ministudy guide genetics exam 4

beginning and end sites of bacterial DNA replication

• begins at the origin of replication and ends at termination sequences opposite to the origin.

• termination utilization substance bind to ter sequences to stop replication forks

• T1 stops counterclockwise

• T2 stops clockwise forks

decide based Meselson Stahl experiment, what model of replication can be inferred for a certain number of generations of cell growth and division

The experiment indicates that DNA replication is semiconservative, where each new DNA molecule consists of one original strand and one newly synthesized strand.

• after 1 gen- half heavy Isemi conservative and dispersive)

• after 2 gen- equal amts of light and half heavy (only conservative)

dnaA

bind to dnaA sequence within oriC to start replication

DnaC

aid dna in recruiting dna helicase to origindn

dna helicase (dna B)

seperates double stranded dna

dna gyrase

removes positive supercoiling ahead of replication forksi

single stranded binding proteins

binds to single straned dna to prevent reformation of helix

primase

makes short rna primers

dna poly 3

makes dna in lading and lagging strandd

dna poly 1

removes rna primers, fill in gaps with dna

dna ligase

attaches okazaki fragments covalently

tus

binds to ter sequences and prevents advancement of replication fork.

initiation of bacterial dna replication

3 types of dna in oric:

dna boxes for bonding of dnaA

AT rich region where strands seperate

GATC methylation sites that help regulate replication

• bidirectional replication

Approx length of telomere overhang

12-16 nucleotides

What is the role of RNA template carried by Telomerase enzyme?

helps maintain the length of dna at chromosome

various mechanisms that ensure DNA replication fidelity

stability of base pairing

structure of dna polym and active site

proofreading of dna polymerase

various restrictions and observations related to DNA polymerase

• can only make dna from 5 to 3 (3 end cant be replicated)

• cant initiate dna synthesis on unprimed dna strand

Three possible models for DNA replication and what kind of strands expected in
daughter DNA molecules for each type. Which one is actually seen?

conservative: 3 new, one old

semi conservative: 2 new, 2 mixed (actual)

dispersive: all 4 mixed

What kind of modification of RNA is carried out by various deaminases?

rna editing- change in rna after it has been made

splicing- introns removed and exons joined

attachment of 7-methylguanosine cap to 5’ end of mrna

attchment of adenine string to 3’ end

Bacterial RNA polymerase holoenzyme components and which subunit helps bind to promoter

made of core enzyme and sigma factor (recognizes promoter).

core enzyme

• two alpha- assmebly of holoenzyme and dna binding

• beta- dna binding and catalytic rna synthesis

• beta prime

• wega- assembly of core enzyme

Given a hypothetical DNA template (3’ to 5’), what would be the RNA transcribed using the template?

complementary + U instead of T

What strand of DNA will the RNA transcript be complementary to? What strand of DNA will the RNA be similar to?

strand transcribed is template strand (rna is complementary to this strand) and opposite strand is coding (sense, nontemplate strand), which is similar to the rna except U instead of T

What is closed complex?

the binding of rna polym to the promoter ( when the sigma factor binds to the promoter and the dna strands have not separated from eachother)

A common mechanism seen in both rho dependent and independent mechanism of bacterial transcription termination

release of the rna dna hybrid region which seperates the rna strand and rna polymerase from the dna strand

Sequence preference/requirement seen in relation to rho independent termination of transcription

• one sequence promotes formation of a stem loop

• second sequence is uracil rich sequence at 3’ end of rna

• rna polym stops at uracil rich sequence is bound to dna. This bonding is weak and the rna disassociates from the dna and stops transcription.

Three different kinds of eukaryotic RNA polymerases and what does each one
transcribe?

rna polym 1, 2 ,3rn

rna polym 1

• all rrnas except for 5S rrna

rna polym 2

• all mrnas

• snras, non coding rna, micrornas, snornas

rna polym 3

• all trna and the 5S gene

Given positions of first base of start codon and last base of stop codon in mRNA. Figure out how many amino acids encoded

((last-first /3)) -1

In eukaryotic transcription, which general transcription factor binds TATA box

TFIID recognizes the tata box

Unusual feature of the 5’ 7-methylguanosine cap on eukaryotic mRNA

• plays role in moving rnas out and in nucleus

• early stages of translation

• intron splicing

• occurs while premrna being made by rna polm 2

5’ 7-methylguanosine cap on eukaryotic mRNA

• rna 5’ removes a phosphate from nucleotide at end of 5’ end

• guanyltransferase attaches guanosine monophosphate to 5’ end

• methyltransferase attaches methyl to the nitrogen at position 7 on guanine base.

Splicing is carried our by which complex?

via a splicesome (composed of snrps- small nuclear rna and a set of proteins)

translation initiation in bacteria

• mrna, initaitor trna, and ribosomal subunits make initiation complex

• tRNA fmet recognizes mrna start codon

  • start codon AUG, GUG, UUG

  • first amino acid is N-methylformylmethionine

Given and anticodon sequence in tRNA, what would be the codon it could bind to and what amino acid would this tRNA carry? Codon table will be provided

given codon is 3’-5’

reverse it

then do complementary base sequencing

use codon table

Shine-Dalgarno sequence (approx location and significance) on bacterial mRNA

it is a ribosome binding site (9 nucleotides long). it is complementary to portion of 16S rrna. left of IF3. facilitates binding of mrna to 30S subunit.

Subunits of bacterial ribosomes

30S + 50S = 70S

subunits of euk ribosomes

40S + 60S =80S

Role of different initiation factors in translation initiation and why initiator tRNA will first bind to the P site

IF1, IF2, IF3

IF1 and IF2

prevents association between small and large ribosomal subunits and favors their dissociation.

IF3

participates in start codon selection

IF2

promotes binding of initiator trna to small ribosomal subunit

helps dissociate initiation factors, allowing two ribosomal subunits to assemble.

why initiator tRNA will first bind to the P site

short polypep is attached to trna located on P site. This is to ensure the correct start of translation and proper positioning of first amino acid on the chain.

When release factors function and what kind of enzymatic activity they activate when they bind to the appropriate site on the ribosome

release factors are proteins that recognize a stop codon and terminate translation, released completed polypeptide. RF1 or RF2 bind to stop codon on A site and RF3 binds at another location. After binding of RF1/RF2 and RF3, bond between polypep and trna is hydrolized and polypep and trna releases from ribosome. Ribosomal subunits, mrna, and release factors then disassembled.

release factors and what they recognize

RF1- UAA and UAG

RF2- UAA and UGA

RF3- also required

Mother’s genotype that can give a certain kind of coiling in water snails

DD and Dd gives dextral, dd gives sinistral (only mother geno)

Explanation for genomic imprinting related Angelman syndrome

occurs with deletion in chromosome 15 when inherited from the female parent. Thin, hyperactive, seizures, repetitive symmetrical muscle movements

• results from lack of UBE3A expression (codes protein that regulates protein degredation)

• paternal copy is silenced

Explain basis of variegation (black, white) phenotype in mouse fur pigmentation (dosage compensation)

1. to start both x are active

2. one x is for black, the other for white

3. one of the x becomes barr body randomly

4. this embryonic cells will give rise to many cells with inactivated x and thus will not display that color

   1. HAPPENS IN early embryonic development

T/F statement related to inheritance of mitochondrial genome mutations in humans

Maternal inheritance has to do with the mitochondria and chloroplasts being passed on from the cytoplasm for mitochondrial diseases or cytoplasmic traits.