Exam 1 Cards Combined

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  1. What is the function of anhydrases?
    They remove water from a substrate.
  2. What is the difference between a synthase and a synthetase?
    Both enzymes catalyze chemical synthesis. Synthetases involve concurrent hydrolysis of a nucleoside triphosphate such as ATP whereas sythases do not.
  3. What is the function of hydrolases?
    They break chemical bonds with the addition of a water molecule.
  4. What is the function of isomerases?
    They rearrange the atoms of a substrate without changing the number or type of atoms within it.
  5. What is the function of endo- and exo- nucleases?
    These enzymes digest DNA or RNA. Endonucleases cut in the middle of an oligonucleotide whereas exonucleases cut from the ends of an oligonucleotide.
  6. What is the function of proteases?
    They digest, or break down, proteins.
  7. What is the function of lyases?
    They break chemical bonds without addition of water or oxygens.
  8. What is the function of cyclases?
    They make a cyclic product from a non-cyclic substrate (i.e. AMP into cAMP). Adenylyl cyclases catalyzes the following reaction: ATP -> 3',5' cyclic AMP + PPi.
  9. What type of enzyme is this (hint: it functions as two enzymes in one)?
    It is both a cyclase (because it makes a cyclic product) and a lyase (because it cleaves its substrate without adding water or oxygen to the product).
  10. What is chemical oxidation?
    Oxidation (catalyzed by oxidases) is the loss of electrons by a molecule or atom. For instance, when Fe+2 is oxidized, it becomes Fe+3.
  11. What is chemical reduction?
    Reduction (catalyzed by reductases) is the gain of electrons by an atom or molecule. It causes a reduction in charge.
  12. What is the function of dehydrogenases?
    They oxidize a substrate by moving a hydride ion from the substrate to an acceptor such as NAD+ or NADP+, forming NADH or NADPH, respectively.
  13. What is the function of oxidoreductase enzymes?
    They transfer an electron from a reductant (electron donor) to an oxidant (electron acceptor).
  14. What is the function of kinases and phosphatases?
    Kinases add a phosphate to a substrate. Phosphatases remove a phosphate (Note that a phosphate is a PO4 group and has a net charge of -3).
  15. What is the function of ligases?
    They covalently bond, or ligate, two molecules (DNA ligase, for instance will 'stitch' two DNA strands to one another).
  16. What is an acyl group?
    It is a R-C=O- group, where R represents a single bonded alkyl group.
  17. What is the function of methylases?
    These enzymes add a methyl group (CH3) to a substrate
  18. What are anions and cations?
    Anions are negatively charged molecules. Cations are positively charged molecules.
  19. What is a carbonyl group?
    It is a C=O group with two substituents on the carbon (in addition to the oxygen).
  20. What is the difference between an amine and an amide?
    An amine is a nitrogen with ammonia-like geometry. An amide is an amine coupled to an acyl group (i.e. in a peptide backbone).
  21. What happens during carboxylation and decarboxylation reactions?
    Carboxylation: addition of CO2 to a substrate. Decarboxylation: removal of CO2 from a substrate
  22. What is pyrophosphate and what is its formula and net charge?
    Pyrophosphate (PPi) is an anion composed of two phosphates. It has a formula of P2O7 and a net charge of -4.
  23. What is the function of nucleotide polymerases and what are their substrates?
    They catalyze elongation of RNA and DNA. Their nucleotide substrates are NTP's (for RNA) and dNTP's (for DNA). Note that one PPi is released after each addition step.
  24. What are the chemical parts of a nucleotide? A nucleoside?
    Nucleotides contain a base, a sugar and a phosphate(s). Nucleosides contain only a base and a sugar
  25. What is the chemical difference between the second carbons of RNA and DNA?
    RNA has a 2' OH group. DNA has an H at this position
  26. What is the direction in which DNA and RNA are read and written?
    5' to 3'
  27. The terms 'denaturation' and 'annealing' of double stranded oligos and primers refer to what physical change?
    Strand separation (denaturation) and strand association (annealing)
  28. Which class of enzymes relaxes positive and negative DNA supercoils?
  29. How many chromosomes do diploid human cells have?
  30. How many base pairs does the haploid human genome contain, approximately?
    About 3 billion
  31. What percent of human DNA codes for proteins?
  32. How many proteins do human genes encode, roughly (not including splice variants)?
    About 30,000
  33. The average protein is about __ amino acids long
    About 400
  34. What process often leads to more than one form of mature RNA being formed from a given transcript?
    Alternative RNA splicing
  35. Functionally related genes that appear close to each other in the genome belong to the same ____
    Gene cluster (i.e. beta globin gene cluster).
  36. What is a pseudogene?
    A piece of DNA homologous to a coding segment that does not code for a protein
  37. Compared to pseudogenes, processed psudogenes lack ____...
  38. What is a provirus?
    DNA copies of ancient viruses that have integrated themselves into the genome. There are about a thousand proviruses integrated into the human genome, and they make up about 8% of our DNA
  39. What is a transposable element?
    A piece of DNA that can insert copies of itself in a new location within the genome
  40. What percent of our genome is composed of short interspersed repeat elements (SINEs)?
    About 10%. Note that SINEs are inserted into the genome via reverse transcription
  41. What percent of our genome encodes long interspersed repeat elements (LINEs)?
    About 20%
  42. What is a transposase?
    An enzyme that allows movement of a transposable DNA element. Note that some elements encode their own transposase.
  43. Name two types of SSRs (simple sequence repeats):
    Microsatellites (very short repeats) and minisatellites (14-500 base pair repeats)
  44. What is the function of telomeres?
    They protect the end of chromosomes from degradation.
  45. Where are telomeres found and what is their base sequence?
    Telomeres are found at the ends of chromosomes. They contain 1000-1700 copies of the hexameric sequence TTAGGG.
  46. What is meant by the term mitotic clock?
    It refers to the loss of 50-200 nucleotides from the ends of chromosomes every time a cell divides. When the telomeres are sufficiently shortened, the cell is no longer able to divide.
  47. Name two drugs that inhibit topoisomerases:
    Camptothecin and mAMSA (how?)
  48. What polymerase is often activated in cancer cells?
    Telomerase - this enzyme rejuvenates the telomeres and circumvents the mitotic clock
  49. How is DNA packaged in nucleosomes?
    DNA is wrapped around histone octomers. These are packed together to form chromatin fibers.
  50. Telomerase is a ____
    type of enzyme, reverse transcriptase (it uses an RNA template)
  51. What type of enzyme is encoded by LINEs?
    A reverse transcriptase. This is involved in introducing additional copies of the LINE into the genome.
  52. What is a single nucleotide polymorphism (SNP)?
    It is a common single base substitution between individuals. Rare single base substitutions are called mutations.
  53. Why are simple sequent repeats (SSRs) used as biomarkers?
    SSRs tend to be highly polymorphic, so the number of copies varies from one individual to another. This allows them to be useful biomarkers.
  54. What kind of bond is most critical for DNA recognition by proteins?
    Hydrogen bonding
  55. On which part of the DNA helix do proteins typically make contact with DNA bases?
    In the major groove of DNA
  56. Many proteins contain ____ (structural motif) that can fit in the ____ (location) of DNA to play a role in site specific binding.
    α-helices, major groove.
  57. What is the origin recognition complex (ORC) and what is its function?
    The ORC is a group of proteins that binds DNA at origins of replication. It helps initiate DNA replication in eukaryotes.
  58. What is a helicase and what is its function?
    It is an enzyme that unzips double stranded DNA to form two single strands by hydrolyzing the hydrogen bonds between the two DNA strands.
  59. What is the function of human single stranded DNA binding proteins (SSBs)?
    To stabilize single stranded DNA by preventing re-annealing
  60. What is the function of Topoisomerase I?
    Topo I is an enzyme that removes DNA supercoiling by breaking a single DNA strand, allowing the DNA structure to relax. It then covalently re-connects the DNA strands where they were originally cut.
  61. What disease associated with leukemia is caused by a deficiency of a cellular DNA helicase?
    Bloom's Syndrome.
  62. What syndrome associated with pre-mature aging is caused by a defective helicase?
    Werner's syndrome.
  63. In which direction does the DNA polymerase that synthesizes the leading strand of DNA read its template?
    5' to 3' (all DNA and RNA polymerases synthesize oligonucleotides in this direction).
  64. What are Okazaki fragments and in which direction are they synthesized?
    Okazaki fragments are short fragments of DNA that constitute the DNA lagging strand during replication. They are synthesized in the 5’ to 3’ direction.
  65. List three Human DNA polymerases:
    Pol-α, Pol-δ, and Pol-ε.
  66. What is the function of a primase?
    It associates with DNA polymerase α. The resulting complex synthesizes a short RNA strand that serves as a primer for other DNA polymerases.
  67. What is DNA Pol ε and what is its function?
    It is a high fidelity polymerase with 3' - 5' exonuclease proofreading activity. It is required for leading strand synthesis and is PCNA dependent.
  68. What is the function of DNA Pol δ and what other enzyme does it require for proper function?
    It synthesizes the lagging strand during DNA replication with high fidelity due to its exonuclease activity. It requires PCNA to remain attached to the DNA template.
  69. What is the function of Poly α?
    It works with a primase to make the DNA primers required to initiate DNA-synthesis by pol ε and pol δ, which in turn synthesize the leading and lagging strands, respectively.
  70. What is the function of Proliferating Cell Nuclear Antigen (PCNA)?
    PCNA form a clamp around a DNA polymerase and prevents it from dissociating from the template DNA strand.
  71. What is the function of the minichromosome maintenance complex (MCM)?
    It unzips double stranded DNA, resulting in the formation of single strands (MCM is the human DNA helicase complex).
  72. What is the function of replication factor C (RFC)?
    RFC helps to load DNA poly ε and DNA poly δ onto the template DNA.
  73. What is the function of single strand binding proteins (SSBs)?
    SSBs prevent single stranded DNA fragments from re-annealing. Note that human SSBs are often abbreviated RPA.
  74. What is the function of DNA ligases?
    They covalently join (ligate) DNA ends and Okazaki fragments to one another.
  75. What is the function of DNA Polymerase γ?
    It synthesizes mitochondrial DNA.
  76. What is the function of DNA Polymerase β?
    It maintains the integrity of the genome by participating in excision repair. (Do not confuse this with RNA polymerase β, which synthesizes mRNA!)
  77. Acyclovir is used to inhibit the polymerase of what class of viruses?
    Herpes simplex viruses
  78. Which enzyme is inhibited by the drug azidothymine (AZT)?
    HIV reverse transcriptase
  79. List the four stages of the cell cycle:
    • G1 (growth)
    • S (DNA synthesis)
    • G2 (more growth)
    • M (Mitosis, which itself is divided into several stages)
  80. What is p53 and what is its function?
    It is a tumor suppressor protein that is active at the G1/S checkpoint to prevent cells with DNA damage from replicating.
  81. What syndrome is associated with inherited mutant forms of the p53 tumor suppressor gene?
    Li-Fraumeni syndrome
  82. What process does a cell undergo if its genome is so damaged that it cannot be repaired?
  83. Name three DNA repair pathways:
    Mismatch repair, Excision repair, Removal of Uracil from DNA
  84. Name the three proteins used in prokaryotic mismatch repair:
    Mut S, Mut H, and Mut L
  85. Name two human proteins that are involved in mismatch repair: hMSH and hMLH
  86. What are the functions of Mut S and Mut H in bacteria?
    Mut S recognizes mismatched base pairs while Mut H catalyzes the incision of the section of the strand containing the mismatched base pairs
  87. Name three diseases associated with trinucleotide repeats:
    Fragile-X syndrome, Myotonic Dystrophy, and Huntington's Disease
  88. What are the main steps of excision repair in E.coli?
    Incision, Excision, Resynthesis and Ligation
  89. What complex of proteins is responsible for the repair of pyrimidine dimers in bacteria?
  90. Which DNA repair mechanism is defective in Xeroderma Pigmentosum?
    The excision repair system. As a result, UV-induced DNA damage cannot be effectively repaired.
  91. Deamination of adenine and cytosine by nitrous acid causes these bases to turn into _____ and ______, respectively:
    Hypoxanthine and uracil
  92. What is the major site of alkylation on DNA bases?
    The N7 of guanine. This results in a loss of the guanine residue.
  93. What are intercalators and what do they cause?
    They are polycyclic rings that have the ability to insert themselves between bases of DNA, causing physical distortion of the DNA, ultimately leading to the addition or loss of base pair(s)
  94. What is the functional difference between DNA Poly δ and DNA ligase with respect to lagging strand synthesis?
    DNA Poly δ removes the RNA primers at every Okazaki fragment and fills in the gaps between the fragments. DNA ligase covalently binds the completed Okazaki fragments to one another.
  95. What is the function of restriction endonucleases?
    They are bacterial enzymes that recognize and destroy foreign DNA
  96. How do bacterial enzymes differentiate endogenous DNA from foreign DNA?
    Bacterial DNA is methylated by endogenous enzymes, whereas foreign DNA is not. That way, bacterial enzymes can discriminate between endogenous and invading DNA.
  97. Restriction endonucleases generate DNA fragments that can be fractioned by gel electrophoresis. What is the main determinant of mobility of these fragments?
    Size. Smaller fragments move through the gel faster than larger fragments.
  98. Which technique is most appropriate for differentiating very large DNA fragments (100-1000kb)?
    Pulsified gel electrophoresis
  99. What do Southern blots separate?
    DNA fragments
  100. Once they are run on a gel, how are DNA sequences of interest isolated?
    DNA fragments of interest are hybridized with a radioactive 32-Phosphorous-labeled probe that is complimentary to the fragment
  101. A scientist inserted the CFTR gene into the genome of a mouse. To detect if the gene was integrated, s/he decided to run a Southern blot. List the steps of Southern blotting in order:
    • 1. Cleave genomic DNA with restriction enzymes
    • 2. Perform gel electrophoresis
    • 3. Transfer fragmented DNA from gel to nitrocellulose membrane
    • 4. Hybridize DNA of interest (in this case, CFTR gene) with labeled probe
    • 5. Expose membrane to film and develop.
  102. A physician wants to test a patient for hemoglobin S (sick cell hemoglobin). The only test available in the lab is a Southern blot. Is it possible for the physician to diagnose the patient?
    Yes. Point mutations whose location in the DNA sequence are known can be detected using a Southern blot if the base substitution or deletion is in a sequence recognized by a restriction endonuclease (this would lead to a loss of a restriction site).
  103. A physician wants to test a patient for a newly discovered genetic disease. The nature and location of the mutation causing the disease is not yet known. The only test available in the lab is a Southern blot. Is it possible for the physician to diagnose the patient? If yes, under what condition?
    Yes, but only if the mutation causing the disease is closely associated with a novel sized restriction fragment
  104. What is the location and nature of the mutation that causes sickle cell hemoglobin?
    The mutation involves a change in codon #6 of the beta-globin gene from GAG (glutamate) to GTC (valine)
  105. The mutation causing alpha1-antitrypsin deficiency does not create or destroy a restriction enzyme site. Which laboratory technique is most appropriate for detecting this disorder?
    Allele-specific oligonucleotide probe. Note that these probes can hybridize to DNA only when the nucleotide sequence of the normal and mutant alleles are known.
  106. True or False: When DNA is cleaved into restriction fragments, the pattern of fragments on a blot varies from one individual to another according to where and how many repeat units are located within the genome.
    True. This is due to the polymorphic variability of the human genome.
  107. Which technique is most appropriate to detect the size and amount of specific mRNA molecules?
    Northern blots
  108. Which technique is most appropriate to detect the size and amount of a specific protein?
    Western blots
  109. What is the function SDS-polyacrymalide gel with regards to Western blotting?
    Different proteins carry different charges. SDS is an anionic detergent that denatures proteins and essentially gives them all the same charge. This allows for the separation of peptides according to size instead of charge.
  110. What kind of molecules are used as probes to detect proteins of interest during Western blotting?
    The probes are antibodies specific for target proteins (whereas for Southern and Northern blots, the probes are nucleic acids that are complimentary to a nucleic acid sequence of interest)
  111. What is the first step of the polymerase chain reaction (PCR)?
    Heat denaturation of the double-stranded DNA fragment that is to be analyzed (90 degrees Celsius)
  112. A scientist wishes to amplify a fragment of DNA using PCR. However, the scientist does not know the DNA sequence of the regions that flank the fragment of interest. Is it still possible for the scientist to amplify the DNA fragment of interest?
    No. The sequence of the flanking regions must be known so that appropriate primers may be selected. Without probes that are complimentary to the flanking regions, the DNA of interest will not be amplified.
  113. What is the special feature of the DNA polymerase used in polymerase chain reactions (PCR)?
    It is heat stabilized.
  114. Which technique is most appropriate to amplify a sequence of RNA and how does it work?
    RT-PCR. A reverse transcriptase converts the DNA into a single-stranded cDNA molecule, which can then be amplified using standard PCR techniques.
  115. A scientist decides to use the single-strand conformation polymorphism (SSCP) technique to determine if his DNA sample contains mutations. What is the main determinant of gel migration using this technique?
    Conformation of the DNA single-stands. If a mutation is present, the conformation of the single-strand will be altered, thereby causing the band pattern to differ from that of the normal single-strands.
  116. The Sanger method is used for DNA sequencing and involves dideoxy-NTPs (dd-NTPs). What is the structure and function of dd-NTPs?
    dd-NTP's lack both the 2' and 3' hydroxyl groups on the ribose. Since the 3'-OH group on the ribose is required for chain elongation, incorporation of dd-NTP's will block chain elongation.
  117. Which technique is most appropriate for determining the base sequence of a DNA fragment?
    The Sanger method (see syllabus for detailed explanation)
  118. Which technique is most appropriate for determining if a protein interacts with a particular DNA fragment?
    DNA band shift assay
  119. Which technique is most appropriate to determine the boundaries of protein-DNA interactions?
    DNase I footprinting assay
  120. What is the function of the enzyme DNase I in DNase I footprinting assays?
    DNase I digests DNA. Regions of DNA bound to protein will be protected from digestion. As a result, their corresponding bands will be absent when the DNA is run on a gel.
  121. What are vectors?
    Vectors are DNA molecules that replicate autonomously in a host cell. They are designed to accommodate the insertion of foreign gene sequences.
  122. After a vector is incorporated into a cell, how can recipient cells be sorted from non-recipient cells?
    Vectors usually contain genes that confer resistance to particular drugs. Therefore, only recipient cells will be able to survive once the drug is added to the growth medium.
  123. What is the difference between genomic libraries and cDNA libraries?
    Genomic libraries are constructed from genomic DNA (introns and exons) whereas cDNA libraries are constructed from mRNA (exons only).
  124. What is a plasmid?
    A plasmid is a circular bacterial chromosome that replicates independently of the host chromosome.
  125. Which of the following technique provides a more precise determination of DNA-protein interactions: DNA band shift assays or DNase I footprinting assays?
    DNase I footprinting assays
  126. A scientist wants to determine if a certain transcription factor is present in brain tissue. Which DNA technique is most appropriate to accomplish this task?
    DNA band shift assay
  127. A helicase is an enzyme that unwinds DNA. Why is a helicase not needed for the polymerase chain reaction (PCR)?
    During PCR, the double-stranded DNA is denatured into single-stranded DNA by elevated temperatures, so the enzyme is not needed.
  128. List three differences between RNA and DNA:
    1. The pentose sugar in RNA is ribose rather than deoxyribose, 2. RNA has Uracil (U) instead of Thymine (T), and 3. DNA normally exists as a double helix whereas RNA exists as a single strand.
  129. True or False: mRNA typically exists as a single-stranded molecule
  130. The sequence of RNA transcripts is similar to that of which DNA strand?
    The coding strand (also called the (+) strand). The other strand is called the template or (-) strand.
  131. In which direction is RNA synthesized?
    5' to 3'
  132. Name the three eukaryotic polymerases involved in RNA synthesis:
    RNA polymerase I, II and III
  133. What is the cellular location and function of RNA polymerase I?
    It is found in the nucleolus and transcribes 28S, 18S and 5.8S ribosomal RNAs (rRNA)
  134. What is the cellular location and function of RNA polymerase II?
    It is found in the nucleus and transcribes pre-mRNA
  135. What is the cellular location and function of RNA polymerase III?
    It is found in the nucleus and transcribes tRNA, 5S rRNA and other small RNAs
  136. What are the two subunits of eukaryotic ribosomes?
    60S and 40S. Each of these is composed of multiple rRNA and protein subunits.
  137. Which two transcription factors are required for RNA polymerase I to bind to and transcribe DNA?
    Transcription factors B and S (B for binding, S for stimulating).
  138. What marks the termination site of RNA poly I?
    A string of T residues.
  139. What transcription factors are required to recruit and activate RNA poly III?
    TFIIIA, TFIIIB and TFIIIC (note that the Roman numeral in the name of the transcription factor tells you which polymerase it is associated with)
  140. What conserved sequence in the promoter region directs Poly II binding? What protein binds this sequence?
    The TATA box. The most common sequence is TATAAA. This is bound by the TATA-binding protein (TBP) which is part of TFIID.
  141. What is the purpose of an enhancer sequence?
    Enhancers increase the transcription of neighboring genes. They can be located either upstream or downstream of the gene that is to be transcribed.
  142. Which set of transcriptions factors are required for the initiation of transcription?
    Basal Transcription Factors.
  143. A methylguanylate (m7G) cap is placed at which end of a nascent RNA strand?
    The 5' end. Note that the m7G residue is linked to the RNA via a 5’ to 5’ triphosphate bond.
  144. Cleavage and polyadenylation occur at which end of a pre-mRNA strand?
    The 3' end
  145. Which sequence element signals for cleavage of hnRNA and addition of the poly(A) tail?
    The AAUAA sequence. This is located approximately 15 nucleotides upstream of the site of cleavage and subsequent polyadenylation.
  146. True or False: Poly A tails are encoded within genes?
    False. The tails are added by poly(A) polymerase, a polymerase that does not utilize a template.
  147. What transcription factor reads the AAUAA sequence on pre-mRNA?
    Cleavage and polyadenylation specificity factor (CPSF)
  148. What is RNA splicing?
    The process by which introns are removed from the pre-mRNA molecule
  149. What is the spliceosome and what is its function?
    The spliceosome is a large ribonucleotide protein complex akin to the ribosome. Spliceosomes contain smaller nuclear snRNPs (U1, U2, U4,U5 and U6). This complex removes introns from pre-mRNA molecules.
  150. What is alternative splicing?
    A single pre-mRNA can be spliced in different ways, yielding different mature mRNAs. Thus, a single gene can code for a series of related, but non-identical proteins.
  151. Which rRNAs make up the 40S subunit of eukaryotic ribosomes?
    18S rRNA (and proteins)
  152. Which rRNAs make up the 60S subunit of eukaryotic ribosomes?
    28S, 5.8S and 5S rRNAs (and proteins)
  153. Which rRNA is synthesized outside of the nucleolus?
    5S rRNA (it is synthesized by RNA poly III)
  154. Which RNA polymerase is inhibited by the drug actinomycin D?
    Mammalian RNA polymerase I
  155. Which RNA polymerase is inhibited by the drug alpha-amanitin?
    Mammalian RNA polymerases II and III
  156. Which RNA polymerase is inhibited by the drug rifampicin?
    Bacterial RNA polymerase
  157. True or False: The activation region for the 5S rRNA gene is found within the gene itself?
  158. True or False: Genes that are constitutively expressed contain a TATA box as a promoter?
    False. They generally contain a GC-rich region instead.
  159. What is the only basal RNA polymerase II transcription factor that directly binds to DNA?
  160. What is the function of the RNA Gppp cap?
    It is believed to protect against the degradation of nascent RNA
  161. True or False: All RNAs acquire a poly(A) tail following transcription?
    False. Only those RNAs that are to become mRNAs acquire a poly(A) tail.
  162. Introns in pre-mRNA typically have ___ residues at their 5' end and ___ residues at the 3' end.
    GU, AG
  163. What is the first step of RNA splicing?
    Cleavage of the 5' exon-intron junction by the spliceosome
  164. What is an intron lariat?
    It is an intron that has been circularized with a specific branch point between a 5' G residue and a 3' splice-site A residue linked in a 5' to 2' bond.
  165. Which small nuclear ribonuclearprotein (snRNP) binds to the 5' exon-intron junction?
  166. Which small nuclear ribonuclearprotein (snRNP) binds to the branch point of an intron lariat?
  167. Which small nuclear ribonuclearprotein (snRNP) binds upstream to the 3' intron-exon junction?
  168. Cells in the brain and cells in the liver contain the same DNA. How is it that these cells are different cell types?
    Each cell type has a distinct pattern of gene expression.
  169. What is a housekeeping protein and in which cell type is it found?
    These are proteins associated with basic metabolism, translation, transcription, replication, and cell structure of a cell. They are generally present in all cell types.
  170. What is heterochromatin?
    Heterochromatin is condensed chromatin. It tends to be transcriptionally inactive, and it is less sensitive to DNAse I digestion than euchromatin.
  171. What is euchromatin?
    Euchromatin is relaxed (i.e. non-condensed) chromatin, and is usually associated with transcriptionally active genes
  172. What are hypersensitive sites and where are they located with respect to genes?
    Hypersensitive sites are short regions of chromatin that are exceptionally sensitive (i.e. very accessible) to nucleases such as DNase I. They are often found in the upstream control regions of active genes.
  173. What are locus control regions (LRCs) and how do they work?
    LCRs are chromosomal elements that act over long distances to control the expression of multigene families. They regulate gene expression indirectly by regulating chromatin organization over certain chromosomal domains. Sections of DNA containing LRCs may form loops over desired genes to enhance their expression.
  174. Name a protein complex that can alter chromatin structure via nucleosome remodeling:
  175. What is the function of histone acetyltransferases?
    These enzymes catalyze the acetylation of histones, which leads to the unfolding of chromatin. This increases the accessibility of transcription factors to DNA.
  176. What is the function of DNA methyltransferases?
    These enzymes methylate cytosine residues at carbon 5 after DNA replication has occurred. Methylation of DNA represses gene transcription.
  177. Which amino acid residue in histones is typically most susceptible to acetylation?
  178. Where are CpG islands found?
    They are found in promoter regions of genes that are actively transcribed in all cell types (i.e. housekeeping genes). CpG islands almost always lack methylation.
  179. The assembly of basal transcription factors requires the presence of what other class of transcription factors?
  180. Activators bind to what regulatory regions of DNA?
  181. What is the function of coactivators?
    They allow communication between activators and basal transcription factors
  182. The complex of coactivators binds to which protein?
    TATA Binding Protein (TBP)
  183. What is the function of repressors? To which sequence of DNA do they bind?
    They block the initiation of transcription by interfering with the function of activators. The sequences that repressors bind to are called silencers.
  184. What is the result of activator-coactivator interactions?
    Activator-coactivator interactions allow basal transcription factors to position RNA polymerase II at the beginning of the protein-coding region of a gene and set the polymerase in motion.
  185. True or False: Genes are generally alike with regards to the combination of promoter and enhancer (or silencer) elements they carry?
    False. This is how cells are able to control the transcription of every gene individually.
  186. Under conditions of elevated temperature, cells from all organisms suspend transcription and translation except for which set of genes?
    Genes encoding proteins that help with survival of cells at high temperature (i.e. genes encoding heat shock proteins).
  187. What causes heat shock factor protein (HSF) to become active?
    Heat shock (elevated temperatures). Other stresses (such as toxins) may also activate a heat shock response.
  188. What is the function of heat shock factor (HSF) proteins?
    After heat shock-induced activation, HSF proteins bind to specific DNA sites upstream of certain genes and increase transcription of those genes.
  189. Binding of heat shock factor (HSF) proteins to DNA is not sufficient to increase transcription of heat shock genes. What else must occur after binding (hint: what modification must occur to the HSF proteins because they can become active)?
    Phosphorylation of HSF proteins
  190. Estrogen, testosterone, and progesterone all belong what class of hormones?
    Steroid hormones
  191. Steroid hormones are all derivatives of which metabolite?
  192. What is the mechanism by which steroid hormones affect the transcription of genes?
    Steroid hormones are fat soluble and can therefore diffuse across membranes. They form complexes with their receptors. These complexes translocate to the nucleus where they displace nucleosomes from promoter regions. This facilitates binding of other transcription factors.
  193. What are the DNA binding sites for steroid hormone/receptor complexes called?
    Hormone response elements.
  194. What information can be extracted from DNA microarrays?
    Levels and patterns of gene expression
  195. How are DNA fragments able to attach to the underlying slide of glass in a DNA microarray?
    The DNA stick to the slide because the slides are coated with poly-L-lysine, which is positively charged (recall that DNA is negatively charged because of the phosphates in the backbone).
  196. DNA microarrays are useful in determining what kind of information?
    The relative expression levels of genes. The sample applied to the microarray is fluorescence-labeled cDNA.
  197. How does antisense therapy affect mRNA translation?
    In antisense therapy, a fragment of nucleic acid that is complimentary to an mRNA of interest is introduced into a cell. If the nucleic acid binds to a complementary fragment of mRNA, it blocks ribosomes from translating the mRNA.
  198. In antisense therapy, a nucleic acid fragment is introduced into a cell. How is the antisense nucleic acid fragment protected from intracellular degradation?
    The oxygen atoms that make up the phosphate links between nucleotides of the DNA backbone are replaced by sulfur atoms, rendering the nucleic acid immune to immediate degradation.
  199. What are some problems with antisense therapy that remain to be overcome before clinical use?
    Evaluation of the toxicity of introduced nucleic acids, keeping nucleic acids inside the cells once they are introduced, identifying the genes that are causative of the diseases we intend to treat, etc.
  200. What is RNA interference?
    RNAi is a technique in which double-stranded RNAs homologous to a gene of interest are introduced inside a cell with the goal of silencing that gene.
  201. What is the function of the enzyme Dicer?
    It cleaves double-stranded RNAs into smaller double-stranded RNA fragments called siRNAs.
  202. How do siRNAs silence gene expression?
    siRNAs are separated into single strands. The single strands then bind to the RISC complex, facilitating degradation of complementary mRNAs before they can be translated by ribosomes.
  203. What is the RISC complex?
    It is a protein complex that binds to single strands of siRNAs. The siRNAs serve as a template that recognize complementary mRNAs. Once recognized, the RNase subunit of the RISC complex cleaves the complementary mRNAs so that they cannot be translated.
  204. What subunits make up a eukaryotic ribosome?
    60S and 40S
  205. What is the sedimentation coefficient of eukaryotic ribosomes?
  206. Where are ribosomes usually found in the cell?
    In the cytoplasm or attached to the endoplasmic reticulum
  207. What is the fate of proteins synthesized by ribosomes on the endoplasmic reticulum?
    They are either exported from the cell or become part of the cellular membrane
  208. What is a codon?
    A trinucleotide sequence of mRNA that determines which amino acid is added to a nascent protein during translation
  209. What is the sequence of the start codon?
  210. The start codon codes for which amino acid?
  211. What are the sequences of the stop codons?
    UAA, UAG, and UGA
  212. In which direction does a ribosome read RNA?
    From 5' to 3' (the same direction as nucleic acid synthesis by DNA and RNA polymerases)
  213. What is a peptide bond?
    A covalent bond between an amino group of one molecule and the carboxyl group of another. Peptide bonds are formed between amino acids during protein synthesis.
  214. What is the Wobble Hypothesis?
    There are fewer tRNAs than codons. It was proposed that the 3’ end of the codon allows for a more relaxed bonding with the 5’ base of the anticodon. The potential for non-Watson-Crick base pairing at this position allows a single tRNA to pair with several different codons.
  215. What class of enzymes activate and attach amino acids to their respective tRNAs?
    Aminoacyl tRNA synthetases
  216. What are the three sites on ribosomes that interact with tRNAs during elongation of a peptide?
    A, P and E sites
  217. What is the purpose of elongation factors?
    Elongation factors (EF) position amino acyl-tRNAs on the ribosome and promote RNA translocation
  218. What is monocistronic mRNA?
    mRNA that will code for only one polypeptide sequence. With very few exceptions, eukaryotic mRNA is monocistronic. Bacteria, on the other hand, frequently have polycistronic messages.
  219. In bacteria, the region of the 3’ terminus of the 16S ribosomal RNA is complementary to the _______ (which sequence)
    Shine-Dalgarno Sequence; This is the ribosome binding site on the mRNA. In eukaryotes the equivalent sequence is known as the Kozak sequence.
  220. What is a missense mutation?
    A single base substitution in which one amino acid replaces another
  221. What is a nonsense mutation?
    A change in a codon that converts it to a stop codon, leading to premature termination of translation
  222. What is a frameshift mutation?
    A mutation that causes the codons to be read out of frame, thereby leading to a misinterpretation of mRNA
  223. What is the sedimentation coefficient of bacterial ribosomes?
  224. What is translation?
    The process by which an mRNA template is used to synthesize a polypeptide chain
  225. Every tRNA has a ____ sequence at its 3' end
  226. What kind of bond links the carboxyl group of an amino acid to the 3' CCA sequence of a tRNA molecule?
    An ester bond
  227. What is an aminoacyl-tRNA?
    A tRNA molecule bound to its corresponding amino acid
  228. What is an anticodon?
    A tRNA trinucleotide sequence that is complementary, and therefore binds to, an mRNA codon
  229. What is the first tRNA binds to the small ribosomal subunit?
    Met-tRNA (note that is binds regardless of whether or not there is a codon for methionine)
  230. Which initiation factor is required for the initiator tRNA (Met-tRNA) to bind to the small ribosomal subunit in eukaryotes?
    eIF2 (along with GTP)
  231. To which binding site does the initiator tRNA (Met-tRNA) bind to on the ribosome?
    It binds directly to the P site
  232. True or False: Interaction of the eIF2-GTP-Met-tRNA complex with the 40S ribosomal subunit must occur in the presence of mRNA?
    False, It typically occurs in the absence of mRNA
  233. What is the function of eIF2 during translation?
    It binds the 40S subunit to tRNA
  234. What happens to eIF2 when the anticodon of the initiator tRNA matches the AUG start codon?
    GTP is hydrolyzed, allowing eIF2 to dissociate from the ribosome and the 60S subunit to bind to the 40S subunit
  235. Which elongation factor is required for tRNA to bind to the A site of the ribosome?
  236. Which elongation factor is required for translocation of tRNA from the A site to the P site of the ribosome?
  237. Which enzyme is thought to catalyze the nucleophilic attack on the carbonyl group of the peptidyl-tRNA by the amino group of the aminoacyl-tRNA? Where does this reaction occur on the ribosome?
    The enzyme is peptidyl transferase and it occurs in the A site of the ribosome
  238. What is the function of the soluble protein called termination factor?
    It promotes the cleavage of the polypeptide chain from the tRNA in the P site, releasing the mRNA from the ribosome
  239. What is the shape of a typical tRNA?
  240. What kind of bond links the amino acid residues of a protein to one another?
    Peptide bond
  241. What is a polypeptide?
    A polypeptide is a chain of amino acids linked together by peptide bonds
  242. What is meant by primary, secondary, tertiary, and quaternary structure of a protein?
    Primary: the amino acid sequence. Secondary: helices, beta sheets, and turns. Tertiary: the way the secondary structure elements come together in 3D space. Quaternary: the way multiple proteins come together to form a complex.
  243. What determines most of the structural and functional properties of a protein?
    The protein's amino acid side chains, which are also called R-groups
  244. Which amino acids are positively charged at neutral pH?
    Arginine, lysine, and histidine
  245. Which amino acids are negatively charged at neutral pH?
    Aspartate and glutamate
  246. Which of the 20 standard amino acids are aromatic?
    Phenylalanine, tryptophan, and tyrosine
  247. The amino acid R-groups of water soluble proteins that face the exterior of the protein are usually ________, and those that face the interior of the protein are usually ________.
    Hydrophilic, hydrophobic
  248. Regions of proteins that interact with DNA are usually ___________ charged
    Positively charged because DNA carries a negative charge
  249. What technique can a scientist use to measure the purity of a protein in a sample?
  250. Define specific activity of a protein:
    It is the activity per amount of protein
  251. A scientist inserts a sample of protein in a spectrophotometer and calibrates the instrument to detect absorbance of the sample at a wavelength of 280nm. What is the scientist measuring?
    The content of tryptophan and tyrosine residues in the protein. Absorbance at 280nm is frequently used to determine protein concentration of a purified protein.
  252. How may the activity of a DNA-binding protein be determined?
    By the ability of the protein to band-shift DNA.
  253. What type of bond has the most significant influence on how proteins fold?
    Weak non-covalent bonds. The energy contribution from each individual bond is small, but the net contribution from all the non-covalent interactions is large.
  254. What is a molten globule?
    It is a type of protein folding intermediate
  255. What is the role of chaperone proteins in protein folding?
    They catalyze folding of some proteins
  256. Name two common secondary protein structure elements:
    Alpha-helix and beta-sheet
  257. Describe the hydrogen bonding pattern between amino acid residues in an alpha-helix:
    Hydrogen bonds in an alpha-helix occurs between the oxygen of a carbonyl group and the HN of an amino acid that is four residues down the polypeptide chain
  258. Which amino acid cannot fit in an alpha-helix?
    Proline: this amino acid has a five-member ring and is referred to as the 'helix breaker'
  259. Describe the hydrogen bonding pattern between amino acid residues in a beta-sheet
    In a beta-sheet, hydrogen bonding occurs between backbone atoms within stretches of amino acid residues. At least two (and frequently more) extended polypeptide chains are involved.
  260. What does the drug Kalydeco do?
    It is a treatment for CF patients with a particular mutation (G551D). This mutation appears in 4-5% of patients.
  261. Which amino acid has the smallest side chain?
    Glycine; its side chain is a hydrogen atom
  262. Describe the pathogenesis of inherited Creutzfeldt-Jakob disease:
    The disease is caused by a single amino-acid mutation. This mutation causes prion proteins to switch their conformation from soluble alpha-helices to insoluble beta-sheets. The insoluble beta-sheets can form aggregates that in turn lead to neurological symptoms.
  263. Proteins make a significant contribution to the buffering capacity in cells and plasma. What part of proteins allows them to act as buffers?
    Titratable groups on the amino acid side chains. Note that the pKa of these groups differ depending on the side chain. Also, since the protein concentration in cells and plasma is quite high, proteins have a considerable buffering capacity.
  264. Define pKa:
    The pKa is the pH at which the concentration of the acid form of a molecule is equal to the concentration of the base form of the same molecule. In other words, half the molecules are in the acid form, and half are in the base form.
  265. Define pI (isoelectric point):
    The pI is the pH at which a molecule is electrically neutral
  266. At what pH will a buffered solution be most resistant to changes in the pH after the addition of acid or base?
    At the pKa of the buffer
  267. Which amino acid is capable of forming disulfide bonds?
    Cysteine: disulfide bonds are most often found in oxidizing environments such as outside of the cell
  268. What is the main buffer in blood?
    Carbonic acid/bicarbonate (H2CO3/HCO3-)
  269. What is the main buffer inside cells?
    Phosphate ions
  270. At pH values lower than the pKa, the ________ form of the molecule predominates. At pH values higher than the pKa, the ________ form of the molecule predominates.
    Acid, base
  271. Aspirin is a weak acid at low pH and has a pKa of 3.5. Per unit surface area, will more aspirin be absorbed in the stomach (pH 1.5) or in the intestine (pH 6.5)?
    At a pH below its pKa, aspirin will be in its acid form (RCOOH). At a pH above its pKa, aspirin will be in its base form (RCOO-). Since non-ionized molecules cross cell membranes passively whereas ionized molecules do not, more aspirin will be absorbed in the stomach than in the intestine
  272. What prosthetic group do myoglobin and hemoglobin have in common?
    Both proteins contain a heme prosthetic group.
  273. What is the difference between a prosthetic group and a coenzyme?
    A prosthetic group is firmly attached to a protein and usually cannot be removed during protein purification. A coenzyme is an organic molecule that is less firmly attached.
  274. What is the oxidation number of the heme iron found in oxygenated myoglobin? What is the oxidation number of the heme iron found in deoxygenated myoglobin?
    Iron is in its ferrous state (Fe2+) irrespective of oxygen binding in both myoglobin and hemoglobin.
  275. What amino acid residue in hemoglobin binds iron?
    Histidine (F8). Movement of this residue helps the protein sense whether or not O2 is bound to the heme group.
  276. Carbon monoxide binds to isolated heme molecules much more tightly than oxygen. How is the CO binding affinity of hemoglobin attenuated?
    The ferrous iron in isolated heme binds CO at a 180 degree angle. Histidine E7 in the active site of heme prevents optimal CO binding by forcing the binding geometry to be 120 degrees, which is the optimal binding orientation of oxygen.
  277. What triggers myoglobin to undergo a conformational change when it binds oxygen?
    When it binds to oxygen, the oxygenated ferrous ion moves into the plane of the porphyrin ring, pulling along some of the protein with it. This is mediated by histidine F8.
  278. Describe the shape of the myoglobin oxygen dissociation curve. What does it suggest with regards to the protein's kinetics?
    Hyperbolic. This suggests that simple equilibrium processes are involved in binding and release.
  279. Describe the shape of the hemoglobin oxygen dissociation curve. What does it suggest with regards to the protein's kinetics?
    Sigmoidal. A binding curve with this shape indicates cooperativity among multiple binding sites.
  280. What is the role of myoglobin in muscle?
    It delivers the oxygen required for metabolism in actively exercising muscle.
  281. What is the role of hemoglobin?
    It transports oxygen between the lungs and tissues
  282. How many oxygen molecules do myoglobin and hemoglobin bind to, respectively?
    Myoglobin binds to one oxygen molecule whereas hemoglobin binds up to four oxygen molecules
  283. Myoglobin vs. hemoglobin: which one is an allosteric protein?
    Hemoglobin is an allosteric protein. Myoglobin, which binds only a single molecule of O2, is not.
  284. What is meant by the statement 'the binding of oxygen to hemoglobin is cooperative'?
    It means that binding of oxygen to one site influences the oxygen affinity of the remaining sites on Hb.
  285. What does the Hill coefficient measure? What are its possible values and what do these values indicate?
    It measures the sigmoidal character of a protein's binding curve and indicates the degree of the protein's cooperativity. A Hill coefficient of 1 means no sigmoidal character and no cooperativity. A Hill coefficient greater than 1 means positive cooperativity. Hill coefficients can also be less than one. In this case, binding one ligand inhibits binding of a second.
  286. What is the Hill coefficient of myoglobin?
    1 (one).
  287. The cooperativity of oxygen in hemoglobin suggests that the heme groups communicate with each other. However, they are too far apart to do so directly. How is it that one heme group may affect the oxygen binding affinity of another heme group?
    Heme groups communicate with one another through conformational changes that are transmitted across the hemoglobin subunit interfaces.
  288. Oxyhemoglobin is said to be in which conformational state?
    The relaxed state. (It has oxygen so it is relaxed.)
  289. Deoxyhemoglobin is said to be in which conformational state?
    The taut state
  290. Which hemoglobin conformational state has the greatest affinity for oxygen?
    The relaxed state
  291. How do high CO2 and rising H+ levels (low pH) affect hemoglobin’s affinity for oxygen? What is this effect called?
    Both CO2 and low pH promote the release of oxygen by lowering the oxygen affinity of hemoglobin. This is known as the Bohr effect.
  292. Describe the physical movement that occurs between the subunits of hemoglobin when an oxygen molecule binds to a heme group:
    When oxygen binds to a ferrous iron, one pair of alpha-beta subunits rotates by 15 degrees relative to the other pair of alpha-beta subunits in the hemoglobin heterotetramer.
  293. Where on hemoglobin does carbon dioxide bind?
    Carbon dioxide binds to the N-terminal amino groups of the alpha subunits. Note that this is different from carbon monoxide, which binds to the oxygen binding site.
  294. Describe the mechanism by which the binding of carbon dioxide to hemoglobin reduces oxygen affinity.
    Carbon dioxide reacts reversibly with an N-terminal amino group (in an alpha subunit) to form a carbamate. The carbamate groups form ionic bonds that stabilize the taut (deoxy) state of Hb, thereby lowering the oxygen affinity of hemoglobin.
  295. Because they reduce the oxygen affinity of hemoglobin without binding directly to the site of oxygen binding, both carbon dioxide and protons are called ______________ effectors.
    Negative allosteric.
  296. Which conformational state of hemoglobin has a greater affinity for protons?
    The taut (deoxy) state.
  297. What are the subunits of fetal hemoglobin? What are the subunits of adult hemoglobin?
    Fetal hemoglobin is composed of two alpha and two gamma subunits. Adult hemoglobin is composed of two alpha and two beta subunits.
  298. What is the role of 2,3-bisphosphoglycerate (BPG) with regards to hemoglobin affinity for oxygen? How does high altitude affect levels of 2,3-BPG?
    2,3-BPG reduces the oxygen affinity of hemoglobin. 2,3-BPG levels increase at high altitude where oxygen is scarce.
  299. How many 2,3-BPG binding sites are there in one molecule of hemoglobin and where are they found?
    One. It is located in a central cavity formed between the beta subunits.
  300. Describe the nature of the bond that forms between 2,3-BPG and hemoglobin. Which state does 2,3-BPG stabilize?
    2,3-BPG is negatively charged and binds to hemoglobin primarily through electrostatic interactions. 2,3-BPG reduces oxygen affinity and therefore stabilizes the taut (deoxy) form of hemoglobin.
  301. Why does fetal hemoglobin have a higher oxygen affinity than adult hemoglobin?
    Fetal hemoglobin contains gamma subunits instead of beta subunits. The gamma subunits have fewer positively charged amino acid residues in the 2,3-BPG binding region. Therefore, 2,3-BPG binds to fetal hemoglobin less strongly than to adult hemoglobin. This confers fetal hemoglobin a higher oxygen affinity than adult hemoglobin.
  302. What is the molecular defect associated with sickle cell anemia?
    It is an amino acid substitution of a valine for a glutamate on the exterior of hemoglobin. This results in an altered charge of the beta subunit.
  303. What causes sick cell hemoglobin (HbS) to polymerize?
    The oxygenated form of HbS has normal solubility, but the deoxygenated form is relatively insoluble. In areas of low oxygen (such as high altitude), HbS polymerizes and distorts red cells, leading to clogging of capillaries and blood vessels.
  304. Why do sickle cell anemia symptoms not become apparent until 3 to 6 months after birth?
    It is not until then that the beta subunits of adult hemoglobin are produced. The symptoms associated with sickle cell anemia correlate with decreased synthesis of gamma subunits and increased synthesis of beta subunits.
  305. Name two drugs that are used to treat sickle cell anemia and explain how they work:
    Hydroxyurea (increases the production of gamma subunits of HbF) and erythropoetin (increases proliferation of red cells containing HbF)
  306. What is the oxidation number of the heme iron in methemoglobin?
    Fe3+ (ferric); this is an abnormal state.
  307. List two causes of methemoglobinemia:
    Ingestion of large amounts of oxidizing agents such as nitrates, or mutations near the heme group.
  308. How is methemoglobinemia treated?
    By administration of reducing agents such as vitamin C or methylene blue
  309. What is the defect in alpha-thalassemias and what does it cause?
    Alpha-thalassemias result from a defect in the synthesis of the alpha-subunits of hemoglobin. This leads to an imbalance in the amount of alpha-globin vs. beta-globin.
  310. Myoglobin vs. hemoglobin: which one binds oxygen more tightly?
    Myoglobin binds oxygen more tightly than hemoglobin
  311. What are the two precursors of insulin?
    Preproinsulin and proinsulin
  312. What kind of bond holds the two peptide chains of collagen to one another?
    Disulfide bonds and non-covalent interactions.
  313. What are the two modified amino acids present in collagen?
    Hydroxyproline and hydroxylysine
  314. Which cells produce collagen type III?
  315. Type I collagen is typically found in which tissues?
    Bone, skin, tendons, heart valve
  316. Type III collagen is typically found in which tissues?
    Newborn skin and blood vessels
  317. List the steps of collagen biosynthesis in order:
    • 1) Polypeptide chain synthesis
    • 2) hydroxylation of proline and lysine
    • 3) glycosylation
    • 4) disulfide bond formation at C-terminus
    • 5) triple helix formation
    • 6) secretion
    • 7) hydrolysis of propeptides
    • 8) fibril assembly
    • 9) fiber assembly and formation of cross links
  318. What type of enzyme (and co-factor) is required for hydroxylation of proline and lysine during collagen formation?
    Hydroxylases; ascorbic acid (Vitamin C is the co-factor)
  319. What effect does hydroxyproline have on collagen stability?
    It makes it more stable
  320. What causes collagen to form a triple helix rather than a standard alpha helix or beta sheet?
    The steric repulsion between the prolines and hydroxyprolines
  321. What amino acid is typically found at every third residue in collagen?
  322. What form of collagen is made after hydrolysis of procollagen?
  323. What enzyme helps catalyze the formation of cross links in collagen fibers?
    Lysyl oxidase oxidizes lysine to allysine. This forms a cross-link with unmodified lysines.
  324. What is the cause of scurvy?
    A lack of ascorbic acid (Vitamin C) which leads to a decrease in the hydroxylation of lysines and prolines in collagen
  325. What are the symptoms of scurvy?
    Damage and fragility of many tissues and organs such as the gums, as well as skin lesions and blood vessel fragility
  326. Which condition usually results from a mutation in type I collagen?
    Osteogenesis Imperfecta. In some of the most severe forms, a glycine is replaced with Cys, interfering with the collagen triple helix.
  327. What are the symptoms of Osteogenesis Imperfecta?
    Symptoms include bone deformities, brittle bones, and teeth and fragile blood vessels
  328. What are two causes of Ehlers-Danlos Syndrome?
    1. Improper processing of collagen caused by lack of enzyme (i.e. lysyl oxidase deficiency) and 2. genetic defects in the collagen genes
  329. What are the symptoms of Ehlers-Danlos Syndrome?
    Symptoms include hyperelastic joints and skin hyperextendibility
  330. Keratin is a protein rich in which amino acid?
  331. What is the basic structural unit of collagen?
    The collagen triple helix.
  332. True or False: different types of collagen arise from alternative splicing?
    False. Different types of collagen are encoded by separate genes.
  333. Type II collagen is typically found in which tissues?
  334. Type IV collagen is typically found in which tissues?
    Basement membranes
  335. Which enzyme catalyzes the hydroxylation of proline into hydroxyproline?
    Prolyl hydroxylase
  336. Which enzyme catalyzes the hydroxylation of lysine into hydroxylysine?
    Lysyl hydroxylase
  337. Vitamin C is a cofactor for the hydroxylation of which amino acid present in collagen?
  338. How does the hydroxyproline content of collagen relate to the stability of the collagen molecule?
    The more the hydroxyproline, the more stable the collagen molecule (as defined by higher melting point).
  339. What kind of bond predominates between the three chains of a collagen triple helix?
    Hydrogen bonding between the NH groups of glycine on one chain and the carboxyl groups on another chain
  340. True or False: collagen processing and assembly occur outside the cell (i.e. in the extracellular space)
  341. What is the difference between procollagen and tropocollagen?
    Tropocollagen molecules lack the N- and C- terminus of procollagen and can spontaneously assemble into collagen fibrils
  342. In which tissues are elastin fibers typically found?
    In elastic tissues such as the lungs
  343. What is the most common cross-linkage between elastin molecules? Desmosine linkage, which involves four lysines
  344. In which tissues is keratin typically found?
    Hair and nails
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