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95 Cards in this Set
- Front
- Back
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What are the exceptions to the central dogma? Pg2
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Reverse transcription & non-coding RNAs
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What is the similarity/difference between RNA and DNA? Pg2
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Both have a nitrogenous base attached to 1’C via an N-glycosidic bond, and 1 to 3 phosphate groups on 5’C. RNA has an –OH on its 2’C, while DNA has –H.
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What makes DNA more stable than RNA? Pg 2
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The absence of oxygen in the 2’C position of DNA makes it more stable and less reactive compared to RNA
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Name the various pyrimidines and purines. Pg 3
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Pure As Gold (purines = adenine, guanine). pYrimidines = cYtosine & thYmine (uracil instead of tyhymine in RNA)
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What is the difference between thymine and uracil? Pg 3
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Thymine has an additional –CH3 (methyl) group on it. Thymine is used in DNA, Uracil is used in RNA.
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Cytosines next to guanines (CpG) on the same strand of DNA are most important for? Pg 3
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The CpG can be modified by enzymatic addition of a methyl group. This modification influences the structure of DNA (indirectly) by preventing its expression.
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What is deamination? Pg 3
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The spontaneous removal of an amine group (NH2) from a nucleotide. This is a common type of DNA damage.
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What are the 2 types of deamination that are “easily detected”? Pg 3
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Cytosine -> uracil. Adenine -> hypoxanthine.
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What is unique about the deamination of a methylated cytosine (methyl-cytosine)? Pg 3
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Deamination results in thymine. This deamination is NOT “easily detected” and thus not easily repaired.
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What is the difference between a nucleoside and a nucleotide? Pg 3
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Nucleoside (nucleoside triphosphate) = ribose sugar + nitrogenous base. Nucleotide = ribose sugar + nitrogenous base + 1-3 phosphate groups
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Describe what type of bond holds the phosphate and the nitrogenous to the ribose sugar. Pg 4
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Nitrogenous base = glycosidic bond. Phosphate = ester linkage
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Describe the naming convention used for the phosphates attached to the ribose sugar. Pg 4
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Alpha, beta, gamma, where alpha is the closest to the sugar. Only the alpha phosphate is incorporated into nucleic acids. Hydrolysis of the other 2 phosphates provides energy.
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Describe how nucleotides are joined together. Pg 4
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Phosphodiester bonds (forming a phosphodiester backbone)
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Describe how complementary base-pairs are held together (what bonds hold the 2 strands together ?). Pg 4
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Strands of DNA are held together by H-bonds between the nitrogenous bases.
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What complementary base paring has the strongest bonds? Pg 4
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C-G have 3 H-bonds between them. A-T only has 2.
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What pattern keeps the 2 strands of DNA parallel and always the same distance apart? Pg 4
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Purine is always base-paired with a pyrimidine
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Define complimentarity. Pg 4
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If the sequence of 1 strand of DNA is known, it is very easy to predict the sequence of the other strand
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What is the anti-parallel nature of DNA? Pg 5
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The 2 strands of DNA run in opposite directions
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Where do proteins interact with DNA? Pg 5
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Major and minor grooves
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What is the composition of chromatin? Pg 5
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DNA + proteins. Which can be in 2 forms (heterochromatin or euchromatin)
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During mitosis, describe the condition of the genetic material. Pg 5
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Chromatin becomes very condensed, chromosomes become visible in the heterochromatin form
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Chromosomes are only visible when a cell is dividing and there is no transcription occurring in the cell. What is the state of the chromatin? 1st biomed scribe notes page 4
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Heterochromatin
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Compare: euchromatin vs. heterochromatin Pg 5
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Euchromatin is less dense, more active. Heterochromatin is more dense & relatively TS inactive. Euchromatin also only makes up 10% of the total chromatin in the cell.
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Where are ribosomes synthesized? Pg 5
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Nucleoli (3 of the 4 rRNAs are made in the nucleoli)
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What is the compaction ratio required to get DNA into the nucleus? Pg 5
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10,000:1. 3billion bp of DNA into a 5-8micrometer nucleus
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Why are histones positively charged? Pg 5
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Histones are positively charged to attract the negatively charged DNA
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What forms the nucleosome core (bead)? Pg 5
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(H2A, H2B, H3, H4) x2. A total of 8 histones form the octamer
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What is found between the nucleosome cores? Pg 5
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Histone H1 bound on each side by linker DNA (~50bp)
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What makes up a nucleofilament? Pg 6
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20nm fiber of packed nucleosomes
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How are chromosomes formed? Pg 6
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Neurofilaments are anchored via scaffolding proteins to form chromosomes.
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Explain the effect of acetylation on histones. Pg 6
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The addition of an acetyl group to histones will neutralize the positive charge, and thus weaken its interaction with DNA. This allows proteins involved in replication & transcription to get to the DNA.
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What is the difference b/w HAT vs. HDAC? Pg 6
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HAT (Histone Acetyl Transferase) acetylates, while Histone DeACetylase removes the acetyl group.
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Describe the specific region of the histone that interacts with DNA. Pg 6
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The amino terminus of histones have (+)-charged lysine AAs that interact with the (-)-charged phosphates in DNA
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Where are the HATs located? Pg 7
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Generally, HATs are located on the TSF and/or proteins themselves. (this is for convenience)
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Describe how an acetyl group affects the formation of euchromatin or heterochromatin. Pg 7
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HAT=euchromatin. HDAC=heterochromatin.
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List 4 post-TL modifications that help to make up the “histone code”. Pg 7
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Acetylation, phosphorylation, methylation, & ubiquitination
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In the cell cycle, during what phase is DNA replicated? Pg 7
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S (synthetic) phase
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Describe the role of tumor suppressors in the cell cycle. Pg 7
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Control checkpoints, which can stop the cell cycle. Such as p53, pRB
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Describe the role of proto-oncogenes in the cell cycle. Pg 7
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Send positive signals for continued cycling. Such as c-myc, Ras
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What is checked at G1 and G2? Pg 7
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Basically, whatever was done in the previous part of the cycle. Therefore in G1, the chromosomes are checked to see if they are intact after mitosis. In G2, the DNA is checked to see if they were replicated once, and only once.
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What happens if DNA damage is detected during the cell cycle? Pg 7
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Cell cycle halted > repaired > if unsuccessful, then apoptosis
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Explain why “licensing” occurs during the cell cycle? Pg 7
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In late G1 and S phase, licensing ensures that all regions of DNA are replicated completely, but only once, per cycle.
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Which regions of the genome replicates earlier in S phase? Pg 7
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Regions of the genome that are actively transcribed are replicated earlier in the S phase as opposed to the untranslated regions.
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Define semi-conservative replication. Pg 8
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The new daughter helices contain 1 strand of parental DNA and 1 strand of de-novo DNA
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Describe the purpose of having multiple origins of replication in DNA. Pg 8
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Replication begins at multiple origins of replication to ensure DNA is replicated quickly. The origins of replication enlarge via replication forks that that extend bi-directionally forming a replication bubble.
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In what direction is template DNA read, and in what direction is DNA synthesized? Pg 8
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Read from 3’ to 5’. Synthesized from 5’ to 3’
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Why is the ORC not sufficient to initiate replication of DNA? Pg 9
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Origin Recognition Complex needs “licensing” of the origin in order to replicate
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How does “licensing” of the ORC occur? Pg 9
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In late G1, cdc6 & cdt1 bind to ORC -> recruit mcm > FORMS A PRE-RC COMPLEX (pre-replicative complex) > origin is now “licensed”
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What are the components of the pre-replicative complex (pre-RC)? Pg 9
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ORC + cdc6 + cdt1 + mcm
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Describe the steps that occur after “licensing” in the G1 phase of replication. Pg 9
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In S phase, S-cdk phosphorylates cdc6 and ORC. Cdc6 gets degraded and ORC will release mcm to help open the bubble with its helicase activity.
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What is the function of mcm in initiation of replication? Pg 9
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The helicase activity of mcm separates the 2 strands of DNA and allows the pre-initiation complex to form (which contains DNA pol and other associated proteins)
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When does “firing” occur in the cell cycle? Pg 9
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The origin “fires” when cdc6 and ORC are phosphorylated by S-cdk. This causes the both the disassembly of the pre-RC, and the initiation of DNA rep. ORC binds the origins of both daughter DNAs, but various mechanisms ensure that the pre-RC doesn’t form until the next G1 and the origin is not fired again until the next S cell cycle
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Name the 3 proteins that help alleviate supercoiling that results when the DNA helix is unwound. Pg 10
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Helicase, single strand binding proteins, topoisomerases (I & II)
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Describe the purpose of helicase. Pg 10
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Helicase (enzyme)- including mcm, use ATP to separate the 2 strands, and moves the replication fork forward
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Describe the purpose of single strand binding proteins. Pg 10
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Single strand binding protein- including RPA, bind to single stranded parental strands to prevent re-annealing.
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Describe the purpose of topoisomerases. Pg 10
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Make reversible nicks in the DNA ahead of the replication fork and pass the unbroken strand(s) through the gap, and then reseal the gap. Type 1 makes 1 nick, type 2 causes a dsBreaks.
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What is the problem that supercoiling causes? Pg 11
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Tangling & ds breaks in DNA
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What is the clinical significance of topoisomerases? Pg 11
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Some cancer drugs inhibit topoisomerases to prevent replication of rapidly dividing cells.
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During DNA synthesis, where is the phosphodiester bond formed? Pg 12
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Between the 5’ phosphate of the incoming nucleotide and the 3’OH of the previous nucleotide
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What gives the ability of DNA pol to proofread? Pg 12
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It’s 3’ → 5’ exonuclease activity. It excises the last nucleotide added if it doesn’t bp correctly with the template strand
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The first 3’OH during DNA replication is provided by? Pg 12
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An RNA primer made by primase (an RNA polymerase)
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What is the difference b/w the leading vs. lagging strand? Pg 13
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Leading strand is copied continuously form the origin of replication, in the same direction as the replication fork. The lagging strand is copied discontinuously in small fragments (Okasaki fragments) beginning at the replication fork and moving toward the origin.
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What enzyme removes the RNA primers laid down by DNA primase? Pg 14
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RNA hydrolases
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Like helicase, what cofactor does ligase require in order to function? Pg 14
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ATP
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Give a brief summary of DNA replication. Pg 14
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1.During the G1-phase: Origin + ORC +cdc6 + mcm = pre-RC 2.Phosphorylation in S-phase 3. Helicases & mcm unwind helix 4.RPA (a SSBP) keeps parental strands from re-annealing 5.Topoisomerases prevents supercoiling 6.Primase makes RNA primer 7.Replication via DNA pol 8. RNAse (RNA hydrolase) removes primers 9.Gaps filled by DNA pol 10.DNA ligase seals nicks
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What are epigenetic signals? Pg 15
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Epigenetic signals represent a form of inheritance at the cellular level (in addition to genetic inheritance based on DNA sequence). Epigenetic signals include: DNA methylation and histone modifications, which influence chromatin structure
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What can change the epigenetic signals? Pg 15
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Typically the patterns are maintained during DNA replication, but may be altered over time in response to environmental factors
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When are epigenetic patterns maintained, and when are they completely erased? Pg 15
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Somatic cell replication = epigenetic signals maintained. Formation of gametes = removal of epigenetic signals (DNA methylation), but may not be complete.
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Describe the main difference between how genetic variation occurs between epigenetic signals versus typical Mendelian genetics. Pg 15
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Epigenetic signals do NOT change the nucleotide sequence. Mendelian genetics involves modification of the nucleotide sequence
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During the course of evolution, what has happened to most of the CpG sequences? Pg 16
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Most of the CpG sequences have mutated to TpG (methylated-cytosines). The remaining CpGs are not evenly distributed in the genome, thus giving the name, CpG islands.
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Where are CpG islands typically located? Pg 16, 17
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These C-G rich areas are located at the 5’ end, mostly in regulatory regions of “housekeeping” genes that are constitutively expressed and usually not methylated
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What are housekeeping genes? Pg 16
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“Housekeeping genes” are genes that are constitutively expressed, found at the 5’ end, and not methylated
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Where does DNA methylation occur, and what is its result? Pg 16
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DNA methylation occurs on CpG sequences of the same strand of DNA. It inhibits TS (heritable gene inactivation)
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Where is DNA methylation important? Pg 16
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Normal development, X chromosome inactivation, & imprinting. Necessary to maintain chromosomal stability by keeping repetitive sequences in non-coding regions in a repressed state.
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Explain why CpGs are underrepresented in the genome? Pg 16
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Deamination of methylated-cytosines results in a thymine. This is why methylated-CpG is mutated to TpG, AND explains why CpGs are underrepresented in the genome over time.
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How are CpG islands maintained in the genome? Pg 16
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CpG islands that are not methylated are maintained. (Only methylated-cytosines are susceptible to deamination, resulting in a thymine, and thus not being maintained in the genome)
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How are the same patterns of methylation maintained during DNA replication? Pg 16
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DNA maintenance methylase recognizes hemi-methylated sites and methylates the other newly synthesized strand
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What are the results of abnormal changes in the DNA methylation patterns in DNA? Pg 17
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Affect gene expression, genomic stability, and are associated with the development of cancer (and possibly other diseases/conditions)
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How is the “histone code” maintained during DNA replication? Pg 17
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Similar to methylation of DNA, the parental pattern of histone modification is re-established by proteins that recognize the same modifications they catalyze (reader-writer remodeling complexes to match the ones already bound)
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In what 4 ways are histone tails often modified? Pg 17
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Acetylation, methylation, phosphorylation, ubiquitination (MONO)
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Why are some DNA lost from the ends of chromosomes with every round of DNA replication? Pg 18
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Because of removal of the RNA primer from the end of the lagging strand, the 3’ end of the parental DNA cannot be replicated completely. This is the problem at the end of replication.
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Describe the structure of telomeres. Pg 18
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A folded 3’ overhang that contains tandem copies of 6bp’s, plus proteins that bind to it. The folding provides a structure for proteins to bind.
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Describe the function of telomeres. Pg 18
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They do not encode any proteins. Instead, they protect the ends of chromosomes from fusion and degradation, and distinguish the ends of intact chromosomes from broken ones
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Define senescence. Pg 19
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Telomeric DNA is lost at every cell cycle. When the loss is significant, it will trigger cell cycle checkpoint mechanisms and the cell stops growing permanently. Such cells are said to be senescent. Senescence has been implicated in certain cell populations that may cause common age-related conditions.
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Why is the loss of telomeric material during DNA replication deleterious to DNA? Pg 19
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As Telomeric DNA is lost, fewer (stabilizing) proteins can bind to protect DNA, and the risk of damage to the ends of the DNA increases
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In what type of cells is and isn’t telomerase found? Pg 19
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Not found in most somatic cells. Found in germ-line cells, stem cells, and >85% of cancer cells (expression is associated with immortalization of cell lines)
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How does telomerase form the 3’ overhang? Pg 19
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Telomerase is a ribonucleoprotein that carries its own RNA template complimentary to the G-rich strand of the telomere. It uses its own RNA as a template to synthesize DNA to extend the parental strand of the telomere
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How are telomerases being exploited clinically? Pg 19
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Experimental cancer vaccines are being developed to target telomerases as a tumor-specific antigen
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Describe the sequelae involving telomerase and its relationship to cancer. Pg 20
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In cancer cells, the checkpoint mechanisms that usually leads to senescence fail. Cell replicates its own DNA even though the telomeres are dangerously short. Lack of functional telomeres results in chromosomal instability. Chromosomal rearrangements occur resulting in reactivation of telomerase. The cell becomes immortal.
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How are the proteins in the mitochondria made? Pg 21
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13 are made from mitochondrial DNA, the rest are imported into the mitochondria from proteins made from the nuclear genome
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Describe the structure of mitochondrial DNA. Pg 21
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Single, double-helical circle, no histones. Multiple copies per mitochondria
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How does the replication of mitochondrial DNA resemble that of bacterial DNA replication?
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Mitochondrial DNA, like bacterial DNA replication, is NOT limited to only the S-phase
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How is the mitochondrial DNA more “economical” than nuclear DNA? Pg 21
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Almost every bp of the mitochondrial DNA is used to make a functional product. Compare this to the 2% in the nuclear DNA.
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Why does mitochondrial DNA have a higher mutation rate than nuclear DNA? Pg 21
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Close proximity to oxygen radicals & less efficient repair mechanisms.
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How does mitochondrial DNA damage relate to aging? Pg 21
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Accumulated mutations in mitochondrial DNA have been suggested to contribute to not only decreased efficiency of oxidative metabolism with increased age, but also to the overall aging process.
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