Exam 2: Ch 4 Flashcards
nucleic acid
linear polymer made from 4 types of nucleotide
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
DNA
informational molecule that determines aa sequence
RNA viruses
have short genomes because RNA is less stable than DNA
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
info stored in DNA is arranged in hereditary units called ____
genes
transcription
DNA copied into RNA
nt sequence language of DNA copied (transcribed) into nt sequence
mRNA
direct the synthesis of a specific protein
nt sequence contains info that specifies correct aa sequence
translation
stepwise assembly of aa into proteins using mRNA as a template
nt sequence language is translated into language of proteins
tRNA
brings correct aas into sequence
rRNA
g
gene expression
process of DNA being decoded into proteins in the right cells at the right time in development
DNA vs RNA length
DNA: several hundred million nts
RNA: less than 100 to thousands of nts
all nucleic acids consist of…
base
5-carbon sugar
phosphate
in RNA the sugar is ____
ribose
in DNA the sugar is ____
deoxyribose
purines
adenine
guanine
pair of fused rings
pyrimidines
cytosine
thymine
uracil (RNA only)
single ring
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
name of chemical bond between nts
phosphodiester
one on 5’ side of phosphate and one on 3’ side
why does base pair complementarity exist
b/c of the size, shape and chemical composition of the bases
what forces stabilize DNA double helix
thousands of h-bonds
van der waals interactions between stacked base pairs
nonstandard base pairs
GT
CT
GU
not found naturally in duplex DNA
most DNA is a ___-handed helix
right-handed
3.4 nm per turn and 10-10.5 bases per turn (B form)
helical grooves
major and minor
DNA binding proteins can read the sequence at these grooves
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
DNA double helix is flexible about its _____ axis
long
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
what makes DNA more stable than RNA
having a Hydrogen atom at the 2’ position as opposed to the OH- group in RNA
what does the 2’-hydroxyl group in ____ do?
RNA
participates in slow OH- catalyzed hydrolysis of phosphodiester bonds at neutral pH
denaturation
unwinding and separating of DNA strands
aka. melting
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
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
hyperchromicity
unstacked bases in ssDNA absorb a lot more UV light
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)
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
what causes ssDNA to renature into dsDNA
lowering temp
increasing ion [ ]
neutralizing pH extrme
what does renaturation depend on
time
[DNA]
[ion]
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
topoisomerase I
bacteria and eukaryotic cells
enzyme that relieves torsional stress by unwinding supercoils
nick, rotate, ligate
topoisomerase II
double-strand break
pass through
ligate
why is the presence of thymine instead of uracil important to DNA stability
thymine functions in DNA repair
hairpin
RNA conformation formed by pairing of bases within 5-10 nt
stem-loop
RNA conformation formed by pairing of bases that are separated by > 10-100s of nts
pseudoknot
tertiary structure of RNA formed by cooperation of RNA conformations
ribozyme
catalytic RNA
usually associated with proteins that stabilize the ribozyme
some functions of ribozymes
splicing
splicing
introns cut and removed and remaining exons ligated
miRNA
micro RNA
regulate translation of specific target mRNAs
a template ___ strand is transcribed into a complementary ___ strand by ___ __________
DNA, RNA, RNA polymerase
RNA is synthesized in what direction
5’ —-> 3’
overview of transcription
one DNA strand template determines order of ribonucleoside triphosphate (rNTP) monomer polymerization into a complementary RNA strand
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
is polymerization into RNA energetically favored?
yes, release of PPi in exchange for forming phosphodiester bond
pyrophosphatase also cleaves PPi into Pi (releases energy)
site on DNA where transcription begins is numbered…
+1
downstream
direction in which template DNA is transcribed indicated by (+) sign
upstream
opposite direction RNA polymerase transcribes DNA denoted by (-) sign
RNA polymerase moves down DNA template in what direction
3’ –> 5’
how many steps in transcription
5
step 1 of transcription
initiation: RNA polymerase + initiation factors bind the promoter in dsDNA
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)
step 3 of transcription
template strand enters active site of enzyme
initiation complete when first 2 ribonucleotides are linked by a phosphodiester bond
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
what happens during transcription elongation
1 riboNT at a time is added to 3’ growing (nascent) end
what makes up the elongation complex
RNA polymerase
template DNA
growing (nascent) RNA strand
transcription bubble
12-14 base pairs of melted DNA
rate RNA synthesis occurs at
1000 nt/min at 37C
transcription step 5
termination: finished RNA molecule is released from RNA polymerase
RNA polymerase releases from template DNA
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
operon
common in bacteria
A functioning unit of DNA containing a cluster of genes under the control of one promoter
transcription of an operon produces a _____ strand of _____ that carries the message for….
continuous, mRNA
a related series of proteins
what does each section of mRNA from an operon represent
the unit/gene that encodes one of the proteins in the operon series
coordinate expression
every time RNA polymerase initiates transcription at the promoter of an operon, all the genes of the operon are transcribed and translated
in prokaryotic DNA the genes are closely packed with very few _____ ____ and the DNA is transcribed directly into ______
noncoding gaps, mRNA
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
in ____ cells, translation can occur concurrently
bacterial
primary transcript
pre-mRNA found in eukaryotes before RNA processing into functional mRNA
in eukaryotic cells mRNA must be exported to the _____ before it can be translated into protein
cytoplasm
RNA processing
capping, splicing, polyadenylation
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
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
RNA splicing
internal cleavage of a primary transcript to excise introns and ligate exons
3 main regions of a functional mRNA
3’ and 5’ UTR (untranslated region)
coding region
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
alternative splicing
producing different forms of a protein called isoforms from a single gene by taking out different introns
ex. fibronectin
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
__% of all human genes are expressed as alternatively spliced mRNA
90%
