MCB 450 EXAM2 REVIEW #2

what are the four bases in DNA?

adenine (A), thymine (T), guanine (G), cytosine (C)

what are the ratios of bases in DNA?

A:T = 1, G:C = 1

what are the sugars in DNA & RNA

deoxyribose and ribose

what differs deoxyribose from ribose?

deoxyribose’s 2’C lacks oxygen

sugars in DNA & RNA are linked by ?

phosphodiester bridges. the hydroxyl of sugar bonds to the phosphoryl group

which bases are purines?

adenine and guanine

which bases are pyrimidines?

cytosine & thymine(DNA) or uracil (RNA)

why do phosphodiester bonds have a negative charge?

to repel nucleophilic species that could damge it

why is DNA more stable than RNA

because there is not 2-hydroxyl group

what is a nucleoside?

base bonded to a sugar

what are the nucleosides in DNA?

deoxyadenosine, deoxyguanine, deoxycytidine, thymidine

what are the nucleosides in RNA?

adenosine, guanosine, cytidine, uridine

what is a nucleotide?

a nucleoside jointed to a phosphoryl group through an ester link

what are the building blocks of RNA &DNA?n

nucleoside triphosphates

do DNA & RNA chains have directionality?

yes. ACG and GCA would be different

how is the double helix stabilized?

by hydrogen bonds and hydrophobic effects

what is on the inside and outside of the double helix?

outside: sugar-phosphate groups, inside: purine & pyrimidine

how do bases lie on the helix axis?

perpendicular

what is base stacking?

when base pairs attract each other due to van der waals

what is dissociation of the double helix called?

denaturation or melting

what is the renaturing process of the double helix called?

annealing

what are characteristics of A-DNA?

less hydrated, wider and shorter, base pairs are tilted and not perpendicular

what is the typical type of DNA?

B-DNA

what are the characteristics of Z-DNA?

left handed

phosphoryl groups are zigzagged

narrower

what kind of grooves does DNA have?

major and minor

what is the purpose of the larger size of major grooves in B-DNA?

makes it more accessible for interactions

the axis of the double helix can be twisted into a superhelix through a process called ______

supercoiling

eukaryotic DNA is tightly bound to small basic proteins called _____

histones

what is chromatin?

isolated chromosomes that make up the entire complex of a cell’s DNA and associated protein

what is chromatin made up of ?

repeating units called nucleosomes

what is a stem loop?

when 2 complementary sequences within a single strand come together

what do DNA polymersases do?

promote formation of the bonds joining units. catalyze addition of deoxyribonucleotide units, catalyze phosphodiester linkage

why is binding of a noncomplementary base unlikely?

because it’s energetically weaker

does DNA synthesis require a primer?

yes

what are helicases?

specific enzymes that utilize energy of ATP hydrolysis to power strand separation

what is Werner syndrome?

defect in helicase activity that leads to premature aging

what are topoisomerases?

enzymes that introduce or eliminate supercoils by temporarily cleaving DNA

what does topoisomerase type 1 do?

catalyze relaxation of supercoiled DNA

what does topoisomerase type 2 do?

utilize free energy from ATP to add negative supercoils to DNA

what does exonuclease in DNA polymerase 1 do?

removes mismatched nucleotides from the 3’end of DNA by hydrolysis

what does single strand binding protein (SSB) do?

binds to newly generated single strand regions to precent reforming of the double helix. called the prepriming complex

what primes the synthesis of DNA?

RNA

what does primase do?

synthesizes a short stretch of RNA that is complementary to one of the template DNA strands

what is the site of DNA synthesis called?

replication fork

what is DNA ligase?

enzyme that uses ATP hydrolysis to power joining of DNA fragments

what does DNA polymerase III do?

it grasps the template and only lets go when the template is completely replicated. it has greater processivity and is much faster than polymerase I

what are telomeres?

chromosome ends that protect the ends of DNA

what is telomerase?

an enzyme that contains an RNA molecule that acts as a template for extending the leading strand, which then acts as a template for the lagging strand

normal cells have _____ levels of telomerase

low

cancer cells have ______ levels of telomerase

high

what does it mean for a mismatch to be mutagenic?

it results in permanent damage

what are mutagens?

chemical agents that alter specific bases

reactive oxygen species hydroxyl radical reacts with guanine to form

8-oxoguanine which is mutagenic bc it pairs with an A instead of C

what does adenine deaminate to?

hypoxanthine which pairs with C

what is alkylation

addition of hydrocarbon molecules (smoke, exhaust, mold)

what can electromagnetic radiation and x-rays cause?

single and double strand breaks

what are the three steps of the DNA repair system

1) recognize the offending base

2) remove it (exonuclease from DNA polymerase III)

3) repair gap w/ DNA polymerase and ligase

what do the two proteins involved in the mismatch repair system do?

one is for detecting, one is for recruiting endonuclease that cleaves

what does exonuclease do?

excises incorrect bae

what is direct repair?

when DNA is repaired w/o removing any fragments

what is the most common point mutation?

C:T

what does the nucleotide excision repair system do?

recognize distortions in the DNA double helix caused by a damaged base

why is thymine used instead of uracil in DNA?

to preserve the fidelity of genetic message

what do tumor suppresor genes do?

prevent tumor growth

what is xeroderma pigmentosum (XP)

extreme sensitivity to light

what causes HNPCC?

defective DNA mismatch repair

what is transcription?

synthesis of RNA from a DNA template

what catalyzes synthesis of RNA?

RNA polymerase

what dose RNA polymerase require?

1. a template (DNA)
2. activated precursors (ribonucleoside triphosphates → ATP, GTP, UTP, CTP)
3. divalent metal ions (Mg2+ or Mn2+)

what is the direction of RNA synthesis?

5’→ 3’

what are genes?

segments of DNA that encode various species of RNA

what are the major types of RNA

1) messenger (mRNA) → encodes info for the synthesis of protein

2) transfer (tRNA)

3) ribsomal (rRNA)

what are tRNA and rRNA critical for?

translating mRNA to protein

what does the sigma subunit do?

helps to find the side where transcription begins, participates in RNA synthesis initiation and then dissociates to help another

what are the 3 stages of RNA synthesis?

1) initiation

2) elongation

3) termination

what are promoters

special DNA sequences that direct RNA polymerase to the proper site for initiatoin

what does the upstream (UP) element do

serves to increase efficiency of transcription by creating an additional binding site for polymerase

how does the sigma subunit help polymerase locate the correct start site?

1. decreases affinity of RNA polymerase for general regions of DNA to let the enzyme bind to DNA & rapidly slide along
2. enables RNA polymerase to recognize promoter sites


1. releases once the new RNA chain reaches 9-10 nucleotides and then leaves to assist another

what is closed promoter complex?

when the DNA is double helical

what is open promoter complex?

when DNA is unwound

RNA synthesis can start de novo, which means

without a primer

when does elongation begin?

after the formation of the first phosphodiester bond. the sigma subunit leaves which allows the core enzyme to strongly bind to the DNA template

mistakes in RNA are more common, but

they are less likely to be harmful

what happens during termination of RNA synthesis?

1) formation of phosphodiester linkages stops

2) RNA-DNA hybrid dissociates

3) melted region of DNA reanneals

4) RNA polymerase releases DNA

what is protein dependent termination

when some sites require rho protein to terminate

where is rho protein used

in sequences in the nascent RNA that is rich in C and poor in G

how does rho protein terminate RNA synthesis

ATPase activity of rho enables the protein to pull on the RNA, pursuing RNA polymerase and then collides with it. this breaks the RNA-DNA hybrid helix which stops transcription

examples of antibiotics that inhibit transcription

rifampicin and actinomycin D

what does rifampicin do

interferes w the formation of first phosphodiester linkages in RNA by blocking the channel

what does actinomycin D do

binds tightly and specifically to double-helical DNA & prevents it from being an effective template. it also intercalates

what does beta-galactosidase do

hydrolyzes lactose into galactose and glucose

what is the lac repressor

in the absence of lactose, it binds very tightly and rapidly to the operator, blocking RNA polymerase from using the DNA template

what does catabolite activator protein (CAP) do

when bound to cyclic AMP, it stimulates the transcription of lactose genes. when the concentration of glucose decreases, the concentration of cAMP increases which activates the lac operon

what is catabolite repression

when glucose inhibits expression of the lac operon

3 important characteristics of gene expression to eukaryotes

1) more complex transcriptional regulation

2) extensive RNA processing

3) transcription and translation take place in different cellular components

where does transcription take place in eukaryotes?

in the membrane-bounded nucleus

where does translation take place in eukaryotes?

oustside the nucleus in the cytoplasm

what is alpha-amantin

toxin produced by mushroom Amanita phalloides

how does each RNA polymerase react to alpha-amantin?

I → is insensitive to it

II → binds tightly to it and blocks elongation

III → high concentrations inhibit it

characteristics of RNA polymerase I

located in the nucleoli, transcribes 3 ribosomal RNAs (18s, 5.8s, 28s) as a single transcript