Cell Molec Exam 3: Study Guide Questions

Protein structures have several different levels of organization. The primary structure of a protein is its amino acid sequence. The secondary and tertiary structures are more complicated. Consider the definitions below and select the one that best fits the term "protein domain." A. A small cluster of a helices and b sheets B. The tertiary structure of a substrate binding pocket C. A complex of more than one polypeptide chain D. A protein segment that folds independently E. The smallest portion of a protein capable of inducing formation of antibodies

A protein segment that folds independently

Which inhibitor is mismatched with the reaction it may interfere with? A. Cyanide inhibits cytochrome c oxidase, preventing electron transport in mitochondria B. Penicillin competes with small peptides of the bacterial cell wall C. Alanine is non-competitive inhibitor of pyruvate kinase in glycolysis D. Lithium is an uncompetitive inhibitor of inositol monophosphatase in the brain E. Alanine inhibits hexokinase in the brain in a non-competitive manner

Alanine inhibits hexokinase in the brain in a non-competitive manner

How are most eukaryotic transcription regulators able to affect transcription when their binding sites are far from the promoter? A. by binding to their binding site and sliding to the site of RNA polymerase assembly B. by looping out the intervening DNA between their binding site and the promoter C. by unwinding the DNA between their binding site and the promoter D. by attracting RNA polymerase and modifying it before it can bind to the promoter

B. by looping out the intervening DNA between their binding site and the promoter

The letter E indicates A. A purine-purine base pairing. B. A pyrimidine-pyrimidine base pairing. C. The adenine-thymine base pair. D. The guanine-cytosine base pair. E. None of the abov

C. The adenine-thymine base pair.

The piece of RNA below includes the region that codes for the binding site for the initiator tRNA needed in translation. 5′-GUUUCCCGUAUACAUGCGUCUGGGGAAG-3′ What is the amino acid sequence encoded by the first codons in this mRNA? A. Phe-Pro-Tyr-Thr-Cys-Val-Trp-Gly B. Glu-Gly-Ser-Ala-His-Ile-Arg-Ser-Val C. Val-Ser-Arg-Ile-His-Ala-Ser-Gly-Glu D. Met-Arg-Leu-Gly-Lys

C. Val-Ser-Arg-Ile-His-Ala-Ser-Gly-Glu

in eukaryotic cells, DNA is not "naked," but associated with proteins, especially histones, forming chromosomes. Mutations in eukaryotic cells consist not only of changes in DNA sequence, but also may appear when the number of chromosomes is affected (i.e., some chromosomes are missing or some chromosomes are present inextra numbers). What is the term that describes an incorrect number of chromosomes in the cells of an organism? A. aberration B. non-disjunction C. aneuploidy D. rupture E. None of these

C. aneuploidy

Which letter points to a 5'-phosphate deoxyribose molecule? A. B. C. D. E

D

Match the term with the number of chromosomes per cell type. A. Haploid _____ i. n chromosomes in both somatic cells and gametes B. Diploid _____ ii. somatic cells have multiples (x) of n (xn) chromosomes; gametes have xn/2 C. Monoploid _____ iii. n chromosomes in gametes D. Polyploid _____ iv. 2n chromosomes in somatic cells

Haploid= n chromosomes in gametes Diploid= 2n chromosomes in somatic cells Monoploid= somatic cells have multiples (x) of n (xn) chromosomes; gametes have xn/2? polyploid= n chromosomes in both somatic cells and gametes?

Drawn below are segments of β sheets, which are rigid pleated structures held together by hydrogen bonds between the peptide backbones of adjacent strands. The amino acid side chains attached to the a-carbons areomitted for clarity. For panel (A) and for panel (B), indicate whether the structure is parallel or antiparallel. Draw the hydrogen bonds as three dots (• • •)

I is parallel and ii is anti parallel

Refer to the transcription bubble diagram (above) to fill in the blanks. ______ 5'- ______ 3'- ______ Template strand/Sense strand_ _____ Coding strand/Antisense strand ______ Region of DNA unwinding ______ Region of DNA rewinding

I, vi, ii, iv, v, iii

Which of the following statements is true? A. Peptide bonds are the only covalent bonds that can link together two amino acids inproteins .B. The polypeptide backbone is free to rotate about each peptide bond. C. Nonpolar amino acids tend to be found in the interior of proteins. D. The sequence of the atoms in the polypeptide backbone varies between differentproteins.

Nonpolar amino acids tend to be found in the interior of proteins.

Recall the definition of an antigen as a molecule (or particle) that can induce the formation of specific molecules called antibodies in an organism. Find the incorrect statement. A. A protein molecule usually has many antigenic regions called epitopes. B. A mammal injected with proteins from an individual from a different species will produce antibodies with more efficiency if it is injected with antigens from another species. C. An antibody specially produced against a single epitope is called "monoclonal." D. Generally speaking, lipids and nucleic acids are as effective antigens as proteins and carbohydrates. E. A serum from an animal injected with a molecule with multiple epitopes will contain "polyclonal antibodies

a mammal injected with proteins from an individual from a different species will produce antibodies with more efficiency if it is injected with antigens from another species.

match the types of RNAs with the main polymerase that transcribes them Most rRNA genes_____ 5S rRNA genes_____ tRNA genes_____ protein-coding genes (mRNA)_____ miRNA genes A. RNA polymerase I B. RNA polymerase II C. RNA polymerase III

a, c, c, b, b

Which of the following is not a feature commonly observed in β sheets? A. antiparallel regions B. coiled-coil patterns C. extended polypeptide backbone D. parallel regions

coiled-coil patterns

What equation (below) represents the last step of oxidative phosphorylation? Recall that cyt c ox represents oxidized cyt c and cyt cred indicates the reduced form of cyt c. A. cyt cox + glucose ⇌ cyt cred + CO2 B. cyt cred + O2 ⇌ cyt cox + H2 O C. cyt cox + e- + H+ ⇌ cyt cred + H2 D. cyt cox + O2 ⇌ cyt cred + H2 O E. cyt cred + H2 O ⇌ cyt cox + O

cyt cred +O2--> cyt cox +H2O

What is the difference between intermolecular and intramolecular disulfide bridges and how do they stabilize the quaternary structure of proteins such as immunoglobulins

Intramolecular bonds impart stability to the naive structure of a protein and decrease amyloid aggregation, whereas intermolecular disulfide bonds aid in the process of aggregation

Insulin forms part of the primary signaling system of higher organisms. How does it interact with the intracellular signal transduction pathways? A. It binds a receptor on the surface of cells of a target organ or tissue. B. It enters the cell and interacts with intracellular proteins. C. It is part of the intracellular signal transduction messengers. D. It behaves as a component of the cytoskeleton and it changes a cell's shape and function E. It is a transcription factor that can turn on specific genes.

It binds a receptor on the surface of cells of a target organ or tissue

Which of the following proteins does not belong in this group? A. Ovalbumin B. Ferritin C. Casein D. Keratin E. Serum albumin

Keratin (a fibrous protein, all the others are globular)

You have analyzed several Lineweaver-Burk graphs. One of the advantages of using a Lineweaver-Burk (L-B)over a classical Michaelis-Menten hyperbolic plot is that L-B graphs are straight lines with a constant slope. Whatis the mathematical representation of the slope (m) of a L-B line (of the form y = mx + b)? A. Kmapp /Vmax B. 1/VmaxC. -1/[S] D. Vmax·[E]t E. 1/vo

Kmapp /Vmax

discuss the differences between monoploid and haploid.

Monoploids have a single basic set of chromosomes. Haploids represent individuals having half the somatic chromosome number found in normal individual.

Find the mismatched pair A. Gene regulation—Transcription factors B. Motor—Myoglobin C. Light receptor—Rhodopsin D. Artificial intracellular marker—Cloned green fluorescent protein E. Hormonal signaling—Insulin

Motor—Myoglobin

Globular proteins fold up into compact, spherical structures that have uneven surfaces. They tend to form multisubunit complexes, which also have a rounded shape. Fibrous proteins, in contrast, span relatively large distances within the cell and in the extracellular space. Which of the proteins below is not classified as a fibrous protein? [Hint: What does the suffix -ase indicate?] A. elastase B. collagen C. keratin D. elastin

elastase

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. A. heat B. water vapor C. metal ions D. enzymes E. None of the above

enzymes

indicate whether the following statements are true or false. If a statement is false, explain why it is false. A. Photosynthetic organisms release only O2 into the atmosphere, while nonphotosynthetic organisms release only CO2 . B. The cycling of carbon through the biosphere first requires the incorporation of inorganic CO2 into organic molecules. c. The oxidation of one molecule is always coupled to the reduction of a second molecule. d. During cellular respiration, carbon-containing molecules become successively more oxidized until they reach their most oxidized form, as CO2 .

false: photosynthetic organisms can also release CO2 true true true

Match the letters with the enzymes and macromolecules involved in DNA replicatio A. _____ i) pyrophosphate (Pi) B. _____ ii) template strand C. _____ iii) incoming nucleoside triphosphate D. _____ iv) new strand E. _____ v) DNA polymerase

ii, iv, v, iii, i

Which of the following is not a feature commonly observed in a-helices? A. left-handedness B. one helical turn every 3.6 amino acids C. cylindrical shape D. amino acid side chains that point outward

left-handedness

Which of the following is not an example of a protein with quaternary structure? A. Calmodulin is a Ca2+ -binding protein which is formed by two identical subunits. B. Hemoglobin in adult humans has the composition a 2b 2 . C. The photosynthetic enzyme Rubisco is composed of 8 L subunits and 8 S subunits. D. Myoglobin, an oxygen-binding protein in muscle, consists of a single subunit. E. South American rattlesnake toxin (crotoxin) is a phospholipase A enzyme with twodifferent subunits

myoglobin, an oxygen-binding protein in muscle consists of a singe subunit (tertiary)

Which of the following statements is incorrect? A. We only need to consume vitamins in small amounts B. Vitamins are precursors to some coenzymes C. Some vitamins are fat-soluble whereas others are soluble in water D. All of the above E. None of the above

none of the above

Complete the sentence with the best option provided below. The secondary structures of a protein are the A. regular, repeated folds present in a lowest energy conformation. B. temporary, unstable protein folding conformations. C. interactions between polar amino acid side chains. D. chemical modifications of amino acid side chains.

regular, repeated folds present in a lowest energy conformation.

For each of the following sentences, fill in the blanks with the best word or phrase selected from the list below.Not all words or phrases will be used; each word or phrase should be used only once.The a-helices and β-sheets are examples of protein ____________ structure. A protein such ashemoglobin, which is composed of more than one protein ________________, has ____________structure. A protein's amino acid sequence is known as its _______________ structure. A protein____________ is the modular unit from which many larger single-chain proteins are constructed.The three-dimensional conformation of a protein is its ____________ structure

secondary, subunit, quaternary, primary, domain, tertiary

What is an allosteric site? How does an allosteric site differ from an enzyme's active site or a receptor's binding site?

the allosteric site is where molecules switch the enzyme's biological activity on and off. it differs because it does not bind the substrate but binds another molecule which alters the enzymes shape and function

In principle, a eukaryotic cell can regulate gene expression at any step in the pathway from DNA to the active protein. Place the types of control listed below at the appropriate places on the diagram in the figure below. A. translation control B. transcriptional control C. RNA processing control D. protein activity control

transcriptional control( DNA to RNA transcript) RNA processing control (RNA transcript to mRNA) translation control (mRNA to protein) protein activity control (protein to inactive protein)

Refer to the graphs above. Match the labels with the correct type of inhibition. Hint: One of the answers is notrepresented here. A. Uncompetitive _______ B. Competitive _______ C. Non-competitive _______ D. Allosteric

uncompetitive: C competitive: A non competitive: B

Activated carriers are small molecules that can diffuse rapidly and be used to drive biosynthetic reactions in the cell. Their energy is stored in a readily transferable form such as high-energy electrons or chemical groups. Which of the molecules below donates a chemical group rather than electrons? A. FADH2 B. NADH + H+ and NADPH + H+ C. FMN D. ATP

ATP

A pregnant mouse is exposed to high levels of a chemical. Many of the mice in her litter are deformed, but when they are interbred with each other, all their offspring are normal. Which two of the following statements could explain these results? A. In the deformed mice, somatic cells but not germ cells were mutated. B. The original mouse's germ cells were mutated. C. In the deformed mice, germ cells but not somatic cells were mutated. D. The toxic chemical affects development but is not mutagenic.

A. In the deformed mice, somatic cells but not germ cells were mutated. D. The toxic chemical affects development but is not mutagenic.

In which phase of meiosis does recombination take place? A. Interphase B. Prophase I C. Metaphase I D. Prophase II

B. Prophase I

Consult chapter 5 of Alberts et al. What do you think is the main difference between RNA and DNA? A. RNA is single stranded and DNA is double stranded B. RNA can have catalytic activity but this does not happen with DNA C. RNA has a backbone of ribose-phosphate whereas DNA's backbone is deoxyribose-phosphate D. RNA has uracil instead of thymine E. Other: ______________________

A. RNA is single stranded and DNA is double stranded

What do miRNAs, tRNAs, and rRNAs have in common? A. They do not code for proteins. B. They act in the nucleus. C. They are packaged with other proteins to form RISC. D. They form base pairs with mRNA molecules.

A. They do not code for proteins.

Which statement is false? A. When DNA is being replicated inside a cell, local heating occurs, allowing the two strands to separate. B. Prokaryotic cells have a single DNA replication origin in their chromosomes. C. Meselson and Stahl's experiments ruled out the dispersive model for DNA replication. D. DNA replication is a bidirectional process that is initiated at multiple locations along chromosomes ineukaryotic cells.

A. When DNA is being replicated inside a cell, local heating occurs, allowing the two strands to separate.

The letters B and C point to a ________ base pair forming ________ hydrogen bonds. A. guanine-cytosine/3 B. adenine-cytosine/3 C. adenine-thymine/2D. uracil-adenine/2 E. None of the above.

A. guanine-cytosine/3

The following is correct regarding the oxidoreductase enzymes: A. NADH + H+ /NAD+ are involved in catabolism and NADPH + H+ /NADP+ participate in anabolism B. The oxidation of the reduced member of a redox pair is associated to a DG < 0 C. The reduction of the oxidized member of a redox pair is associated to a DG > 0 D. All of the above E. none of the above

All of the above

Which of the following is an alternative to ATP (DG°' = -31 kJ/mol) as an energy carrier? A. creatine-phosphate B. phosphoenolpyruvate C. diphosphoglycerate D. All of the above E. None of the above

All of the above

Refer to antigen binding sites on antibodies (see diagram below) and explain the statement "Antibodies such as immunoglobulin G are divalent".

Antibodies are proteins from the immune system in response to the presence of foreign substances. Antibodies have two antigen binding sites

The letter A indicates A. A purine-purine base pairing. B. The guanine-cytosine base pair. C. The adenine-thymine base pair. D. A pyrimidine-pyrimidine base pairing E. None of the above

B. The guanine-cytosine base pair.

How long does a human ovum remain arrested in prophase I? A. Nine months; at birth meiosis slowly continues. B. Until puberty; then one ovum enters meiosis II about each month or so. C. Until death D. None of the above

B. Until puberty; then one ovum enters meiosis II about each month or so.

Observe the diagram on the right: What form of DNA is seen here? A. A B) B C) Z

B

The _____ arrow points to the major groove whereas the ______ arrow points to the minor groove. A. yellow B. blue

B(blue) A(yellow)

If the DNA in Eubacteria is not contained in a nucleus, how is it organized? A. It is completely "naked" B. It is associated to proteins but not as organized as the eukaryotic chromosomes C. It is covered by lipids in a disorganized matter D. None of these is correct

B. It is associated to proteins but not as organized as the eukaryotic chromosomes

Which of the following is not a good example of a housekeeping (constitutively expressed) protein? A. DNA repair enzymes B. histones C. ATP synthase D. Hemoglobin

D. Hemoglobin

Find the mismatched pair regarding broad spectrum antibiotics A. Chloramphenicol—prevents protein chain elongation by inhibiting the peptidyl transferase activity B. Streptomycin—disrupts the initiation and elongation steps in protein synthesis .C. Tetracyclines—bind 30S ribosomal subunit, inhibiting the binding of incoming aminoacyl-tRNAs D. None of the above is mismatched

D. None of the above is mismatched

What is the name of the phase between mitotic cycles? A. Telophase B. Anaphase C. Prophase D. Interphase

D. interphase

How is DNA A different from DNA B? Why is it the form most commonly present in cells?

DNA A has a shorter, more compact helical structure whose base pairs are not perpendicular to the helix-axis as in B-DNA. B-DNA is most stable under physiological conditions

The typical form of Down Syndrome occurs when a human individual has an extra chromosome 21 (chromosomes are grouped from A to G according to their size and centromere position; the sex chromosomesare in their own category). In some individuals with Down Syndrome, the characteristic symptoms are less severe, and they are said to have Familial Down Syndrome. Find the incorrect statement regarding Familial Down Syndrome. A. The age of the parents is not an important contributing factor. B. It is hereditary (i.e., it runs in families, hence the name) C. It is caused by a Robertsonian translocation (i.e., a piece of chromosome 21 attaches itself to chromosome 13or 14) D. All of the above are incorrect E. None of the above are incorrect

E. None of the above are incorrect

In 2018, a new category of enzymes was officially established by the IUPAC-IUBMB. This category is EC 7. What type of reactions are catalyzed by EC 7 enzymes?

EC 7 enzymes catalyze reactions involving the formation of carbon-carbon bonds

A non-competitive inhibitor has a very similar structure to that of the enzyme's substrate and hence it modifies the apparent Km. A. True B. False

False

The correct folding of proteins is necessary to maintain healthy cells and tissues. Unfolded proteins are responsible for such neurodegenerative disorders as Alzheimer's, Huntington's, and Creutzfeld-Jacob disease (the specific faulty protein is different for each disease). What is the ultimate fate of these disease-causing, unfolded proteins? A. They are degraded. B. They bind a different target protein. C. They form structured filaments. D. They form protein aggregates

They form protein aggregates

An enzyme's Km is the concentration of substrate at which vo reaches ½ Vmax. A. True B. False

True

Which type of inhibitor can only bind to the enzyme-substrate [S] complex? A. Uncompetitive B. Competitive C. Non-competitive D. Allosteric

Uncompetitive

Meiotic recombination produces new genetic information in sister chromatids. This happens during prophase I. Order the stages of prophase I chronologically: A. ____ Diplotene.-The synaptonemal complex disassociates; homologous pairs remain attached (chiasmata). B. ____ Zygotene.-A synaptonemal complex is formed between homologous chromosomes. C. ____ Diakinesis.-Nuclear membrane disintegrates and chromosomes fully condense prior to metaphase I. D. ____ Leptotene.-Chromosomes start condensing and attaching to the nuclear membrane via telomeres. E. ____ Pachytene.-Non-sister chromatids undergo crossing over of genetic material.

_4___ Diplotene.-The synaptonemal complex dissociates; homologous pairs remain attached (chiasmata). ___2_ Zygotene.-A synaptonemal complex is formed between homologous chromosomes. __5__ Diakinesis.-Nuclear membrane disintegrates and chromosomes fully condensed prior to metaphase ___1_ Leptotene.-Chromosomes start condensing and attaching to the nuclear membrane via telomeres __3__ Pachytene.-Non-sister chromatids undergo crossing over of genetic material.