Chapter 13- Bacterial Genome Replication and Expression

What did Griffith observe in his transformation experiments?

The change of nonvirulent organisms into virulent ones via transformation

What did Avery, MacLeod and McCarty show in 1944?

That the transforming principle was DNA

What blocked the transformation of nonvirulent bacteria in Avery, MacLeod’s and McCarty’s experiment?

DNase

Hershey and Chase used what as a model?

Bacteriophage T2 infection

Hershey and Chase labeled DNA with _ and a protein coat labeled with …

³²P , ³⁵S

What did Hershey and Chase find?

Only DNA entered the cell, but protein was not involved in the new virus production

What are the nucleic acids

DNA and RNA

Nucleic acids are polymers of

nucleotides

Nucleic acids are linked together by

phosphodiester bonds

DNA and RNA differ in

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

DNA is mostly found in

nucleus and nucleoid

RNA is mostly found in

the cytoplasm

DNA is ___ prone to UV damage

more

RNA is ___ prone to UV damage

less

DNA carries what

genetic information

RNA does what

involved in protein synthesis and sometimes gene expression regulation

Nucleoside vs Nucleotide

Nucleotide has phosphate

DNA bases

adenine, guanine, cytosine, thymine

Sugar in DNA

deoxyribose

Phosphodiester bond

phosphate is esterified to sugar carbon

What is the sugar phosphate backbone of DNA?

covalent bonds between the 3’-hydroxyl of one sugar and 5’-phosphate attached to an adjacent sugar

What are the pyrimidine bases?

Cytosine, Thymine, Uracil

What are the purine bases?

Adenine, Guanine

What is the structure of DNA?

an antiparallel double-stranded helix

Adenine and thymine pair by

2 hydrogen bonds

Guanine and cytosine pair by

3 hydrogen bonds

When the 2 strands of DNA twist around eachother they form

major and minor grooves

Supercoling

DNA is helical, forming a coil

SUpercoiling…

provides stability and controls gene expression

RNA is a polymer of

ribonucleotides

RNA contains the bases

adenine, guanine, cytosine and uracil

RNA sugar

ribose

Most RNA molecules are ___, some are __

single stranded; double stranded

What are the four components of an amino acid?

1. Central Carbon

2. Carboxyl Group

3. Amino group

4. Side chain

The carboxyl group in an amino acid is aka

C-terminus

The amino group is aka

N-terminus

Amino acids can be ___, ____, or ____ depending on side chain

polar, nonpolar, charged

Polymers of amino acids are linked by ____ between C and N

peptide bonds

Primary structure of proteins

amino acid sequence

Secondary Structure of Proteins

alpha helices or beta sheets

Tertiary structure of Proteins

3D structure

Quaternary structure of proteins

2 or more polypeptide strands interacting

DNA synthesis is

semiconservative

how is DNA synthesis semiconservative?

each daughter cell obtains one old and one new strand

DNA in most bacteria is

circular

DNA replication is _____ from a single origin

bidirectional

Replication fork

where DNA is unwound

Replicon

portion of genome that contains an origin and is replicated as a unit

Replisome

multiple proteins involved in replication

What catalyzes synthesis of complementary strand of DNA?

DNA polymerase

What direction does DNA synthesis proceed in?

5 to 3

DNA synthesis forms

phosphodiester bonds

What components are required for DNA synthesis?

1. template

2. primer

3. Deoxynucleotide triphosphate

4. Enzyme

What does a template do in synthesis?

Directs synthesis of complementary strand

What is a primer in DNA synthesis?

a short DNA or RNA strand

DNA piolymerase III

adds nucleotides to the new DNA chain

Helicase

unwinds DNA strands

Single-stranded DNA binding proteins

coat single stranded DNA to protect it from coiling

Topoisomerase

relieve twise generated by rapid unwinding of double helix, prevents supercoiling

Primase

synthesizes short complementary strands of RNA primers (~10 nucleotides) needed by DNA polymerase

DNA polymerase synthesis is in ___ direction only

5 to 3

The lagging strand is synthesized in short fragments called

Okazaki fragments

What is needed for the synthesis of each Okazaki fragment?

a new primer

In E Coli, when DnaA proteins bind to the origin of replication what happens

strands bend and separate

After strands bend and separate, what happens

DnaB and other helicases separate strands, and SSB attach

After other strands separate and SSB attaches what happens in E coli

Primase synthesizes RNA primer

After RNA primer is synthesizes what happens in E. coli?

Lagging and leading strand is synthesized

After lagging and leading strand is synthesized, what happens in e. coli?

DNA polymerase I removes RNA primers and fills gaps with DNA

After RNA primers are removed and filled what happens in E. coli?

Okazaki fragments are joined by DNA ligase

DNA ligase

forms a phosphodiester bond between 3’-OH of growing strand and 5’-phosphate of an Okazaki fragment

what enzyme carries out proofreading?

DNA polymerase III

Proofreading

removal of mismatched base from 3’ end of growing strand by exonuclease activity of enzyme

When does replication stop in E. coli?

when replisome reaches termination site on DNA

_____ chromosomes are separated by topoisomerase

catenated

Gene

basic unit of genetic information

Template strand of DNA directs

mRNA synthesis

mRNA synthesis is read in the ___ direction

3 to 5

Sense (complementary) DNA strand

has same bucleotide seuqnce as mRNA except in DNA bases

The ____ is located at the start of the gene

promoter

Promoter

recognition/binding site for RNA polymerase that orients polymerase

What sequence is important for translation initiation?

Shine-Dalgarno

Coding region of DNA begins with DNA sequence:

3’-TAC-5’

The coding region of DNA produces codon

AUG

Transcription

RNA synthesis from DNA template

RNA produced from transcription has ___ sequence to DNA template

complementary

Three types of RNA produced from transcription

tRNA, rRNA, mRNA

tRNA

carries amino acids during protein synthesis

rRNA

components of ribosomes

mRNA

carries the message for protein synthesis

What is an operon?

Cluster of genes under the control of a single promoter and usually functioning together in a metabolic pathway

5 polypeptides that create core enzyme

2 alpha subunits

1 beta

1 beta’

1 omega subunit

Sigma factor

enzyme without catalytic activity that helps the core enzyme recognize the start of genes

RNA polymerase holoenzyme

core enzyme + sigma factor

What is the only thing that can begin transcription?

holoenzyme

____ helps position the core enezyme at the promoter

sigma factor

After binding, what unwinds DNA?

RNA polymerase

Transcription bubble

region that moves with the polymerase as it synthesizes mRNA and where a temporary RNA:DNA hybrid is formed

What is incorporated into RNA complementary to DNA template?

ATP, GTP, CTP and UTP

RNA synthesis proceeds in a ___ direction

5 to 3

transcription termination occurs when

core RNA polymerase dissociates from template DNA