Exam 2: Ch 4 Flashcards Preview

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Flashcards in Exam 2: Ch 4 Deck (87):
1

nucleic acid

linear polymer made from 4 types of nucleotide

2

nucleic acids 4 things

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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DNA

informational molecule that determines aa sequence

4

RNA viruses

have short genomes because RNA is less stable than DNA

5

all forms of life use ___ to encode genetic info

DNA

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

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info stored in DNA is arranged in hereditary units called ____

genes

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transcription

DNA copied into RNA

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

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mRNA

direct the synthesis of a specific protein

nt sequence contains info that specifies correct aa sequence

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translation

stepwise assembly of aa into proteins using mRNA as a template

nt sequence language is translated into language of proteins

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tRNA

brings correct aas into sequence

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rRNA

g

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gene expression

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

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DNA vs RNA length

DNA: several hundred million nts

RNA: less than 100 to thousands of nts

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all nucleic acids consist of...

base

5-carbon sugar

phosphate

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in RNA the sugar is ____

ribose

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in DNA the sugar is ____

deoxyribose

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purines

adenine

guanine

pair of fused rings

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pyrimidines

cytosine

thymine

uracil (RNA only)

single ring

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nucleic acid strand structure

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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name of chemical bond between nts

phosphodiester

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

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why does base pair complementarity exist

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

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what forces stabilize DNA double helix

thousands of h-bonds

van der waals interactions between stacked base pairs

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nonstandard base pairs

GT

CT

GU

not found naturally in duplex DNA

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most DNA is a ___-handed helix

right-handed

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

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helical grooves

major and minor

DNA binding proteins can read the sequence at these grooves

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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

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DNA double helix is flexible about its _____ axis

long

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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

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what makes DNA more stable than RNA

having a Hydrogen atom at the 2' position as opposed to the OH- group in RNA

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what does the 2'-hydroxyl group in ____ do?

RNA

participates in slow OH- catalyzed hydrolysis of phosphodiester bonds at neutral pH

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denaturation

unwinding and separating of DNA strands

aka. melting

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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

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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

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hyperchromicity

unstacked bases in ssDNA absorb a lot more UV light

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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)

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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

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what causes ssDNA to renature into dsDNA

lowering temp

increasing ion [ ]

neutralizing pH extrme

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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

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topoisomerase I

bacteria and eukaryotic cells

enzyme that relieves torsional stress by unwinding supercoils

nick, rotate, ligate

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topoisomerase II

double-strand break

pass through


ligate

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why is the presence of thymine instead of uracil important to DNA stability

thymine functions in DNA repair

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hairpin

RNA conformation formed by pairing of bases within 5-10 nt

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stem-loop

RNA conformation formed by pairing of bases that are separated by > 10-100s of nts

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pseudoknot

tertiary structure of RNA formed by cooperation of RNA conformations

46

ribozyme

catalytic RNA

usually associated with proteins that stabilize the ribozyme

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some functions of ribozymes

splicing

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splicing

introns cut and removed and remaining exons ligated

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miRNA

micro RNA

regulate translation of specific target mRNAs

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a template ___ strand is transcribed into a complementary ___ strand by ___ __________

DNA, RNA, RNA polymerase

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RNA is synthesized in what direction

5' ----> 3'

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overview of transcription

one DNA strand template determines order of ribonucleoside triphosphate (rNTP) monomer polymerization into a complementary RNA strand

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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)

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site on DNA where transcription begins is numbered...

+1

56

downstream

direction in which template DNA is transcribed indicated by (+) sign

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upstream

opposite direction RNA polymerase transcribes DNA denoted by (-) sign

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RNA polymerase moves down DNA template in what direction

3' --> 5'

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how many steps in transcription

5

60

step 1 of transcription

initiation: RNA polymerase + initiation factors bind the promoter in dsDNA

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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)

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step 3 of transcription

template strand enters active site of enzyme

initiation complete when first 2 ribonucleotides are linked by a phosphodiester bond

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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

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what happens during transcription elongation

1 riboNT at a time is added to 3' growing (nascent) end

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what makes up the elongation complex

RNA polymerase

template DNA

growing (nascent) RNA strand

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transcription bubble

12-14 base pairs of melted DNA

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rate RNA synthesis occurs at

1000 nt/min at 37C

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transcription step 5

termination: finished RNA molecule is released from RNA polymerase

RNA polymerase releases from template DNA

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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

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transcription of an operon produces a _____ strand of _____ that carries the message for....

continuous, mRNA

a related series of proteins

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what does each section of mRNA from an operon represent

the unit/gene that encodes one of the proteins in the operon series

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coordinate expression

every time RNA polymerase initiates transcription at the promoter of an operon, all the genes of the operon are transcribed and translated

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in prokaryotic DNA the genes are closely packed with very few _____ ____ and the DNA is transcribed directly into ______

noncoding gaps, mRNA

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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

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in ____ cells, translation can occur concurrently

bacterial

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primary transcript

pre-mRNA found in eukaryotes before RNA processing into functional mRNA

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in eukaryotic cells mRNA must be exported to the _____ before it can be translated into protein

cytoplasm

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RNA processing

capping, splicing, polyadenylation

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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%