BIO353 Exam 2

What is NOT the function of a kinase? 1) an enzyme that catalyzes the rearrangement of bonds within a single molecule 2) an enzyme that catalyzes a change in the position of a specific chemical group within a single molecule 3) an enzyme that catalyzes the oxidation of a molecule by removing a hydride ion 4) an enzyme that catalyzes the addition of phosphate groups to other molecules

1, 2, 3

What processes do take place in the mitochondria? 1) citric acid cycle 2) conversion of pyruvate to activated acetyl groups 3) oxidation of fatty acids to acetyl CoA 4) glycolysis

1, 2, 3

Which of the following statements about the proteasome is TRUE? 1) Ubiquitin is a small protein that is covalently attached to proteins to mark them for delivery to the proteasome. 2) Proteases reside in the central cylinder of a proteasome. 3) Misfolded proteins are delivered to the proteasome, where they are sequestered from the cytoplasm and can attempt to refold. 4) The protein stoppers that surround the central cylinder of the proteasome use the energy from ATP hydrolysis to move proteins into the proteasome inner chamber.

1, 2, 4

Which of the following does describes a mechanism of post-translational control of gene expression? 1) the alternative splicing of a gene, leading to the production of a muscle-specific protein 2) the action of gene-specific transcription factors in binding to proximal control elements of the promoter 3) the activation of a protein when it is phosphorylated by a protein kinase 4) translational inhibition of an mRNA by the binding of a protein at the 5´ untranslated region of the message.

1, 3, 4

The human genome is a diploid genome. However, when germ-line cells produce gametes, these specialized cells are haploid. What is the total number of chromosomes found in each of the gametes (egg or sperm) in your body?

23

Which of the following DNA strands can form a DNA duplex by pairing with itself at each position? 5´-AAGCCGAA-3´ 5´-AAGCCGTT-3´ 5´-AAGCGCAA-3´ 5´-AAGCGCTT-3´

5´-AAGCGCTT-3´

Intron

A noncoding, intervening sequence within a eukaryotic gene.

What best describes the phosphorylation event that occurs during the process known as "oxidative phosphorylation"?

A phosphate group is added to ADP

TRUE or FALSE: There are two major stages of photosynthesis: (1) Light Reactions, in which light drives the formation of small energy carrying molecules and (2) Dark reactions, in which carbon assimilation reactions occur in a light-independent manner.

False (don't call them Dark reactions)

The complete set of information in an organism's DNA is called its

Genome

Which of the following processes do NOT take place in the mitochondria? citric acid cycle conversion of pyruvate to activated acetyl groups oxidation of fatty acids to acetyl CoA glycolysis

Glycolysis

Which of the following processes do NOT take place in the mitochondria? 1) citric acid cycle 2) conversion of pyruvate to activated acetyl groups 3) oxidation of fatty acids to acetyl CoA 4) glycolysis

Glycolysis

During Stage 2 of oxidative phosphorylation, ATP synthesis is powered by movement of __________ ions through the _________

H+; ATP synthase

At first glance, it may seem that living systems are able to defy the second law of thermodynamics. However, on closer examination, it becomes clear that although cells create organization from raw materials in the environment, they also contribute to disorder in the environment by releasing....

Heat

Electron carriers in the ETS of respiration are arranged _____.

In such a way that the amount of energy released by the oxidation of the preceding carrier is more than the energy required for the reduction of the subsequent carrier.

Pros of Introns

Increase the coding potential of the cell's genome via alternative splicing: More than one pattern of splicing can occur for a single RNA. ("Alternate splicing"). Speeds up the emergence of new proteins during evolution

Why is ATP uniquely qualified as the currency of energy exchange?

It carries two high-energy phosphoanhydride bonds AND It occupies an intermediate position in the bond energy cascade.

Which of the following statements describes the mitochondrial outer membrane?

It is permeable to molecules with molecular mass as high as 5000 Daltons

Pigment

Light-absorbing molecule

Which of the following statements about the proteasome is FALSE? 1) Ubiquitin is a small protein that is covalently attached to proteins to mark them for delivery to the proteasome. 2) Proteases reside in the central cylinder of a proteasome. 3) Misfolded proteins are delivered to the proteasome, where they are sequestered from the cytoplasm and can attempt to refold. 4) The protein stoppers that surround the central cylinder of the proteasome use the energy from ATP hydrolysis to move proteins into the proteasome inner chamber.

Misfolded proteins are delivered to the proteasome, where they are sequestered from the cytoplasm and can attempt to refold. (***Once proteins are sent to the proteasome, proteases degrade them. Chaperone proteins provide a place for misfolded proteins to attempt to refold.***)

Pyruvate can be converted into many other molecules by various biosynthetic and metabolic pathways, which makes it a central hub in the regulation of cellular metabolism. Which of the following molecules is NOT made from pyruvate? oxaloacetate ethanol lactate NADH

NADH (***Pyruvate cannot be converted into NADH, but it can be converted into the other metabolites in one or two steps.***)

The most abundant energy-rich small molecules (activated carriers) produced by the TCA cycle (tricarboxylic acid cycle OR citric acid cycle) are _________.

NADHs

Even though cellular macromolecules contain a large number of carbon and hydrogen atoms, they are not all spontaneously converted into CO2 and H2O. This absence of spontaneous combustion is due to the fact that biological molecules are relatively __________ and an input of energy is required to reach lower energy states

Stable

Euchromatin

The less condensed form of eukaryotic chromatin that is available for transcription and expresses genes (and therefore proteins).

Which of the following cells rely exclusively on glycolysis to supply them with ATP? anaerobically growing yeast aerobic bacteria skeletal muscle cells plant cells

anaerobically growing yeast (****All the other cells can perform oxidative phosphorylation to generate additional ATP.****)

You are a virologist interested in studying the evolution of viral genomes. You are studying two newly isolated viral strains and have sequenced their genomes. You find that the genome of strain 1 contains 25% A, 55% G, 20% C, and 10% T. You report that you have isolated a virus with a single-stranded DNA genome. Based on what evidence can you make this conclusion?

because double-stranded genomes have equal amounts of A and T

Plastocyanin (PC)

blue-colored, hydrophilic, and water soluble protein

The energy used by the cell to generate specific biological molecules and highly ordered structures is stored in the form of......

chemical bonds

Which of the following steps or processes in aerobic respiration include the production of carbon dioxide?

conversion of pyruvate to acetyl CoA (**One carbon is oxidized and released as carbon dioxide when pyruvate is converted to acetyl CoA**)

miRNAs, tRNAs, and rRNAs all _________

do not code for proteins

Photoexcitation

electrons in a pigment molecule transfer from low energy ground state to a high-energy orbital excited state by absorbing photon energy

The advantage to the cell of the gradual oxidation of glucose during cellular respiration compared with its combustion to CO2 and H2O in a single step is that

energy can be extracted in usable amounts (***The amount of free energy released by glucose oxidation is the same as combustion, and the amount of CO2 released is the same.****)

Catalysts are molecules that lower the activation energy for a given reaction. Cells produce their own catalysts, called _________

enzymes

In the absence of oxygen, yeast cells can switch to a completely anaerobic metabolism called fermentation. Which of the following is a final product of fermentation in yeast? a) lactate b) ethanol c) acetaldehyde d) pyruvate

ethanol (OH-H2C-CH3)

What chemical groups are used to construct a DNA molecule?

five-carbon sugar, phosphate, nitrogen-containing base

Photosystems

functional unit of light reactions containing an antenna complex and a reaction center complex, which consist of chlorophylls, accessory pigments, and associated proteins

The N-terminal tail of histone H3 can be extensively modified, and depending on the number, location, and combination of these modifications, these changes may promote the formation of heterochromatin. What is the result of heterochromatin formation?

gene silencing

Which of the following polymers of glucose is used as a vehicle to store energy reserves in animal cells glucagon glycogen starch glycerol

glycogen

Reaction Center

has a "special pair" of chlorophylls that convert solar energy into chemical energy by transferring electrons from the chlorophyll to an electron acceptor molecule (by photoreduction).

Plastoqunione (Q)

hydrophobic and lipid soluble quinone (small molecule)

The concentration of H+ ions inside the mitochondrial matrix is lower than it is in the cytosol or the mitochondrial intermembrane space. What would be the IMMEDIATE effect of a membrane-permeable compound that carries and releases protons into the mitochondrial matrix?

inhibition of ATP synthesis

Cytochrome B6/f complex

integral membrane proteins anchored to thylakoid membranes

Total nucleic acids are extracted from a culture of yeast cells and are then mixed with resin beads to which the polynucleotide 5´-TTTTTTTTTTTTTTTTTTTTTTTTT-3´ has been covalently attached. After a short incubation, the beads are then extracted from the mixture. When you analyze the cellular nucleic acids that have stuck to the beads, which of the following is most abundant?

mRNA (***mRNA is the only type of RNA that is polyadenylated, and its poly-A tail would be able to base-pair with the strands of poly T on the beads and thus stick to them. DNA would not be found in the sample, because the poly-A tail is not encoded in the DNA and long runs of T are rare in DNA.***)

Which of the following statements about miRNAs is FALSE? One miRNA can regulate the expression of many genes. miRNAs are transcribed in the nucleus from genomic DNA. miRNAs are produced from rRNAs. miRNAs are made by RNA polymerase.

miRNAs are produced from rRNAs

The DNA from two different species can often be distinguished by a difference in the

ratio of A + T to G + C

Which of the following chemical groups is NOT used to construct a DNA molecule?

six-carbon sugar

Which of the following examples does NOT describe a mechanism of post-transcriptional control of gene expression? the alternative splicing of a gene, leading to the production of a muscle-specific protein the action of gene-specific transcription factors in binding to proximal control elements of the promoter the activation of a protein when it is phosphorylated by a protein kinase translational inhibition of an mRNA by the binding of a protein at the 5´ untranslated region of the message.

the action of gene-specific transcription factors in binding to proximal control elements of the promoter

Exon

the coding sequences which is expressed in the final mRNA

A neuron and a white blood cell have very different functions. For example, a neuron can receive and respond to electrical signals, while a white blood cell defends the body against infection. This is because

the neuron expresses some mRNAs that the white blood cell does not (***Different cell types express different mRNAs, leading to differences in protein expression. There are proteins common to all cells in multicellular organisms. Although it is true that the neuron and white blood cell within an individual have the same genome, this does not explain why these two cells have different functions. Differentiated cells still need to transcribe and translate genes.***)

photoreduction

the transfer of the photoexcited electron itself from one molecule to a high-energy orbital of another molecule

The distinct characteristics of different cell types in a multicellular organism result mainly from the differential regulation of the

transcription of genes transcribed by RNA polymerase II (***The major cause of differences between different cell types is in the differential expression of protein-coding genes transcribed by RNA polymerase II, because these genes encode, not only the specific proteins characteristic of different cell types, but also the transcription regulators required to maintain and control this pattern of expression. All genes are replicated equally when cells divide. The expression of housekeeping genes does not differ much from cell to cell, because they mainly encode the proteins that are necessary for all cells to live. The general transcription factors bind to the TATA box and do not mediate differential gene expression.***)

Which of the following structural characteristics is NOT normally observed in a DNA duplex?

uniform left-handed twist

Although the chromatin structure of interphase and mitotic chromosomes is very compact, DNA-binding proteins and protein complexes must be able to gain access to the DNA molecule. Chromatin-remodeling complexes provide this access by

using the energy of ATP hydrolysis to move nucleosomes

Cons of Introns

wasteful: both material and energy wise.

Fatty acids can easily be used to generate energy for the cell. Which of the following fatty acids will yield more energy? A) H3-CH2-CH2-CH2-CH2-CH2-CH2-CH = CH-COOH B) CH3-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-COOH C) CH3-CH = CH-CH2-CH2-CH2-CH2-CH = CH-COOH D) CH3-CH2-CH2-CH2-CH2-CH2-CH2-COOH

B. (***This fatty acid has 10 carbons and has a completely saturated hydrocarbon tail. The total number of carbons determines how many acetyl CoA molecules can be derived from it; in this case it is 5. The fact that all hydrocarbon bonds are saturated means that an FADH2 molecule will be generated in the first step of the fatty acid cycle, converting a carbon-carbon single bond into a carbon-carbon double bond. If that bond is already reduced, the cycle begins at the second step. As a result, FADH2 is not generated in that cycle, lowering the total number of cofactors that can be used by the electron-transport chain to generate a proton gradient.***)

During respiration, energy is retrieved from the high-energy bonds found in certain organic molecules. Which of the following, in addition to energy, are the ultimate products of respiration?

CO2 and H2O

Oxidation is a favorable process in an aerobic environment, which is the reason cells are able to derive energy from the oxidation of macromolecules. Once carbon has been oxidized to __________, its most stable form, it can only cycle back into the organic portion of the carbon cycle through __________

CO2, Photosynthesis

Of all the biological molecules containing high-energy phosphate bonds, which one is the key driver of most phosphorylation reactions and the transfer of metabolic energy?

ATP (adenosine triphosphate)

Which of the following is NOT part of the process known as "oxidative phosphorylation"? 1) Molecular oxygen serves as a final electron acceptor. 2) FADH2 and NADH become oxidized as they transfer a pair of electrons to the electron-transport chain. 3) The electron carriers in the electron-transport chain toggle between reduced and oxidized states as electrons are passed along. 4) ATP molecules are produced in the cytosol as glucose is converted into pyruvate.

ATP molecules are produced in the cytosol as glucose is converted into pyruvate. (***During glycolysis, ATP generation occurs simultaneously with two of the key reactions that convert glucose to pyruvate in the cytosol. This production of ATP in the absence of oxygen is not part of oxidative phosphorylation; it is referred to as "substrate-level phosphorylation.***)

The TCA cycle enzymes are primarily regulated via _______ regulation.

Allosteric

What best describes the function of a kinase?

An enzyme that catalyzes the addition of phosphate groups to other molecule

Pyruvate is an important metabolic intermediate that can be converted into several other compounds, depending on which enzyme is catalyzing the reaction. Which of the following CANNOT be produced from pyruvate in a single enzyme-catalyzed reaction? lactate oxaloacetate citrate alanine

Citrate

Glycolysis occurs in __________, producing the product of __________, and produces __________ ATPs per glucose (net gain) molecule.

Cytosol, Pyruvate, Two

In a DNA double helix, the two _______ run __________

DNA strands; antiparallel

How does the cell determine which parts of the RNA transcript to remove during splicing?

Each intron contains a few short nucleotide sequences that act as cues for its removal. These sequences are found at or near each end of the intron. The cutting is done by snRPS

The second law of thermodynamics states that the disorder in any system is always increasing. In simple terms, you can think about dropping NaCl crystals into a glass of water. The solvation and diffusion of ions is favored because there is an increase in......

Entropy (Delta S)

A chemical reaction is defined as spontaneous if there is a net loss of free energy during the reaction process. However, spontaneous reactions do not always occur rapidly. Favorable biological reactions require __________ to selectively speed up reactions and meet the demands of the cell

Enzymes

Heterochromatin

Eukaryotic chromatin that remains highly compacted during interphase and is generally not transcribed.

TRUE or FALSE: ATP produced by the light reactions of photosynthesis can be transported out of the chloroplast for driving otherwise endergonic reactions in the cytosol.

FALSE

TRUE or FALSE: All photo-excited chlorophylls and accessory pigments can transfer their excited electrons to the high-energy orbital of another molecule.

False

TRUE or FALSE: There are two major stages of photosynthesis: (1) Light Reactions, in which light drives the formation of small energy-carrying molecules and (2) Dark Reactions, in which carbon assimilation reactions occur in a light-independent manner.

False

Overall, DNA and RNA molecules carry _____ charge due to the phosphate groups in their backbones.

Negative

Glycolysis is an anaerobic process used to catabolize glucose. What does it mean for this process to be anaerobic?

No oxygen is required (***Glycolysis takes place in the cytosol, and although oxidation of glucose is taking place, no molecular oxygen is used.***)

Which of the following stages in the breakdown of the piece of toast you had for breakfast generates the most ATP?

Oxidative phosphorylation (produces about 28 molecules of ATP)

Location of P700 chlorophylls

PSI

Location of P680 chlorophylls

PSII

What photosystem produces oxygen?

PSII

What type of macromolecule helps package DNA in eukaryotic chromosomes

Proteins

The final metabolite produced by glycolysis is ___________.

Pyruvate

DNA is an information storage molecule, whose sequences serve as a template to make _______

RNA

You are studying a disease that is caused by a virus, but when you purify the virus particles and analyze them you find they contain no trace of DNA. Which of the following molecules are likely to contain the genetic information of the virus?

RNA

How are introns removed?

RNA splicing

The purpose of fermentation is to _________.

Regenerate NAD+ so the cell can keep glycolysis going to generate more ATP in the absence of oxygen.

The enzyme that catalyzes the first step of CO2 fixation is_______________.

Rubisco (RuBP)

In Stage 2 of carbon assimilation reactions ATP and NADPH are used to reduce 3-phosphoglycerate into glyceraldehyde 3-phosphate. These reactions are ________ reactions of steps 6-7 in glycolysis

The reverse

Which of the following does not occur before a eukaryotic mRNA is exported from the nucleus?

The ribosome binds to the mRNA (***Ribosomes are in the cytosol and will bind to the mRNA once it has been exported from the nucleus.***)

What makes P680 and P700 special?

They can absorb photons to dramatically change their free energy levels and transfer excited (energized) electrons to an electron acceptor

Photosynthesis is a process that takes place in chloroplasts and uses light energy to generate high-energy electrons, which are passed along an electron-transport chain. Where are the proteins of the electron-transport chain located in chloroplasts?

Thylakoid membrane

In stage 1 of photosynthesis, a proton gradient is generated and ATP is synthesized. Where do protons become concentrated in the chloroplast?

Thylakoid space

Regulation of gene expression in prokaryotic cells occurs mainly at the level of _______.

Transcription

In eukaryotes, the primary protein factor that selects the template DNA strand for RNA transcription is______

Transcription Factors

Resonance Energy Transfer (RET)

Transfer of excitation energy from one photoexcited electron to an electron in an adjacent pigment molecule

TRUE or FALSE: In reality, the ratio of NADPH/ATP produced by the light reaction is NOT always 1:1.

True

TRUE or FALSE: Plants cannot use chloroplast to replace mitochondria to supply their ATP needs.

True

According to current thinking, the minimum requirement for life to have originated on Earth was the formation of a

molecule that could catalyze its own replication (***Although providing a template is an important step in self-replication, it would not by itself be sufficient. Being a double-stranded DNA helix and being a molecule that could direct protein synthesis are likely stages in the evolution of the cell that must have succeeded the formation of the first self-replicating molecules.***)

How does the ubiquitin protein get degraded in the cell?

piggybacks with payload or identifies itself as a damaged protein

Antenna Complex

pigments that absorb photons and pass energy to neighboring pigments, eventually to the reaction center complex (by RET).

Osmosis describes the movement of water across a biological membrane and down its concentration gradient. In chemiosmosis, useful energy is harnessed by the cell from the movement of __________ across the inner mitochondrial membrane into the matrix __________ a concentration gradient

protons, down

What structural characteristics are normally observed in a DNA duplex?

purine-pyrimidine pairs, external sugar-phosphate backbone, antiparallel strands