Module 1 Flashcards
1A - Amino Acids - Carbohydrates and Lipids - Membrane Receptor & Transport; Material Transport - Enzymes 1B ECM, DNA & Protein Synthesis, Gene Expression and Mutations, Bioenergetics, Biological Oxidation & Oxidative Phosphorylation
- Which of the following amino acids, when deficient, will cause a deficit of catecholamines as part of the sympathetic nervous system response?
a. Tryptophan
b. Histidine
c. Tyrosine
d. Glutamate
c. Tyrosine
Catecholamines (norephinephrine, epinephrine) are derived from tyrosine. The protein amino acids phenylalanine and tyrosine serve as precursors of epinephrine, norepinephrine, and DOPA (dihydroxyphenylalanine). (p19 Harpers)
- Selenium deficiency in the diet, leading to Keshan disease, a condition characterized by heart failure, also impairs the body’s ability to clear free radicals. The amino acid that requires selenium is?
a. Synthesized in the nucleus
b. Produced during translation through modification of cysteine
c. Synthesized in the ribosomes
d. Produced during translation through modification of serine
d. Produced during translation through modification of serine.
Selenocysteine is structurally similar to cysteine; both derived from serine. It has selenium residue instead of sulfur. Impairments in human selenoproteins have been implicated in tumorigenesis and atherosclerosis, and are associated with selenium deficiency cardiomyopathy (Keshan disease). (p286 Harpers)
- Which of the following amino acids will most likely cause akink in a helical peptide?
a. Serine
b. Alanine
c. Proline
d. Cysteine
c. Proline
Proline, owing to its uncanny structure (imino acid), causes it to disrupt helices by introducing folds and kinks.
- Glutathione is a tripeptide composed of the following, EXCEPT?
a. Cysteine
b. Glutamate
c. Methionine
d. Glycine
c. Methionine
Glutathione is a tripeptide that is composed of (Glu-Cys-Gly) Glutamate, Cysteine, and Glycine that participates in the metabolism of xenobiotics and the reduction of disulfide bonds, is linked to cysteine by a non-α peptide bond. (Harper p23)
- In sickle cell anemia, the altered hemoglobin structure has which of the following changes to the amino acids involved?
a. Polar to non-polar
b. Basic to acidic
c. Acidic to basic
d. Non-polar to polar
a. Polar to non-polar
Sickle cell is a disease that results from a substitution of a polar amino acid known as glutamate with a nonpolar one valine at position six of the beta polypeptide unit of hemoglobin. The substitution happens as a result of a change in one of the bases in the beta-globin gene from adenine to thymine. (Harper p417)
- A patient is diagnosed with familial hypercholesterolemia where there is a mutation in the receptors needed for lipoprotein transport and docking into the liver. Which of the following is a most likely outcome?
a. Poor wound healing
b. Hemolytic anemia
c. Decreased plasma lipoproteins
d. Early onset cardiovascular disease
d. Early Onset Cardiovascular Disease
Inherited defects in lipoprotein metabolism lead to the primary condition of either hypo- or hyperlipoproteinemia. For example, familial hypercholesterolemia (FH), causes severe hypercholesterolemia and is also associated with premature atherosclerosis. (Harpers p275)
- Which of the following stabilizes the secondary structure of peptides?
a. Salt bridges
b. Hydrophobic interactions
c. Peptide bonds
d. Hydrogen bonds
d. Hydrogen Bonds
Secondary structures are usually the general conformation or how the peptide is folded. Alpha helices, which is one of the abundant secondary structures for globular proteins, are stabilized by hydrogen bonding between the amide nitrogens and carbonyl carbons of peptide bonds. While for the Beta Sheets, which can be found more prominent in fibrillar proteins, are also being stabilized by hydrogen bonds for folding and alignment.
- A patient with osteogenesis imperfecta has a mutation in the gene encoding for collagen leading to poor bone and soft tissue maturation and development. The resulting collagen protein most likely has an altered?
a. Primary protein structure
b. Secondary protein structure
c. Primary, Secondary, Tertiary, and Quarternary protein structures
d. Tertiary protein structure
c. Primary, Secondary, Tertiary, and Quarternary protein structures
Osteogenesis Imperfecta (brittle bones) is characterized by abnormal fragility of bones. -Exome sequencing has emerged as an alternative to whole genome sequencing as a means for diagnosing rare or cryptic genetic diseases like the osteogenesis imperfecta. -Since it affects the sequencing, it has already affected the protein structure starting from the primary.
- Which of the following amino acids is neutrally charged at physiologic pH?
a. Histidine [Considered correct after revisions]
b. Aspartate
c. Arginine
d. Leucine
a. Histidine (Considered Correct after Revisions) AND d. Leucine
Histidine plays unique roles in enzymatic catalysis. The pKa (6.0) of its imidazole proton permits histidine to function at neutral pH as either a base or an acid catalyst without the need for any environmentally induced shift.
Leucine is an amino acid with aliphatic side chains that is branched and it is a non-polar which makes it a neutrally charged at physiologic pH
- A mutation in the peptide portion of a glycoprotein will most likely impair?
a. Cell-to-cell communication
b. Stability of connective tissue
c. Activation of thyroid hormones
d. Intercellular transport of lipids
a. Cell-to-cell communication
Glycoproteins are covalently associated with carbohydrates and it is functionally active in cell to cell interactions.
- An ion transporter containing 5 sub-units uses which level/s of protein structure?
a. Quaternary only
b. Primary, Secondary, Tertiary, and Quarternary
c. Primary, Secondary and Tertiary only
d. Primary and Secondary only
b. Primary, Secondary, Tertiary, and Quarternary
Many proteins consist of more than one polypeptide chain in their functional states. Each polypeptide chain in such a protein is called a subunit. -All levels of protein structure are used in 5 sub-units ion transporter since polypeptide chain will not be produced when it does not start with the primary protein structure which is responsible for the sequence of the chain. In secondary structure, it is responsible for the folding of the chain. In tertiary structure, it is responsible for the 3-D folding pattern. Then, quaternary structure is the arrangement of subunits and the nature of their interactions.
- A procedure that obliterates disulfide bonds between proteins, as in rebonding of hair, alters which level of protein structure?
a. Primary
b. Secondary
c. Tertiary
d. Both primary and secondary
c. Tertiary
Tertiary protein structures are stabilized by noncovalent and covalent interactions; and some of these are hydrophobic interactions, hydrogen bonds, salt bridges, and disulfide bonds – where the sulfhydryl groups of cysteinyl residues in a tertiary protein are bonded. Any alterations affecting these interactions in particular, like the disulfide bond, will lead to the denaturation of a tertiary protein.
- Which of the following amino acids actively participates in N-linked glycosylation?
a. Asparagine
b. Tyrosine
c. Histidine
d. Serine
a. Asparagine
Glycoproteins are proteins that contain oligosaccharide chains (glycans) covalently bound to amino acids. This bond is formed from a process called glycosylation, which is the enzymatic attachment of sugars, and the linkage can either be O-linked or N-linked.
- Ganglioside GM1 serves as the receptor for the cholera toxin, which is responsible for causing voluminous diarrhea in cholera. To gain entry into intestinal cells, the cholera toxin specifically binds to the
a. Alcohol head group
b. Monosaccharide (glucose or galactose) moiety
c. Oligosaccharide moiety
d. Phosphate group
c. Oligosaccharide
Moiety Gangliosides are glycosphingolipids, which contain sphingosine and sugar residues as well as a fatty acid. GM1, a complex ganglioside, is known to be the receptor in the human intestine for cholera toxin. Merritt et al. (1994) states that cholera toxin (CT) links to the pentasaccharide moiety of ganglioside GM1.
Please refer to the image. Technically, D-mannose and Dgalactose are _____ with respect to each other.
a. Diastereoisomers
b. Enantiomers
c. None of the choices
d. Constitutional Isomers
a. Diastereoisomers
Diastereoisomers are a type of stereoisomer that are not mirror images of each other. This is as opposed to enantiomers, which are non-superimposable mirror images, and constitutional isomers, which differ in the way the components of the molecule are attached and arranged. (Tymoczko, Berg & Stryer, 2015, pg. 168)
- When glycoproteins lose these saccharide residues from their oligosaccharide chains, they are endocytosed by the liver and thus cleared from circulation.
a. Galactose
b. Fucose
c. Sialic acid
d. Mannose e. N-acetylgalactosamine
c. Sialic Acid
“Loss of terminal sialic acid residues accelerates clearance of plasma glycoproteins from the circulation.”
- The following statements regarding glycosaminoglycans are correct, EXCEPT
A. They extend perpendicularly from core proteins of proteoglycans in a bottlebrush-like structure.
B. As a group, they are considered as the heteropolymeric type of polysaccharides.
C. Genetic inability of the body to break them down leads to development of mucopolysaccharidoses.
D. An example would be a repeating disaccharide unit containing neuraminic acid and galactosamine.
d. An example would be a repeating disaccharide unit containing neuraminic acid and galactosamine.
This choice is incorrect, as the structure of a glycosaminoglycan consists of a repeating disaccharide unit containing an amino sugar and uronic acid. Reference: Module 1A.5 Carbohydrates of Physiological Significance PDF, Page 11
- Medications such as Ibuprofen (Advil) and Mefenamic acid (Dolfenal) work by inhibiting or preventing the production of prostaglandins, eicosanoids responsible for mediating pain and inflammation. Which of the following enzymes is the most likely target of these drugs for inhibition?
a. Cyclooxygenase
b. Phosphodiesterase
c. Nucleotide cyclase
d. Lipoxygenase
a. Cyclooxygenase
Indomethacin and ibuprofen inhibit cyclooxygenases by competing with arachidonate. (Rodwell, Bender, Botham & Kennelly, 2018, pg. 226) Reference: Rodwell, V. W., Bender, D. A., Botham, K. M, Kennelly, P. J. & Weil, P. A. (2018). Harper’s illustrated biochemistry [31st ed.]. McGraw-Hill Education.
- Which of the following is the most appropriate nomenclature for alpha-linoleic acid? Examine the image carefully!
a. Omega-9 PUFA
b. 18:3 (Δ 9,12,15)all-cis
c. 18:3 (Δ 9,12,15)all-trans
d. Omega-3 MUFA
e. 20:4 (Δ 1,9,12,15)all-cis
b. 18:3 (Δ 9,12,15)all-cis
Carbon atoms are counted from the carboxyl carbon (C-1). Succeeding carbons C-2, C-3, and C-4 are also known as ⍺, 𝛽, and 𝛾 carbons. DΔN denotes the number of double bonds (D) and position (N) from the carboxyl carbon (C-1). Trans isomers have hydrogen on opposite side; cis isomers have hydrogen bonds on the same side. Structure shows an 18-carbon fatty acid with 3 double bonds located at the 9th, 12th, and 15th carbon from C-1 all in the cis formation (18:3Δ9,12,15)-all cis. Reference: Dr. Van Haute - Lecture on Carbohydrates and Lipids of Physiologic Significance (Part 3)
- The straight-chain form of a monosaccharide derivative will be unable to cyclize if
a. At least one of the parent monosaccharide’s hydroxyl groups is replaced by a hydrogen.
b. When a hydroxyl group of a parent monosaccharide has been replaced with an amino group.
c. The carbonyl group of the parent monosaccharide’s aldose or ketose is reduced to an alcohol.
d. When there is one carboxyl group on each end of the straight-chain monosaccharide.
c. The carbonyl group of the parent monosaccharide’s aldose or ketose is reduced to an alcohol.
Cyclic structures are formed by the reaction between the aldehyde or ketone group with an alcohol. Loss of aldehyde or ketone by reduction prevents cyclization. (Tymoczko, Berg, and Stryer, 2015, pg. 169-170) Reference: Tymoczko, J. L., Berg, J. M., & Stryer, L. (2015). Biochemistry: A short course (p. 169-170). New York: W.H. Freeman & Company.
- Which of the following occurs during the cyclization of a linear fructose molecule?
a. A ketal is formed following a nucleophilic attack on the hemiketal group by a hydroxyl group from another monosaccharide.
b. Two forms that are non-superimposable mirror images of each other emerge in solution at equilibrium.
c. A hemiacetal is formed following a nucleophilic attack on the ketone group by a hydroxyl group on the same molecule.
d. A hemiketal is formed following a nucleophilic attack on the aldehyde group by a hydroxyl group on the same molecule.
e. A new asymmetric carbon is designated, with two anomeric forms of the molecule emerging at equilibrium.
e. A new asymmetric carbon is designated, with two anomeric forms of the molecule emerging at equilibrium.
Anomers are isomers that differ at a new asymmetric carbon atom formed on ring closure. Furanose-ring of fructose has anomeric forms ⍺ and 𝛽 at the anomeric carbon C2 (see image below). These two structures are present at equilibrium. (Tymoczko, Berg, and Stryer, 2015, pg. 170) Reference: Tymoczko, J. L., Berg, J. M., & Stryer, L. (2015). Biochemistry: A short course (p. 170). New York: W.H. Freeman & Company.
- Which of the following carbohydrates would not be able to lose its electrons to oxidize another chemical species?
- Sucrose
- Lactose
- Fructose
- Galactose
- Glucose
a. Sucrose
Reducing agents are capable of reducing its electrons to oxidize another chemical species. Since sucrose is a non-reducing sugar, it may not perform such function. Reference: Handout 1 Carbohydrate and Lipid Chemistry, Module 1A, Dr. Van Haute’s Lecture
- Compared with palmitic acid (16:0), oleic acid (18:1 Δ 9 cis) has a lower melting point because oleic acid has
- a kink produced by the double bond.
- a longer hydrocarbon chain.
- a trans-double bond at carbon 9.
- a more saturated chain.
a. a kink produced by the double bond.
Oleic acid contains a double bond, hence making it an unsaturated fatty acid. Melting point of fatty acids decreases/lowers because of this double bond, which produces a kink in the chain. Reference: Rodwell, V., Bender, D., Botham, K., Kennelly, P., & Weil, A. P. (2015b). Harper’s Illustrated Biochemistry (30th ed., p. 213). McGraw-Hill Education / Medical.
- A medication called Montelukast (brand name, Singulair) antagonizes or blocks the leukotrienes responsible for bronchoconstriction (narrowing of the airways) during asthmatic attacks. Leukotrienes are eicosanoids derived specifically from which of the following? Choose the best answer.
- Eicosapolyenoic acid
- Arachidonic acid
- Ceramide
- Phosphatidylinositol
b. Arachidonic Acid
Leukotrienes are derived from arachidonic acid through the lipoxygenase pathway. Reference: Rodwell, V., Bender, D., Botham, K., Kennelly, P., & Weil, A. P. (2015b). Harper’s Illustrated Biochemistry (30th ed., p. 240). McGraw-Hill Education / Medical.
- Antiphospholipid antibody syndrome (APLAS), a disorder strongly associated with recurrent miscarriages, frequently manifests as having detectable antibodies in the blood directed against
- phosphatidylinositol.
- phosphatidylserine.
- phosphatidylcholine.
- phosphatidylethanolamine.
- diphosphatidylglycerol.
e. Diphosphatidylglycerol
Antibodies against diphosphatidylglycerol (cardiolipin) often develop in antiphospholipid antibody syndrome (APLAS). Reference: 2023 Biochem Ratio
- Plasmalogen and platelet activating factor specifically have which of the following distinctive components in their structures?
- A mono- or oligosaccharide attached to sn-3 of glycerol via a glycosidic bond
- An amino alcohol head group attached to sn-3 of glycerol via a phosphodiester bond
- A hydrocarbon chain attached to sn-1 of glycerol via an ether bond
- A fatty acid attached to sn-2 of glycerol via an ester bond
c. A hydrocarbon chain attached to sn-1 of glycerol via an ether bond
The fatty acid at the sn-1 carbon of a glycerophospholipid is replaced by an unsaturated alkyl group attached by an ether (rather than an ester) linkage to the core glycerol molecule References: Rodwell, V. W., Bender, D. A., Botham, K. M., Kennelly, P. J., & Weil, P. A. (2018). Harpers illustrated biochemistry. New York: McGraw-Hill Medical. Ferrier, D. R. (2017). Lippincott illustrated reviews: Biochemistry. Philadelphia: Wolters Kluwer.
- Lung surfactant keeps alveoli from collapsing especially during expiration (exhalation). The major component of lung surfactant, dipalmitoylphosphatidylcholine (that is, phosphatidylcholine wherein the 2 fatty acid esters are palmitic acid; see structure in image) is a
- Sphingophospholipid
- Glycerophospholipid
- Ether glycerolipid
- Glycosphingolipid
b. Glycerophospholipid
A glycerophospholipid consists of a glycerol backbone and an ester. In the structure, the one encircled is a glycerol backbone connecting the 2 esters and phosphatidylcholine. In DPPC, positions 1 and 2 on the glycerol are occupied by palmitate. Reference: Ferrier, D. R. (2017). Lippincott illustrated reviews: Biochemistry. Philadelphia: Wolters Kluwer.
- When two carbohydrates are epimers,
- One is an aldose and the other is a ketone
- They rotate plane-polarized light in the same direction
- One is a pyranose and the other is a furanose
- They differ in the configuration around one carbon atom only
- They differ in length by one carbon
d. They differ in the configuration around one carbon atom only
Isomers that differ in configuration of the -OH and -H on carbon atoms 2, 3, and 4 of glucose are defined as epimers of each other.
- This is a key molecule needed for protein degradation
a. Clathrin
b. Ubiquitin
c. Heat shock protein
d. COPI
b. Ubiquitin
Lysosomal protease, a major pathway for protein degradation, does not use ATP but involves ubiquitin. Ubiquitin is a small, highly conserved protein that tags various proteins for degradation in proteasomes. The ubiquitin pathway is associated with the disposal of misfolded proteins and regulatory enzymes that have short half-lives. Polyubiquitinated target proteins enter proteasomes in the cytosol, which is composed of 4 rings with the protease active sites and 1 or 2 caps that recognize the polyubiquitinated substrates and initiate degradation. Target proteins unfold via ATPase in the cap. Target proteins are degraded to small peptides in the core and further degraded by cytosolic peptidases once out of the proteasome. Reference: Harper’s Illustrated Biochemistry 31st edition. Chapt. 49
- Alternating charged and uncharged series
a. Nuclear importation
b. Nuclear exportation
c. Mitochondrial importation
d. Peroxisomal importation
e. ER importation
b. Nuclear exportation
- N-terminal signal of 5 to 10 hydrophobic amino acids
a. Peroxisomal importation
b. ER importation
c. Mitochondrial importation
d. Nuclear importation
e. Nuclear exportation
b. ER importation
- Positively charged amino acids series
a. Nuclear importation
b. Mitochondrial importation
c. ER importation
d. Peroxisomal importation
e. Nuclear exportation
a. Nuclear importation
In nuclear import, proteins to be imported carry a nuclear localization signal (NLS). One example of an NLS is the amino acid sequence (Pro)2(Lys)3-Arg-Lys-Val, which is markedly rich in basic residues.
- After protein synthesis, what is the correct sequence of events for exocytosis?
a. Nucleus to Golgi Complex to ER to Plasma Membrane
b. ER to Mitochondria to Golgi Complex to Plasma Membrane
c. Plasma Membrane to Golgi to ER to Nucleus
d. ER to Golgi Complex to Vesicles to Plasma Membrane
d. ER to Golgi Complex to Vesicles to Plasma Membrane
Proteins synthesized and sorted in the RER branch include many destined for various membranes (eg, of the ER, Golgi apparatus [GA], plasma membrane [PM]) as well as lysosomal enzymes, and also those for export from the cell via exocytosis (secretion).These various proteins may thus reside in the membranes or lumen of the ER, or follow the major transport route of intracellular proteins to the GA. In the secretory or exocytotic pathway, proteins are transported from the ER → GA→ PM and then released into the external environment. Reference: Harper’s Illustrated Biochemistry 30th ed. Chap 49 pg. 608
- 3 amino acids at carboxy terminus
a. Peroxisomal importation
b. Nuclear importation
c. Mitochondrial importation
d. ER importation
e. Nuclear exportation
a. Peroxisomal importation
Reference: Doc Raymond ppt
- Alternating positively charged amino acids with hydrophobic amino acids
a. Mitochondrial importation
b. ER importation
c. Nuclear importation
d. Nuclear exportation
e. Peroxisomal importation
a. Mitochondrial importation
Reference: Doc Raymond ppt
- Which of the following vesicles is responsible for anterograde protein transport?
a. V Snares
b. COPI
c. T Snares
d. COPII
d. COPII
A number of proteins possess the amino acid sequence KDEL (Lys-Asp-Glu-Leu) at their carboxyl terminal KDEL-containing proteins first travel to the GA in vesicles coated with coat protein II (COPII). This process is known as anterograde vesicular transport. In the GA they interact with a specific KDEL receptor protein, which retains them transiently. They then return to the ER in vesicles coated with COPI (retrograde vesicular transport), where they dissociate from the receptor, and are thus retrieved. HDEL sequences (H = histidine) serve a similar purpose. Reference: Harper’s Illustrated Biochemistry 30th ed. Chap 49 pg. 621
- Sphingomyelin is a molecule identified in a plasma membrane. Which of the following describes its location in that membrane?
a. Intercalated between phospholipids
b. The outer membrane leaflet
c. Extending into the environment
d. In a transmembrane arrangement
b. The outer membrane leaflet
Sphingomyelin are found in the outer leaflet of the cell membrane and are particularly abundant in specialized areas of the plasma membrane known as lipid rafts. Reference: Harper’s Illustrated Biochemistry 31st ed. Chap 21 pg. 200
- A plasma membrane is observed to have caveolae. These structures are:
a. Composed of disorderly phospholipids
b. Cholesterol-enriched membrane invaginations
c. Intercalated between cholesterol molecules
d. Components of phospholipids
b. Cholesterol-enriched membrane invaginations
Lipid rafts are specialized areas of the outer leaflet of the lipid bilayer enriched in cholesterol, sphingolipids, and certain proteins. Caveolae may derive from said lipid rafts. Reference: Harper’s Illustrated Biochemistry 31st ed. Chap 40 pg. 466
- A ligand receptor is identified in a plasma membrane of a living cell. The arrangement of that ligand receptor within the membrane is best described as a/an:
a. Lipid-anchored protein
b. Glycolipid
c. Integral membrane protein
d. Peripheral protein
c. Integral membrane protein
Most membrane proteins fall in the integral class, meaning that they interact extensively with the phospholipids and require the use of detergents for their solubilization. Reference: Harper’s Illustrated Biochemistry 31st ed. Chap 40 pg. 464-465
- The degradation of improperly folded Endoplasmic Reticulum proteins occurs in the:
a. Mitochondria
b. Lysosomal compartment
c. ER lumen
d. Proteasome in the cytoplasm
d. Proteasome in the cytoplasm
Improperly folded ER proteins are exported and degraded in the cytosol. Dr. Raymond Cruz’ ppt. Slide 51
- Which of the following statements regarding membranes is FALSE?
a. Proteins are the most abundant type of macromolecules within cell membranes
b. The model that best describes the plasma membrane is the fluid mosaic model
c. Membrane leaflets have an asymmetric distribution
d. Plasma membranes are selectively permeable structures of eukaryotic cells
a. Proteins are the most abundant type of macromolecules within cell membranes
The basic structure of all membranes is the lipid bilayer. This bilayer is formed by two sheets of phospholipids in which the hydrophilic polar head groups are directed away from each other and are exposed to the aqueous environment on the outer and inner surfaces of the membrane. Reference: Harper’s Illustrated Biochemistry 30th ed. Chap 40 pg. 497
- Lactate dehydrogenase has five isoenzymes. The following statements regarding these isoenzymes of LDH are true EXCEPT:
a. They produce different migration patterns during electrophoresis
b. They are made up of different subunits
c. They are characteristically produced by different types of tissues
d. They bind to the same substrate but produce different products
d. They bind to the same substrate but produce different products
Lactate dehydrogenase is comprised of two domains, an N-terminal NAD+-binding domain and a C-terminal binding domain for the second substrate, pyruvate. Reference: Harper’s Illustrated Biochemistry 30th ed. Chap 5 pg. 40
- Identify the type of inhibitor
a. Non-competitive
b. All of the choices
c. Competitive
d. Uncompetitive
c. Competitive
Competitive - inhibitor has no effect on Vmax but raises K′m
- The removal of a hydrogen ion from water by one aspartic acid residue in the active site of HIV protease makes water more nucleophilic; the donation of another hydrogen ion by another aspartic acid residue facilitates the breakdown of the tetrahedral intermediate. Identify the mechanism of action.
a. Covalent catalysis
b. General acid/base catalysis
c. Proximity and orientation effect
d. Desolvation effect
e. Strain effect
b. General acid/base catalysis
- Identify the enzyme class.
a. Oxidoreductase
b. Isomerase
c. Hydrolase
d. Lyase
b. Isomerase
Isomerase, a class of enzymes that catalyze reactions involving a structural rearrangement of a molecule. This step in glycolysis is catalyzed by triose phosphate isomerase. Isomerases catalyze isomerization reactions (geometric/structural changes). This step completes the first phase of glycolysis. Reference: Cruz, R. (n.d.).Powerpoint presentation: Enzymes.
- Which of the following is a correct enzyme: cofactor pair?
a. Lysyl oxidase: Cuprous ion
b. Prolyl hydroxylase: Pyridoxal phosphate
c. Aspartate aminotransferase: Thiamine pyrophosphate
d. Alanine aminotransferase: Biotin
a. Lysyl Oxidase: Cuprous Ion
- Transaminase enzymes require pyridoxal phosphate
- Prolyl hydroxylase requires Ascorbic Acid (Vitamin C), NOT pyridoxal phosphate
- Lysyl Hydroxylase requires Ascorbic Acid (Vitamin C) and Cuprous Ion
- All of the following statements are true of collagen EXCEPT:
a. It has glycine residues at every third position of the alpha chain
b. It has many different genetic types
c. It undergoes extensive post translational modification
d. It has intramolecular desmosine cross-links in its structure
d. It has intramolecular desmosine cross-links in its structure
- True of bone tissue:
a. Osteoclasts synthesize most of the proteins found in bone
b. The inorganic component is mainly hydroxyapatite
c. The major protein is Type IV Collagen
d. The sole cation that can be incorporated in bone tissue is calcium
b. The inorganic component is mainly hydroxyapatite
- Glycosaminoglycans (GAG) are also known as mucopolysaccharides. What is the primary defect seen in the group of diseases generally referred to as mucopolysaccharidoses (MPS)?
a. A defect in the Golgi complex
b. Accumulation of GAG in the cell
c. A mutation in the DNA for GAGs
d. Impaired GAG synthesis
b. Accumulation of GAG in the cell
The mucopolysaccharidoses (MPSs) are a family of inherited disorders of GAG degradation. (Rodaks, p.481)
They are due to lysosomal storage abnormalities, which allow the proliferation and non-degradation of GAG in cells. There is no synthesis abnormality involved because the problem is in degradation. No DNA mutation or Gogli complex defect is involved.
- A 40-year-old female presents with a low grade fever, nonproductive cough and was diagnosed with pneumonia. She was advised to take erythromycin. Which of the following is the mechanism of action of erythromycin?
a. inhibits the initiation factor 1
b. inhibits the 50s ribosomal subunit
c. binds to the Shine Dalgarno sequence
d. inhibits the incoming aminoacyl tRNA
b. Inhibits the 50s ribosomal subunit
- There is only one kind of amino acyl tRNA synthetase
a. True
b. False
b. False
Each codon represents a particular amino acid, and each codon (20) is recognized by a specific tRNA
- A 4 month old infant with rhinitis and coughing was tested positive for Bordella pertussis. He was given an antibiotic that inhibits translocation of peptidyl-tRNA on 70s ribosomes. This patient is most likely treated with
a. erythromycin
b. tetracyclin
c. streptomycin
d. lincomycin
a. Erythromycin
Erythromycin is an antibiotic that inhibits protein synthesis by inhibiting translocation during translation. It specifically acts on the 50s subunit of the ribosome.
Tetracyclin inhibits aminoacyl tRNA binding on the A-site
Streptomycin inhibits codon-anticodon initiation and elongation
Lincomycin inhibits peptidyl transferase
- A mutation that replaces pyrimidine with purine
a. transversion
b. frameshift
c. transition
d. silent
a. transversion
Single-base changes (point mutations) may be transitions or transversions. In the former, a given pyrimidine is changed to the other pyrimidine or a given purine is changed to the other purine. Transversions are changes from a purine to either of the two pyrimidines or the change of a pyrimidine into either of the two purines, as shown in Figure 37–3.
- Which of the following regulators are said to act in “trans”?
a. the lac operator and the mammalian transcription factors
b. the lac repressor and the mammalian enhancers
c. the lac transcription factors and the mammalian activators
d. the tryp operon co-repressor and the lac operator
c. the lac transcription factors and the mammalian activators
Regulatory elements Classified into two types, based on their “location”
- Cis-acting elements - DNA sequences that exert their effect only on nearby genes Example: TATA box, enhancers and silencers ν
- Trans-acting elements - Regulatory proteins that bind to such DNA sequences Example: Reference: Gene Expression Compendium by Sheila Maria P. Torres M.S.
- Which of the following statements describes how glucagon stimulates transcription of PEPCK gene
a. binding of the glucagon by cell surface receptors initiates a chain of events that results in the phosphorylation of CREB protein
b. glucagon forms a complex with adenylate cyclase resulting in the synthesis of cAMP and activation of protein kinase
c. glucagon forms a complex with glucocorticoid response elements associated with PEPCK
d. binding of glucagon to the CRE that activates PEPCK gene
a. binding of the glucagon by cell surface receptors initiates a chain of events that results in the phosphorylation of CREB protein
- Complex IV of the electron transport chain catalyzes the transfer of reducing equivalents from cytochrome c to molecular oxygen, resulting in the formation of water. Complex IV is thus a/an
a. oxygenase
b. oxidase
c. hydroperoxidase
d. dehydrogenase
b. oxidase.
Oxidase removes hydrogen from a substrate and transfers it to oxygen to form water or hydrogen peroxide Reference: Page 4/8 of the handout on Biological Oxidation provided by Dr. Van Haute
- Consider a biochemical reaction that started with equal amounts of substrate and product, and was allowed to reach equilibrium. If the value of the equilibrium constant (Keq) is 5.1, this means that
a. ΔG0’ is positive
b. ΔG0’ is zero
c. –RT(ln Keq) is negative
d. ln Keq is negative
c. –RT(ln Keq) is negative
Reference: Doc Van Haute’s Handout on Bioenergetics
- The proliferation of cytotoxic T-cells is impaired upon infection with HIV-V. The defect has been traced to the expression of the viral-encoded enzyme that inactivates a host cell nuclear protein required for DNA replication. Which protein is a potential substrate for the viral enzyme?
a. Catabolite activator protein
b. TATA binding protein
c. Single Strand Binding Protein
d. Cap Binding Protein
c. Single Strand Binding Protein
Explanation# 1:
- Prokaryotic Enzymes of Replication The single-stranded DNA that result from the helicase action is coated with single-stranded DNA-binding protein that prevents reannealing of parental strands and prevent hairpins and other super secondary structures from forming in the sing stranded DNA
Explanation# 2:
- SSBs bind ssDNA with high affinity and in a sequence-independent manner and, in doing so, SSbs help to form central nucleoprotein complex substrates for DNA replication, recombination, and repair processes.
- Which of the following types of mutation describes sickle cell anemia
a. transversion, nonsense
b. transition, missense
c. transversion, missense
d. transition, nonsense
c. Transversion, Missense
Purine- Adenine, Guanine (A & G)
Pyrimidines- Cytosine, Thymine (C & T)
Point Mutation Types:
- Transitions- interchanges of purines (A G) or pyrimidines (C T).
- Transversions- interchanges of purine for pyrimidine bases or vice versa.
- Ex. (A C), (A T), (G C), (G T)
Substitution Mutation Types:
- Silent mutations have no effect on the protein.
- Missense mutations result in a single amino acid change in the translated sequence.
- Nonsense mutations result in an amino acid codon being replaced by a “stop” codon. Nonsense mutations end translation prematurely and result in a truncated protein.
- MELAS Syndrome (Mitochondrial Encephalopathy, Lactic Acidosis, and Stroke-like episodes) is an inherited condition caused by mitochondrial DNA or tRNA mutations that result in electron transport chain complex deficiency. One form of such disease results in mitochondrial Complex IV deficiency. For patients with this type of the disease, what would be the net ATP produced for one molecule of NADH as an electron carrier?
a. 0
b. 1
c. 4
d. 2
d. 2
Complex 4 transfers 2 hydrogen ions to the interstitial space. Since it is inhibited and then instead of 10 hydrogen ions only 8 hydrogen ions will be formed. Since 4 hydrogen ions are required for 1 ATP synthesis. Therefore 2 ATP will be produced Reference: handout in Oxidative phosphorylation provided by Dr. Van Haute
- A university student takes some tablets she is offered at a club, and without asking what they are, she swallows them. A short time later, she started to hyperventilate and feel hot all over. She was brought to the ER, where her temperature was found to be 41ºC. What is the most likely action of the tablets she took?
a. Stimulation of mitochondrial ATP synthesis
b. Uncoupling of mitochondrial electron transport and oxidative phosphorylation
c. Stimulation of ATP transport out of the mitochondria into the cytosol
d. Inhibition of mitochondrial electron transport
e. Inhibition of ADP transport into mitochondria to be phosphorylated
b. Uncoupling of mitochondrial electron transport and oxidative phosphorylation
- In redox reactions, these 2 groups of coenzymes react directly with substrates to obtain their reducing equivalents.
a. NADH and FADH2
b. H2O and CO2
c. NAD+ and FAD
d. NADPH and ATP
c. NAD+ and FAD
“NAD+ and FAD reacts directly with H+ to form NADH+ and FADH2 respectively.”
Redox Reactions (Oxidation-reduction reactions)
- Chemical reaction that involves a transfer of electrons between two chemical species (atom, molecule, or ion)
- What is Reduced is the one accepting electrons. (the fuel in this example is carbohydrate)
- Which of the following examples show negative transcriptional control?
a. any situation that inactivates repressor
b. inhibition of EF2
c. binding of transcription factor to the inducer
d. protein blocks the access of RNA Polymerase to the gene’s promoter region
d. protein blocks the access of RNA Polymerase to the gene’s promoter region
Types of Gene Regulation:
- Positive Regulation (Positive Transcriptional Control) – Expression of the genetic information is increased by the presence of specific regulatory element (activator/inducer)
- Negative Regulation (Negative Transcriptional Control) – Expression of the genetic information is diminished by specific regulatory element (repressor).
The repressor binds to the Operator to block the RNA polymerase from “going” to the structural gene in order to prevent it from transcribing unnecessary/unneeded protein. Reference: Doc Shiela’s Compendium on “Gene Regulation and Mutation”
- A biochemical reaction occurs spontaneously if
a. Both ΔE and ΔS are positive, with ΔE having a much greater magnitude
b. The ΔE is negative, while the ΔS is positive
c. Both ΔE and ΔS are negative, with ΔS having a much greater magnitude
d. The ΔE is positive, while the ΔS is negative
b.The ΔE is negative, while the ΔS is positive
- Examine the following statements. Which statement best describes the direction a biochemical reaction will take?
a. Under standard conditions, a reaction will proceed in a forward direction if the free energy ΔG0’ is positive.
b. The direction of a reaction is independent of the initial substrate and product concentrations, because the direction is determined by the change in free energy.
c. One can easily determine the rate at which a reaction’s equilibrium can be reached by looking at the ΔG0’.
d. A reaction with +ΔG0’ proceeds in a forward direction if the substrate concentration is raised high enough, and its product is rapidly cleared by a subsequent reaction.
d. A reaction with +ΔG0’ proceeds in a forward direction if the substrate concentration is raised high enough, and its product is rapidly cleared by a subsequent reaction.
Recall that metabolic pathways must have an overall negative △ G°(provided by ATP hydrolysis) to favor the formation of products over the formation of reactants. In that same vein, it is possible for reactions in the pathway with positive △ G°’ to proceed in the forward direction if:
- The concentration of that reaction’s substrate is raised to a high enough level. This increase in substrate concentration is provided by the reaction preceding the + △ G°’ reaction in question along the metabolic pathway.
- The concentration of that reaction’s product is decreased to a very low level. This occurs when the subsequent reaction (which uses the + △ G°’ reaction’s product as substrate) clears the product.
These 2 processes cause disequilibrium as far as the + △ G°’ reaction is concerned because of more substrate and less product than usual compared to the levels present at equilibrium. In order to obtain equilibrium again, the + △ G°reaction has to move forward. This reiterates the fact that the direction if a reaction is dependent on the initial substrate and product concentration as reflected in Keq. While the general principle is “larger and more negative G°-> spontaneous remains true, △ G°, however is not an indicator of the velocity of the reaction or the rate at which equilibrium can be reached. This actually depends on the efficiency and amount of enzyme available to catalyze the reaction.
- Examine the following statements regarding molecular oxygen, and choose the one which is the most accurate.
a. It has a high positive redox potential, thus easily reduces other molecules.
b. It has a negative redox potential, thus easily oxidizes other molecules.
c. It has a negative redox potential, thus easily reduces other molecules.
d. It has a high positive redox potential, thus easily oxidizes other molecules
d. It has a high positive redox potential, thus easily oxidizes other molecules
Redox Potential (E0’)
- A measure (in volts) of the energy change when that compound accepts e–
- Expression of the willingness of a compound to accept electrons.
- The more positive the Redox Potential, the more willing it is to accept electrons.
- (More positive = Better as Oxidizing agent) That’s why it can easily oxidize other molecules.
In contrast:
- The more negative the Redox Potential, the more willing it is to give off electrons.
- (More negative = Better as Reducing agent)
