Advanced Biochemistry Exam Preparation Guide

Course Introduction

Advanced Biochemistry delves into the molecular mechanisms underpinning cellular processes, exploring the structure and function of biomolecules such as proteins, nucleic acids, lipids, and carbohydrates. The course emphasizes enzyme kinetics, regulation of metabolic pathways, and the integration of metabolism in various physiological contexts. It also covers advanced topics such as signal transduction, molecular genetics, and bioenergetics, while introducing contemporary biochemical techniques and analysis methods. Designed for upper-level undergraduates and graduate students, this course equips learners with a deep understanding of biochemical processes and practical skills essential for research and professional applications in the life sciences.

Recommended Textbook

Biochemistry 4th Edition by Christopher K. Mathews

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29 Chapters

733 Verified Questions

733 Flashcards

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Chapter 1: The Scope of Biochemistry

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Sample Questions

Q1) Which of the following organelles is found in plant cells, but not in animal cells

A)chloroplast

B)Golgi apparatus

C)mitochondrion

D)smooth endoplasmic reticulum

E)rough endoplasmic reticulum

Answer: A

Q2) The synthesis of which molecule is considered by many to be the root of biochemistry since it was the first synthesis of a biological molecule from non-biological precursors?

A)DNA

B)urea

C)glucose

D)glycine

E)adenosine triphosphate (ATP)

Answer: B

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Chapter 2: The Matrix of Life: Weak Interactions in an Aqueous Environment

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Q1) Glutamic acid contains two carboxylic acid groups (pKa values of 2.2 and 4.2)and an amine group (pKa 9.7). What is the pI for glutamic acid?

A)3.2

B)6.0

C)6.5

D)7.0

E)none of the above

Answer: A

Q2) Which of the following atoms could interact through a hydrogen bond?

A)the oxygen of a ketone and the hydrogen of an aldehyde

B)the oxygen of methanol and a hydrogen on the methyl carbon of methanol

C)the hydrogen of an amine and the oxygen of an alcohol

D)the hydrogen on an aromatic ring and the oxygen of carbon dioxide

E)none of the above

Answer: C

Q3) Imidazole is a commonly used buffer in biochemistry labs. With a pKa of 7.0, what would be the ratio of base to acid at pH 7.4?

Answer: 2.5 11ea7cd4_c4a8_33b6_a2ab_b9ca760947d7_TB2679_00

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Chapter 3: The Energetics of Life

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Sample Questions

Q1) Calculate the \(\Delta\)G\(\circ\)'for the oxidation of succinate to fumarate, a step in the citric acid cycle.

FAD + 2H+ + 2e- \(\rarr\) FADH2 E\(\circ\)' = - 0.22 V fumarate + 2H+ + 2e- \(\rarr\) succinate E\(\circ\)' = + 0.03 V

Answer: E\(\circ\)'= - 0.25 V \(\Delta\)G\(\circ\)' = -nFE\(\circ\)' = -(2)(96.5 kJ/V/mol)(-0.25 V)= 48.3 kJ/mol

Q2) Which of the following best describes biochemical systems with respect to the first law of thermodynamics?

A)most biochemical systems operate at constant volume

B)most biochemical systems operate at constant temperature

C)most biochemical systems operate at constant pressure

D)most biochemical systems operate with a constant number of molecules

E)none of the above

Answer: C

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Chapter 4: Nucleic Acids

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Q1) Which of the following is correctly paired with the type of tautomerization(s)that occurs?

A)adenine: keto-enol

B)cytosine: amino-imino and keto-enol

C)guanine: amino-imino

D)thymine: keto-enol

E)none of the above

Q2) Which of the following base pairs would have 2 hydrogen bonds and a distance between C-1' of 1.08 nm?

A)A-C

B)G-C

C)A-T

D)G-T

E)none of the above

Q3) Which of the following is correctly paired?

A)adenine: pyrimidine

B)RNA: ribose containing nucleic acid

C)thymine: purine

D)uracil: purine

E)DNA: ribose containing nucleic acid

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Chapter 5: Introduction to Proteins: the Primary Level of Protein Structure

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Q1) The prevalence of the trans orientation in peptide bonds results in the R-groups of adjacent amino acids being oriented approximately ______ degrees with respect to each other.

A)30

B)60

C)90

D)120

E)180

Q2) In the sequence of cytochrome c, the presence of cysteine at position 17 in hundreds of different species indicates that this particular amino acid is _________.

A)conserved

B)mutated

C)homologous

D)variable

E)none of the above

Q3) What is the pI for the following peptide: Ala-Glu-Val-Asp-Lys-Leu

Q4) Draw each of the structures of aspartic acid that predominate at pH 1, 3, 7, and 11.

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Chapter 6: The Three-Dimensional Structure of Proteins

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Q1) Which of the following causes denaturation of a protein when disulfide bonds are present?

A)heat

B)pH changes

C)reducing agent

D)detergent

E)all of the above

Q2) The two amino acids most often found in a polyproline II helix are proline and _______.

A)alanine

B)glycine

C)serine

D)lysine

E)histidine

Q3) Draw a section of antiparallel \(\beta\)-sheet showing two sheets with three residues in each sheet. Clearly show the hydrogen bond pattern between the two sheets.

Q4) Show the most likely interaction that would occur between a serine residue and a glutamine residue.

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Chapter 7: Protein Function and Evolution

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Sample Questions

Q1) Which of the following mutations in the coding strand of DNA would be the most likely to cause a serious mutation?

A)AGA \(\rarr\) CGA

B)ATA \(\rarr\) TTA

C)GAA \(\rarr\) AAA

D)TAA \(\rarr\) TGA

E)ACT \(\rarr\) AGT

Q2) Which immunoglobulin is the only one to occur in a dimeric form?

A)IgA

B)IgD

C)IgE

D)IgG

E)IgM

Q3) Myoglobin without a heme group would be considered a(n)_______.

A)apoprotein

B)holoprotein

C)apoenzyme

D)holoenzyme

E)none of the above

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Chapter 8: Contractile Proteins and Molecular Motors

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Sample Questions

Q1) Which form of myosin is found in striated muscle?

A)I

B)II

C)IV

D)VI

E)all of the above

Q2) Which of the following motor proteins is correctly paired with both its binding target and its direction of movement?

A)myosin II: actin filament, moves towards (-)end

B)myosin V: actin filament, moves towards (+)end

C)kinesin: actin filament, moves towards (+)end

D)cytoplasmic dynein: microtubule, moves towards (+)end

E)axonemal dynein: microtubule, can move in either direction

Q3) Which of the following only occurs when ATP (not ADP)is bound to the myosin head?

A)actin is released from its binding site on myosin

B)weak binding of myosin head to actin

C)strong binding of myosin head to actin

D)power stroke of muscle contraction

E)none of the above

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Page 10

Chapter 9: Carbohydrates: Sugars, Saccharides, Glycans

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Sample Questions

Q1) Dihydroxyacetone is classified as a(n)_______.

A)aldotriose

B)ketotriose

C)aldotetrose

D)ketotetrose

E)none of the above

Q2) Gluconic acid is derived from ________ while glucuronic acid is derived from _______.

A)glucose; gulose

B)gulose; glucose

C)glucose; glucose

D)glucose; galactose

E)galactose; glucose

Q3) Of the following phosphate esters of monosaccharides, which has the most spontaneous \(\Delta\)G\(\circ\)´ of hydrolysis?

A)\(\alpha\)-D-glucose-6-phosphate

B)\(\beta\)-D-glucose-6-phosphate

C)\(\beta\)-D-glucose-1-phosphate

D)\(\alpha\)-D-fructose-6-phosphate

E)D-glyceraldehyde-3-phosphate

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Chapter 10: Lipids, Membranes and Cellular Transport

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Q1) Which of the following mechanisms of membrane transport is correctly defined?

A)simple diffusion: uses concentration gradient to move highly polar molecules and ions across membranes

B)facilitated diffusion: uses proteins such as ion channels to move substances against their concentration gradient across a membrane

C)primary active transport: uses ATP hydrolysis to move ions against their concentration gradient across a membrane

D)secondary active transport: uses ATP hydrolysis along with an ion gradient to move polar molecules or ions against their concentration gradient across a membrane E)all of the above

Q2) Draw the following fatty acid: 18:3c\(\Delta\)9,12,15 as it would appear at physiological pH. With reference to the omega carbon, what type of fatty acid is this? Draw the result if this fatty acid underwent partial hydrogenation to produce 18:1t\(\Delta\)11

Q3) Draw a molecule of phosphatidylserine with palmitic acid (16:0)and oleic acid (18:1c\(\Delta\)9)present. Make sure to put the saturated and unsaturated fatty acids in their proper location.

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Chapter 11: Enzymes: Biological Catalysts

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Q1) What are the expected changes in kinetics in the presence of a competitive inhibitor?

A)Vmax decreases, KM appears to decrease

B)Vmax does not change, KM appears to decrease

C)Vmax decreases, KM appears to increase

D)Vmax does not change, KM appears to increase

E)Vmax decreases, KM does not change

Q2) Which of the following cofactors is used during the activation and transfer of carbon dioxide?

A)nicotinamide adenine dinucleotide (NAD)

B)thiamine pyrophosphate

C)biotin

D)coenzyme A

E)tetrahydrofolate

Q3) In a Lineweaver-Burke plot, what does the slope represent?

A)KM

B)Vmax

C)Vmax/KM

D)KM/Vmax

E)none of the above

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Chapter 12: Chemical Logic of Metabolism

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Q1) Which of the following statements regarding the general concepts of metabolism is true?

A)once glucose is converted to pyruvate, there is no way to convert pyruvate back to glucose

B)when triacylglycerols are used as fuel, only the fatty acids can be metabolized, the glycerol is a waste product

C)amino acids serve as substrates for many pathways including glycolysis and the citric acid cycle

D)the citric acid cycle is generally considered an anabolic pathway while gluconeogenesis is generally considered a catabolic pathway

E)none of the above

Q2) Pyruvic acid has the formula C3H4O3. Write the reaction for its complete combustion. What is its respiratory quotient? Does this mean that it is more oxidized or less oxidized than glucose?

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Chapter 13: Carbohydrate Metabolism: Glycolysis,

Gluconeogenesis, Glycogen Metabolism, and the Pentose

Phosphate Pathway

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Q1) What is the link between glutathione and the pentose phosphate pathway (PPP)?

A)during the oxidative phase, thiol groups on glucose-6-phosphate dehydrogenase become oxidized and must be reduced by glutathione

B)glutathione acts as an inhibitor of glucose-6-phosphate dehydrogenase

C)NADPH from the PPP is needed to keep glutathione in its reduced state

D)phosphopentose epimerase often produces free radicals that are quenched by glutathione

E)none of the above

Q2) During aerobic glycolysis, pyruvate is most likely oxidized to ________ while in anaerobic glycolysis, pyruvate is converted to _________.

A)acetaldehyde; ethanol

B)acetyl CoA; glyceraldehyde

C)acetyl CoA; lactate

D)acetaldehyde; lactate

E)none of the above

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Chapter 14: Citric Acid Cycle and Glyoxylate Cycle

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Sample Questions

Q1) The oxidation reactions that convert pyruvate to CO2 are specifically catalyzed by ______ enzymes.

A)oxygenase

B)oxidase

C)decarboxylase

D)dehydrogenase

E)none of the above

Q2) Which of the following reactions is commonly used to replenish intermediates of the citric acid cycle?

A)citrate \(\rarr\)oxaloacetate + acetyl CoA

B)oxaloacetate \(\rarr\) aspartate

C)glutamate \(\rarr\) \(\alpha\)-ketoglutarate

D)malate \(\rarr\) pyruvate

E)all of the above

Q3) What is the source of acetyl-CoA for the glyoxylate cycle?

A)pyruvate

B)amino acids

C)fatty acids

D)cholesterol

E)all of the above

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Chapter 15: Electron Transport, Oxidative Phosphorylation, and Oxygen Metabolism

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Q1) __________ increases oxygen consumption while decreasing ATP synthesis, but ____________ decreases both oxygen consumption and ATP synthesis.

A)rotenone; valinomycin

B)azide; 2,4-dinitrophenol

C)antimycin A; nigericin

D)2,4-dinitrophenol; oligomycin

E)cyanide; valinomycin

Q2) Which of the following correctly indicates the number of protons pumped into the intermembrane space at each complex of electron transport for each FADH2 that is oxidized by the electron transport pathway?

A)II: 2 III: 4 IV: 2

B)II: 0 III: 2 IV: 4

C)II: 2 III: 2 IV: 2

D)II: 0 III: 4 IV: 2

E)II: 0 III: 2 IV: 2

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Page 17

Chapter 16: Photosynthesis

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Q1) In the mechanism of Rubisco, what role does the Mg2+ play?

A)neutralizes negative charges of active site Asp and Glu, enabling ionization of CO2

B)activates water molecule that hydrates the carboxy-\(\beta\)-keto intermediate C)complexes with the phosphate on C-1 to hold ribulose-1,5-bisphosphate in the active site

D)repels the product, 3-phosphoglycerate, allowing it to leave the active site more rapidly

E)none of the above

Q2) Which of the following carbohydrates is the most common molecule exported by photosynthetic cells for use in other parts of the plant?

A)amylose

B)amylopectin

C)glucose

D)sucrose

E)fructose

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Chapter 17: Lipid Metabolism I: Fatty Acids, Triacylglycerols, and Lipoproteins

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Q1) Which of the following events occurs first in the process of transporting an LDL into a cell?

A)formation of a coated pit with the aid of clathrin

B)receptor-mediated endocytosis

C)fusion of the clathrin-lined vesicles to produce an endosome

D)fusion of the cell membrane around the LDL particle

E)interaction of apoprotein B-100 with the LDL receptor

Q2) Which of the following enzymes of fatty acid synthesis is most analogous to thiolase when considering that fatty acid synthesis is analogous to a reversal of \(\beta\)-oxidation?

A)\(\beta\)-ketoacyl-ACP synthase

B)\(\beta\)-ketoacyl-ACP reductase

C)3-hydroxyacyl-ACP dehydratase

D)enoyl-ACP reductase

E)thioesterase

Q3) If gadoleic acid (20:1c\(\Delta\)9)underwent complete mitochondrial oxidation to CO2, how many ATP could be produced assuming that all reduced electron carriers are re-oxidized by the mitochondrial electron transport chain?

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Chapter 18: Interorgan and Intracellular Coordination of Energy Metabolism in Vertebrates

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Q1) For skeletal muscle, which of the following correctly pairs the activity state with the source of energy?

A)resting: glucose

B)resting: amino acids

C)exertion: glucose

D)exertion: fatty acids

E)none of the above

Q2) For each of the following tissue types, list the fuel(s)stored, preferred fuel(s)and exported fuel(s)under normal conditions.

Tissue

fuel(s)stored

preferred fuel(s)exported fuel(s)Brain

Highly active skeletal muscle

Heart

Adipose

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Chapter 19: Lipid Metabolism Ii: Membrane Lipids, Steroids,

Isoprenoids, and Eicosanoids

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Q1) Which of the following is used to activate phosphatidic acid for conversion to various phospholipids?

A)ATP

B)UTP

C)CTP

D)GTP

E)TTP

Q2) The synthesis of phosphatidylethanolamine in prokaryotes involves _________________ while in mammals _______________ occurs.

A)reaction of CDP-diacylglycerol with ethanolamine; decarboxylation of phosphatidylserine

B)decarboxylation of phosphatidylserine; reaction of CDP-ethanolamine with diacylglycerol

C)reaction of phosphoethanolamine with diacylglycerol; reaction of CDP-ethanolamine with diacylglycerol

D)decarboxylation of phosphatidylserine; reaction of CDP-diacylglycerol with ethanolamine

E)reaction of CDP-diacylglycerol with ethanolamine; reaction of phosphoethanolamine with diacylglycerol

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Chapter 20: Metabolism of Nitrogenous Compounds I:

Principles of Biosynthesis, Utilization, and Turnover

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Q1) Which of the following correctly explains the covalent modification used to control glutamine synthetase?

A)uridylylation activates, deuridylylation inhibits B)uridylylation inhibits, deuridylylation activates C)adenylation activates, deadenylation inhibits

D)adenylation inhibits, deadenylation activates E)phosphorylation inhibits, dephosphorylation activates

Q2) Which of the following metabolites is elevated as a result of low folate levels and poses a risk for cardiovascular disease?

A)homocysteine

B)methionine

C)5-formyl-THF

D)formate

E)none of the above

Q3) Which of the following is an essential amino acid for humans?

A)alanine

B)serine

C)tyrosine

D)cysteine

E)histidine

Page 22

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Chapter 21: Metabolism of Nitogenous Compounds II:

Amino Acids, Porphyrins, and Neurotransmitters

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Q1) Bilirubin is conjugated with _________ to increase its solubility for excretion.

A)phospholipids

B)glycine

C)glucuronic acid

D)taurine

E)all of the above

Q2) Which of the following molecules derived from tyrosine is correctly defined?

A)dopamine: thyroid hormone

B)dopaquinone: precursor for melanins

C)thyroxine: catecholamine

D)norepinephrine: thyroid hormone

E)all of the above

Q3) Which amino acid utilizes nitrogen and carbon from adenine in the synthesis of its R-group?

A)histidine

B)arginine

C)lysine

D)asparagine

E)all of the above

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Chapter 22: Nucleotide Metabolism

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Q1) What molecule(s)is(are)the source of the two nitrogen atoms for pyrimidine synthesis?

A)asparagine

B)glutamine, glutamate

C)aspartate, carbamoyl phosphate

D)carbamoyl phosphate, glutamine

E)aspartate, glutamate

Q2) Which of the following correctly describes the activity or regulation of E coli ribonucleotide reductase?

A)the overall activity of the enzyme is controlled by ATP and dATP

B)the specificity of the enzyme is controlled by all four dNTPs

C)a tyrosine free radical participates in the reaction

D)the reduction is not a result of simple hydride transfer

E)all of the above

Q3) Which enzyme of the pyrimidine synthesis pathway is the most highly regulated?

A)carbamoyl phosphate synthetase

B)aspartate transcarbamoylase

C)orotate phosphoribosyltransferase

D)UMP kinase

E)nucleoside diphosphate kinase

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Chapter 23: Mechanisms of Signal Transduction

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Q1) In the presynaptic neuron, ______ influx causes neurotransmitter release while in the postsynaptic neuron, ______ enters the cell following opening of ion channels.

A)Na+; K+

B)K+; Na+

C)Ca2+; K+

D)Ca2+; Na+

E)Na+; Ca2+

Q2) Glucocorticoids are thought to function as anti-inflammatory agents since they are able to stimulate the synthesis of what protein?

A)tumor necrosis factor (TNF)

B)platelet-derived growth factor (PDGF)

C)transforming growth factor \(\beta\) (TGF-\(\beta\))

D)nuclear factor-kappa B (NF-\(\kappa\)B)

E)inhibitor-kappa B\(\alpha\) (I\(\kappa\)B\(\alpha\))

Q3) Insulin activates glycogen synthase while glucagon inhibits glycogen synthase. Explain the intracellular mechanisms that are used to bring about this activity.

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Page 25

Chapter 24: Genes, Genomes and Chromosomes

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Q1) What technique is used to amplify portions of DNA, usually about 500 base pairs in size?

A)DNA sequencing

B)polymerase chain reaction

C)cloning

D)restriction digestion

E)electrophoresis

Q2) What structure is responsible for linking the centromeres to the spindle fibers during mitosis?

A)metaphase plate

B)nucleosome

C)kinetochore

D)centromere scaffold

E)none of the above

Q3) What is the typical percentage of lysine + arginine in histone proteins?

A)<5%

B)5-10%

C)10-20%

D)20-35%

E)>35%

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Chapter 25: DNA Replication

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Q1) What feature of the telomerase enzyme allows it to synthesize DNA without the use of a DNA or RNA primer?

A)it synthesizes new DNA in a 3' to 5' direction

B)it contains an RNA oligonucleotide complementary to the telomeric sequence

C)since the telomeric sequence is a 15 base repeat, it is synthesized separately from the replication process and merely sealed in place by the ligase action of telomerase

D)telomeric DNA forms a hairpin that is used to create its own complimentary primer

E)none of the above

Q2) Which of the following DNA polymerases is correctly defined?

A)polymerase I: DNA repair

B)polymerase I: RNA primer excision

C)polymerase II: DNA repair

D)polymerase III: nucleotide incorporation during replication

E)all of the above

Q3) For the following sequence, indicate the RNA primer that would be needed to start synthesis of the Okazaki fragment.

5'-A-A-C-T-A-G-A-C-C-A-G-A-3'

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Chapter 26: DNA Restructuring: Repair, Recombination, Rearrangement, Amplification

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Q1) One mechanism to introduce greater diversity into antibody sequences is somatic hypermutation. What enzyme is responsible for somatic hypermutation in the DNA sequences that code for antibodies?

A)deoxyadenosine deaminase

B)deoxycytidine deaminase

C)deoxyadenosine transaminase

D)purine-pyrimidine transposase

E)none of the above

Q2) In antibody light chain production, combination of V and J regions occurs at the _____ level; combination of J and C regions occurs at the _____ level.

A)DNA; DNA

B)DNA; RNA

C)DNA; protein

D)RNA; RNA

E)RNA; protein

Q3) Show the common base pair seen between 8-oxoguanine and adenine.

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Chapter 27: Information Readout: Transcription and Post-Transcriptional Processing

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Q1) What is required for conversion from the closed-promoter complex to open-promoter complex?

A)ATP binding

B)ATP hydrolysis

C)GTP binding

D)GTP hydrolysis

E)DNA bending

Q2) Give the mRNA sequence that would result from the following sense strand: 5'-A-T-C-T-C-G-A-T-C-G-T-A-C-G-A-T-G-T-C-A-3'

Q3) As RNA polymerase moves along the DNA, it creates a single stranded region of about 18 base pairs that is called a ________________.

A)transcription bubble

B)transcription single-stranded region

C)transcription droplet

D)transcription vesicle

E)transcription bead

Q4) Draw a transcription bubble, clearly labeling the proteins and nucleic acids involved in the process.

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Chapter 28: Information Decoding: Translation and Post-Translational

Protein Processing

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Q1) Which of the following is an intermediate in the reaction catalyzed by aminoacyl-tRNA synthetase?

A)pyrophosphorylated 3' hydroxyl on the tRNA

B)aminoacyl phosphate

C)aminoacyl pyrophosphate

D)aminoacyl adenylate

E)none of the above

Q2) A repetitive mRNA of GAG could produce which of the following?

A)polyglutamate

B)polyleucine

C)polyleucine, polyserine, or polyproline

D)polyarginine, polyglycine or polyglutamate

E)none of the above

Q3) During apoptosis, proteolysis is catalyzed by ______________ enzymes.

A)ubiquitin

B)autophagic lysosomal protease

C)phagocytic protease

D)HSP protease

E)caspase

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Chapter 29: Regulation of Gene Expression

Available Study Resources on Quizplus for this Chatper

25 Verified Questions

25 Flashcards

Source URL: https://quizplus.com/quiz/65207

Sample Questions

Q1) What elements are contained within the promoter of the lactose operon?

A)operator and CRP site

B)operator and repressor

C)CRP site and repressor

D)operator, CRP site and repressor

E)none of the above

Q2) Show how glutamine interacts with an A-T base pair as seen in the cI and Cro repressors.

Q3) Which of the following accounts for the greater complexity in eukaryotic transcriptional control when compared with prokaryotic control?

A)physical separation of transcription from translation

B)the presence of chromatin instead of naked DNA

C)the larger size of the chromosomes

D)the presence of introns

E)none of the above

Q4) Design an antisense RNA that prevents the start of translation for any mRNA in an E. coli cell.

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