BSCI330 Exam 2

Which of the following is true about the ends labeled end A and end B in the actin filament depicted below:

a) End A is the minus end. In a shrinking filament, loss of actin from end A is faster than addition of actin to end B.

b) End B is the plus end. In a growing filament, addition to end B is faster than loss from end A.

c) If addition at end B is balanced with loss at end A, a phenomenon called "treadmilling" occurs.

d) All of the above statements are true.

d) All of the above statements are true.

Which of the following is TRUE about enzyme catalysts?

a) Enzymes do not change the △G for a chemical reaction

b) Enzymes increase the activation energy for a chemical reaction

c) Enzymes shift the reaction equilibrium to favor the products

d) Enzymes stabilize the products

a) Enzymes do not change the △G for a chemical reaction

Enzymes are catalytic proteins, speeding up cellular reactions to allow life. Enzymes do not alter delta G. They cannot make a reaction occur spontaneously if it is thermodynamically unfavorable and they cannot alter the concentrations of reactants and products. Enzymes equally catalyze the forward and reverse reactions. Enzymes lower activation energy for a catalyzed reaction.

Which of the following is true about the ends labeled end A and end B in the actin filament depicted below:

a) End A is the minus end. In a shrinking filament, loss of actin from end A is faster than addition of actin to end B.

b) End B is the plus end. In a growing filament, addition to end B is faster than loss from end A.

c) If addition at end B is balanced with loss at end A, a phenomenon called "treadmilling" occurs.

d) All of the above statements are true.

d) All of the above statements are true.

Which of the following is TRUE about enzyme catalysts?

a) Enzymes do not change the △G for a chemical reaction

b) Enzymes increase the activation energy for a chemical reaction

c) Enzymes shift the reaction equilibrium to favor the products

d) Enzymes stabilize the products

a) Enzymes do not change the △G for a chemical reaction

Enzymes are catalytic proteins, speeding up cellular reactions to allow life. Enzymes do not alter delta G. They cannot make a reaction occur spontaneously if it is thermodynamically unfavorable and they cannot alter the concentrations of reactants and products. Enzymes equally catalyze the forward and reverse reactions. Enzymes lower activation energy for a catalyzed reaction.

Which of the following statements about the genetic code is false?

a) Some amino acids are encoded by more than one codon

b) All amino acids are encoded by more than one codon

c) One codon always encodes for the same amino acid

d) Stop codons do not code for amino acids

b) All amino acids are encoded by more than one codon

In order to accommodate 20 different amino acids, the genetic code must use combinations of at least 3 nucleotides, which is called a codon. Since there are more codons than amino acids, most amino acids have multiple corresponding codons. Translation begins with the AUG (Met) codon and ends at the stop codon (don't encode any amino acid). Each mRNA has 3 potential "reading frames", so the ribosome must choose one and remain consistent, or garbled translation occurs

Which of the following statements about glycolysis is TRUE?

a) It cannot occur in the absence of oxygen

b) It produces a net output of 4 ATP

c) It uses the energy released from reduction of G3P to allow the oxidation of NAD+ and the generation of ATP

d) All of the above

e) None of the above

e) none of the above

Which of the following characteristics would be most likely to allow a protein to serve as a molecular integrator?

a) Contains a heme prosthetic group

b) A structure that is all alpha-helical

c) Multiple phosphorylation sites

d) The presence of a GTPase domain

c) Multiple phosphorylation sites

Which of the following statements about the genetic code is TRUE?

a) Some codons do not encode any amino acid

b) Most amino acids are encoded by more than one codon

c) The initiation codon establishes the reading frame for the ribosome

d) Every possible codon has some function in translation

e) All of the above

e) All of the above

In order to accommodate 20 different amino acids, the genetic code must use combinations of at least 3 nucleotides, which is called a codon. Since there are more codons than amino acids, most amino acids have multiple corresponding codons. Translation begins with the AUG (Met) codon and ends at the stop codon (don't encode any amino acid). Each mRNA has 3 potential "reading frames", so the ribosome must choose one and remain consistent, or garbled translation occurs.

Which of the following is NOT catalyzed by an aminoacyl-tRNA synthetase?

a) Attachment of amino acid to AMP

b) Attachment of amino acid to tRNA

c) Proofreading to ensure the correct amino acid is attached to the tRNA

d) Formation of a peptide bond between two amino acids

e) None of the above (i.e. all are performed by the aminoacyl-tRNA synthetase)

d) Formation of a peptide bond between two amino acids

In protein translation, amino acids are coupled to tRNA by aminoacyl-tRNA synthetase. Each amino acid has a distinct synthetase. Amino acid is first "activated" by conjugation to AMP. Amino acid is then transferred from AMP to tRNA. Once translation is complete, the synthetase proofreads it for accuracy.

Many enzymes that perform redox reactions in cells require NAD+. The NAD+ would be considered

a) An allosteric regulator

b) A coenzyme

c) A chaperone

d) A motif

b) A coenzyme

Non-protein molecules which aid in some protein function are called prosthetic groups. Enzyme prosthetic groups are referred to as cofactors. Organic molecules that act as cofactors are often called coenzymes. NAD+ is an example of a non-protein molecule that aids in a protein function, redox reactions. Therefore NAD+ is a cofactor or coenzyme.

Which of the following components of the protein synthesis pathway does NOT hydrolyze either ATP or GTP hydrolysis as part of its function?

a) EF-Tu

b) Aminoacyl-tRNA synthetase

c) elF2

d) Ribosome

d) Ribosome

So we know that aminoacyl tRNA synthetase couples amino acids to tRNA and AMP and also proofreads translation. EF-Tu is an elongation factor used to bind aminoacyl-tRNA synthetase to the ribosome.

One measure of the binding interaction between a protein and its ligand is the dissociation constant, Kd. Which of the following is true about this value?

a) The Kd is equal to koff/kon

b) The lower the Kd, the weaker the binding

c) The higher the Kd, faster the on rate for binding

d) The lower the Kd, the faster the off rate for dissociation

e) None of the above

a) The Kd is equal to koff/kon

Kd is a dissociation constant. Kon is the rate of the forward association and Koff is the rate of backward dissociation. Ka, an association constant, measures the strength of binding such that Ka= Kon/Koff. Kd is 1/Ka (the reverse of Ka). Therefore Kd= koff/kon. Lower dissociation rates=lower Kd values= stronger binding.

Which of the following is NOT a property of the homeodomain DNA binding motif?

a) Contains 3 alpha-helices

b) Contains a structure very similar to a helix-turn-helix

c) Contains a zinc ion

d) Makes contacts in both the major and minor grooves of DNA

c) Contains a zinc ion

A helix-turn-helix is one of the simplest DNA-binding motifs. A homeodomain is a special case of the helix-turn-helix motif. It's a larger structure that includes a helix-turn-helix region plus other highly conserved structures (including a third alpha helix). This conserved structure suggests that all homeodomains are presented to DNA in the same fashion.

Which of the following is NOT a reason for a molecular tunnel structure in an enzyme?

a) It prevents the reaction intermediates from diffusing away

b) It prevents reactive intermediate species from interacting with water

c) It isolates toxic intermediate products from harming the cell

d) It slows down the reaction to allow for greater regulation

e) None of the above

d) It slows down the reaction to allow for greater regulation

Some enzymes perform multiple sub-reactions that must occur at distinct active sites. The structures of such enzymes may act as tunnels to direct the intermediate products from one active site to the next- the intermediates never leave the enzyme. This prevents diffusion of intermediates, prevents decomposition of unstable molecules, and speeds up reaction rates.

Which of the following statements is TRUE about the homeodomain motif?

It contains a helix-turn-helix motif

A helix-turn-helix is one of the simplest DNA-binding motifs. A homeodomain is a special case of the helix-turn-helix motif. It's a larger structure that includes a helix-turn-helix region plus other highly conserved structures (including a third alpha helix). This conserved structure suggests that all homeodomains are presented to DNA in the same fashion.

Which of the following is a property of a non-competitive reversible inhibitor?

It reduces the Vmax without affecting the Km

A non-competitive inhibitor reversibly binds away from the active site to cause change in enzyme structure that lowers catalytic efficiency. It lowers Vmax and does not affect Km or substrate binding.

Which of the following steps in protein synthesis requires GTP hydrolysis?

Attachment of amino acid to tRNA

One measure of the binding interaction between a protein and its ligand is the dissociation constant, Kd. Which of the following is true about this value?

The lower the Kd, the stronger the binding

Lower dissociation rates=lower Kd values= stronger binding.

Which of the following DNA binding motifs does NOT also contain a dimerization region?

Homeodomain

Which of the following is a function of acetylation as a post-translational modification of proteins?

It neutralizes the charge on a lysine residue

Explain how a non-competitive inhibitor works to inhibit enzyme function. Include the effects of Vmax and Km.

A non-competitive inhibitor reversibly binds away from the active site to cause change in enzyme structure that lowers catalytic efficiency. It lowers Vmax and does not affect Km or substrate binding.

List 3 different covalent post-translational modifications that can be used to regulate CYTOPLASMIC proteins. Please also indicate the amino acid that is modified.

Phosphorylation- modifies tyrosine, serine and threonine

Ubiquitylation- modifies lysine.

Methylation- modifies lysine.

List ONE specific mechanism that enzymes can use to stabilize the transition state of a chemical reaction.

A transition state for a reaction is an intermediate form between product and reactant, with a specific structure.

Mechanisms that enzymes can use to stabilize the transition state of a chemical reaction include:

Enzyme binds 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 charges that favor a reaction

Enzyme strains the bound substrate molecule, forcing it toward a transition state to favor a reaction

Many antibiotics are translation inhibitors. Briefly explain how they are able to selectively affect prokaryotic cells. Also explain why some may have side effects on eukaryotic cells (even if they do not inhibit general translation in eukaryotic cells).

Antibiotics are translation inhibitors that selectively affect prokaryotic cells due to differences between prokaryotic and eukaryotic ribosomes. Some have side effects on eukaryotic cells because they inhibit mitochondrial ribosomes and mRNA on mitochondrial ribosomes.

Transcription of most genes is regulated by the binding of specific transcription factors. List TWO mechanisms that these proteins can use to increase the transcription of a gene

In order to increase the transcription of a gene, there are 5 mechanisms:

-Some transcription factors help to unpack chromatin, making the gene accessible to RNA polymerase and the initiation complex

-Some transcription factors control the recruitment of RNA polymerase and/or the general transcription factors to the promoter

-Some transcription factors may regulate the switch from initiation to elongation

-Some transcription factors help recruit histone-modifying enzymes to change the local chromatin structure

-Some transcription factors bend DNA to allow long-distance interactions between gene regulatory regions

Many pharmaceutical drugs work by inhibiting G-protein coupled receptors (GPCR). Briefly describe how the signal of ligand binding to GPCR is transduced across the plasma membrane into an intracellular signal. Do NOT describe subsequent activation of intracellular effector proteins or second messengers

G-Protein coupled receptors are multi-pass transmembrane proteins. They indirectly regulate the activity of a nearby target protein that is located in the membrane. GPCRs contain a GTP binding protein complex that acts as the "middle man" between an activated receptor and its target. Ligand binding to G-protein coupled receptors causes conformation changes in the receptor. This changes GDP to GTP, and the G protein dissociates from the receptor. From there, the alpha subunit separates from beta/gamma subunits.

A common theme among cell surface receptors is the use of a kinase cascade to transduce the signal. Briefly explain the advantage of this signaling strategy.

The kinase cascade allows for faster and more efficient signal transduction.

The amount of a protein produced by a cell can be regulated at many different steps. Please describe 3 specific ways. NOT including regulation of mRNA transcription, by which the amount (NOT the activity) of a protein can be regulated. Be specific in how the mechanism affects protein levels (i.e. what it actually does).

Phosphorylation: The addition of a negatively charged phosphate group to the R-group of serine, threonine, and/or tyrosine. This reaction is catalyzed by a class of enzymes known as protein kinases. Phosphorylation is reversible and phosphate removal is catalyzed by protein phosphatases. Each phosphate group adds two negative charges to the protein, which can drive major structural changes or changes in protein solubility. The added phosphate group may create a new recognition site that allows other proteins to bind to the phosphorylated protein.

Addition of 2 negative charges to R group of serine, threonine or tyrosine which can drive major changes in structure and solubility and may create a new recognition site that allows proteins to bind to the phosphorylated protein.

Ubiquitylation: Ubiquitin is a small protein that is covalently attached to proteins. It serves as a tag that can either mark proteins for degradation or direct it to specific locations in the cells.

Please fully describe all levels of protein structure presented in lecture. Your description should include the chemical properties that determine each level of protein structure.

Primary: linear sequence of amino acid residues, determined by mRNA code,2 in combination with the protein's environment it determines the rest of the structures

Secondary: folding and twisting of the peptide backbone, held together by weak H-bonds between C=O (carbonyl) and N-H (amine) groups in the backbone. R groups stick out from the backbone. Two well known secondary structures- alpha helices and beta sheets

Tertiary: 3D arrangement of secondary structures, held together by noncovalent attractions between R-groups/between R-groups and their environment i.e. lipid bilayer. R-group interaction leads to folding of secondary structures into 3D (tertiary structure) that assume the lowest possible energy state

Quaternary: Arrangement of multiple tertiary structures, held together by weak bonds and some disulphide bonds. (Homomers-identical subunit polypeptides, Heteromers- different polypeptides). Can be simple (hemoglobin: 2 copies each of 2 subunits) or complex (RNA polymerase II contains 17 subunits, 11 different polypeptide chains)

A common theme among cell surface receptors is the generation of second messengers to transduce the signal. Briefly explain two advantages of this signaling strategy.

Second messengers are helpful for secretion and amplification of messages. In the G-Protein coupled receptors, Ca2+ is a common second messenger that allows for the signal to be disseminated throughout the cell.

Explain what is meant by "allosteric regulation"

Allosteric regulation occurs when a regulatory molecule binds to an allosteric site on the molecule. This causes conformational change that can either activate or inhibit the enzyme.

The components of a signal transduction pathway are often assembled into a higher order complex to increase the speed and efficiency of signaling. Describe ONE way that these complexes can be assembled

The kinase cascade allows for faster and more efficient signal transduction. This is because the enzymes are all very close together in proximity which allows the signal to fall in a ladder-like fashion down the signal pathway.

Practice Essay

Describe the general mechanism of action of each of the following types of enzymes: Irreversible inhibitor, Competitive reversible inhibitor, non competitive reversible inhibitor (for competitive and non competitive include vmax and km information)

Irreversible inhibitor: substance that permanently blocks the action of the enzyme

Competitive reversible inhibitor: competes with the substrate for binding at the active site of the enzyme. Vmax stays the same and Km increases

Non competitive reversible inhibitor: reversibly binds away from the active site to cause change in enzyme structure that lowers catalytic efficiency. It lowers Vmax and does not affect Km or substrate binding.

Describe ONE function that the 5'7- methylguanosine cap performs for an RNA molecule

5' cap is added to the RNA after it is transcribed from DNA so that it can be recognized when it will be sent to the cytoplasm for translation

Briefly describe the 3 main post-transcriptional processing events for eukaryotic mRNA

Addition of the 5' cap

Addition of the 3' polyAtail

Splicing out introns