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bio 315 > exam 2 > Flashcards

exam 2 Flashcards

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Biology 101 flashcards
1
Q

describe the ikea manual analogy

A

the central dogma is like an ikea manual in swedish
- dna is like the swedish manual, we cant understand it but it holds important information for how to build the furniture
- rna is like the translator that puts the dna into understandable terms for the protein, like how we need the instructions to be in english to make the furniture
- protein is like the finished product, everything comes together to build the furniture

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1
Q

the central dogma allows for

A

flexibility with protein production

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2
Q

do all genes express at equal amounts and produce equal amounts of proteins?

A

NO

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3
Q

what does the example of tubulin vs kinetochore proteins say about gene expression

A

they do not all produce equal amounts of proteins, more tubulin is needed for interphase than kinetochore

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4
Q

mRNA transcription is essentially…

A

protein coding

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5
Q

describe the difference in structure between RNA and DNA (sugars and bases)

A

sugar - RNA has ribose (OH group), DNA has deoxyribose (H group)

base - RNA has CH group on URACIL, DNA has CH3 group on THYMINE

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6
Q

give a general description of how DNA is transcribed into RNA

A

DNA is unwinded via DNA polymerase, RNA polymerase binds to the 3’ end and adds corresponding rna bases to dna bases, creating a single mRNA strand

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7
Q

what regulates mRNA transcription

A

transcription factors

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8
Q

what do transcription factors do?

A

bind to specific DNA motifs in promotor to activate/deactivate transcription

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9
Q

what happens if the sequence or coding is off during mRNA transcription?

A

the protein will not be made properly - no function or improper function

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10
Q

what is example of a gene that requires multiple transcription factors to be transcribed? how many does it need?

A

collagen - 3

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11
Q

why do some genes need more than one transcription factor to activate transcription? what do TFs sometimes bind to in order to stabilize this bond?

A

-the TFs bonds can be weak, but when combined they synergize to keep bonds strong and last longer/more productive connections

-some TFs will additionally bind to an enhancer in a regulator region to stabilize the bonds

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12
Q

what molecule utilizes cooperative binding? what does it suggest

A

transcription factors
- accidental binding is less likely

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13
Q

for TFs that cant reach the chromatin to access the motifs needed, what is used instead?

A

pioneer TFs

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14
Q

what do pioneer tfs do and what are some examples?

A

they initiate chromatin opening at dna motifs - Sox2 Oct4 FoxA

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15
Q

what molecule has specialized structures to bind to dna motifs within compact chromatin

A

pioneer TFs

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16
Q

T/F: most TFs are pioneers and dont need help from chromatin modifying proteins or other pioneers

A

FALSE

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17
Q

why are pioneer TFs important

A

help with specificity and maintenance

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18
Q

what is an important idea about bond strengths and stable interactions?

A

many weak bonds between 2 molecules=specific stable interactions

  • just bc a bond is strong does not mean its the best and most productive bond for those molecules
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19
Q

what is an example of a chromatin modifying protein? what do they do

A

histone modifiers can use histone PTMS to alter the charge of their tails and loosen/tighten interactions with DNA

20
Q

what is an example of enzyme in a PTM of histones that TIGHTENS chromatin

A

acetylation - HDACs (histone deacetylases) close chromatin by removing acetylation from histone tails

21
Q

what is an example of enzyme in a PTM of histones that LOOSEN chromatin

A

acetylation - HATs (histone acetyl transferases) close chromatin by adding acetylation from histone tails

22
Q

what impact does methylation have on chromatin compactness

A

is does not alter the charge of the histone tails, but by recruiting other proteins that remodel chromatin it can alter gene expression and function - can either tighten or open depending on which protein remodelers are recruited

23
Q

what important amino acid is abundant in histones and give it its positive charge

A

lysine

24
Q

make a histone tail charge more positive/ dna charged negatively causes chromatin to…

A

TIGHTEN

25
Q

remodeling proteins need ____ to act on histones

A

ATP

26
Q

what three ways can remodeling proteins change histones

A
  1. nucleosome shift
  2. swap in histone variants
  3. remove an entire nucleosome
27
Q

what are the two types of histones and which is more abundant in cell nuclei?

A
  1. canonical - most abundant in nucleus of cell
  2. variants
28
Q

when are canonical core histones produced

A

during S phase - cell division

29
Q

what do variant histones do and when can they be added?

A
  • make significant changes
  • can be added in a non dividing cell
30
Q

using the example of H3.3, explain what kind of histone it is and the implications it has in cancer

A

H3.3 is a histone variant that makes a small change but has big consequences as it is associated with cancers, especially brain cancers

31
Q

why is H3.3 more prevalent in brain cancers compared to other cancers like intestinal cancer?

A

our neuronal turnover is much slower than our intenstinal cell turnover, so variants are impactful for longer as they are not removed and replaced as quickly in neurons as they are in intestinal cells

32
Q

How did most researchers think the “new ring” was formed BEFORE they tried expressing GFP in bacteria?

A

by a jellyfish-specific enzyme

33
Q

How did the researchers know if their theory about the new ring being formed in GFP was right or wrong?

A

they knew they were wrong because GFP did glow green in bacteria

34
Q

Is this Green Fluorescent Protein (GFP) the same protein or different from the one that glows blue?

A

it’s a different protein and does not need calcium to glow green

35
Q

Dr. Chalfie was particularly excited about the idea of GFP because he wanted to use it to label specific cells and track them during development. In the image above, he illustrates how this would work. Given what we discussed in class about transcription, what might make a promoter “neuron-specific”?

A
  • it contains TF binding sites for TFs that are only expressed in neurons
  • it is found in front of genes that are only expressed in neurons
36
Q

In this illustration, Dr. Chalfie shows how you can both express GFP in a particular cell type AND attach it to a particular protein you want to track. This strategy has been used thousands of times with success to visualize different proteins in a cell, but it doesn’t always work well. Looking at the image and considering what we know about protein folding and function, why might this not work well for some proteins?

A

adding a big extra protein domain affects the function, binding interactions, proper degradation, and stability of the “favorite protein”

37
Q

Dr. Schekman and his lab members generated a system for making genetic mutants in yeast to identify genes that encode proteins required for protein trafficking and secretion. What types of proteins might this method uncover

A

ER proteins, Golgi proteins, vesicle forming proteins, membrane-bound signaling receptors

38
Q

Why do the sec1 mutant cells have increased enzyme activity at 4 hours?

A

after switching to 37C the enzyme cannot be secreted from sec1 mutants

39
Q

Why might the sec1 mutant cells show a drop in enzyme activity at >5 hours?

A

sec1 is an essential gene, so the cells start to die after being at 37C for too long

40
Q

Although the sec1 mutant cells can survive at the “permissive” temperature, they are not 100% normal. Which of the following issues are they most likely to have?

A

they are smaller than normal cells

41
Q

Dr. Schekman and his lab want to test if the function of the yeast sec1 protein is conserved in human cells. What experiment should they do?

A
  • add a normal copy of the human sec1 gene back into the mutant yeast and see if it rescues the phenotype
  • mutate the human sec1 gene homolog and see if it has the same phenotype
42
Q

Why did the authors show the Coomassie blue stained gel alongside the “H3-methyl” and “H3-acetyl” results?

A
  • to show that the H3-methyl and H3-acetyl signals were detected on a protein of similar size to a histone
  • to confirm that they loaded similar amounts of protein extracted from micro and macronuclei
43
Q

In class I explained that HAT enzymes add acetylation to histone tails, neutralizing their positive charge and changing their interaction with DNA. What does the data in panel A indicate about the chromatin status of macronuclei versus micronuclei?

A

that macronuclei likely have more open chromatin than that of micronuclei

44
Q

Given what I told you in class about HAT activity and its effect on chromatin, what do you hypothesize about HMT enzymes and the methylation they add to histones?

A

methylation likely also correlates with open chromatin

45
Q

go to figure 4 panel A from the paper we read for week 5 hw:

what does panel A indicate?

A
  • Lysine (K) 27 may be the site of H3 methylation that caused the signal in Figure 1, but this does not prove it
  • Lysine (K) 4 may be the site of H3 methylation that caused the signal in Figure 1, but this does not prove it
46
Q

go to figure 4 panel B from the paper we read for week 5 hw:

Panel B shows Histone H3 isolated from human HeLa cells to compare with that of Tet macronuclei. Why do you hypothesize that human cells have a different signal pattern than Tet?

(added info: in humans, histone H3 lysine 9 methylation is heavily enriched at repetitive genomic regions, such as ancient viral sequences)

A
  • HeLa cells come from a cancerous tumor
  • Tet and human are evolutionarily distant species, so there may be many reasons
  • human cells don’t have two nuclei, so they cannot separate active and silent chromatin
47
Q
A

bio 315 (1 decks)

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