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BIOCHEM C785 Biochemistry/BIOCHEM C785 Biochemistry
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The correct answer is 3' TAT TCG CAT 5'. Remember complementary means “Matching or Pairing” You have to remember to pay attention to your numbers as well as your letters (A-T, G-C, 5'-3'). The correct answer is 3’ ATG CGA ATA 5’ (original sequence) 5’ TAC GCT TAT 3’ (complementary sequence) But we asked for it in the 3’ direction, so mirror answer to give correct answer: 3’ TAT TCG CAT 5’ If you chose 3' TAC GCT TAT 5', this is incorrect. Although the nucleotides are in the correct order, the 5' and 3' are in the wrong place. DNA strands that are complementary run in opposite directions. This means that if one strand starts with a 3', the the complementary strand must start with a 5'. If none of the answer choices give the correct answer in 5' ---> 3', then you need to write its mirror, which will run from 3' ---> 5'. 3’ GAT AGC ATA 5’ 5’ ATA AGC GTA 3’ 2
Tyr Val Tyr Ile Gln Ile Ile Asp Val The correct answer is Ile Asp Val. We are starting at the coding strand, and have to remember the relationship between coding DNA and mRNA. These two strands are non- complementary and parallel. So we copy the coding strand , change T ---> U, and then write the mRNA sequence: 3’ ATG CAG ATA 5’ coding 3’ AUG CAG AUA 5’ mRNAMirror by changing orientation: 5’ AUA GAC GUA 3’ Read chart Ile Asp Val (chart is in direction of 5' ---> 3') Leu His Lys 3
Tyr Tyr Arg Ile Met Ala Ser Val Ile The correct answer is Ser Val Ile because 5’ TAT TAC CGA 3’ template is complementary and antiparallel so 3’ AUA AUG GCU 5’ but it is in the wrong orientation, so mirror 5’ UCG GUA AUA 3’ and read the chart Ser Val Ile Ser His Gln 4
dNTPs, Primer, RNA Polymerase, template RNA
dNTPs, Primer, DNA Polymerase, template DNA The correct answer is dNTPs, Primer, DNA Polymerase, template DNA. Notice that all components are about DNA. The Primer is even a DNA Primer. ATP, Primer, mRNA polymerase; template mRNA Acetyl CoA, RNA primer, DNA Ligase, Template phosphate 5
The correct answer is 32. 2x2x2x2x2= 64 10 6
The correct answer is 5' AUC GUA ACA 3' Ile Val Thr 5’ AUG GUA ACA 3’ 5’ AUC GCA ACA 3’ 7
Silent The correct answer is silent mutation. The nucleotide sequence changes, but it codes for the same amino acid. The coding sequence 5' TAC 3' corresponds to the mRNA sequence 5' UAC 3' (Tyr), and the coding sequence 5' TAT 3' corresponds to the mRNA sequence 5' UAU 3' (Tyr). Since the C changed to at T, this is a point mutation. If the point mutation results in the same amino acid in the new sequence as in the original sequence, the point mutation is a silent mutation. Missense Nonsense Insertion 8
Option 1
A DNA-binding protein blocks RNA Polymerase from binding to the promoter sequence, facilitating the transcription of the MECP2 gene. Transcription factors are unable to bind to the transcription start site of the MECP gene because nucleosomes are tightly packed together. The answer is "Transcription factors are unable to bind to the transcription start site of the MECP2 gene because nucleosomes are tightly packed together." Think "increased space gives increased access and increased expression." Gene expression is increased when nucleosomes are widely spaced and transcription factors and RNA Polymerase are able to bind to the transcription start site of the gene. In this question, decreased expression is resulting from decreased space between the nucleosomes, so the RNA Polymerase and transcription factors have decreased access to the transcription start site of the gene. Transcription activators cause nucleosomes to separate, exposing the MECP2 gene. RNA Polymerase binds to the MECP2 gene and begins translation. 13
The homologous chromosome is used to replace the incorrectly added base with the correct one. DNA Polymerase removes the incorrect base and adds in the correct base. The correct answer is "DNA Polymerase removes the incorrect base and adds in the correct base." DNA Polymerase repairs mismatch errors that occur during DNA replication. Thymine dimers occur. Distortion of the double helix occurs and is repaired by RNA Polymerase. 14
Removal of a single damaged nucleotide Damage to a few or several nucleotides are identified, then many nucleotides are removed and all are replaced to repair the DNA segment The correct answer is "Damage to a few or several nucleotides are identified, then many nucleotides are removed and all are replaced to repair the DNA segment." In nucleotide excision repair, several nucleotides are removed whereas, in BER (base excision repair), a single nucleotide is removed. Required when there are breaks in the double stranded DNA strand which causes discontinuity in both strands Insertion of a thymine dimer
Ionic bonds will continue to form, allowing the protein to fold as normal. Hydrophobic interactions will continue to occur resulting in normal folding. Ionic bonds will no longer form, potentially causing the protein to misfold. The correct answer is "Ionic bonds will no longer form, potentially causing the protein to misfold." Since arginine is a positively-charged amino acid, it would have formed an ionic bond with a negatively-charged amino acid in the protein. Leucine is not charged and is hydrophobic, so it will not form this same ionic bond, and could lead to protein misfolding. Hydrophobic interactions will be broken, potentially causing aggregation. 16
Option 1 Option 2 Option 3 The correct answer is "phenylalanine" and "methionine." Phenylalanine and methionine are both nonpolar (hydrophobic) amino acids, and they interact in the core of the protein through hydrophobic forces. If you chose, "Glutamine" and "Alanine," this is an incorrect answer. Glutamine is a polar amino acid, which should form a hydrogen bond to another polar amino acid, and alanine is a hydrophobic amino acid, which should interact with another hydrophobic amino acid to form hydrophobic interactions. Option 4 17
Hydrophobic interactions Hydrogen bonds Disulfide bonds The correct answer is covalent (disulfide) bonds. Hydrophobic interactions are disrupted by heat. Hydrogen bonds and ionic bonds are both disrupted by pH and by salt. Ionic bonds 18
Ionic bond
Nothing they will bind normally The hydrogen bond will no longer be formed, and the protein will be misfolded The correct answer is "The hydrogen bond will no longer be formed, and the protein will be misfolded. Glutamine is a polar amino acid (NH and also C=O), and alanine is a nonpolar (hydrophobic) amino acid (CH3), and so alanine will not interact with the polar amino acid glutamine. Nothing, they will form a hydrophobic interaction They will form a disulfide bond 23
Disulfide bond formation by cysteine amino acids Iron deficiency Aggregation of hydrophobic amino acids The correct answer is "Aggregation of hydrophobic amino acids." Alzheimer's disease results from abnormal protein aggregation in the brain. Ionic bonds formed by hydrogen bonding of amino acids 24
Hydrogen bonds Hydrogen bonds and ionic bonds are affected by a change in pH. Hydrogen bonds and ionic bonds are also affected by a change in salt concentration. Ionic bonds Hydrogen bonds and ionic bonds are affected by a change in pH. Hydrogen bonds and ionic bonds are also affected by a change in salt concentration. Hydrophobic interactions Disulfide bonds 25
Primary Secondary The correct answer is "secondary." Primary structure is formed by joining together amino acids through peptide bonds. Secondary structure is formed by hydrogen bonds between backbone amino acids. Tertiary structure is formed form interactions between
amino acid side chains. Quaternary structure is formed from interactions between amino acid side chains. Proteins with quaternary structure have two or more subunits. Tertiary Quaternary 26
Ionic Disulfide Charged Peptide The correct answer is "peptide bonds." The primary structure is built by hooking together amino acids to make the amino acid backbone of the protein. The amino acids are joined together by peptide bonds. 27
A protein has optimal function in its primary structure. All proteins carry out cellular functions when they have obtained their final quaternary structure. Ionic bonds between the backbone groups of amino acids stabilize a protein's tertiary structure. The hydrophobic effect primarily contributes to a single subunit protein's tertiary structure. The correct answer is "the hydrophobic effect primarily contributes to a single subunit protein's tertiary structure." The hydrophobic effect drives the formation of the core of a protein, which is the predominant contributing factor to the protein's tertiary structure. 28
Ionic bonds Hydrophobic interactions The correct answer is "Hydrophobic interactions." Heat will disrupt hydrophobic interactions. Ionic bonds are disrupted by changes in pH and by salt, and disulfide bonds are disrupted by reducing agents. Disulfide bonds None of the above 29
Hemoglobin binds oxygen in a cooperative manner, while Myoglobin binds oxygen with a relatively higher affinity and stores oxygen.
Carbon dioxide is converted to bicarbonate and binds to hemoglobin, which shuttles the carbon dioxide to the lungs so that it can be exhaled out of the body. Carbon dioxide flows through the bloodstream to the lungs so that it can be exhaled out of the body. Carbonic anhydrase helps carbon dioxide stick to hemoglobin, which shuttles the carbon dioxide to the lungs. In the lungs, Carbonic Anhydrase converts carbon dioxide to a gas so that it can be exhaled out of the body. Carbonic anhydrase converts carbon dioxide to bicarbonate, which can flow through the bloodstream to the lungs. In the lungs, Carbonic Anhydrase converts bicarbonate back to carbon dioxide so that it can be exhaled out of the body. The correct answer is, "Carbonic anhydrase converts carbon dioxide to bicarbonate, which can flow through the bloodstream to the lungs." In the lungs, carbonic anhydrase converts bicarbonate back to carbon dioxide so that it can be exhaled out of the body.) CO2 is a waste product produced in the tissues from aerobic respiration. The CO is converted to bicarbonate (HCO3-) in the tissues as a way to shuttle CO2 to the lungs so that it can be exhaled out of the lungs. In the lungs, HCO3- is converted back to CO2, and CO2 is exhaled out of the body. 33
Hemoglobin adopts the T-state conformation and the heme groups become planar. Hemoglobin adopts the R-state conformation and the heme groups become planar. The correct answer is, "Hemoglobin adopts the R-state conformation and the heme group becomes planar." When hemoglobin binds oxygen (in the lungs) in changes into the R-state and the heme groups take on a planar shape. Think of hemoglobin as becoming relaxed as it binds more oxygen, just like you might if you stop and take a deep breath. Think CHART in the tissues, the opposite in the lungs: C for high CO2, H for high H+, A for acidity, R for release of oxygen, and T for T state, or benT heme. Hemoglobin adopts the T-state conformation and the heme groups become bent. Hemoglobin adopts the R-state conformation and the heme groups become bent. 34
Hemoglobin will switch into the R-state and deliver oxygen Hemoglobin will bind and store oxygen Hemoglobin will switch into the T-state and deliver oxygen The correct answer is "Hemoglobin will switch into the T-state and deliver oxygen," because Hemoglobin switches into the T-state and delivers oxygen in the acidic (low pH) environment of exercising muscle tissue. Think CHART: C for high CO2, H for high H+, A for acidity, R for release of oxygen, and T for T state. Hemoglobin will switch into the R-state and bind oxygen 35
The hemoglobin curve will shift to the right when there is a high concentration of H+ (protons) and the concentration of CO2 is high. The correct answer is, "The hemoglobin curve will shift to the right when there is a high concentration of H+ (protons) and the concentration of CO2 is high." A right shift in the hemoglobin curve correlates with a decrease in pH. At low pH, H+/proton concentration is high (this occurs in muscle tissue and tells hemoglobin to release oxygen). In the muscle tissue, at low pH, CO2 concentration is high because it is being produced by the muscles.Think CHART in the tissues, the opposite in the lungs: C for high CO2, H for high H+, A for acidity, R for release of oxygen, and T for T state, or benT heme. The hemoglobin curve will shift to the left when there is a high concentration of H+ (protons) and the concentration of CO2 is low. The hemoglobin curve will shift to the right when there is a low concentration of H+ (protons) and the concentration of CO2 is low. The hemoglobin curve will shift to the left when there is a high concentration of H+ (protons) and the concentration of CO2 is high. 36
The amount of A would decrease The amount of D would increase The amount of C would decrease The amount of E would increase The correct answer is, "The amount of E would increase." If enzyme 4 is inhibited, then D will no longer be made, so C will be converted to E. Thus, E would increase. 37
The amount of compound C would build up The amount of compound B would build up The correct answer is, "The amount of compound B would build up." When an enzyme is inhibited within a pathway, the enzyme’s substrate builds up and its subsequent products will decrease. The amount of compound D would increase The amount of compound A would decrease 38
Kinase The correct answer is, "Kinase." A kinase ‘kindly’ adds a phosphate to a molecule and that phosphate can be removed by a phosphatase. Another way to remember this is that a kinase is "kind and giving" of a phosphate (from ATP). Phosphatase
Option 1 Option 2 Option 3 The correct answer is Option 3, methanol. Alcohol dehydrogenase converts ethanol to acetoacetate, which means that ethanol is the substrate of the enzyme. A competitive inhibitor should have a similar structure as the substrate of the enzyme, since they both compete to bind to the active site of the enzyme. The structure of methanol is very similar to the structure of ethanol. Option 4 43
Communicative Non-competitive Competitive The correct answer is, "Competitive." Competitive inhibitors compete with substrate to bind to the active site of an enzyme and can be out-competed by high concentrations of substrate. Saturated 44
Serotonin AcCoA N-acetyl-serotonin Melatonin The correct answer is, "Melatonin." Since melatonin is the product of the pathway, it can act as a feedback inhibitor by giving a message (feedback) to one of the first enzymes in the pathway, and shut down the pathway. 45
The correct answer is Step 2. The induced fit model describes how substrate binds to the enzyme and forms an enzyme-substrate complex, in which the enzyme wraps itself around the substrate to convert the substrate into product. Step 2 represents the formation of the enzyme-substrate complex. 3 4 46
The correct answer is B, because B is the substrate of enzyme 2. When an enzyme is inhibited within a pathway, the enzyme’s substrate builds up and its subsequent products will decrease. C E
The correct answer is 30. Two ATPs are made from Glycolysis, four is the net loss in the Cori Cycle, 6 is how many ATP are used in the Cori cycle, and 30 is the correct answer. From glycolysis through the ETC, we will produce about 30 ATP. 48
Catabolic Anabolic The correct answer is "anabolic," because ATP is being built by adding a phosphate to ADP to make ATP. Ants like to build (anabolic). In a catastrophe, everything falls apart (catabolic). Dehydration Hydrolysis 49
Acetyl CoA; GTP, ATP Pyruvate; ATP, NADH Acetyl CoA; NADH, FADH
The correct answer is 9 rounds of beta oxidation. 20 carbons/2= 10. 10 -1 for the number of rounds = 9 rounds. 19 20 54
Fermentation Citric acid cycle Glycolysis In Beta-Oxidation, fatty acids are broken down to produce AcCoA and in each round of Beta-Oxidation, NADH and FADH2 are produced. In glycolysis, glucose (six carbons) is cut in half and makes two pyruvates (three carbons each). Two ATPs are needed to start the first steps, and four ATPs are made through substrate-level phosphorylation, giving a net of two ATPs formed. Two NAD+ are also required, which results in the formation of two NADH. Beta-Oxidation 55
NADH is an electron shuttle that carries electrons to the electron transport chain. The correct answer is, "NADH is an electron shuttle that carries electrons to the electron transport chain." NADH and FADH2 are produced by the Citric Acid Cycle and carry electrons to the Electron Transport Chain. NADH is a proton shuttle that carries protons to the electron transport chain. NADH is a high energy molecule that directly fuels all cellular work. NADH is an electron shuttle that carries electron to the Krebs cycle. 56
They are small and can only use glucose as an energy source They do not have mitochondria, so they have to function by anaerobic metabolism The correct answer is, "They can only perform anaerobic metabolism because they lack mitochondria, the organelle where aerobic metabolism occurs." They have a specialized citric acid cycle that allows them to undergo anaerobic metabolism 57
When oxygen is present, pyruvate is converted lactate during fermentation When oxygen is not present, pyruvate enters the mitochondrial matrix and is converted to lactate When oxygen is present, pyruvate is converted to acetyl-CoA in the mitochondrial matrix The correct answer is, "When oxygen is present, pyruvate is converted to acetyl-CoA in the mitochondrial matrix." If it has oxygen, it undergoes aerobic metabolism. If it does not, it is converted into lactic acid in the cytosol in fermentation. When oxygen is present, pyruvate produces glucose to reverse the cycle 58
The starchy foods lead to an increase in acetyl-CoA, which is necessary for fatty acid synthesis. The correct answer is, "The starchy foods lead to an increase in acetyl-CoA, which is necessary for fatty acid synthesis." Glucose and fatty acids do not share similar structures, so glucose cannot be stored as fatty acids.Glucose is stored as glycogen, and most of our energy is stored as triglycerides. Glucose does result in glycosylation, although most of the material is used in fatty acid synthesis. Glucose is processed to acetyl-CoA through glycolysis, and then pyruvate is converted, in the mitochondrion, to acetyl-CoA. If there are high levels of acetyl-CoA present, acetyl-CoA is used to produce fatty acids. Carbohydrates and fatty acids have similar molecular structures. This allows for carbohydrates to be directly stored as fat. The diet has caused a buildup of glycogen in the adipose and muscle cells. An increase in carbohydrates leads to protein glycosylation that results in decreased triglyceride synthesis in the kidneys. 59
Gluconeogenesis Glycogenolysis Glucagon Glycogenesis The correct answer is, "Glycogenesis." After eating a candy bar, Maria will have a lot of glucose in her bloodstream, so insulin will be secreted to lower blood glucose levels. Insulin stimulates the production of glycogen, through glycogenesis, to store excess glucose. Glucagon is not a process. Glucagon is the hormone that is secreted by the alpha cells of the pancreas when the blood sugar is low. Insulin is the hormone that is secreted by the beta cells of the pancreas when the blood sugar is high.
This molecule is the primary component of the lipid bilayer. The correct answer is "This molecule is the primary component of the lipid bilayer." The molecule shown is a phospholipid, which contains a polar phosphate head group and two fatty acid tails. This molecule is the major energy storage molecule found in adipose tissue. This molecule is the precursor to a variety of eicosanoids, including prostaglandins. This molecule is a polysaccharide that stores glucose in the liver and muscle. 65
Iron Glucose Vitamin A The correct answer is, "Vitamin A." Vitamin A is a fat-soluble vitamin that needs fat in order to be absorbed. Insulin 66
Option 1 The correct answer is Option 1, arachidonic acid, which is made from essential fatty acids. Arachidonic acid is best recognized by its characteristic "hairpin" and polyunsaturated structure. Eicosanoids have twenty carbon atoms. Option 2 Option 3 Option 4 67
Long-chain unsaturated The correct answer is, "Long chain unsaturated." This fatty acid has a single double bond, and it has more than 12 carbons. Long-chain saturated Medium-chain unsaturated Medium-chain saturated Short-chain unsaturated
Short-chain saturated 68
Liquid Solid The correct answer is, "Solid." It is a long-chain saturated fatty acid. Long-chain fatty acids have more than 12 carbon atoms, and they have no double bonds. Since the chain is so long, it is a solid at room temperature and stacks well. Bilayer Phospholipid 69
During fasting, these individuals will produce excessive amounts of ketone bodies. They should avoid intake of carbohydrates and instead focus on a high-fat diet. They should ensure that they eat frequently so that their body has adequate supplies of glucose. The correct answer is, "They should ensure that they eat frequently so that their body has adequate supplies of glucose." Individuals that are not able to breakdown lipids should limit their intake of lipids and consume more protein and carbohydrates instead. They will break down CH3(CH2)8CH=CH(CH2)10COOH without a problem. 70
Triglycerides could not be broken down to release fatty acids for beta-oxidation. The correct answer is, "Triglycerides could not be broken down to release fatty acids for beta-oxidation." Lipase is an enzyme that breaks down triglycerides to release the three fatty acids from glycerol. The fatty acids are then used to produce energy when they are broken down through beta oxidation. Triglycerides could not be broken down to release glucose in response to glucagon signaling. Gluconeogenesis could not occur and glucose would have to be taken in from the individual's diet. Amino acids could not be broken down to acetyl-CoA which decrease ATP formed by the electron transport chain.