microbio exam 3

What is a genome

all DNA present in a cell or virus

How many sets of genomes do Bacteria and Archaea generally have

one set, haploid

How many sets of genomes do eukaryotes have

two sets, diploid

What is a genotype

the specific set of genes an organism possesses

What is a phenotype

collection of observable characteristics

What is the central dogma of DNA

DNA breaks down into RNA through transcription, RNA breaks down into proteins through translation

What is the flow of genetic information?

DNA

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transcription of DNA

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tRNA mRNA rRNA

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Translation of RNA

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Protein

What links the nucleic acids of DNA and RNA together

phosphodiester bonds

How do DNA and RNA differ?

the nitrogenous bases they contain, the sugars they contain, and whether they are single or double stranded

What bases does DNA have

Cytosine, Guanine, Adenine, and Thymine

What bases does RNA have

cytosine, adenine, Uracil and guanine

What bases are pyrimidines

cytosine, uracil and thymine

what bases are purines

guanine and adenine

what is messenger RNA

mRNA has proteins

what is ribosomal RNA

rRNA makes ribosomes

what is transfer RNA

tRNA brings amino acids

what are the polymers of amino acids linked by

peptide bonds

what is replication

a process of preserving genetic information during cell division

how is the complementary strand formed

according to base pairing rules (e.g. AT/GC)

what is semiconservative replication

daughter DNA molecules consist of one old and one new strand

the DNA in most bacteria is…

circular

where does replication begin

origin of replication

DNA polymerase

synthesize complementary strand of DNA, synthesize DNA in 5’ to 3’ direction, five types

what does DNA polymerase require

a template, a primer, and a deoxynucleoside triphosphate

what does the polymerase template do

it directs synthesis of complementary strand; read in 3’-5’ direction

what does the primer of polymerase do

DNA poly cannot start from scratch; needs free 3’-OH end

DNA polymerase III

multifunctional, complex of 10 proteins

what ae the three core enzymes of DNA poly III

two replicate one DNA strand and the third replicates other; each catalyse DNA strand synthesis; proof reading

B-clamp of poly III

associated with each core enzyme; teathers core to the DNA

t-(tau) complex

clamp loader; includes proteins for loading b-clamp onto DNA; also holds holoenzyme together

helicases

separate DNA strands, a head of replication fork; needs ATP

single stranded DNA binding proteins (SSB)

keep two strands apart

DNA gyrase (topoisomerase)

unwinds supercoiled DNA by breaking one strand of DNA to relieve tension from rapid unwinding of double helix

primase

synthesizes short complementary strands of RNA primers (~10 nucleotides); cannot start without short sequences

DNA A proteins

bind oriC (origin of replication) causing bending and separation of strands

DNA B

helicase (5-3); breaks hydrogen bonds holding two strands together; promotes DNA primase activity; involved inn primosome assembly

SSBP

coats template strand for lagging strand synthesis

primase

synthesizes RNA primer; one in case of leading strand and several for lagging strand synthesis

B-clamp loader

loads B-clamp onto template

B-clamp

tether core enzyme to strand

DNA poly I

removes RNA primers using 5-3 exonuclease activity; replace with DNA using 3-OH end of adjacent dNTP

DNA ligase

seals gaps between replaced DNA and existing DNA

leading strand synthesis

synthesized continuously from 3-5 template; core poly is able to move along direction of fork

lagging strand synthesis

synthesized in fragments from 5-3 template; core poly cannot move in same direction of fork; new primer is needed for each Okazaki fragment

Okazaki fragments

formed with core poly moving opposite to fork direction

what is the termination of replication

when the replisome reaches termination site (or when two forks meet) on DNA causing replication to stop

what are two problems of chromosomes separation

the formation of catenates (interlocked chromosomes) and dimerized chromosome (joining of two chromosomes to form one large one)

what do ribosomes do

perform protein synthesis

what is sigma factor

binds with gene and allows RNA poly to bind

In DNA how does the sequence go?

promotor → leader → coding → trailer → terminator

how does the RNA sequence run?

leader → coding → trailer

what is a gene

the basic unit of genetic information that can also be defined as the nucleic acid sequence that codes for a polypeptide, tRNA or rRNA

what is a cistron

segment of gene that encodes a single polypeptide

template DNA strand

directs RNA synthesis and is read in 3’ to 5’ direction

complementary DNA strand

coding strand, same nucleotide sequence as mRNA except in thymine, read 5’ to 3’; also called sense strand

promotor strand

located upstream of gene, specifies which strand from two strands serves as template, functions to orient poly

what strand serves at the recognition/binding site for RNA polymerase

promotor strand

leader sequence

is transcribed into mRNA, not translated; is at 5’ end of mRNA

which strand includes Shine-Dalgarno sequence

leader sequence

coding region

begins with DNA sequence 3’-TAC-5’ produces codon 5’-AUG-3’; codes for first amino acids N-formylmethionine

what does the coding region end with

stop codon which signals end of translation

trailer

down stream coding region, transcribed but not translated, prepare RNA-pol release from template

terminator

just after trailer, sometimes overlapping; signals to stop transcription

continuous coding region in bacteria usually

sometimes interrupted by non-coding region called introns

why are introns removed

removed from mRNA before translation to make protein

what are DNA sequences that code for tRNA and rRNA considered

genes

polycistronic mRNA

codes multiple genes at once

leader → coding region 1 → spacer → coding region 2 → trailer

cistronic mRNA

only codes one gene at a time

leader → coding region → trailer

core enzyme

5 polypeptides subunits: 2a, B B’; catalyzes RNA synthesis

holoenzyme

core enzyme +sigma factor i. e. (2a, B B’, w) + o; only thing that can begin transcription

sigma factor lacks

polymerase activity which helps core enzyme recognize the start of genes

three stages of transcription

elongation, initiation, termination

initiation stage

recognition, transcription bubble formation, and open complex formation

what is recognition in initiation

transcription factor o recognize -35 sequence and settle down holoenzyme

what is transcription bubble formation in initiation

o and core enzyme undergo conformational change, causes DNA to separate at -10 AT rich region

what is open complex formation in initiation

o interacts with one of DNA strand and stabilize RNA pol-template DNA interaction; open complex has region of app 16-20 unwound DNA

elongation

DNA unwinding, sliding (along template) and RNA synthesis

transcription termination

occurs when core RNA poly dissociates from template DNA

factor independent terminator

do not require any aid for termination

factor dependent terminator

require the aid of the rho factor for termination

codon

set of three nucleotides, specifies amino acid, anticodon on tRNa is complementary

reading frame

the way in which nucleotides are grouped in codon for reading the message

start codon

start site for translation, always AUG

sense codon

the 61 codons that specify amino acids

stop (nonsense) codon

the three codons used as translation termination signals; do not encode amino acids

code degeneracy

up to six different codons can code for a single amino acid

codon bias

not all codons of an AA used at same frequency

tRNA

forms tertiary structure due to base pairing within tRNA molecule

anticodon

present at anticodon arm, binds codon

acceptor 3’ end

present at acceptor arm, binds amino acid, sequence is CCA

wobble base pairing

loose base pairing - 3rd position of codon less important than 1st or 2nd; eliminates need for unique tRNA for each codon

two rare amino acids into polypeptides

selenocysteine and pyrrolysine

aminoacyl-tRNA synthetase

attaches the specific amino acid to a specific tRNa to create a charged tRNA which requires ATP

16S rRNA

binds leader sequence in mRNA for protein synthesis initiation; binds protein needed for initiation of translation; binds 3’ CCA end of amino acyl-tRNA

23S rRNA

it is the ribozyme; catalyzes peptide bond formation

transpeptidation reaction

amino group of the A site amino acid reacts with the carboxyl group of the C-terminal amino acid on the P site tRNA

translocation

peptidyl tRNA moves from A to P site; ribosome moves one codon

constitutive genes

housekeeping genes are expressed continuously by the cell; replacement of worn out parts

inducible genes

genes that code for inducible enzymes needed only in certain environments; making more or less protein if conditions change

negative control of Lac operon

enzymes normally not produced unless lactose is present; inducible