Exam 1

T/F The main role for phosphatidic acid is energy storage

False

T/F Cytidine monophosphate is a component of rRNA

False

T/F In bacterial mRNA the recognition site for ribosome binding is called the start codon

False

T/F In a typical protein, heating or boiling will break peptide bonds

False

What is the function of smooth endoplasmic reticulum (SER)

Lipid and hormone synthesis

Which macromolecules makes up the main part of SER?

Phospholipids

Chemical structure of the molecules that makes up the main part of the SER

What bond connects two monomers of peptidoglycan in bacteria?

beta-1,4-glycosidic bond

Which of the following proteins can break the covalent bond connecting monomers of a typical bacterial cell wall?

A) nuclease A

B) lipidase

C) phosphatase

D) glycosidase

E) antibodies

D) Glycosidase

T/F Enzymes increase the rates of metabolic reactions by altering the equilibrium of the reaction

False

T/F Enzymes increase the rates of metabolic reactions by making non-spontaneous reactions spontaneous

False

T/F Enzymes increase the rates of metabolic reactions by changing the activation energy of the reaction

True

T/F Enzymes increase the rates of metabolic reactions by causing the overall delta G of the reaction to become more negative

False

Compare and contrast the structural features of DNA and RNA as described in class (including secondary structure). Please include the chemical structure of the sugars.

DNA and RNA are both nucleic acids composed of long chains of nucleotides however DNA is made of the sugar deoxyribose which does not contain a 2’ hydroxyl group while RNA is made with the sugar ribose which does contain a 2’ hydroxyl group. DNA also has A, T, C, and G as it’s nitrogenous bases while RNA has A, U, C, and G. Finally DNA has a double helix secondary structure formed by hydrogen bonding of base pairs, while RNA folds into hairpins, loops, and stem loops formed through intramolecular base pairing.

What is the main role of tRNA in cellular organisms? In molecular terms, describe how tRNA accomplishes this task, including relevant bonds needed.

tRNA's primary function is to bring specific amino acids to the ribosome in accordance with the codons on the mRNA template, enabling the assembly of amino acids into a polypeptide chain. Each tRNA has a specific amino acid attached to its 3' end via an ester bond. tRNA molecules have a specific anticodon that is complementary to the mRNA codon. This base pairing occurs via hydrogen bonds between the complementary bases of the codon and the anticodon. Once the tRNA is positioned in the ribosome, its attached amino acid is brought into proximity with the growing polypeptide chain. The ribosome catalyzes the formation of a peptide bond between the amino acid from the tRNA and the last amino acid of the polypeptide chain.

The GENERAL structure of two ordinary monomers of mRNA and the
COVALENT bond that connects the monomers

What is the enzyme that forms the covalent bond that connects two ordinary monomers of mRNA?

RNA polymerase

Would the structure of two ordinary monomers of mRNA be considered a high energy compound?

Yes, due to the presence of triphosphates

What is the definition of a high energy compound?

A high-energy compound is a molecule that stores and releases a significant amount of energy during chemical reactions, usually through the breaking of high-energy phosphate bonds

A genetically engineered cell produces the mRNA for the gene of interest, but the protein encodedby the gene is not produced. Which signal is most likely to be deactivated?
A) promoter
B) start codon
C) operator
D) origin
E) terminator

B) Start codon

Which molecule is the electron acceptor in the forward direction of this reaction?

NADP+

Which molecule is the reductant in the forward direction of this reaction?

NADPH

During AEROBIC exercise, highly reduced compounds produce more ATP per carbon atom than more oxidized compounds. During aerobic respiration, which of the following will produce the MOST ATP? And why?
(a) Fructose, a carbohydrate
(b) Hexanoic acid, a 6-carbon saturated fatty acid
(c) Homo-glutamic acid, (glutamic acid with an extra –CH2- group in the side chain)

(b) Hexanoic acid, a 6-carbon saturated fatty acid

Fatty acids are more reduced than carbohydrates and generate more ATP per carbon via beta oxidation

What is the role of the TCA cycle in degrading the highly reduced compounds during aerobic exercise?

Breaks down acetyl-CoA to generate NADH and FADH₂ for oxidative phosphorylation.

What is the role of O2 in making ATP when degrading the highly reduced compounds during aerobic exercise?

Final electron acceptor in the electron transport chain and forms water after accepting electrons.

T/F Electrons from highly reduced compounds are transferred to ADP to make ATP. And why?

False, Electrons from highly reduced compounds (such as NADH and FADH₂) are transferred through the electron transport chain (ETC) to ultimately drive the production of ATP, but they are not transferred directly to ADP.

Given your knowledge of redox and oxidative phosphorylation, explain in molecular terms why highly reduced compounds produce more ATP per carbon atom than more oxidized compounds.

More reduced molecules release more energy per oxidation step, leading to higher ATP yield

For a MEMBRANE-SPANNING protein, which of the following amino acids
would tend to be in contact with the hydrocarbon part of the membrane?

I

Q

S

P

I

Glutathione is a natural reductant in cells. This TRIPEPTIDE is composed of gamma-glutamyl-cysteinyl-glycine. “Gamma-glutamyl” means that the carboxyl group for the FIRST peptide bond comes from the SIDE CHAIN of glutamate. Draw the structure of the tripeptide glutathione at pH 7, showing the peptide bonds very clearly

Look at the structure of glutathione. What chemical feature most likely contributes to the role of glutathione as a reductant? Justify your answer.

The thiol (-SH) group of cysteine allows it to donate electrons

Draw a titration curve for glutathione, showing pKa value and pI.

Estimate the pI of glutathione, based on the information provided in class.

Transcribe the DNA template strand below.
DNA template strand: 3’- T A C C G C G C A T T C A T T - 5’

5’-AUGGCGCGUAA-3’

What determines the strength of secondary structure?

The pH of grapefruit juice is 3.25. What is the [H+]? Please state units.

10⁻³^.²⁵ M

The pKa of butanoic acid is 4.87. A student mixes 120 mL of 0.45 M butanoic acid with 50 mL of 0.3 M NaOH and adds water to give a final volume of 1 L. What is the pH of the final solution?

To make an amino acid buffer at pH 5.4, which amino acid
would be the BEST choice? Three-letter ________ one-letter _____

HIs, H

A student starts with 0.175 liter of a 0.25 M solution of the amino acid histidine at the pKa of the side chain. The student then adds 50 ml of 100 mM HCl and
dilutes the mixture to 1 L. What is the final pH?

Draw the entire amino acid at pH 7

Draw the entire titration curve of this amino acid. Label the axes and write each pKa. Label the pI.

The molecule on the left side of the arrow is called phosphoenolpyruvate.
According to the thermodynamics lecture, what is/are the driving force(s) for the reaction below?

High phosphoryl transfer potential, Increased entropy upon hydrolysis

Define “essential” amino acid.

Draw a dipeptide at pH 7 containing 2 ESSENTIAL amino acids.

In mad cow disease, the infectious agent is a “prion protein” that has misfolded, leading to certain death within 5 years. MONOMERS of the normal and disease-causing protein forms are shown below. For EACH of the four LEVELS of protein structure, compare and contrast the structures of the twoprotein forms. (Based on the drawings AND description, what is the same and what differs between the two? Give numbers; for example, how many of each structural feature do you see?

Primary: No change

Secondary: Shift from alpha helices to beta sheets

Tertiary: More aggregation in diseased form

Quaternary: Formation of insoluble fibrils

What is a peptide bond?

The peptide bond is a covalent bond between the amine group (NH₂) of the incoming amino acid and the carboxyl group (COOH) of the last amino acid in the chain