Micro Bio exam #3 ch.13

define genome

all genetic information that defines an organism (DNA)

what is the polymer of nucleic acids

DNA and RNA

how are DNA and RNA linked

phosphodiester bonds

what are the three parts of a nucleotide?

1. Deoxyribose sugar

2. Phosphate group

3. Nitrogenous base

what are the two nitrogenous bases and which are which

– Purines: adenine (A) and guanine (G)

– Pyrimidines: cytosine (C) and thymine (T

what kind of charge does a phosphate have and why

negative because DNA makes it acidic

the OH is on the _’ and the phosphate is on the _’

3 OH′

5 Phosphate

what is the amino acid structure

• carboxyl group

• amino group

• side chain

how are amino acids linked ?

peptide bonds between carbon and nitrogen

what are the levels of a protein structure?

• Primary structure—amino acid sequence

• Secondary structure—alpha helices or beta sheets

• Tertiary structure—3-D structure

• Quaternary structure—2 or more polypeptide strands

interacting.

when does DNA replication occur?

each time new cells are produced through binary fission

what are the three steps in order for replication?

1) Initiation

2) Elongation

3) Termination

define semiconservative

each daughter cell obtains one old and one new strand

where is DNA unwound?

The Origin of Replication (OriC)

What direction does replication go?

Replication is bidirectional and moves in two directions —> creating two forks

when does replication end?

the ter site

DnaA

binds to OriC and separates strands

Helicase

*unwinds DNA strand

helicase ring encircles the DNA and distrupts H-bonds

• moves along the replisome (genome being replicated)

DNA polymerase III

catalyses synthesis of complementary strand of DNA

what direction does DNA get synthesized?

5’ → 3’ direction

what bonds are formed when DNA is being synthesized?

phosphodiester bonds

what end are nucleotides added to?

ONLY the 3’ end of the growing strand

primase

synthesizes short complementary strands of RNA primers

what makes up a primisome?

helicase + primase

DNA Polymerase III

main replicator

Tau

mediates the polymerase attachments to the primisome (helicase+primase)

clamp

stabilizes Polymerase III to the DNA

clamp loader complex

mediates the polymerase attachments to the clamps

Single-stranded DNA binding proteins (SSBs)

they coat single stranded DNA to protect it from damage

Topoisomerase

relieve twist generated by the rapid unwinding of double helix

• prevents super coiling

• AKA DNA gyrase

the OH end is the…?

3’ end

in what direction can the leading strand be synthesized?

continuously in the direction of the helicase movement

in what direction can the lagging strand be synthesized?

the other direction in short fragments (Okazaki Fragments)

• each Okazaki fragment has their own primer

DNA polymerase I

removes RNA primer and fills gaps with DNA

DNA ligase

join Okazaki Fragments

what is the order of events for replication?

• DnaA binds to oric

• helicase unwinds double helix

• SSB attaches to replisome

• primase synthesizes RNA primers on each template

• DNA polymerase III synthesizes lagging strands

• DNA polymerase I removes RNA primers and fills gaps with DNA

• DNA ligase joins okazaki fragments

define Gene

basic unit of genetic information

define operon

functional unit of DNA that consists of a cluster of related genes that get transcribed together

what occurs during Initiation (transcription)

RNA polymerase holoenzyme binds to the promoter region

what occurs during elongation of DNA (replication)

The RNA chain is extended by the addition of ribonucleotides

what occurs during termination for transcription

RNA polymerase detaches from the DNA, after the transcript is made

where does the RNA polymerase bind on the DNA?

on the -10 and -35 regions of DNA in the promoter region

where does RNA transcription begin on DNA

at the +1 nucleotide

RNA polymerase

carries out transcription by making RNA copies from the DNA template strand

core polymerase

elongation phase of transcription

sigma factor

required for initiation of transcription

• helps core enzyme detect the promoter

what makes up the holoenzyme for transcription?

core polymerase enzyme + sigma factor

monocistronic vs. polycistronic

mRNA molecule that included information for one protein vs multiple proteins (operons)

what is the order of transcription

1) RNA polymerase holoenzyme scans DNA for promoter sequence

2) binds to the promoter sequence —> forms a closed complex

3) RNA polymerase unwinds DNA and begins transcribing RNA with rNTPs

4) sigma factor leaves the complex

Rho-dependent termination

Rho protein catches up to the RNA polymerase and knocks it off

• due to the pause site sequence on the DNA that makes RNA polymerase move slower

Rho-independent

sequence on the mRNA causes hairpin and NusA binds to hairpin, knocking RNA polymerase off the DNA

what are the three letter words called and what do they code for?

codons and they code for specific proteins

what brings the codons to the mRNA

tRNA

what are the machines that read the mRNA and convert that information into protein?

ribosomes

what occurs during translation

mRNA is decoded and tRNA brings the codons which are amino acids that end up being covalently bonded to form a polypeptide

what are the two functional regions of tRNA?

anticodon = hydrogen bonds with the mRNA codon

3’ (acceptor) = binds the amino acid

what are the three stages for protein synthesis

1) initiation

2) elongation

3) termination

what happens during initiation for protein synthesis (translation)

two ribosomal units come together onto the first amino acid

what happens during elongation for protein synthesis

amino acids are sequentially added as directed by mRNA transcript

what happens during termination for protein synthesis

the ribosomes release the completed protein and recycle the ribosomal units

how do ribosomes find the right reading frame?

the Shine-Dalgarno sequence that pairs with the 16s RNA of the small ribosomal unit

APE

acceptor = receives tRNA carrying amino acid

peptidyl = hold tRNA attached to growing polypeptide

exit = empty tRNA leaves ribosome

16S rRNA

used for initiation of translation

• binds to Shine-Dalgarno and 3’CCA end

23S rRNA

ribozyme catalyzes peptide bond formation (links all the proteins together)