LEC21: Overview of Gene Expression; Nucleic Acid Structure Flashcards Preview

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Flashcards in LEC21: Overview of Gene Expression; Nucleic Acid Structure Deck (34):
1

 Almost all somatic cells contain very similar genetic information. Name three types of normal cells that have quite a different genetic content? How do cells that have very similar genetic information look and act so differently? 

blood cells, surface skin cells, bone cells, cardiac muscle cells, skeletal muscle cells, neuron are different cell types 

although they have the potential for same info, set of genes that's active/expressed in each are different 

this differentiation = how a primoridal cell gets to be a certain kind of cell, by expressing certain genes and not others 

long-term regulation of gene expression 

2

Describe four steps in gene expression at which regulation can occur

1) transcription: increase transcription initiation rate, recruitment of RNA Polymerase II

2) mRNA processing: if stabilize or slow down mRNA decay rate, can make more protein, which means more enzyme --> more activity

3) translation 

4) post-translation: increase activity of pre-existing protein

5) protein decay: if slow down an enzyme's decay/turnover rate, have more steady state levels of protein it acts on, get more activity 

3

what is an advantage of regulating an early step in gene expression? 

advantage of regulating a late step in gene expression?

if regulate transcription (early step), it's very slow but safe 

if regulate post-translationally, it's energetically expensive 

4

what holds 2 strands of double-stranded DNA together? covalent bonds? 

NO COVALENT link between 2 strands, only Hydrogen bonds

5

why is it easier for cellular RNA to form intramolecule double-stranded structures than it is for chromosomal DNA? 

have complementarity within an RNA strand; can loop back on itself, form double strandedf RNA structure

6

what does it mean that genes have tissue specificity?

nearly all cells have same or v. similar coding info, but have diff structure/function due to differential gene expression

7

what is the flow of genetic information, from a protein-coding gene to the protein? 

in nucleus:

1) DNA is acted on by RNA Polymerase II

produces pre-mRNA

2) pre-mRNA is processed to mRNA

3) mRNA exported to the cytoplasm 

4) mRNA is translated by ribosome into protein

8

how much of our genome do protein coding genes constitute?

only 1-2% of whole genome is protein coding genes

9

what is a pre-ncRNA? what does it become? how much of genome does it comprise?

pre-non coding RNA 

product of some DNA's transcription 

does not code for a protein 

90% of the genome is transcribed to give a ncRNA

10

what is unique about RNA re: its regulatory function in humans?

many genes code for RNA only, w/ no protein produced

 

11

what are the different types of non-coding RNA (ncRNA)?

what is their function and location in the cell? 

1) rRNA: ribosomal rNA, goes to nucleolus 

2) tRNA: transfer RNA, used in translation, so in cytoplasm

3) miRNA: micro RNA, regulate translation, so in cytoplasm

4) lnc RNA: long non-coding RNA, regulatory function; many come back, bind to DNA, inhibit transcription

12

why does a liver cell's gene expression program change depending on conditions? explain

this is short term regulation 

different cells do different things at different times 

liver cell has many fxns: can express genes that go thru enzymes that make glucose; if eating glucose now, liver cells won't make glucose; if you're starving, will make glucose 

thus its gene expression program changes depending on conditions

13

do all cells in the body contain all genes? why do they do different things then? 

insulin example

all cells in the body have insulin gene 

but no cells in body make insulin except beta cells of pancreas 

thus beta cells have insulin gene "on," every other cell in body has insulin gene off 

this is how gene expression is regulated

14

what's a nucleotide? what are the components of a nucleotide?

nucleotide = basic unit of nucleic acid chain

base + sugar + phosphate 

 

15

what is a nucleoside?

base + ribose sugar

16

what are the bases of nucleic acids?

"puragold, cut the pi" 

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17

how are purines numbered? 

pyrimidines? 

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18

what's the ribose carbon's structure?

where does the purine/pyrimidine base link to the ribose sugar? 

where does the phosphate connect to the ribose sugar?

 

1' position: purine/pyrimidine base 

2' position: OH group RNA ONLY!

3' position: OH group

5' position: phosphate group 

 

 

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19

name this

 

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adenosine-5'-monophosphate

 

20

name this

 

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21

name this 

how are the phosphates named? 

how are they re: ionization at physiological pH?

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1st phosphate attached to sugar: alpha phosphate

2nd: beta

3rd: gamma

all ionized at physiological pH

22

what links 2 nucleotides?

3'-to-5' phosphodiester bond between the 3' OH and 5' phosphate

 

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23

what is the convention for reading DNA?

5' to 3' directionality 

from 5' triphosphate to 3' OH 

 

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24

what varies re: DNA/RNA? what determines our DNA sequence?

phosphate-sugar chain is invariant 

BASE varies 

this determines our DNA sequence

25

how do strands of double stranded DNA run?

how do strands connect?

antiparallel to each other in double helix

G-C and A-T base pairs stabilize via H-bonds, base stacking, and other hydrophobic interactions

26

what are available H groups of double stranded DNA used for?

binding by "DNA binding partners"

27

what can single stranded RNA interestingly do?

single stranded RNA can form intramolecular base pairs

28

what is a reverse transcriptase enzyme

transcription can be reversed, w/ RNA serving as template to syntehize DNA by a reverse transcriptase enzyme

29

what is the intrinsic melting temperature of double stranded DNA or intramolecular double-stranded RNA?

what makes a higher melting temp? a lower melting temp?

temperature at which the 2 strands separate

higher melting temperature: higher G-C content (b/c form 3 H-bonds)

lower melting temperature: higher A-T content (b/c form 2 H-bonds)

30

what balances the negative charges that DNA/RNA present int he cell? 

low molecular weight aliphatic cations that counteract the negative balance of the DNA 

they're also important for RNA function 

 

 

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31

what is the primary structure of DNA? 

the phosphate-sugar-base chain 

32

what is the secondary structure of DNA? 

what makes it happen?

complementary double-stranded DNA helix 

happens b/c of complementary base pairing 

33

what is the minor groove? the major groove?

minor groove: 3.4 A

major groove: where proteins bind DNA; 36 A

34

what is the basis of nucleic acid probe technology? think annealing

single stranded, "melted" DNA can "reanneal" to original double-stranded state b/c strings of "complementary" (G/C, A/T, A/U) base pairs can find themselves in solution 

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