Unit 3 Microbiology Exam

Ch 13-16

13 Define a genome.

All the genetic information that defines an organism.

13.2 What are the monomers of nucleic acids?

nucleotides

13.2 What type of bonds link nucleotides together?

phosphodiester bonds

13.2 What are the 3 parts of the chemical structure of a DNA nucleotide?

deoxyribose sugar, phosphate group, and a nitrogenous base

13.2 What are the two types of nitrogenous bases?

purines (adenine and guanine) and pyrimidines (cytosine and thymine)

13.2 What is the difference between a deoxyribose and ribose sugar?

A ribose has an OH group on its 2’ carbon, which makes it less chemically stable.

13.2 Which nitrogenous bases are considered purines?

adenine and guanine

13.2 Which nitrogenous bases are considered pyrimidines?

cytosine, thymine, and uracil

13.2 What is attached to the 3’ carbon on a nucleotide?

a hydroxide group

13.2 What is attached to the 5’ carbon on a nucleotide?

a phosphate group

13.2 Between a hydrogen and phosphodiester bond, which is weaker and why?

A hydrogen bond is weaker, because it needs to be able to separate in order for replication to occur.

13.2 What is the structure of an amino acid?

central carbon, proton, carboxyl group, side chain, and amino group

13.2 What is the bond that links amino acids to create polymers? What 2 atoms is the bond between?

A peptide bond between nitrogen and carbon.

13.2 What is the primary structure a polypeptide?

amino acid sequence

13.2 What is the secondary structure a polypeptide?

alpha helices or beta sheets

13.2 What is the tertiary structure a polypeptide?

3D structures (determines function)

13.2 What is the quaternary structure a polypeptide?

2+ polypeptide strands that interact

13.2 What is the central dogma of biology?

DNA → transcription → RNA → translation → protein

13.2 What needs to happen in terms of genetic information whenever new cells are produced by binary fission?

DNA replication

13.3 List the 3 general steps of DNA replication.

initiation, elongation, and termination

13.3 Why is DNA replication considered a semiconservative process?

In a new daughter cell, there DNA is comprised of one parental strain and one newly synthesized strand.

13.3 What is the shape of DNA in most bacteria?

circular

13.3 Where does DNA start unwinding in bacteria?

origin of replication (OriC)

13.3 Does DNA replication in bacteria occur unidirectionally or bidirectionally?

bidirectionally

13.3 Where does DNA replication stop in a bacterial chromosome?

ter site

13.3 Which protein binds to the oriC and causes the DNA strands to separate?

DnaA (initiation proteins)

13.3 What is the purpose of helicase?

To provide the force needed to move the replisome by disrupting H bonds. Essentially it unwinds the DNA strands.

13.3 What does DNA polymerase do?

It catalyzes the synthesis of the complementary strand in the 5’ to 3’ direction.

13.3 What 3 things does DNA polymerase require?

1. template strand

2. primer - short RNA strand with 3’-OH

3. dNTPs - free floating deoxynucleotide triphosphates

13.3 Why is the hydroxide group on the 3’ carbon important?

It used as an attachment point for new nucleotides.

13.3 In which direction does replication go?

5’ to 3’

13.3 What is the job of the enzyme primase?

It synthesizes the short complementary RNA primers needed by DNA polymerase.

13.3 Which 2 enzymes make up the primisome?

helicase and primase

13.3 What is the primary DNA polymerase used in prokaryote DNA replication?

polymerase III

13.3 Which protein helps polymerase attach to the primisome?

Tau

13.3 What stabilizes the interaction between polymerase III and DNA?

clamp

13.3 What mediates polymerase binding to the clamp?

clamp loader complex (CLC)

13.3 Why are single-stranded DNA binding proteins necessary in DNA replication?

They protect the ssDNA, since it is more prone to breakage.

13.3 What is the function of topoisomerase? What is another name for it?

It relieves the tension built up by the rapid unwinding of DNA by breaking and resealing H bonds. It also goes by the name DNA gyrase.

13.3 Which strand is synthesized continuously and which strand is synthesized in fragments?

The leading strand is synthesized continuously and the lagging strand is synthesized in fragments.

13.3 What are the fragments of the lagging strand called?

Okazaki fragments

13.3 What does polymerase I do?

It removes the RNA primers from the Okazaki fragments and fills in the gaps with DNA?

13.3 Which enzyme links the Okazaki fragments together?

DNA ligase

13.3 Put the enzymes used in replication in order from when they are used.

DnaA (initiation proteins) → helicase → SSB → primase → DNA polymerase III → DNA polymerase I → DNA ligase

13.4 Provide the definition of a gene.

The basic unit of genetic information. It codes for a functional product.

13.4 How might several genes exist in tandem with one another?

They all share one operon.

13.4 What is another name for the ribosomal binding site?

Shine-Dalgarno sequence

13.5 What 2 sites on the DNA does RNA polymerase bind to? What is this collectively called?

The -10 and -35 nucleotide region make up the promoter.

13.5 Where on the DNA does transcription start?

+1 nucleotide

13.5 What does the ribosome use to know when to start and stop translation?

start and stop codons

13.5 What are the 2 components of an RNA polymerase?

core polymerase and sigma factor

13.5 What is the purpose of the sigma factor?

It helps the core enzyme locate the promoter.

13.5 What is the purpose of a “housekeeping” sigma factor?

It recognizes the consensus sequence at the -10 and -35 positions.

13.5 What is another name for the consensus sequences at the -10 and -35 relevant to the +1 nucleotide positions?

TATA box

13.5 Why are there different types of sigma factors?

Each one controls transcription differently.

13.5 What is the difference between polycistronic and monocistronic?

Polycistronic means there are multiple genes aligned with one promoter, while monocistronic means there is one gene with one promoter.

13.5 What are the 4 steps that encompass the initiation of transcription?

1. RNA polymerase holoenzyme scans the DNA for promoter

2. Closed complex formed as it binds to the promoter sequence

3. RNA polymerase unwinds DNA and begins transcribing RNA with rNTPs (ribonucleoside triphosphates)

4. Sigma factors leave complex

13.5 Describe elongation.

A 17-bp transcription bubble is moved along with RNA polymerase as it sequentially adds ribonucleotides.

13.5 What are the 2 known transcription termination signals?

Rho-dependent and Rho-independent

13.5 What does Rho-dependent termination rely on?

A pause site near the 3’ end of the DNA that slows RNA polymerase down to allow the Rho protein to catch up to it and knock it off

13.5 What does Rho-independent termination rely on?

A GC-rich region with 4-8 consecutive Us on the RNA which forms a hairpin that NusA protein binds to knock RNA polymerase off

13.6 How many possible codons are there? How many specify amino acids and how many are stop codons?

64 total: 61 specify amino acids and there are 3 stop codons

13.7 What is the machine or site responsible for translation?

Ribosome

13.7 What is the direction of translation?

N-terminal to C-terminal

13.7 What are the 2 functional regions of a tRNA?

The anticodon, which hydrogen bonds to the mRNA to specify the amino acid and the 3’ (acceptor) end which is bound to the amino acid

13.7 How do ribosomes find the correct reading frame?

The upstream and untranslated leader RNA has a purine-rich sequence. Also the Shine-Dalgarno sequence is complementary to the 3’ end of 16S rRNA of the 30S subunit

13.7 What are the 3 sites of the ribosome?

Acceptor (receives the tRNA carrying amino acid), Peptidyl (holds tRNA attached to growing polypeptide), Exit (empty tRNA leaves)

13.7 What is the importance of 16S rRNA?

It is needed for the initiation of translation, as it binds to the Shine-Dalgarno sequence and binds to the 3’CCA end of the aminoacyl-tRNA

13.7 What is the importance of 23S rRNA?

It catalyzes the formation of the peptide bonds

13.7 What do 16S and 23S rRNA have in common?

They contribute to the ribosome structure.

13.7 What are the 3 phases of the elongation cycle of protein synthesis?

Aminoacyl-tRNA binding, transpeptidation reaction, and translocation

13.7 What are 2 ways to change the effects of a protein after it is done being translated?

Post-translational modification and folding

13.8 Define a polyribosome. Why might a bacteria use this?

A complex of mRNA with several ribosomes used to increase efficiency by coupling RNA polymerase activity with translation.

14 Why might a bacteria not always express all its genes?

It is energy intensive and some genes may only be necessary in specific environments.

14.1 What are 4 levels that gene regulation occurs at?

1. Alteration of DNA sequence

2. Transcription control

3. mRNA stability control

4. Translational control

14.2 What is a constitutive gene?

Also known as a housekeeping gene, are genes that encode enzymes for the central metabolic pathway as the cell needs a constant supply of active enzymes. Transcription is always on for these.

14.2 What is the difference between inducible and repressible genes?

Inducible genes’ default is off and can be turned on, while repressible genes’ default is on and can be turned off

14.2 Why is β-galactosidase considered an inducible gene?

Its purpose id to hydrolyze lactose into galactose and then glucose, so it is only active in the presence of lactose. Its default is off.

14.2 What is a transcription factor?

A DNA-binding regulatory protein that controls the initiation of transcription at gene promoters

14.2 What are the 2 forms of regulatory proteins?

Repressors that bind to the regulatory DNA sequences and prevent transcription, while activators stimulate transcription.

14.2 What does a ligand do to a regulatory protein?

It alters its DNA binding affinities, which then activates their ability to either repress or stimulate transcription. Some repressors need to bind to a small ligand first, while most repressors must bind to a small ligand.

14.2 Are genes that encode regulatory proteins usually transcribed together or separately from their target gene?

Separately

14.2 How does negative transcriptional control work?

A repressor protein binds to the operator to stop RNA polymerase from binding to it an initiating transcription

14.2 How does positive transcriptional control work?

An activator protein binds to an activator binding site upstream from the promoter that encourages RNA polymerase to bind to it

14.2 What is another name for a ligand?

Inducer

14.2 What is a ligand called when it is necessary for a repressor to bind to the operator?

Corepressor

14.2 What is included in an operon?

All the structural genes and the DNA regulatory sequences that control transcription (promoter + operator + structural genes)

14.2 What is the gene product of a gene that is outside the operator, bunt controls the operon?

Regulatory protein

14.2 In E. coli, how are the enzymes for glucose utilization expressed?

Constitutively

14.2 What is the inducer ligand for the lac operon in E. coli?

Lactose

14.2 What is lacI in relation to the lac operon?

The regulator gene upstream from the lac operon, which produces the repressor protein for this operon

14.2 What is lacP in relation to the lac operon?

The promoter of the lac operon

14.2 What is lacO in relation to the lac operon?

The operator of the lac operon

14.2 What happens at the lac operon when there is no lactose present?

The repressor binds to the operate to inhibit the transcription of the structural genes

14.2 What happens at the lac operon when there is lactose present?

β-galactosidase converts lactose into allolactose, which binds to the repressor and prevents it from binding to the operator. This allows the structural genes to be transcribed.

14.2 What are the structural genes of the lac operon and what do they encode?

lacz (β-galactosidase), lacY (permease), lacA (transacetylase)

14.2 What does permease do?

It imports lactose into the cell

14.2 When does cyclic AMP (cAMP) accumulate in E. coli?

When the cell is starved for carbon

14.2 What activator protein does cAMP combine with?

cAMP receptor protein (CRP)

14.2 When cAMP binds to CRP, what do they do?

They bind to the DNA to recruit RNA polymerase