CHE 311- Final Exam

The pH of the mitochondrial matrix is ___________, which is ___________ than that of the intermembrane space.

7.9; higher

What is true of the enzyme glycogen phosphorylase, which breaks down glycogen?

It is inhibited by glucose 6-phosphate and by ATP.

In eukaryotic cells, what is the final electron acceptor in the electron transport chain?

O2

(Q006) Which characteristic of a replicating RNA polymerase allows multiple transcripts to be made simultaneously from the same region of DNA?

The RNA transcript dissociates from the DNA template immediately once complete.

(Q022) What can happen if heterochromatin spreads inappropriately into an area with active genes?

The active genes can become silenced.

(Q004) The consistent diameter of the DNA double helix arises because of which property?

base pairing of pyrimidines with purines

(Q020) Shown below is a schematic of an interphase chromosome. Which region is most likely to contain the highest density of genes?

euchromatin between telomere and centromere

How many oxidation reactions occur during the citric acid cycle?

four

(Q009) What performs the function of bacterial sigma factor in eukaryotes?

general transcription factors

The cytochrome complexes contain heme prosthetic groups, which have a higher redox potential than the iron-sulfur centers found in other electron-transport chain complexes like NADH dehydrogenase. Where in the electron-transport chain would the cytochrome complexes thus be located relative to iron-sulfur center complexes?

later in the chain

(Q017) What is the name of the type of damage caused by an improperly paired base in the DNA?

mismatch

(Q020) Which double-strand break repair mechanism is a simple ligation mechanism?

non homologous end joining

(Q003) The type of bond that holds together neighboring subunits in a single strand of DNA is a

phosphodiester bond.

The first step of glycolysis uses one ATP molecule in order to

phosphorylate glucose

(Q008) Eukaryotic repressor proteins can decrease transcription using which of the following mechanisms?

preventing the assembly of the transcription initiation complex

(Q013) What is the name of the protein that binds the two separated DNA strands to keep them from base pairing again before they can be replicated?

single-strand binding protein

(Q016) Which of the following is NOT a common source of DNA damage for cells in our bodies?

soap

The low redox potential of NADH means that it has a

tendency to give up electrons

(Q006) The part of the DNA molecule that carries the information for producing proteins is

the order of the nucleotide bases.

The energy to generate ATP in step 7 of glycolysis comes from which?

the oxidation of glyceraldehyde 3-phosphate

(Q005) Excess amounts of the amino acid tryptophan result in downregulation of the expression of the enzymes required for its synthesis due to

the repressor binding to the operator.

What is gluconeogenesis?

the synthesis of glucose from pyruvate

(Q015) What is a function of the nucleolus?

to assemble ribosomal RNA and proteins into ribosomes

(Q001) The process of gene expression always involves which process(es) described in the central dogma?

transcription

(Q003) Which of the following is the main point of control for regulating gene expression levels?

transcription

Glycolysis produces ___________ ATP molecules, whereas the complete oxidation of glucose to water and carbon dioxide produces ___________ ATP molecules.

two; thirty

the technique that scientists used to determine that hemoglobin was a single large macromolecules rather than a loose conglomeration of small organic molecules was?

ultracentrifugation

how does phosphorylation of a protein affect its activity?

Could increase or decrease activity

When food is plentiful, animals can store glucose as what?

Glycogen

(Q012) In eukaryotes, multiple genes can be expressed simultaneously by

the binding of a specific transcriptional regulator to several genes.

(Q025) DNA is a better molecule for long-term storage of genetic information than RNA because

the deoxyribose sugar stabilizes DNA chains.

What is the function of a kinase?

to add a phosphate group to a molecule

(Q021) Heterochromatin can spread along a chromosome until it encounters a

barrier DNA sequence

(Q002) At which step of gene expression can cells amplify the number of copies of a protein made from a single gene?

both transcription and translation

which method is the most suitable for determining the three-dimensional structure of an extremely large integral membrane protein complex?

cryoelection microscopy

(Q009) The technique whereby human chromosomes are stained and identified is called a

karyotype

(Q022) Protein concentration can be regulated by all of the steps listed EXCEPT

DNA replication.

(Q001) Transplanting the nucleus of an epithelial cell into an egg cell lacking genetic information leads to the formation of

a normally developing embryo.

(Q016) When are chromosomes in their most compacted form?

during mitosis

What is the role of oxygen in the electron transport chain?

electron acceptor

(Q018) What types of bonds are formed between histone proteins and DNA to form nucleosome core particles?

electrostatic interactions

The first living things on Earth probably generated ATP by what mechanism?

fermentation

(Q007) If lactose and glucose are both available to a bacterial cell, which carbon source(s) will be used?

glucose

The food molecule whose breakdown generates most of the energy for a majority of animal cells is

glucose

Individuals with inherited diseases causing mitochondrial dysfunction typically experience which of the following symptoms?

heart problems

Biochemical subcompartments that form inside the nucleus are distinct from their immediate surroundings because of the?

high concentrations of interacting proteins and RNA.

(Q007) The bonds that link two DNA strands together are

hydrogen bonds.

(Q005) If one end of a DNA strand has a phosphate group on it, the chemical group on the other end must be

hydroxyl.

Gluconeogenesis requires a total of ___________ ATP and GTP molecules combined.

six

If cells that cannot carry out fermentation were grown in anaerobic conditions, at which step would glycolysis halt?

step 6: where NAD+ is converted to NADH

In addition to being converted to acetyl CoA for the citric acid cycle, pyruvate made during glycolysis can be used for

synthesis of alanine and fermentation.

Q008) Which of the following is found only in eukaryotic genomes, and NOT in prokaryotic genomes?

telomeres

Why is the presence of oxygen required for the citric acid cycle to operate?

because the NADH passes its electrons to oxygen in the electron transport chain to renew NAD+

(Q002) A housekeeping gene is a gene whose cellular function is

important for processes found in all cell types.

(Q006) In which direction, and on which strands does DNA replication proceed from a replication origin on a chromosome?

in both directions, on both strands

Protons are pumped across the mitochondrial inner membrane to accumulate in the

intermembrane space

What is the fermentation product produced in an anaerobic muscle cell?

lactic acid

(Q013) The reading frame to use for translating an mRNA into functional protein is determined by the

location of an AUG.

(Q010) In the cell, enhancer sequence functions are limited in their range of action by the formation of ___________ that hold specific genes and enhancers in close proximity.

loops

(Q007) Which type of RNA is converted into protein for performing its cellular function?

mRNA

(Q017) Noncoding RNAs include all of the following EXCEPT

mRNA.

(Q018) MicroRNAs block the expression of a specific gene product by binding to the ___________ and inhibiting ___________.

mRNA; translation

Which of the following correctly matches the cellular location with the production of ATP by oxidative phosphorylation in that cell type?

plasma membrane—bacteria

(Q016) The control of a gene product's levels or activity after transcription has taken place is called

post-transcriptional control.

(Q004) Mutations in which of the following elements would abrogate RNA polymerase's ability to activate gene expression?

promoter

(Q020) What is the name of the complex that degrades proteins that have reached the end of their lifespan, are damaged, or are misfolded?

proteasome

(Q020) Long noncoding RNA (lncRNA) can function as a(n)

protein scaffold.

How is pyruvate imported into the mitochondrial matrix for use in the citric acid cycle?

proton gradient-driven symport

(Q009) Which of the following mechanisms describes how eukaryotic activator proteins can regulate chromatin packaging to enhance transcription?

recruiting chromatin-remodeling complexes to eject or slide nearby nucleosomes

Chlorophyll appears green because it ________ light.

reflects green light.

(Q010) The splicing of introns out of an mRNA molecule is catalyzed by

RNA molecules that base pair with the splice sites to promote intron removal.

(Q005) Why does RNA polymerase make more mistakes than DNA polymerase?

RNA polymerase does not have proofreading activity.

(Q012) The information in an mRNA molecule is converted into protein sequence using

three consecutive bases, with no overlap between triplets.

Shown is a chloroplast with labeled structures. The photosynthetic machinery is found in which of the compartments shown?

thylakoid membrane

During glycolysis, the number of ATP consumed (per glucose molecule) is ___________, while the number produced is ___________.

two; four

Which of the following is a mobile electron carrier in the electron-transport chain?

ubiquinone

(Q006) Generally, bacterial promoters that are regulated by transcriptional activators bind ___________ to RNA polymerase on their own, but promoters that are regulated with transcriptional repressors bind ___________ to RNA polymerase.

weakly; strongly

(Q005) The sequence at which DNA replication begins tends to have which characteristic?

AT-rich

Which of the following has the lowest electron affinity?

NADH dehydrogenase complex

In what form do plant and animal cells store fat?

Triacylglycerol

When nutrients are plentiful, plants can store glucose as what?

Starch

When fatty acids are oxidized to produce acetyl CoA, each cycle of the reaction removes how many carbon atoms from the fatty acid molecule?

2

From one glucose molecule, how much net energy (in the form of ATP and NADH) is produced during glycolysis?

2 ATP, 2 NADH

When ATP is abundant, which processes are likely to occur?

Glycogen synthesis, gluconeogenesis

What type of enzyme catalyzes the rearrangement of chemical bonds within a single molecule?

Isomerase

Where does the oxidative (oxygen-dependent) stage of the breakdown of food molecules occur in a eukaryotic cell?

Mitochondrion

How do enzymes maximize the energy harvested from the oxidation of food molecules?

They allow the stepwise oxidation of food molecules, which releases energy in small amounts.

Fatty acids can be used to produce energy by conversion to ___________ in the ___________ of the cell.

acetyl CoA; mitochondria

How does binding of GTP and GTP-binding protein affect this activity?

always activates the protein.

(Q015) How do tRNAs become attached to the correct amino acid?

aminoacyl-tRNA synthetases

(Q014) A transcriptional regulator that activates expression of additional transcriptional regulators that induce production of a particular cell type or organ is called a

master regulator.

The proton flow through the transmembrane H+ carrier of ATP synthase results in

mechanical rotation that is converted into the chemical-bond energy of ATP.

(Q018) What recognizes the stop codons in an mRNA?

release factor

(Q012) What is the name of the enzyme that fills the sequence gaps after primers are removed from a newly synthesized DNA strand?

repair polymerase

(Q004) What is the name of the DNA sequence where replication begins?

replication origin

(Q008) The energy for the polymerization reaction in DNA synthesis is powered by

the breaking of high-energy phosphate bonds in the deoxynucleotides.

(Q002) When Griffith injected heat-killed infectious bacteria mixed with live harmless bacteria, he found that the mice died because

the live harmless bacteria were transformed into infectious bacteria.

The number of ATP molecules that could be synthesized from the energy released by the transfer of two electrons from NADH to molecular oxygen is ___.

2.5

Glycolysis alone captures approximately what percentage of the free energy available in a molecule of glucose?

10%

(Q010) Which of the following describes the chromosomal makeup of a somatic cell of a human biological male?

22 pairs of autosomes + 1 X chromosome + 1 Y chromosome

Which of the numbers represents the most permeable membrane of the mitochondrion?

3 outer membrane

(Q001) If a stretch of DNA on the parental strand of a replicating chromosome has the sequence 5′-AGCTCGATCGGCTA-3′, what will the sequence of the newly synthesized strand made from this stretch of template be?

3′-TCGAGCTAGCCGAT-5′

(Q011) Export of RNA from the nucleus requires the RNA to have which characteristic(s)?

5′ cap and poly-A tail

In the presence of high levels of ___________, the enzyme phosphofructokinase is inhibited.

ATP

Most of the energy released by oxidizing glucose is saved in the high-energy bonds of what molecules?

ATP and other activated carriers

Which of the following are required for glycolysis to take place?

ATP, ADP, NAD+, and Pi

Stage two of photosynthesis (or the light-independent reactions) uses which input molecules to produce organic food molecules?

ATP, NADPH, CO2

Which two-carbon molecule enters the citric acid cycle?

Acetyl CoA

The citric acid cycle converts the carbon atoms in acetyl CoA to which of the following?

CO2

The major products of the citric acid cycle are

CO2 and NADH

Each molecule of acetyl-CoA entering the citric acid cycle produces two ___________ and four ___________.

CO2; activated carriers

(Q010) How does Polymerase help maintain the accuracy of DNA replication?

DNA polymerase can cut out improperly base-paired nucleotides and add the correct one during synthesis.

(Q004) Which of the following is a difference between the mechanisms of DNA polymerase and RNA polymerase?

DNA polymerase needs a base-paired 3′ −OH for a polymerization reaction to occur; RNA polymerase can polymerize two nucleotides without a base-paired 3′ −OH.

Which of the following processes generates the largest number of ATP molecules?

Electron transport chain

Why do cells use enzymes to harvest energy from food molecules rather than by direct oxidation?

Enzymes transfer energy from food to carrier molecules in small steps.

After an overnight fast, most of the acetyl CoA entering the citric acid cycle is derived from what type of molecule?

Fatty amino

Under anaerobic conditions, which metabolic pathway regenerates the supply of NAD+ needed for glycolysis?

Fermentation

How do fermentation reactions in oxygen-starved muscle cells and anaerobically grown yeast cells differ?

Fermentation in muscle cells produces lactate and in yeast produces ethanol plus CO2.

Useful energy is obtained by cells when sugars derived from food are broken down by which processes?

Glycolysis, the citric acid cycle, and oxidative phosphorylation

In the electron transport chain, the oxygen atoms in O2 become part of which of the following molecules?

H2O

(Q019) How does methylation of histone tails affect the accessibility of DNA?

It can have different effects depending on the location.

Which is true of gluconeogenesis?

It consumes four molecules of ATP and two molecules of GTP to produce one molecule of glucose.

(Q001) Which of the following is a function of the protein component of chromosomes?

It packages the DNA strands

(Q013) A reporter gene is an experimentally engineered regulatory DNA sequence from a gene of interest that has been fused to a gene that encodes a protein that is easily observed experimentally. Why is this approach useful?

It provides information into where and when a gene is expressed.

(Q014) What is the function of a topoisomerase in DNA replication?

It relieves the tension in DNA strands.

What is true of the phosphorylation of glucose in step 1 of glycolysis?

It traps the sugar inside the cell.

(Q012) What is the relationship between genome size and organismal complexity?

More complex organisms generally have larger genomes but there are many notable exceptions.

(Q019) What is the benefit of protein synthesis in polyribosomes?

More protein can be produced from a single RNA.

The citric acid cycle produces which activated carriers that transfer high-energy electrons to the electron-transport chain?

NADH and FADH2

If cells were undergoing glycolysis but could not carry out fermentation, what products would build up in the cytosol?

NADH and pyruvate

(Q013) Which of the following is true about "junk DNA"?

Portions of junk sequence are conserved between species and thus may be functional.

(Q019) Which protein complex mediates the RNAi silencing process by inhibiting RNA polymerase via histone methylation and heterochromatin formation?

RITS

(Q003) Which nucleic acid often base pairs with itself to fold into complex three-dimensional shapes in the cell?

RNA

(Q023) Which of the following properties could help RNA be both an information storage unit and a self-replicating molecule?

RNA can act as a template for making copies of itself.

(Q017) The catalytic sites for peptide bond formation during translation is found in which part of the ribosome?

large subunit RNAs

Chemical modification likes phosphorylation and acetylation of proteins occur on ________ of amino acids and can affect interaction of proteins with other cell components or structures?

Side Chains.

Co2 is released in which steps of the citric acid cycle?

Steps 3 and 4

Cytochrome c oxidase catalyzes the reaction that reduces molecular oxygen (two oxygen atoms) to two water molecules. The electrons are added sequentially, and during the process cytochrome c oxidase must bind the oxygen tightly in the active site. Why?

Superoxide radicals are formed as an intermediate, and are dangerous to the cell.

(Q018) What is the first step that must occur to repair damage on one strand of the double helix?

The damaged region must be removed.

The NADH generated during glycolysis and the citric acid cycle feeds its high-energy electrons to which of the following?

The electron transport chain

Shown below is the ATP hydrolysis cycle of a motor protein. What sentence BEST describes the state of the motor protein in "C"?

The hydrolysis of ATP and ADP caused a conformational change in the protein.

What does it mean for a bond to be "high energy," such as the bonds between phosphate groups in ATP?

The hydrolysis of the bond is energetically favorable.

(Q019) In bacteria, how does the cell recognize which strand is the newly synthesized strand and thus contains the mismatch?

The newly synthesized strand is unmethylated.

(Q011) How are the primers from which DNA synthesis starts different from the DNA itself?

The primers are made up of RNA not DNA.

In eukaryotic cells, why must metabolism be tightly regulated?

The substrates involved in metabolic reactions can be used by a number of different enzymes.

(Q024) Why is RNA thought to predate DNA in evolution?

The sugar in RNA is easier to make with the organic molecules that were present on primitive Earth.

How do the high-energy electrons of activated carriers contribute to forming the high-energy phosphate bonds of ATP?

They are used by the electron-transport chain to make a proton gradient.

(Q011) ___________ is a sequence of DNA that contains the information required for making a particular functional RNA or protein.

a gene

(Q021) Single nucleotide changes from unrepaired DNA damage that lead to uncontrolled cell division can lead to which of the following conditions?

cancer

(Q014) Which of the following specialized DNA sequences provides an attachment point for the segregation of duplicated chromosomes?

centromeres

In oxidative phosphorylation in mitochondria, high-energy electrons are transferred to the electron-transport chain from activated carriers like NADH. Stage 1 of photosynthesis also uses an electron-transport chain to pump protons and make ATP. In this case, where do the high-energy electrons come from?

chlorophyll

(Q011) Many transcriptional regulators function together to decide the expression level of a particular gene. This describes the concept of

combinatorial control.

(Q007) The structural feature of DNA that hints at the mechanism for its replication is the

complementary base pairing

(Q002) Meselson and Stahl performed a classic experiment to explore three models for the mechanism of DNA replication. Which of the models held that the two parental strands would remain associated after replication?

conservative

(Q003) Using the technique shown below, Meselson and Stahl did an experiment where they grew cells in heavy medium for many generations, then after a single generation in light medium, they observed a single band of intermediate weight after centrifugation. This experiment ruled out which model of DNA replication?

conservative

Glycogen synthetase enzyme, which forms glycogen from glucose, is activated by excess

glucose 6-phosphate

transfer of a phosphate from which molecule to ADP is energetically UNFAVORABLE?

glucose 6-phosphate