Genetics: Chromosomes, Transcription, Translation Flashcards
How does a genome differ from a gene?
Genome is entirety of genetic data for species, gene contains code for a single protein (or can be code for multiple proteins depending on how it is spliced together)
Prokaryotic vs. Eukaryotic Genome (Size, Shape, Introns/Exons)
Prokaryotic has fewer BPs, usually a single circular DNA strand, almost all coding for proteins
Eukaryotic has more BPs, usally multiple straight chromosomes, very little actually codes for proteins
What are Homologous Chromosomes?
Chromosome pairs, (one from mom, one from dad), may have different genotypes for genes on them
Diploid vs. Haploid?
Diploid: Double set of chromosomes
Haploid: Single set of chromosomes
Mitosis
Duplication of cell (prophase, prometaphase,metaphase,anaphase, telophase)
Meiosis
Creation of haploid sex cells for reproduction
What are the 3 components of a nucleotide?
Nitrogenous base (adenine, thymine, cytosine, guanine), deoxyribose sugar, phosphate group
Draw the 4 nucleotides
Guanine, Adenine, Thymine, Cytosine
Which nucleotides are purines?
Adenine, Guanine (these are the ones with 2 rings)
Which nucleotides are pyrimidines?
Thymine for DNA, Cytosine, Uracil for RNA (these are the ones with one ring)
Which nucleotides pair up, how many ___ bonds does each pair have?
C - G three hydrogen bonds
A - T or A - U two hydrogen bonds
What does semiconservative DNA look like? draw and explain
Semiconservative means that in replication one strand comes from the parent DNA and one strand is the newly created strand
Prokaryotic vs. Eukaryotic origins of replication?
Prokaryotic: One replication fork, creates an entirely new circular chromosome of DNA (still semiconservative). Replication occurs in both directions at once and occurs in the cell’s cytoplasm (outside nucleus)
Eukaryotic: Multiple replication forks, happening at the same time. Replication only occurs in one direction, and it occurs within the nucleus
Prokaryotic vs. Eukaryotic origins of replication?
Prokaryotic: One replication fork, creates an entirely new circular chromosome of DNA (still semiconservative). Replication occurs in both directions at once and occurs in the cell’s cytoplasm (outside nucleus)
Eukaryotic: Multiple replication forks, happening at the same time. Replication only occurs in one direction, and it occurs within the nucleus
List as many challenges as you can come up with related to DNA replication (at least 3)
- how do you start? what opens up the double stranded DNA?
- What keeps the double stranded DNA from closing right away?
- As the strands of DNA unwind, the composite structure begins to wind up like messy string, creating supercoils.
- Occasionally the wrong nucleotide is put down by DNA polymerase.
- Our chromosomes are huge and we have a lot of them, so it must take a really long time
- We need 3’ carbons to add 5’ carbon phosphate groups of the inserted nucleotides to.
- At the 3’ end of DNA strands, even primers cannot provide the 3’ carbon necessary for replication
What property of DNA polymerases improves fidelity (accuracy) in replication?
DNA polymerases have “checking” exonucleases. Exonuclease goes reverse of synthesis (3’ to 5’) to catch errors. MSH2,MSH3, MSH6, MLH1, PMS2 identify mismatched nucleotides, and identify which DNA strand is the parent strand so they know which nucleotide is wrong. Exonuclease then fixes it up
What are the 3 main types of DNA polymerases in eukaryotes? What are their key differences?
DNA polymerase delta: most of the synthesis on the lagging strand during DNA replication
DNA polymerase alpha: exists in a complex with primase, does not have proofreading capabilities, but can only put in nucleotides. Not as efficient, but used to resolve okazaki fragments and initiate replication.
DNA polymerase epsilon: most of the synthesis on the leading strand during DNA replication
Processivity?
The ability of a polymerase to remain bound to its template and replicate DNA. Defined as #bases synthesized per binding event
What is the clamp protein?
The clamp protein stabilizes DNA and DNA polymerases, increasing their processivity by passing the DNA through a donut-hole-like opening
Leading vs. Lagging replication?
DNA unwinding only occurs in one direction, but the antiparallel individual strands of DNA both need to be replicated. The DNA strand facing 3’-5’ can be read 3’-5’ and synthesized 5’-3’ as the DNA strand is opened up and new nucleotides on the 5’ end become available. But on the other strand, DNA replication is going the opposite direction from DNA unwinding. This means that short bursts of replication are performed, and then the fragments (okazaki fragments) are fused together. Lagging strand replication is not as efficient
List all the steps and molecular players necessary in overarching DNA replication.
Initiation: DNA is opened up at site of origin. Helicase unwinds DNA. Topoisomerase relieves tension in superwound DNA (topo I cuts one strand of DNA and unwraps it. topo II cuts two strands of DNA and pushes macro-scale loops through). Primase sets RNA primers down (RNA is less stable than DNA so it’s easier to get off later. Primase can lay down RNA primers without needing an initial 3’ carbon to attack, which is why it’s used). Single Strand Binding Protein (SSBP) attach to both unwound strands and keep them from coming back together.
Elongation: DNA polymerase (delta for leading, epsilon and alpha for lagging) goes through the opened strands and fills in nucleotides to compliment the template strand (nontemplate strand is what the DNA will look exactly like, template is what the DNA is paired to). Sliding clamp stabilizes DNA polymerase
Termination: Nucleases remove RNA primers and replace them with DNA. Ligase creates covalent bonds between okazaki fragments
What molecules are involved with mismatch repair?
MSH2, MSH3, MSH6, identify mismatches. MLH1, PMS2 identify which strand was the parent strand, Exonuclease I goes in and replaces the incorrect nucleotide
Why is mismatch repair important?
If you didn’t fix the mismatched nucleotides you would get mutant DNA strands –> Mutant RNA strands –> Mutant proteins. This is the source of 15% of all genetic diseases
Explain how genetically inherited errors in the mismatch repair system would lead to an increased risk of cancer?
If you don’t identify errors you will have a faster rate of mutation accumulation and eventually will build a cancerous cellular genome.
Aside from DNA repair, what other processes protect chromosomes?
Telomeres are a buffer on the 3’ end of DNA to solve the end replication problem. Telomerase creates telomere buffer regions in cells that need to continue replicating.
Centromeres guarantee that each daughter cell gets the correct number and type of chromosomes
What is an incorrect number of chromosomes called?
aneuploidy
What are sister chromatids?
identical copies of chromosomes, held together by the centromere until cell division
What two problems are present in the replication and movement of linear chromosomes?
end replication problem: initiation of replication requires an available 3’ carbon. Eventually this primer is removed and a polymerase downstream fills in the gap. But on the furthest 3’ end of the DNA strand there isn’t anything downstream to use to fill in, so it gets cut.
DNA ends are also sensitive to degradation. If the ends of a chromosome degrade the cell will freak out and fuse the two strands in a chromosome together, which means the chromosomes won’t be able to split during mitosis.
What is a telomere?
Telomeres are repeated segments of DNA at the 3’ end of a DNA strand that are basically a buffer region that can be degraded without impacting the protein that eventually is translated from the RNA which is transcribed from the DNA
What types of cells is telomerase active in?
Bone Marrow, Embyronic, maybe hair cells. Anything with a high level of mitosis, because the telomeres shorten with each round of mitosis otherwise.
What are the 4 histone proteins?
H2A, H2B, H3, H4
What is a nucleosome?
An octomer of histone proteins (2 of each H2A, H2B, H3, H4) Nucleosomes are positively charged and have negatively charged DNA wrapped around them. These nucleosomes decrease the space that DNA takes up in the cell.
How is DNA packed?
DNA is wrapped around nucleosomes which, when combined with H1 histone protein, form a chromatosome. A bunch of ochromatosomes (H1 + nucleosome) are coiled together to form a fiber. This fiber is coiled to form the chromatid structure.
What is the difference between euchromatin and heterochromatin?
Euchromatin is “open” and the genes on this DNA strand are being expressed. Heterochromatin is “closed”, and genes on this DNA are not being expressed.
What does acetylation do?
Acetylation decreases the positive charge on a nucleosome and allows DNA to open up and be expressed a bit.
What does methylation do?
Methylation creates “breaks” in cytosine’s integration with the rest of the gene sequence, and decreases the ability of the cell to express the methylated gene.
In eukaryotes, the 5’ end of mature mRNA is:
A. Always an A
B. Added to the RNA during splicing
C. Added by an enzyme carried on the CTD of RNA polymerase II
D. Added in the cytoplasm before translation begins
E. Added in the nucleus after poly(A) addition
Added by an enzyme carried on the C Terminal Domain of RNA polymerase II
C is correct. The enzymes that add the 5’-7-methyl-G cap are carried by the CTD of RNA
polymerase. A is false because the first nucleotide incorporated is not always an A. B is incorrect
because addition of the 5’ cap happens very early (within the first 25 nucleotides of mRNA
synthesized). D is incorrect because addition of the cap occurs in the nucleus, not the cytoplasm.
E is incorrect for the same reason as B.
Several types of small RNAs play important roles in preparing larger RNAs for their roles in translation. Which type of small RNA plays a role in guiding chemical modifications and endonucleolytic cleavages of rRNA? A. hnRNA B. smRNA C. snoRNA D. tRNA
snoRNA
C is correct. A is incorrect because hnRNAs is a general term for a large heterogeneous group
of RNAs. B is incorrect because smRNAs is a made-up term. D is incorrect because tRNAs are
often the targets of guide RNAs, but tRNAs do not direct RNA modifications.
Many of the transitions that occur during translation involve initiation or elongation factors that move on and off the ribosome at specific steps. A common feature of these factors is that:
A. They are encoded within introns of mRNAs
B. They are GTPases
C. They are snRNPs
D. They enter the cytoplasm bound to mRNAs
E. They are composed entirely of RNA
They are GTPases (they all take GTP and turn it into GDP plus a free phosphate group)
B is correct. Many initiation factors and elongation factors hydrolyze GTP to provide energy
to drive the conformational changes that occur as a part of translation, and are, thus, GTPases.
Translation of an mRNA ends when:
A. A termination codon moves into the A site of the ribosome
B. A terminator tRNA moves into the P site of the ribosome
C. The ribosome reaches the polyA tail of the mRNA
D. EF1a enters the P site of the ribosome
A is correct. Termination codons enter the A site and this triggers the binding of termination
factors which release the growing peptide from the tRNA in the P site and trigger dissociation of
the ribosomal subunits from mRNA.
A protein required by RNA polymerases I, II, and II to bind to their respective promoters is: A. TFIIH B. TFIIIA C. TFIIB D. TFID E. TBP
E is correct. TBP (TATA Binding Protein). This is the only protein common to the
transcription pre-initiation complexes of all three eukaryotic nuclear polymerases and it is
required by all three to bind to their promoters.
