Genetics: Chromosomes, Transcription, Translation Flashcards
(104 cards)
1
Q
How does a genome differ from a gene?
A
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)
2
Q
Prokaryotic vs. Eukaryotic Genome (Size, Shape, Introns/Exons)
A
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
3
Q
What are Homologous Chromosomes?
A
Chromosome pairs, (one from mom, one from dad), may have different genotypes for genes on them
4
Q
Diploid vs. Haploid?
A
Diploid: Double set of chromosomes
Haploid: Single set of chromosomes
5
Q
Mitosis
A
Duplication of cell (prophase, prometaphase,metaphase,anaphase, telophase)
6
Q
Meiosis
A
Creation of haploid sex cells for reproduction
7
Q
What are the 3 components of a nucleotide?
A
Nitrogenous base (adenine, thymine, cytosine, guanine), deoxyribose sugar, phosphate group
8
Q
Draw the 4 nucleotides
A
Guanine, Adenine, Thymine, Cytosine
9
Q
Which nucleotides are purines?
A
Adenine, Guanine (these are the ones with 2 rings)
10
Q
Which nucleotides are pyrimidines?
A
Thymine for DNA, Cytosine, Uracil for RNA (these are the ones with one ring)
11
Q
Which nucleotides pair up, how many ___ bonds does each pair have?
A
C - G three hydrogen bonds
A - T or A - U two hydrogen bonds
12
Q
What does semiconservative DNA look like? draw and explain
A
Semiconservative means that in replication one strand comes from the parent DNA and one strand is the newly created strand
13
Q
Prokaryotic vs. Eukaryotic origins of replication?
A
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
14
Q
Prokaryotic vs. Eukaryotic origins of replication?
A
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
15
Q
List as many challenges as you can come up with related to DNA replication (at least 3)
A
- 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
16
Q
What property of DNA polymerases improves fidelity (accuracy) in replication?
A
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
17
Q
What are the 3 main types of DNA polymerases in eukaryotes? What are their key differences?
A
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
18
Q
Processivity?
A
The ability of a polymerase to remain bound to its template and replicate DNA. Defined as #bases synthesized per binding event
19
Q
What is the clamp protein?
A
The clamp protein stabilizes DNA and DNA polymerases, increasing their processivity by passing the DNA through a donut-hole-like opening
20
Q
Leading vs. Lagging replication?
A
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
21
Q
List all the steps and molecular players necessary in overarching DNA replication.
A
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
22
Q
What molecules are involved with mismatch repair?
A
MSH2, MSH3, MSH6, identify mismatches. MLH1, PMS2 identify which strand was the parent strand, Exonuclease I goes in and replaces the incorrect nucleotide
23
Q
Why is mismatch repair important?
A
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
24
Q
Explain how genetically inherited errors in the mismatch repair system would lead to an increased risk of cancer?
A
If you don’t identify errors you will have a faster rate of mutation accumulation and eventually will build a cancerous cellular genome.
25
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
26
What is an incorrect number of chromosomes called?
aneuploidy
27
What are sister chromatids?
identical copies of chromosomes, held together by the centromere until cell division
28
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.
29
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
30
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.
31
What are the 4 histone proteins?
H2A, H2B, H3, H4
32
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.
33
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.
34
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.
35
What does acetylation do?
Acetylation decreases the positive charge on a nucleosome and allows DNA to open up and be expressed a bit.
36
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.
37
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.
38
```
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.
39
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.
40
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.
41
```
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.
42
```
In eukaryotes, promoters of tRNA genes:
A. Are usually recognized by TFIIIC
B. Are usually recognized by TFIIB
C. Usually lie near the 3’ end the gene
D. Usually contain TATA boxes
```
A is correct. RNA polymerase III is the enzyme that recognizes promoters within tRNA genes.
Therefore, only a General Transcription factor with a III in its name would be relevant here and
so B is incorrect. C is incorrect because the promoters of tRNA genes lie within the gene, near the
center. TATA boxes are found in some Pol II promoters but not in the promoters of tRNA genes,
so D is incorrect.
43
An antibody to Protein X is used on a Western blot of nuclear protein extracts from various
tissues. The results show the following protein band sizes for each tissue: Brain - 70 kilodaltons
(KDa), Liver - 50 KDa; Muscle - 40 KDa and 50 KDa, Pancreas - 70 and 40 KDa. One likely
explanation is:
A. Tissue-specific post-translational modifications
B. Tissue-specific alternative polyadenylation sizes
C. Tissue-specific alternative splicing
D. Presence or absence of mRNA cap structures
E. Tissue-specific tRNAs
C is correct. Alternative splicing in different tissues can result in mRNAs with different
coding sequences and different sized proteins. A is incorrect since most post-translational
modifications (e.g. adding a few phosphate or methyl groups) will not result in size differences of
this magnitude. B is incorrect since different size poly(A) tracks will affect the size of the mRNA
but not protein. D is incorrect since the absence of a cap would affect protein levels not their size.
E is incorrect since tissue-specific tRNAs would not change the sequence or size of the proteins.
44
A DNA-binding transcription factor binds to a gene’s enhancer. The transcription factor binds
a nuclear protein containing a histone acetyltransferase (HAT) activity. This results in strong
transcription from the gene’s promoter, which is close to the enhancer. What effect is the
recruitment of this HAT cofactor likely to have on the transcribed gene’s promoter?
A. The HAT enhances the activity of polyadenylation factors that increase the length of the
transcribed RNA
B. The HAT dephosphorylates the DNA-binding transcription factor causing it to no longer
bind to DNA
C. The HAT will acetylate histones, resulting in opening of chromatin at the promoter and
allowing RNA Pol II to bind and initiate transcription of the gene
D. The HAT removes methyl groups from DNA, repressing transcription of the adjacent
gene
C is correct. The DNA-binding transcription factor recruits a coactivator with HAT activity.
The DNA loops bringing the enhancer close to the promoter and HAT acetylates histones causing
the nucleosomes to move and create an open site at the promoter that allows access to Pol II. A,
B, and D are incorrect. There is little evidence that HAT cofactors act on poly(A) factors,
enhancer binding transcription factors, or DNA demethylases. Also, A and D activities do not
result in transcriptional activation and in B, HATs acetylate proteins, not dephosphorylate them.
45
A eukaryotic gene (gene Z) is expressed in tissues A and B. The intact genomic copy of the
gene is 15,000 bp long. The mature mRNAs expressed from gene Z in each tissue are sequenced.
The RNA from tissue A is 750 nucleotides long while that from tissue B is 600 bp long. RNAs
from both tissues have the same nucleotide sequence through the first 250 bp, then completely
diverge. However, the sequence of the final 56 nucleotides prior to the poly(A) tail is identical for
transcripts from both tissue types. RNAs from both tissues have average poly(A) lengths of 200
nucleotides. Translation of the RNAs produces two functional proteins of differing molecular
weights. The most likely explanation for the differences and similarities between the RNAs
transcribed from gene Z RNA in these two tissues is:
A. Different usage of alternative splice sites in gene Z mRNA in the two tissues
B. Different transcriptional start sites for gene Z in the two different tissues
C. Use of different alternative 3’ cleavage sites generating different 3’ ends on the RNA
D. Differential RNA editing in the two tissues
A is correct. Differential RNA splicing is consistent with the data. Gene Z is described as
being 15,000 bp long with a 750 bp transcript in tissue A and a 600 bp transcript in tissue B. The
sequence heterogeneity is between the middle of the two transcripts, but not at the two ends
indicating that transcription in both tissues begins and ends at the same site in gene Z, ruling out
answers B and C. Differential RNA editing is ruled out by the extent of the heterogeneity. In
humans, RNA editing occurs at the single nucleotide level, not over long contiguous stretches of
RNA. This eliminates D.
46
Several types of RNA editing have been found in humans. C to U editing is responsible for:
A. Creation of a premature stop codon in mRNA normally encoding Apo-B-100
B. Changes in only the Apo-B-100 RNA and protein sequence, but not size of the protein
C. Creation of new translational start sites in many different mRNAs as a normal part of
RNA processing
D. Formation of the Iron Response Element in ferritin and transferrin mRNAs
A is correct. This particular example is emphasized because of its clinical consequences. C to
U editing is relatively rare in mammals (thus, answer C is incorrect), although high-throughput
RNA sequencing is discovering new instances. The canonical example in humans is the editing of
mRNA encoding apolipoprotein B mRNA (answer A). If editing creates a stop codon, then protein size, not just squence, may be affected (so answer B is incorrect). The Iron Response
Element does not rely on RNA editing to generate it (answer D is incorrect).
47
MicroRNAs are produced from:
A. mRNAs degraded as a result of nonsense-mediated decay
B. Capped and polyadenylated transcripts of introns
C. Capped and polyadenylated tRNAs
D. RNAs derived from transposable elements
B is correct. MicroRNAs often arise from introns (but are also found elsewhere in the
genome); the pre-miRNAs are usually transcribed by RNA Pol II and are capped and
polyadenylated. However, before they leave the nucleus they are processed, which removes their
poly(A) tails as well as additional 5’ and 3’ flanking sequences. A, C, and D are incorrect: they
are not modified tRNAs; they are not transcribed by RNA Pol III (as are tRNAs); they are not
derived from transposons.
48
MicroRNAs regulate gene expression. They act as part of the RISC complex and bind to:
A. Regions of mRNAs with complementary nucleotide sequences, triggering either mRNA
degradation or inhibition of translational initiation
B. Intron/exon boundaries in newly synthesized mRNAs, inhibiting correct splicing
C. The first AUG in mRNAs, thereby inhibiting translation
D. The 5’-leader regions of mRNAs, triggering 5’-Cap release and mRNA degradation
A is correct. MicroRNAs in their final forms are bound by a protein complex called RISC. In
the cytoplasm, miRNAs bind to mRNAs (commonly at 3’-ends) with regions of homology (thus,
C and D are incorrect). If the match is perfect, the RISC complex cuts the mRNA, which is
rapidly degraded. If the match is less extensive, RISC remains bound to the mRNA and miRNA
and interferes with translation of the mRNA. RISC does not affect RNA splicing (B is incorrect).
49
What is the central dogma?
DNA--> transcribed into RNA --> translated into Protein
50
What are the main types of RNA, and what are they used for?
mRNA is used as a sequence of codons for translation into protein.
tRNA is paired with amino acids and then paired with codons to create peptide chains
rRNA is used to create ribosomes, which are the factory in which proteins are made
also siRNA (small, interfering RNA, often used to silence RNA strands), snoRNA (small nucleolar RNA, guide chemical/structural modification of rRNA, tRNA, siRNA)
51
Draw an overview of the central dogma
Strand of DNA (top strand is nontemplate, bottom strand is template). Make a copy of the nontemplate strand (but with Us replacing Ts)/ also known as complement of template strand. RNA is spliced (introns removed) 5' capped and 3' poly(A) tail added, and sent to the ribosomes to make proteins.
52
Differences in transcription between eukaryotes and prokaryotes?
Prokaryotes: transcription and translation occur in the same cellular region, simultaneously. No RNA splicing necessary. All genes are transcribed by a single RNA polymerase.
Eukaryotes: transcription is in the nucleus, translation is in the cytoplasm. genes code for individual proteins. There are significant amounts of non-coding DNA (over 90%), so RNA splicing is required. DNA is packaged around nucleosomes. Multiple classes of genes (tRNA, rRNA, siRNA, snoRNA, mRNA)
53
What is RNA Polymerase I used for?
transcribes rRNA genes
54
What is RNA Polymerase II used for?
transcribes mRNA genes, microRNAs (regulation) snRNA (RNA splicing)
55
What is RNA Polymerase III used for?
transcribes tRNA, the 5S rRNA gene, and some siRNAs
56
What is an RNA promoter region?
A region of DNA where transcription is initiated. Initial binding site and a lot of binding sites for transcription factors throughout
57
What is an RNA enhancer region?
A region of DNA where activators can bind. Also known as a transcription factor, an activator increases the likelihood (probability distribution/kinetics is really the name of the game here) that transcription will occur.
58
Which polymerase type (I, II, or III) interacts with the TATA box and the initiator element?
RNA Polymerase II. TATA box is bound to by TATA binding protein. TATA box is about 30 bp away from start of gene. Initiator element is found about 1 bp away from the start of the gene.
59
What are the differences between dispersed and focused promoters?
Dispersed: Multiple start sites, less effectively regulated. Instead of TATA boxes, there are CpG islands (Cytosine phosphate Guanine). This is for housekeeping genes, genes that always need to be on.
Focused: A single start site on the gene, TATA and Initiator elements. These are usually regulated genes. 20% of promoters are focused promoters
60
What transcription factors are common with RNA Polymerase II?
TFIIA, TFIIB, TfiID, TFIIE, TFIIF, TFIIH, TATA binding factor.
Notice that all of these have TFII in them (expect TATA)
61
What is the process of Polymerase II transcription?
TBD binds TAA box
TFIIA and TFIIB stabilize TBP binding to TATA box DNA strand.
TFIIB positions polymerase II, TFIIF & TFIIE & TFIIH assist with polymerase II
TFIIH helicase unwinds DNA.
TFIIH kinase phosphorylates C terminal domain, transcription starts
62
What are the major similarities and differences between all the RNA polymerases?
Each RNA polymerase has a specific DNA sequence structure that it uniquely looks for.
Each RNA polymerase is recruited by a combination of promoter/enhancer factors.
Each Polymerase interacts with TATA-Binding Protein and TFIIB protein
Pol I uses ribosomal initiator
Pol II uses TATA and initiator box
Pol II recognizes internal sites within the gene (A & B or C)
63
What would happen if your RNA polymerase was inhibited?
you wouldn't have transcription and wouldn't be able to make proteins
64
What does prokaryotic transcription look like?
There's only one RNA polymerase. Promoters have short, consistently conserved sequences prior to the gene that are recognized by the polymerase.
The RNA polymerase requires a sigma factor to recognize these sequences. RNA polymerase binds to sigma factor.
65
Draw the mRNA structure
5' cap, untranslated region (leader region), start codon, gene, stop codon, untranslated region (trailer), poly(a) tail
66
When do the poly(a) tail and 5' cap get added?
Poly(a) tail is added after RNA has been made. 5' cap is one of the first things added, during elongation. Both occur in nucleus before splicing.
67
How does DNA know what's an intron and what's an exon to splice correctly?
Introns always start with GU and end with AG. Exons are short and have some exon factors bound. These, the size, and the intron start/stop regions are identified to find the right places for splicing
68
What is the 5' cap's function? What is its structure?
Makes mRNA resistant to degradation (buffer) and boosts initiation of translation. It's some weird bond between two 5' carbons of guanosine and a methyl group. Capping occurs as mRNA is transcribed
69
How does Polymerase II help form the 5' Cap?
As Pol II is transcribed, its C terminal domain is phosphorylated. The phosphorylated CTD attracts/binds capping proteins. These proteins are transferred to the 5' end of mRNA and create the cap
70
What is the poly(a) tail?
Polyadenylation is done by Poly(a) polymerase, and functions to keep the mRNA stable (buffer), helps transport the mRNA out of the nucleus, and increases translation. Poly(a) is added to cleaved 3' mRNA
71
What happens when the poly(a) tail degrades?
The DNA strand will eventually also erode and the cell will be destroyed.
72
What do snRNPs do?
snRNPs (small nuclear ribonucleo proteins) are RNA-protein combinations that make up a large part of the spliceosome, a protein complex used to splice exons together.
73
How is pre-mRNA spliced?
U1 snRNPs bind near the first intron junction (GU).
U2 snRNPs bind at some adenine inside the intron
U4/5/6 snRNPs bind near the other end of the intron (AG).
The G from U1 forms a bond with the A from U2, and cleaves the bond from the exon.
The exon is then ligated to the previous exon.
74
What happens when splicing goes wrong?
15% of all genetic diseases are caused by splicing errors
You'll get defective protein, point mutations, insertions, deletions, frame shifts.
75
What's different about the mitochondrial genome?
Distinct from the cell's genome: has own tRNA, rRNA, mRNA. Circular. mRNA codes for proteins involved in the electron transport chain and oxidative phosphorylation (producing energy)
76
Is the mitochondria independent from the cell?
No, many proteins are actually made from cellular RNA and then transported into the mitochondria through the TIM and TOM protein translocases (translocate proteins)
77
Difference between prokaryotic and eukaryotic ribosomes
Prokaryotic is smaller (70s) than Eukaryotic (80s)
78
What are ribosomes made up of?
4 subunits (28s, 18s, 5.8s, 5s) and some ribosomal proteins
79
What does tRNA do?
matches amino acids with codons presented in the ribosomes
80
What is aminoacyl-tRNA synthetase?
aminoacyl-tRNA synthetase identifies amino acids and tRNA that need to match up and puts them together. It takes two steps to do this. First, the tRNA is charged with an amino acid. Then, this charge is converted into a covalent bond.
81
What are the steps of translation?
Initiation, elongation, termination! Methionine starts, then the ribosome elongates the protein, and then a stop codon finishes stuff up.
A - P sites
Amino acid site is where the new tRNA matched with codon lands. The P site is where the old peptide chain is hanging out. The A-site amino acid attacks the peptide chain and removes it from the p-site tRNA. This p-site tRNA leaves and the a-site tRNA-peptide chain combo moves over to the a-site
82
What step initiates translation?
Methionine (AUG) always starts translation. eIF2 (eukaryotic initiation factor 2) brings the methionine tRNA to the small ribosome (40S unit), and waits until the methionine codon matches it. GTP is used to start the chain.
83
What is a polysome?
mRNAs can be translated by multiple ribosomes simultaneously! poly-ribosome action
84
What happens when splicing is messed up?
There might be a stop codon in an intron, so the protein is finished off early. But the exon has some bound proteins (exon junction complexes), that would have normally be removed as the ribosome pushed along the RNA strand. If these are still around, Upf proteins will degrade the RNA strand/protein before it can be used or mess anything up.
85
What is EF1 used for?
EF1 is a G-protein that drives aminoacyl-tRNA to the A site in a ribosome
86
In what ways does gene expression vary in the body?
Gene expression varies with age, and it varies depending on what cells are being looked at.
87
Is gene expression related to disease? How?
Yes! Changed gene expression is the cause of many diseases. Overexpression of telomerase gene allows cancer proteins to continue being coded even when the cell should be senescent. Over expression of genes that push a cell towards mitosis would also cause cancer.
88
What are some methods of gene expression regulation?
DNA methylation, Histone Acetylation, steriod/ligand binding. Regulation of transcription, translation, post-translation protein modification. siRNA (silencer RNA)
89
At what steps can gene expression regulation occur?
Mostly transcription control and post-translation modification, but also translation control, RNA transport control
90
What are housekeeping and regulated genes?
Housekeeping genes are always active to some extent and don't fluctuate much. Regulated genes are controlled by active gene regulation, and vary more in their level of activation.
Housekeeping gene example: basic cellular functions like creating rRNA, tRNA
Regulated gene example: Cell-type specific, neuron development, stomach acid producing enzymes
91
What are enhancers?
Short regions of DNA that can be bound by activator proteins which increase likelihood that transcription of a certain gene will occur. Enhancers allow for spatial, temporal, and hormonal control (binding proteins may not be present in the brain, so genes for liver function don't show up).
92
What are promoters?
Regions of DNA that initiate transcription of a certain gene
93
How can you classify transcription factors?
1. Presence of DNA binding motif (helix-turn-helix for bacteria, zinc finger homeobox or basic helix-loop-helix for eukaryotes)
2. Repressor or activator?
3. Chromatin modification (acetylase or deacetylase activity. Open or closed chromatin)
94
What is a consensus sequence? Draw a consensus sequence
A probabilistic sequence describing the likelihood that a certain nucleotide shows up in a sequence
95
What do transcription factors do?
Transcription factors will find sequence-specific binding domains on DNA strands. After binding, the transcription factors either activate or repress transcription. Activation TFs will interact with Pol II and general transcription factors to encourage transcription. Repressor TFs will block other factors from binding.
Transcription factors may be able to cause acetylation or deacetylation on the histones. Transcription factors could also be ligands that bind directly to DNA and disrupt transcription.
96
What is the general structure of transcription factors?
Binding domain, activation or repression domain.
97
Draw how glucocorticoid receptor, in the presence of steroid, influence transcription
normally glucocorticoid receptor is bound to heat shock protein. In the presence of steroids with higher binding affinity, GR will dump HSP and pick up steroid. This newly formed molecule will sneak through the nuclear membrane and attach to DNA.
98
How is chromatin structured? How is it remodeled?
8 histone proteins form 1 nucleosome. Nucleosomes wind up and clump together to form chromatin. Chromatin can be remodeled by acetylation. Enhancer recruits coactivator that acetylates histones and opens up chromatin.
99
How are regulated genes regulated?
Either actively repressed or actively promoted. If a resting repressor is on the gene, it takes additional factors to remove the repressor and allow for gene expression. Or it may be actively promoted, going from neutral to being promoted. Active repression is better than just leaving something neutral, because then the gene will never be expressed by chance.
100
What does methylation do to gene expression?
Methylation sticks methyl groups on cysteines and interrupts DNA, silencing gene expression.
101
How does methylation affect cancer?
Methylation of tumor suppression genes decreases the ability of the cell to regulate against abnormal growth.
102
What do insulators do?
Insulators prevent promoters and enhancers from one gene from messing with the expression of another gene. They do this by isolating a gene along a DNA strand. All DNA activity should then be independent of whether there are something going on in a nearby gene. Insulators use insulator-binding protein to create these isolated loops
103
How does splicing effect gene expression?
Splicing allows for alternate proteins to come out of the same basic DNA. Splicing, if done well, increases the versatility and efficiency of our genome. If messed up, splicing guarantees major errors in body function. Splicing can be normal (find all exons, eliminate all introns), or it can be messy (exon skipping, intron retention, alternative 5' or 3' site, mutually exclusive exons show up)
104
What is ubiquitination?
ubiquitin is a small regulatory protein that marks other molecules for degradation by the proteasomes around. ubiquitin is used to regulate protein levels via degradation.
