity ultimately control
what proteins do and what reactions occur in the cell
a protein can be unfolded by a process called
denaturation
primary structure is held together by what kind of bonds?
Covalent and peptide bonds
primary part of proteins bonds are between
carboxy group of one amino acid and the amino group of a second amino acid
What agents can disrupt primary structures?
Proteases (enzymes)
Secondary bonds held together by
H-bonds between carboxy and amide of polypeptide backbone
secondary part of proteins bonds are between
H-bonds between carboxyl and amide groups of peptide bonds
what agents can disrupt secondary structure?
Heat, high salt, since they’re dependent on partial charges
Tertiary bonds held together by
H-bonds
Hydrophobic
Electrostatic (ionic)
Van der Waals
disulfide
Tertiary part of proteins bonds are between
H-bonds between R-groups of amino acids
What agents can disrupt tertiary structure?
Heat, pH change, Detergent, organic solvent, and reducing agent and high salt
Quaternary bonds held together by
H-bonds, Hydrophobic, electrostatic (ionic), van der waals, and disulfide
Quaternary protein bonds are between
bonds between different polypeptide chains
what agents disrupt quaternary structure?
Heat, pH change, detergent, organic solvent, reducing agent, and high salt
define allosteric regulation
molecule binds outside the proteins active site/binding site and changes the proteins shape and activity
Explain how kinases and phosphates work to regulate protein function
kinases add a phosphate to turn on or off a protein
Phosphatases remove a phosphate to turn on or off the protein
Both to regulate the protein
Protein molecules that have a quaternary structure must have two or more of which of the following?
polypeptide chains
Protein molecules that have a quaternary structure must have two or more polypeptide chains. If a protein molecule exists as a complex of more than one polypeptide chain, then these interacting polypeptides form its quaternary structure. Though proteins with quaternary structure may have a variety of features (including extensive secondary structures, disulfide bonds, antigen binding sites, and domains), these do not define this level of protein structure. Proteins with quaternary structure are composed of more than one polypeptide chain, and therefore have multiple N- (and C-) termini.
How do most motor proteins ensure their movements are unidirectional?
Choose one:
A. Their asymmetrical structures support movement in only one direction.
B. They hydrolyze their bound GTP, effectively preventing movement in the reverse direction.
C. They couple a conformational change to a thermodynamically unfavorable reaction.
D. They couple a conformational change to the formation of an ATP molecule from ADP and Pi.
E. They couple a conformational change to the hydrolysis of an ATP molecule.
E. They couple a conformational change to the hydrolysis of an ATP molecule.
Correct. To achieve such directionality, one of the steps must be made irreversible. For proteins that are able to move in a single direction for long distances, this irreversibility is achieved by coupling one of the conformational changes to the hydrolysis of an ATP molecule that is tightly bound to the protein—which is why motor proteins are also ATPases. A great deal of free energy is released when ATP is hydrolyzed, making it very unlikely that the protein will undergo a reverse shape change, as required for moving backward.
Which parts of amino acids are involved in a peptide bond?
Choose one:
A. amino group of one amino acid and side chain of the other
B. carboxyl groups of both amino acids
C. side chains of both amino acids
D. amino group of one amino acid and carboxyl group of the other
E. amino groups of both amino acids
F. carboxyl group of one amino acid and side chain of the other
D. amino group of one amino acid and carboxyl group of the other
A disulfide bond is a(n) ___ interaction within the protein
covalent
The disulfide bond is a covalent interaction within the protein. Disulfide bonds help stabilize a favored protein conformation. Covalent disulfide bonds form between adjacent cysteine side chains by a reaction between their polar –SH groups.
Investigators are studying a protein that must be phosphorylated to be activated. Which method could be used to separate the phosphorylated form of the protein from the form that lacks an activating phosphate group?
Choose one:
A. velocity sedimentation
B. equilibrium sedimentation
C. differential centrifugation
D. ion-exchange chromatography
E. gel-filtration chromatography
D. ion-exchange chromatography
hich statement concerning feedback inhibition is false?
Choose one:
A. Feedback inhibition is difficult to reverse.
B. Feedback inhibition can work almost instantaneously.
C. Feedback inhibition regulates the flow through biosynthetic pathways.
D. Feedback inhibition is a feedback system for controlling enzyme activity.
E. In feedback inhibition, an enzyme acting early in a reaction pathway is inhibited by a later product of that pathway.
A. Feedback inhibition is difficult to reverse.
Feedback inhibition is not difficult to reverse. Rather, it is very easy to do so. In feedback inhibition, for example, an enzyme acting early in a reaction pathway is inhibited by a molecule produced later in that pathway. Thus, whenever large quantities of the final product begin to accumulate, the product binds to an earlier enzyme and slows down its catalytic action, limiting further entry of substrates into that reaction pathway. Feedback inhibition can work almost instantaneously and is rapidly reversed when product levels fall.
Mutations in the nucleic acid sequence of a gene can sometimes direct the substitution of one amino acid for another in the encoded protein. Which amino acid substitution would be most likely to severely disrupt the normal structure of a protein?
Choose one:
A. tryptophan to phenylalanine
B. asparagine to threonine
C. leucine to isoleucine
D. alanine to glycine
E. methionine to arginine
E. methionine to arginine
In an α helix, hydrogen bonds form between which of the following?
Choose one:
A. acidic and basic amino acid side chains
B. every other amino acid
C. every fourth amino acid
D. the peptide bonds and DNA
E. nonpolar amino acid side chains
C. every fourth amino acid
What does the primary structure of a protein refer to?
Choose one:
A. the locations of the peptide bonds that form the protein’s backbone
B. the linear amino acid sequence of the protein
C. the overall three-dimensional shape of the protein
D. the locations of the protein’s α helices and β sheets
E. the structure that forms first as the protein folds into its most stable form
B. the linear amino acid sequence of the protein
Which of the following best describes the stable protein–ligand interaction that is represented in the image? Be sure to use the image as a guide but apply your knowledge regarding how protein and ligand commonly interact with each other. A note of caution though: the red lines in the figure are merely representing interactions and are not meant to be quantified.
Choose one:
A. The formation of a set of very few weak, noncovalent interactions maintains the interaction between protein and ligand.
B. The formation of a set of many weak, noncovalent interactions maintains the interaction between protein and ligand.
C. The formation of a set of many weak, covalent interactions maintains the interaction between protein and ligand.
D. The formation of a set of very few weak, covalent interactions maintains the interaction between protein and ligand.
B. the formation of a set of many weak, noncovalent interactions maintains the interaction between protein and ligand
Which of the following chemical group interactions may be represented by the red lines in the image?
Choose one:
A. a –CH2CH3 of the ligand interacting with a –NH3+ of the protein
B. a COO– of the ligand interacting with a –CH2CH3 of the protein
C. an –OH of the ligand interacting with a –CH2CH3 of the protein
D. an –OH of the ligand interacting with an –SH of the protein
d. An -OH of the ligand interacting with an -SH of the protein
The antibody is composed of __ polypeptide chains
4
If SDS-PAGE were used for a pure sample of this protein that was preincubated with mercaptoethanol, then there would be ____ bands expected
2
In a globular protein, where would the amino acid tryptophan most likely be found?
Choose one:
A. exposed at the protein’s surface
B. located at the protein’s C-terminus
C. buried in the protein’s interior
D. hydrogen-bonded to cysteine
E. located at the protein’s N-terminus
C. buried in the proteins interior
. In a globular protein, the amino acid tryptophan would most likely be found buried in the interior of the protein. Nonpolar, hydrophobic amino acids, such as tryptophan, tend to cluster in the interior of the folded protein to avoid contact with the aqueous cytosol.
Which is true of prion proteins?
Choose one or more:
A. They can spread from one organism to another.
B. They cannot spread from cell to cell.
C. They are misfolded forms of normal proteins.
D. They form unstable protein aggregates.
A. They can spread from one organism to another
C. They are misfolded forms of normal proteins
Which part of an amino acid gives it its unique properties?
Choose one:
A. amino group
B. α-carbon
C. carboxyl group
D. side chain
E. peptide bond
D. side chain
Hydrogen bonds between which types of atoms have been found to stabilize a polypeptide’s folded shape?
Choose one or more:
A. backbone and side-chain atoms
B. multiple carbon atoms
C. side-chain atoms
D. backbone atoms
A. backbone and side-chain atoms
C. side-chain atoms ‘
D. backbone atoms
What is the definition of a protein-binding site?
Choose one:
A. the portion of a protein that attaches to the cell membrane and tethers the protein as a peripheral membrane protein
B. any region on a protein’s surface that interacts with another molecule through noncovalent bonding
C. a pocket on a protein where a small molecule can be covalently attached and thus modify the protein
D. the region of the cell where proteins are assembled based on information from the genetic code
B. any region on a proteins surface that interacts with another molecule through noncovalent bonding
most likely to be found on the interior of a protein and explain why?
alanine; glycine
glycine is smaller, nonpolar, smallest amino acid, usually found on the inside
most likely to be found on the interior of a protein and explain why?
serine; phenylalanine
since serine is polar, it would be on the outside of the cell based on the OH group
most likely to be found on the interior of a protein and explain why?
glutamic acid; asparagine
There is no charge on asparagine. The lower the charge the more likely it is to be inside
most likely to be found on the interior of a protein and explain why?
methionine;cysteine
both nonpolar but cysteine is smaller, Also two cysteines form disulfide bonds
look at vmax and km graphs
look
in cells ATP is made in the following way: ADP + Pi—–> ATP.
what happens in cells that keeps this rxn from reaching chemical equilibrium?
ATP is consumed
in order for a reaction to proceed efficiently in a cell it must have
A negative charge in free energy so -deltaG
and
A specific, active enzyme to catalyze the reaction
The reaction sucrose —> glucose + fructose has a deltaG of -12 kJ/mole in a typical cell and is catalyzed by the enzyme lysosome. What is true?
In the presence of lysosomes, the delta G for this reaction would become less negative.
Substrate X can be converted into product B or A depending on whether Enzyme B or A is active. Enzyme B has a Km= 10^-3M which is product B and Enzyme A has a Km= 10^-7M which is product A. Which product is most likely to be made and why?
The answer is product A because A lower Km means the enzyme has a higher affinity for the substrate (it binds and works efficiently even at low substrate concentrations).
How can proteins that exists in the aqueous environment of the cytosol contain nonpolar amino acids?
Protein folds so that non-polar amino acids are inside of the protein
primary structure is held together by ______ bonds while secondary structure is held together by______ bonds.
peptide (covalent); hydrogen
Which type of amino acid is most likely to be found on the inside of a protein in the cytosol?
Nonpolar with a short side chain
in secondary structure
Hydrogen bonds between polar peptide bonds are responsible for forming secondary structure.
allosteric regulation is
noncompetitive inhibitor
What do you pair SDS-PAGE with
molecular weight
