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Cellular and Molecular Biology > Exam 2: Ch 4 > Flashcards

Exam 2: Ch 4 Flashcards

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1
Q

nucleic acid

A

linear polymer made from 4 types of nucleotide

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2
Q

nucleic acids 4 things

A

nucleotide sequence determines aa sequence (and thus the structure and function of all proteins)

critical functional components of ribosomes

catalyze rxns in cells (ex. formation of peptide bonds)

regulate expression of genes

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3
Q

DNA

A

informational molecule that determines aa sequence

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4
Q

RNA viruses

A

have short genomes because RNA is less stable than DNA

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5
Q

all forms of life use ___ to encode genetic info

A

DNA

implies that all life descended from a common ancestor based on storage of info in nucleic acid sequence

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6
Q

info stored in DNA is arranged in hereditary units called ____

A

genes

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7
Q

transcription

A

DNA copied into RNA

nt sequence language of DNA copied (transcribed) into nt sequence

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8
Q

mRNA

A

direct the synthesis of a specific protein

nt sequence contains info that specifies correct aa sequence

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9
Q

translation

A

stepwise assembly of aa into proteins using mRNA as a template

nt sequence language is translated into language of proteins

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10
Q

tRNA

A

brings correct aas into sequence

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11
Q

rRNA

A

g

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12
Q

gene expression

A

process of DNA being decoded into proteins in the right cells at the right time in development

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13
Q

DNA vs RNA length

A

DNA: several hundred million nts

RNA: less than 100 to thousands of nts

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14
Q

all nucleic acids consist of…

A

base

5-carbon sugar

phosphate

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15
Q

in RNA the sugar is ____

A

ribose

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16
Q

in DNA the sugar is ____

A

deoxyribose

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17
Q

purines

A

adenine

guanine

pair of fused rings

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18
Q

pyrimidines

A

cytosine

thymine

uracil (RNA only)

single ring

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19
Q

nucleic acid strand structure

A

pentose-phosphate backbone with bases extending as side groups

5’ end has hydroxyl or phosphate on 5’ end carbon of terminal sugar

3’ end has hydroxyl on 3’ carbon of terminal sugar

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20
Q

name of chemical bond between nts

A

phosphodiester

one on 5’ side of phosphate and one on 3’ side

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21
Q

why does base pair complementarity exist

A

b/c of the size, shape and chemical composition of the bases

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22
Q

what forces stabilize DNA double helix

A

thousands of h-bonds

van der waals interactions between stacked base pairs

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23
Q

nonstandard base pairs

A

GT

CT

GU

not found naturally in duplex DNA

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24
Q

most DNA is a ___-handed helix

A

right-handed

3.4 nm per turn and 10-10.5 bases per turn (B form)

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25
helical grooves
major and minor DNA binding proteins can read the sequence at these grooves
26
A form
in lab conditions where most H2O is removed wider and shorter than B form wider and deeper major groove, and narrower and shallower minor grooveq
27
DNA double helix is flexible about its _____ axis
long
28
unlike the a-helix in proteins there are no H-bonds ______ to the axis of the DNA helix
parallel this allows DNA to bend when complexed with a DNA binding protein critical to the dense packing of DNA in chromatin
29
what makes DNA more stable than RNA
having a Hydrogen atom at the 2' position as opposed to the OH- group in RNA
30
what does the 2'-hydroxyl group in ____ do?
RNA participates in slow OH- catalyzed hydrolysis of phosphodiester bonds at neutral pH
31
denaturation
unwinding and separating of DNA strands aka. melting
32
how is denaturation/melting achieved
raising the temp of a soln of DNA thermal energy increases (inc. molecular motion) and breaks H-bonds and dispersion forces that stabilize DNA
33
at near denaturation temp what happens to DNA
a small increase in temp causes the rapid loss of stabilizing interactions, which causes the strands to separate almost simultaneously
34
hyperchromicity
unstacked bases in ssDNA absorb a lot more UV light
35
melting temp Tm of DNA depends on
proportion of GC to AT (more GC = higher Tm) ion [ ] b/c negatively charged phosphates are shielded by positively charged ions pH (extremes lower Tm)
36
how does pH affect denaturation
at low pH bases are protonated (positively charged) and repel each other at high pH bases dissociate (negatively charged) and repel each other
37
what causes ssDNA to renature into dsDNA
lowering temp increasing ion [ ] neutralizing pH extrme
38
what does renaturation depend on
time [DNA] [ion]
39
nucleic acid hybridization
technique used to study the relatedness of 2 DNA samples detect and isolate specific DNA molecules in a mixture of DNA sequences
40
topoisomerase I
bacteria and eukaryotic cells enzyme that relieves torsional stress by unwinding supercoils nick, rotate, ligate
41
topoisomerase II
double-strand break pass through ligate
42
why is the presence of thymine instead of uracil important to DNA stability
thymine functions in DNA repair
43
hairpin
RNA conformation formed by pairing of bases within 5-10 nt
44
stem-loop
RNA conformation formed by pairing of bases that are separated by > 10-100s of nts
45
pseudoknot
tertiary structure of RNA formed by cooperation of RNA conformations
46
ribozyme
catalytic RNA usually associated with proteins that stabilize the ribozyme
47
some functions of ribozymes
splicing
48
splicing
introns cut and removed and remaining exons ligated
49
miRNA
micro RNA regulate translation of specific target mRNAs
50
a template ___ strand is transcribed into a complementary ___ strand by ___ __________
DNA, RNA, RNA polymerase
51
RNA is synthesized in what direction
5' ----> 3'
52
overview of transcription
one DNA strand template determines order of ribonucleoside triphosphate (rNTP) monomer polymerization into a complementary RNA strand
53
transcription polymerization rxn
bases in template DNA base pair with complementary rNTPs which are joined by RNA polymerase nucleophilic atk of 3' oxygen in growing RNA chain on a-phosphate of next nucleotide, forming a phosphodiester bond and releasing PPi
54
is polymerization into RNA energetically favored?
yes, release of PPi in exchange for forming phosphodiester bond pyrophosphatase also cleaves PPi into Pi (releases energy)
55
site on DNA where transcription begins is numbered...
+1
56
downstream
direction in which template DNA is transcribed indicated by (+) sign
57
upstream
opposite direction RNA polymerase transcribes DNA denoted by (-) sign
58
RNA polymerase moves down DNA template in what direction
3' --> 5'
59
how many steps in transcription
5
60
step 1 of transcription
initiation: RNA polymerase + initiation factors bind the promoter in dsDNA
61
step 2 of transcription
RNA polymerase + initiation factors separate DNA strands and melt 12-14 base pairs around start site (located on template strand in promoter region)
62
step 3 of transcription
template strand enters active site of enzyme initiation complete when first 2 ribonucleotides are linked by a phosphodiester bond
63
step 4 of transcription
RNA polymerase dissociates from promoter DNA and transcription factors strand elongation occurs where RNA polymerase moves along template DNA and opens dsDNA
64
what happens during transcription elongation
1 riboNT at a time is added to 3' growing (nascent) end
65
what makes up the elongation complex
RNA polymerase template DNA growing (nascent) RNA strand
66
transcription bubble
12-14 base pairs of melted DNA
67
rate RNA synthesis occurs at
1000 nt/min at 37C
68
transcription step 5
termination: finished RNA molecule is released from RNA polymerase RNA polymerase releases from template DNA
69
structure of RNA polymerase
2 large subunits B' and B 2 copies of smaller alpha subunit 1 copy of a fifth subunit w that isn't used for transcription
70
operon
common in bacteria A functioning unit of DNA containing a cluster of genes under the control of one promoter
71
transcription of an operon produces a _____ strand of _____ that carries the message for....
continuous, mRNA a related series of proteins
72
what does each section of mRNA from an operon represent
the unit/gene that encodes one of the proteins in the operon series
73
coordinate expression
every time RNA polymerase initiates transcription at the promoter of an operon, all the genes of the operon are transcribed and translated
74
in prokaryotic DNA the genes are closely packed with very few _____ ____ and the DNA is transcribed directly into ______
noncoding gaps, mRNA
75
since DNA is not found in a nucleus in prokaryotes, ribosomes.....
can immediately begin translation at the mRNA start sites as they emerge from RNA polymerase translation begins even as the 3' end of the mRNA is still being synthesized by RNA polymerase
76
in ____ cells, translation can occur concurrently
bacterial
77
primary transcript
pre-mRNA found in eukaryotes before RNA processing into functional mRNA
78
in eukaryotic cells mRNA must be exported to the _____ before it can be translated into protein
cytoplasm
79
RNA processing
capping, splicing, polyadenylation
80
capping
5' cap (7-methylguanylate) attached to terminal nt of RNA by a 5', 5' triphosphate linkage protects mRNA from enzymatic degradation and assists in exportation to cytoplasm bound by a protein factor required to begin translation
81
poly-A tail
endonuclease cleaves the end so a 3'-hydroxyl can acquire adenylic acid residues (100-250) poly(A) polymerase is part of a complex of proteins that locate and cleave a transcript and then add the right # of A residues
82
RNA splicing
internal cleavage of a primary transcript to excise introns and ligate exons
83
3 main regions of a functional mRNA
3' and 5' UTR (untranslated region) coding region
84
repeated exons and thought to have evolved by...
accidental duplication of a length of DNA between two sites in adjacent introns results in insertion of a string of repeated exons, separated by introns, between the original two introns
85
alternative splicing
producing different forms of a protein called isoforms from a single gene by taking out different introns ex. fibronectin
86
fibronectin
long, adhesive protein secreted into extracellular space that binds other proteins together what and where it binds depends on which domains are spliced together from alternative splicing
87
__% of all human genes are expressed as alternatively spliced mRNA
90%

Cellular and Molecular Biology (34 decks)

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