1035 Lecture 3 and 4 Practice Questions

Identify the three components in the figure of a generalized nucleotide below. Optional follow-up question: Would this nucleotide be found in DNA, RNA, or both? How do you know?

1. nitrogenous base 2. 5-carbon sugar (ribose) 3. phosphate group Optional follow-up answer: the nucleotide would be found in RNA because it contains the sugar ribose. DNA nucleotides contain the sugar deoxyribose which does not have the hydroxyl group on the 2' carbon.

TRUE or FALSE: The sequence of amino acids in a protein is sufficient to determine its 3-D structure. True False

TRUE. A protein's amino acid sequence contains all of the information to determine its 3-D shape. Polypeptide chains fold into the lowest energy conformation to form proteins. Other proteins called chaperones are often required to help a protein fold into its lowest energy state. How do we know this? Take a purified protein and expose it to a denaturant (urea), a solvent that interferes with noncovalent interactions. When the denaturant is removed, the polypeptide returns to its original conformation!

The 20 common amino acids can be classified into the following groups based on their side chains: basic polar (positively charged) acidic polar (negatively charged) uncharged polar nonpolar Use the dropdown menus to classify the amino acids below.

1. Uncharged polar. The amide nitrogen (N) strongly attracts electrons (asparagine). 2. Nonpolar. Carbon (C) and hydrogen (H) attract electrons relatively equally, resulting in relatively nonpolar covalent C - H bonds in the side chain (valine). 3. Uncharged polar. Oxygen strongly attracts electrons, making the hydroxyl group (-OH group) polar (serine).

Once an mRNA is produced, its message can be decoded on ribosomes. The ribosome is composed of two subunits: the _______ subunit, which catalyzes the formation of the peptide bonds that link the amino acids together into a polypeptide chain, and the _________ subunit, which matches the tRNAs to the codons of the mRNA. During the chain elongation process of translating an mRNA into protein, the growing polypeptide chain attached to a tRNA is bound to the __ site of the ribosome. An incoming aminoacyl-tRNA carrying the next amino acid in the chain will bind to the __ site by forming base pairs with the exposed codon in the mRNA. The end of a protein-coding message is signaled by the presence of a stop codon, which binds the _________ called release factor.

1. large 2. small 3. P 4. A 5. protein

The figure below shows part of a polypeptide chain. The N-terminus is on the ______ side and the C-terminus is on the _______ side. Amino acid sequences are always read from the___________________ .

1. left 2. right 3. the N-terminus to the C-terminus

Identify the parts of the generalized amino acid in the figure below. Optional follow-up: practice drawing a generalized amino acid without looking at your lecture notes, textbook, or other sources. Use "R" to represent the side chain. Label the alpha carbon, amino group, and carboxyl group.

1.amino group 2. alpha-carbon 3. side chain 4. carboxyl group

Identify the components of the polypeptide chain in the figure below. Optional follow-up: drawing a short polypeptide without looking at your lecture notes, textbook, or other sources. Represent the side chains as "Rs." Label the peptide bonds, carboxyl terminus, and amino terminus.

1.amino terminus (N-terminus) 2. polypeptide backbone 3. side chain 4. carboxyl terminus (C-terminus) 5. peptide bond

DNA and RNA nucleotides contain different five-carbon sugars. DNA nucleotides contain the sugar deoxyribose and RNA nucleotides contain the sugar ribose. A. On the left side of the figure, what do the 1' - 5' red labels refer to? B. On the right side of the figure below, which sugar is deoxyribose and which sugar is ribose?

A. On the left side of the figure, the 1'-5' red labels indicate different carbon atoms in the sugar molecules and are referred to as the 1-prime carbon (1'-carbon), the 2-prime carbon (2'-carbon), etc. Note: carbon and hydrogen atoms are not shown explicitly. Carbon atoms are represented at intersections or ends of lines. Because carbon atoms are involved in four bonds, the number of hydrogen atoms attached to a carbon atom is equal to four minus the number of bonds involving the carbon atom. B. Deoxyribose is the sugar on the bottom right (think deoxy -> lost an oxygen). Ribose is the sugar on the top right.

The five types of nitrogen-containing rings (bases) found in DNA and/or RNA nucleotides are shown in the figure below. A. How are purines and pyrimidines different? B. Which bases are present in both DNA and RNA and which are found only in DNA or RNA? C. Create or find a mnemonic device to remember which bases are purines and which are pyrimidines.

A. Pyrimidines are smaller, only consisting of a six-membered nitrogen-containing ring, while purines are bulkier, consisting of a six-membered and five-member nitrogen-containing ring fused together. B. DNA contains adenine (A), thymine (T), cytosine (C), and guanine (G). RNA contains adenine (A), uracil (U), cytosine (C), and guanine (G).

A protein chain folds into its stable and unique three-dimensional structure, or conformation, by making many noncovalent bonds between different parts of the chain. Such noncovalent bonds are also critical for interactions with other proteins and cellular molecules. Identify the class of amino acids that is most important for each of the interactions detailed below. Note: an amino acid class may be used more than once or not at all. A. forming ionic bonds with negatively charged DNA B. tightly packing the hydrophobic interior core of a globular protein C. forming hydrogen bonds to aid solubility in water

A. basic polar B. nonpolar C. uncharged polar

When using a repeating trinucleotide sequence (such as 5′-AAC-3′) in a cell-free translation system, you will obtain _____. A. three different types of peptides, each made up of a single amino acid. B. peptides made up of three different amino acids in random order. C. peptides made up of three different amino acids, each alternating with each other in a repetitive fashion. D. polyasparagine, as the codon for asparagine is AAC.

A. is correct. An mRNA composed of a trinucleotide repeat of AAC can be "read" in three different frames: AAC, ACA, and CAA. Thus, this mRNA will yield polyasparagine (codon = AAC), polythreonine (codon = ACA), and polyglutamine (codon = CAA).

Which amino acid would you expect a tRNA with the anticodon 5′-CUU-3′ to carry? A. lysine B. glutamic acid C. leucine D. phenylalanine

A. is correct. As is conventional for nucleotide sequences, the anticodon is given reading from 5′ to 3′. The complementary base-pairing occurs between antiparallel nucleic acid sequences, and the codon recognized by this anticodon will therefore be 5′-AAG-3′.

Which of the following are possible base compositions for double-stranded DNA? A. Option 1 B. Option 2 C. Option 3 D. All of the above E. None of the above

A. is correct. In double-stranded DNA, A base-pairs with T and C base-pairs with G. U would not be in DNA.

Step 1: a charged tRNA molecule carrying an amino acid base-pairs to the mRNA codon exposed at the [ Select ] site on the ribosome. Step 2: the [ Select ] end of the polypeptide chain is uncoupled from the tRNA at the [ Select ] site and joined by a peptide bond to the amino acid attached to the tRNA at the A site. Step 3: the large subunit shifts relative to the small subunit, moving the tRNAs that were previously in the P and A sites into the E and P sites, respectively. Step 4: the small subunit moves exactly [ Select ] nucleotides along the mRNA molecule, bringing it back to its original position relative to the large subunit. The movement ejects the spent tRNA from the [ Select ] site.

Answer 1:A Answer 2carboxyl Answer 3:P Answer 4three Answer 5:E

The α-helix and β-sheet are common folding patterns present in proteins. Which of the following statements is TRUE? A. Both result from hydrogen bonds between the polypeptide backbone and amino acid side chains. B. Both result from hydrogen bonds between the amino acid side chains. C. Both result from hydrogen bonds between the N-H and C=O groups in the polypeptide backbone. D. There are no similarities.

C is correct!

Polar covalent bonds are formed when the electrons in the bond are not shared equally between the two nuclei. Which one of these molecules contains polar covalent bonds? Optional follow-up: what types of molecules can form hydrogen bonds? A. methane B. propane C. water D. all of the above

C is correct. In a water molecule, the oxygen and hydrogens form polar covalent bonds. This is because oxygen is more electronegative and attracts electrons more strongly than hydrogen. As a result, oxygen in a water molecule has a partial negative charge and the hydrogens have partial positive charges. A, B, and D are incorrect. Methane and propane are both hydrocarbons (molecules formed of only carbon and hydrogen). Carbon and hydrogen have similar electronegativities and thus form nonpolar covalent bonds. Optional follow-up: Hydrogen bonds are noncovalent bonds that form between water molecules or other polar molecules due to the partial positive and negative charges (see figure below). In the context of cellular biology, hydrogen bonds commonly form when molecules contain oxygen or nitrogen. This is because both oxygen and nitrogen are more electronegative than hydrogen (attract electrons more strongly) and will form polar covalent bonds with hydrogen, resulting in partial positive and partial negative charges. Hydrocarbons do not engage in hydrogen bonding because carbon and hydrogen have similar electronegativities and share the electrons more equally, forming nonpolar covalent bonds.

Which of the following molecules is thought to have arisen first during evolution? A. protein B. DNA C. RNA D. All came to be at the same time.

C. is correct. Because RNA is known to catalyze reactions within the cell, because the components of RNA are thought to be more readily formed in the conditions on primitive Earth, and because RNA can contain genetic information, it is the most likely of the three molecules to have arisen first in evolution.

According to the conventional way of writing the sequence of a peptide or a protein, which is the C-terminal amino acid in the peptide: Pro-Val-Thr-Gly-Lys-Cys-Glu? A. Proline (Pro) B. Glycine (Gly) C. Glutamic acid/glutamate (Glu) D. cannot be determined

C. is correct. By convention, amino acid sequences are written with the N-terminal amino acid first and C-terminal amino acid last.

DNA replication is considered semiconservative because _________. A. after many rounds of DNA replication, the original DNA double helix is still intact. B. each daughter DNA molecule consists of two new strands copied from the parent DNA molecule. C. each daughter DNA molecule consists of one strand from the parent DNA molecule and one new strand. D. new DNA strands must be copied from a DNA template.

C. is correct. During DNA replication, each parental DNA strand serves as a template to produce a new strand of DNA and the resulting daughter helices include one parental and one newly synthesized DNA strand.

TRUE or FALSE: All genes are segments of DNA that contain instructions for making a particular protein. a) True b) False

Genes are segments of DNA that contain instructions for making a particular RNA molecule (genes can code for proteins or non-coding RNA molecules). Protein-coding genes are transcribed to messenger RNA (mRNA) and the mRNA is then translated to make proteins. Non-coding RNA genes are transcribed to non-coding RNA molecules such as ribosomal RNA (rRNA), transfer RNA (tRNA), microRNAs (miRNA), and others.

Which of the following is NOT a function of RNA? A. form the core of the ribosome's structure and catalyze protein synthesis B. regulate gene expression C. genetic material for cells D. code for proteins

The correct answer is C

Match each polymeric macromolecule to its monomeric subunits. a) carbohydrate (polysaccharide) b) ribonucleic acid c) deoxyribonucleic acid d) protein

a) monosaccride b) nucleotide (adenine, uracil, cytosine, and guanine) c) nucleotide (Adenine, thymine, cytosine, guanine) d)amino acid

You are trying to make a synthetic copy of a particular protein but accidentally join the amino acids together in exactly the reverse order. One of your classmates says the two proteins must be identical, and bets you $20 that your synthetic protein will have exactly the same biological activity as the original. After having read this chapter, you have no hesitation in staking your $20 that it will not. What particular feature of a polypeptide chain makes you sure your $20 is safe and that the project must be restarted?

As a peptide bond has a distinct chemical polarity, a polypeptide chain also has a distinct polarity. The reversed protein chain cannot make the same noncovalent interactions during folding and thus will not adopt the same three-dimensional structure as the original protein. The activities of these two proteins will definitely be different, because the activity of a protein depends on its three-dimensional structure. It is unlikely that the reverse chain will fold into any well-defined, and hence functionally useful, structure at all, because it has not passed the stringent selective pressures imposed during evolution.

You have a piece of DNA that includes the following sequence: 5′-ATAGGCATTCGATCCGGATAGCAT-3′3′-TATCCGTAAGCTAGGCCTATCGTA-5′ Which of the following RNA molecules could be transcribed from this piece of DNA? A. 5′UAUCCGUAAGCUAGGCCUAUGCUA-3′ B. 5′AUAGGCAUUCGAUCCGGAUAGCAU-3′ C. 5′UACGAUAGGCCUAGCUUACGGAUA-3′ D. None of the above.

B is correct!

Both DNA and RNA are synthesized by covalently linking a nucleoside triphosphate to the previous nucleotide, constantly adding to a growing chain. In the case of DNA, the new strand becomes part of a stable helix. The two strands are complementary in sequence and antiparallel in directionality. What is the principal force that holds these two strands together? A. ionic interactions B. hydrogen bonds C. covalent bonds D. van der Waals interactions

B is the correct answer!

Which of the following ratios of nucleotides is constant for DNA? A. A + T = G + C B. A + G = T + C C. A + C = U + G D. A + U = G + C

B. is correct. A base-pairs with T, so the number of A's will be equal to the number of T's. Similarly, the number of C's will be equal to the number of G's. If you add together the number using one from each base-pair (say, A + G) that will be equal to adding together the number of the remaining one from each base pair from each set (in this case, T + C).

In eukaryotes, but not in prokaryotes, ribosomes find the start site of translation by _________. A. binding directly to a ribosome-binding site preceding the initiation codon. B. scanning along the mRNA from the 5′ end. C. recognizing an AUG codon as the start of translation. D. binding an initiator tRNA.

B. is correct. In prokaryotes, ribosomes will bind directly to a ribosome-binding site preceding the initiation codon while eukaryotes will scan along the mRNA from the 5′ end to find the translational start site. In both prokaryotes and eukaryotes, the AUG codon must be recognized by the ribosome, which leads to the binding of an initiator tRNA.

The sequences of two tripeptides are written below. Would you expect to find them in the inner core or on the surface of a cytosolic protein? Note: serine, threonine, and tyrosine all have polar side chains while alanine, glycine, and leucine all have nonpolar side chains. serine-threonine-tyrosine (Ser-Thr-Tyr) alanine-glycine-leucine (Ala-Gly-Leu) A. Both in the inner core. B. both on the surface. C. Ser-Thr-Tyr in the inner core and Ala-Gly-Leu on the surface. D. Ser-Thr-Tyr on the surface and Ala-Gly-Leu in the inner core.

D. Ser-Thr-Tyr on the surface and Ala-Gly-Leu in the inner core. Serine, threonine, and tyrosine all have polar side chains and would most likely be found on the surface of the protein, interacting with the aqueous environment of the cytosol. Alanine, glycine, and leucine all have nonpolar side chains that are likely buried in the interior of the protein to minimize the energetically unfavorable interactions of these hydrophobic side chains with water in the cytosol.

Which of the following is a monosaccharide? A. C6H12O6 B. C3H6O3 C. C5H10O5 D. all of the above E. none of the above

D. is correct. Monosaccharides have the chemical formula: (CH20)n where n is 3, 4, 5 or 6.

You have a segment of DNA that contains the following sequence: 5′-GGACTAGACAATAGGGACCTAGAGATTCCGAAA-3′ 3′CCTGATCTGTTATCCCTGGATCTCTAAGGCTTT-5′ You know that the RNA transcribed from this segment contains the following sequence: 5′-GGACUAGACAAUAGGGACCUAGAGAUUCCGAAA-3′ Which of the following choices best describes how transcription occurs? A. The top strand is the template strand; RNA polymerase moves along this strand from 5′ to 3′. B. The top strand is the template strand; RNA polymerase moves along this strand from 3′ to 5′. C. The bottom strand is the template strand; RNA polymerase moves along this strand from 5′ to 3′. D. The bottom strand is the template strand; RNA polymerase moves along this strand from 3′ to 5′.

D. is correct. The bottom strand can hybridize with the RNA molecule and thus is the template strand. The polymerase moves along the DNA in a 3′-to-5′ direction, because the RNA nucleotides are joined in a 5′-to-3′ polarity.

As a protein is made, the polypeptide is in an extended conformation, with every amino acid exposed to the aqueous environment. Although both polar and charged side chains can mix readily with water, this is not the case for nonpolar side chains. Explain how hydrophobic interactions may play a role in the early stages of protein folding, and have an influence on the final protein conformation.

One reason that nonpolar groups are excluded from an aqueous environment is that a hydrophobic surface would organize water into a highly structured network of hydrogen bonds, which is energetically unfavorable. Thus, you would expect that nonpolar amino acids would group together early, forming "hydrophobic pockets," while the polar and charged side chains remain at the interface of the surrounding solution. In the final, folded protein, most of the nonpolar amino acids will remain buried inside the protein. This fold is more stable because nonpolar atoms are prevented from contact with water and remain in contact with each other.

What influence, if any, does a protein's structure have on its function?

Protein structure --> Protein function A protein's structure is intimately linked to its function. All proteins function by engaging in highly specific interactions with other molecules. To engage in these specific interactions, proteins must have a particular structure. Thus, a protein's structure is integral to its function.

The molecule below is _____ . A. GTP B. TTP C. dGTP D. dTTP E. CTP

dTTP stands for deoxythymidine triphosphate. This is one of the four nucleoside triphosphate that make up DNA. Without memorizing the entire chemical structure, you would be able to see that the sugar in the center is deoxyribose because it does not have a hydroxyl group on the two-prime carbon. You then know that the molecule is either dGTP or dTTP. Next, without memorizing the exact chemical structure of the four nitrogenous bases, you know that guanine is a purine and thus has two nitrogen-containing rings while thymine is a pyrimidine and thus has one nitrogen-containing ring. Therefore, the molecule must be dTTP.