BIOCHEMISTRY EXAM QUESTION AND ANSWERS 100% CORRECT.

DNA replication is ___________, which allows each of the two strands to serve as a _______ for the new strands. b. semiconservative, template - ANSWERS-DNA replication is semiconservative, meaning that each new duplex has one original (parent) strand and one new strand. Because the two parent strands are separated during replication and the base pairing is predictable, each parent strand can serve as a template for the new strand synthesis. .Which of the following enzymes does NOT assist the DNA polymerase on the lagging strand to overcome its two problems? (Recall that the DNA polymerase can only make DNA in the 5'->3' direction, and it must bind a double-stranded nucleotide polymer before it can start making its own DNA polymer.) c. Helicase - ANSWERS-Helicase unwinds the double stranded DNA to allow for replication, but this is not a problem for the DNA polymerase. .Several components of cigarette smoke, including benzopyrene, insert themselves (intercalate) into the DNA and lead to several types of mutations such as frameshift mutations, including both insertions and deletion. Which of the following repair pathways would be used to repair this type of damage? c. Nucleotide Excision Repair - ANSWERS-Nucleotide excision repair is used to repair deletions, insertions, and helix-distorting lesions, such as thymine dimers. .Maternal smoking during pregnancy is hazardous yet common in many places. Many studies have associated prenatal smoking to unhealthy physical and psychological outcomes for the baby. Researchers know that maternal smoking affects are epigenetic in nature. Which of the following events can be considered epigenetic in nature? a. Changes in chromatin structure - ANSWERS-Frame shift mutations are a kind of mutations which result from addition of deletion of a nucleotide base resulting in an altered reading frame and ultimately a different protein, than the one the gene originally encoded. Frameshift mutations are genetic changes because they alter the DNA sequence, whereas epigenetic changes do not alter the DNA sequence. Epigenetic changes are modifications to genomic structure (not sequence) that are caused by the external environment. These environmental factors affect the overall chromatin structure to allow more or less "access" to the DNA by gene expression machinery to turn the genes "on" or "off". In other words, epigenetics can alter gene expression without changing the underlying DNA sequences. The changes may or may not be heritable, depending on the location and circumstances. .Blood type is an example of what type of inheritance? a. Codominance - ANSWERS-The genes that produce the A and B antigen proteins can both be expressed independently, and a heterozygote (someone with both genes) will be produce both A and B proteins - neither will dominate the other. The is an example of codominance. .What is the expected probability that a child will have an autosomal dominant disease if their father is heterozygous for the allele and their mother is homozygous for the normal allele? a. 50% - ANSWERS-If D is the disease-conferring dominant allele and d is the normal allele, the father has the genotype Dd and the mother's genotype is dd. Each child can only inherit a d allele from their mother, and they have a 50% chance of inheriting the D allele from their father. As a result, the expected probability that their child will inherit the disease is 50%. .The physical trait of lip protrusion exhibits a characteristic type of inheritance, as shown by the pedigree above. What type of inheritance best describes this inheritance pattern? a. Incomplete dominance - ANSWERS-The correct answer is incomplete dominance. The blending of the large and small lip protrusion into an intermediate, medium lip protrusion, as well as the presence of all three variations in the offspring, demonstrate a clear example of incomplete dominance. .The normal sequence of a section of the HLA-B27 gene, a genetic marker of the inflammatory disease Ankylosing spondylitis, is given below. Match each mutation of the sequence to the type of mutation it exhibits. A genetic code table is provided for your use in answering the question. 5'- CGG CAG AAU UUA -3' 5'- CAG CAG AAU UUA -3' - Missense mutation 5'- CGG CAG AAA UUU A-3' - Insertion 5'- CGG CAG AAC UUA -3' - Silent mutation 5'- CGG CAG AAU UA -3' - Deletion 5'- CGG UAG AAU UUA-3' - Nonsense mutation - ANSWERS-Silent mutations are those in which the amino acid encoded doesn't change as a result of the mutation. Missense mutations are those in which the amino acid encoded changes to a different amino acid as a result of the mutation. Nonsense mutations are those in which the amino acid encoded changes to a stop codon as a result of the mutation, yielding a smaller protein. Insertions are the inclusion of extra nucleotides compared to the original sequence. They can result in other mutations, such as nonsense mutations. Deletions are the removal of nucleotides compared to the original sequence. They can result in other mutations, such as nonsense mutations. .PCR is a powerful tool that can do all of the following.... b. detect mutations that lead to disease c. copy small segments of DNA, less than 6kb d. amplify DNA from samples that have just a few cells - ANSWERS-PCR's ability to amplify is powerful, and products can even be generated from samples with just a few cells. PCR is less reliable for amplifying large segments of DNA greater than 6 kb, though some careful changes to the techniques can allow it. .Which of the following is a required "ingredient" in a PCR reaction? a. DNA nucleotides b. DNA primers c. DNA polymerase - ANSWERS-The primers used in PCR are made from DNA, rather than RNA. RNA primers are used in DNA replication inside the cell, but the quick degradation of RNA makes it less useful for PCR reactions. Instead, PCR reactions contain primers made of DNA to anneal to the region of DNA that will be amplified and serve as a starting point for DNA polymerase. .Which of the following changes can be detected using PCR? a. Differences in DNA sequence b. Insertions c. Deletions - ANSWERS-Differences in DNA sequence can be detected since these changes can alter the ability of primers to anneal to the DNA. They can also be detected by DNA sequencing of the PCR product. Epigenetic changes are not detectable via PCR because they don't affect the DNA sequence. .A small segment of Kevin's green opsin gene is shown below. What would be the resulting mRNA sequence? Kevin's opsin gene at nucleotide positions 936 to 941. 5'-G.C.C.T.A.G-3' (coding strand) 3'-C.G.G.A.T.C-5' (template strand) c. 5'-GCCUAG-3' - ANSWERS-This sequence is the same as the coding sequence, and the "T" bases have been replaced with "U", as is found in RNA. .The gene for blue opsin protein is located on chromosome 7, a non-sex chromosome. What kind of inheritance pattern would you expect to see with color blindness due to a mutated blue opsin? a. An equal distribution of blue color blindness between males and females. - ANSWERS-The blue opsin gene is located on a somatic (non-sex) chromosome, and therefore will be inherited with the same frequency for both sexes. .In Kevin's case, a specific kind of mutation in the opsin gene resulted in the premature termination of the translation process. This resulted in a shorter opsin protein than usual. What specific mutation could have caused this? c. Nonsense mutations - ANSWERS-Missense mutations are point mutations that change a single base pair in a codon such that the codon now encodes a different amino acid. In Kevin's case, a nonsense mutation, which is a point mutation that changes a single base pair in a codon to a stop codon resulted in termination of the translation signal. This further led to the synthesis of truncated protein. .After consultation with a genetic counselor and an examination of extended family history, the following pedigree was generated. Who did Kevin most likely inherit this mutation from? a. Maternal grandfather - ANSWERS-Red-green color blindness occurs more frequently in males than females because these genes are located on the X chromosome, and males inherit only one X chromosome and will express whatever alleles are on that chromosome. Females, on the other hand, inherit two X chromosomes, and thus have two alleles for each gene. If one of the alleles is mutated on one X chromosome, there is usually a correct allele on the other that can provide the needed gene. A woman must have two mutated opsin alleles to be color blind, while men need only one. This is known as sex-linked inheritance. Kevin inherited his Y chromosome from his father and his X chromosome from his mother, so his X chromosome with the defective opsin gene most likely came from his maternal grandfather and was passed to him by his mother. Thus, both grandfathers is not correct because his paternal grandfather would have contributed a Y chromosome. .The nonsense mutation that causes Kevin's color blindness could have resulted from a malfunction of __________. b. DNA polymerase - ANSWERS-Helicase unwinds the DNA during replication, but doesn't add or remove nucleotides. The correct choice is the DNA polymerase. DNA polymerase could have added an erroneous nucleotide, and it's proofreading activity could have missed it. While this type of event is rare, DNA polymerase is known to make a mistake that it doesn't correct about one in one hundred million! .Primary structure consists of the order of ______ in a protein. These are held together with ______ bonds that are formed by a ______ reaction. a. Amino acids, peptide, dehydration - ANSWERS-Correct Correct! .Several types of side chain interactions stabilize the tertiary structure of proteins, including which of the following? c. Ion pairs, hydrophobic interactions, hydrogen bonds, disulfide bonds - ANSWERS-The stability of a tertiary structure of a protein depends on the various interactions and bonds that occur between the side chains of different amino acids. .Which of the following statements is true about the secondary structure of proteins? a. It includes alpha helices as a common form. c. It includes beta pleated sheets as a common form. d. It involves hydrogen bonding between the backbone atoms. - ANSWERS-A secondary structure of protein consists of hydrogen bonds between backbone atoms, includes alpha helices and beta sheets as common forms. .In order to fulfill their function, proteins must fold in proper, three-dimensional conformations. Which one of the following molecules, available in a cell, is likely to help a protein fold properly? b. Chaperone - ANSWERS-Chaperones are helper proteins that ensure proper protein folding by stabilizing the polypeptide until the correct structure is fully formed. .Which of the following is true about a misfolded protein? a. It can be degraded by the cell. b. It can cause protein aggregation. d. It can be the result of denaturation. e. It will lose its normal function. - ANSWERS-Misfolded proteins can be the result of denaturation, are usually degraded by the cell into amino acids, lose their normal function, and may even lead to detrimental protein aggregation, as in the case of Alzheimer's disease. .Which of the following amino acids would you expect to find in the interior of a protein most often? - ANSWERS-Hydrophobic amino acids want to avoid water, and are most often found in the hydrophobic interior of the protein. While charged and polar amino acids can be found in the interior of the protein, they are also commonly found on the exterior of the protein where they can interact with water. .Which of the following amino acids would you expect to find most often on the exterior surface of a protein? - ANSWERS-Aspartic acid is a charged amino acid that interacts well with water and is often found on the exterior surface of a protein. .Which part(s) of the amino acid below can be involved in peptide bond formation? b. A - Amino group - ANSWERS-Peptide bonds are formed between the amino group (A) and carboxylic acid group (B) of amino acids. .Which part(s) of the amino acid below contributes to tertiary structure stabilization? c. D - R group - ANSWERS-The backbone carboxylic acid is involved in peptide bond formation and primary structure. Tertiary structure is stabilized primarily by interactions between different R groups. .Drag the name of the protein structure level to the part of the amino acid that primarily contributes to that structure level. - ANSWERS-Correct! The backbone of the amino acid participates primarily in primary and secondary structure while the R group stabilizes tertiary and quaternary structure. .In the pathway above, which compound could accumulate and trigger feedback inhibition? c. End Product - ANSWERS-The substrate is the start of the pathway, and therefore cannot inhibit anything before itself. While the amount of substrate could be reduced, and thereby slow product formation, the substrate itself is not part of feedback inhibition. In order to regular the amount of a product from a pathway, cells often use feedback inhibition. When the end product is no longer needed (or needed at a reduced rate), the product begins to accumulate and bind to enzymes in the pathway. This binding can inhibit the action of that enzyme by noncompetitive inhibition, thus slowing the pathway and reducing the amount of product made. .A substrate binds to an enzyme at a specific site, referred to as a(n)_________________. b. Active site - ANSWERS-The active site of an enzyme is the site where the substrate specifically binds to the enzyme and the reaction is carried out. .You are in charge of designing a drug that inhibits the activity of a specific enzyme. An important criteria for the drug selection is to ensure that the drug is directly in competition with the original substrate when binding to the active site of the enzyme. Which of the following kind of inhibitor would be an ideal choice? a. Competitive inhibitor - ANSWERS-A competitive inhibitor competes with the substrate for access to enzyme's active site and inhibits the enzyme. .Which of the following factors can affect the protein folding and activity of an enzyme? a. pH b. Heat d. Reducing agents - ANSWERS-Several factors can denature a protein and affect enzyme activity, including: reducing agents, pH, heat, and salt concentration. .One way a cell can avoid overproduction of a molecule is by using a particular type of inhibition in which the molecule itself acts as an inhibitor for an enzyme in its production pathway. This type regulation is known as ___________ inhibition. b. feedback - ANSWERS-The purpose of feedback inhibition in a cell is to prevent overproduction of the product. Feedback inhibition works by inhibiting an enzyme using the product of the very same reaction the enzyme catalyzes or a product from the same enzymatic pathway. .In the pathway above, what will happen to the levels of Second Intermediate Substrate if Enzyme 1 is inhibited as a result of feedback inhibition? c. Decrease - ANSWERS-Inhibition of an enzyme earlier in the pathway will prevent the product(s) of that enzyme from forming, thereby preventing the action of subsequent enzymes and formation of their respective products. For example, inhibition of Enzyme 1 would lead to a decrease in First Intermediate Substrate, which then reduces the levels of Second Intermediate Substrate because Enzyme 2 has less substrate on which to act. Thus, the levels of Second Intermediate Substrate will decrease as a result of feedback inhibition. .What type of enzyme adds a phosphate to another molecule? b. Kinase - ANSWERS-Protease enzymes break peptide bonds to digest proteins. Kinases add phosphates to molecules while phosphatases remove them. Kinases are enzymes that use a phosphate donor, usually ATP, to add a phosphate to another molecule. Phosphatases have the opposite role - they remove phosphate groups from molecules. .Which of the following are possible effect(s) that phosphorylation/dephosphorylation can have on the activity of an enzyme? b. Turn the enzyme "off". c. Turn the enzyme "on". - ANSWERS-Some enzymes are activated by phosphorylation while others are deactivated by the addition of a phosphate. Adding or removing a phosphate group to an enzyme affects the activity, and the type of effect is specific to the enzyme. For some enzymes, phosphorylation activates the activity of the enzyme, while other enzymes can be deactivated by phosphorylation. .In the enzymatic cycle, the enzyme shape is changed when [Substrate binds] and resumes its original shape when [Product is released] after [Substrate is converted to product]. - ANSWERS-An enzyme is a catalyst, meaning that it can catalyze the same reaction over and over again. Substrate binding can alter the conformation (or shape) of an enzyme, so it must resume its original shape when product is released, after substrate is converted to product, to allow it to perform the same reaction again. .The rate of an enzyme reaction can be increased by which of the following: b. Decreasing the activation energy of the reaction - ANSWERS-Enzymes do not directly affect the temperature of a cell. The rate (or speed) of a chemical reaction depends on the size of the activation energy barrier. Increasing temperature can provide the energy needed to get over the activation barrier, while lowering the temperature will reduce the available energy to overcome the barrier. However, enzymes cannot affect the temperature around them. Instead, enzymes decrease the activation energy of a reaction, thus allowing more reactions to take place at any given temperature. .Statins are a class of medications that target the enzyme HMG-CoA reductase in the pathway for cholesterol synthesis, as shown below. Compared to a patient that is not on a statin medication, In a patient taking a statin medication the concentration of cholesterol would [decrease], the concentration of HMG-CoA would [increase], and the concentration of Acetoacetyl CoA would [stay the same]. - ANSWERS-Recall that inhibiting an enzyme generally leads to an increased concentration of the substrate of the inhibited enzyme and a decrease in its product (or products further down the pathway).