MMU Microbiology Exam 5 Study Guide

What is the central dogma of biology?

Flow of information in a prokaryotic cell.

Flow of central dogma?

DNA, Transcription, RNA, Translation, Protein

Where does transcription and translation occur in prokaryotes?

cytoplasma

Define a gene

segment of dna that codes for a functional product

Describe the initiation of transcription in prokaryotes.

Promoters are dna sequences that signal where to start transcription

What are some of the DNA sequences and proteins involved in starting transcription?

RNA polymerase, promoters, sigma factors, consensus sequence.

RNA polymerase is responsible for?

polyermizing rna

Promoters indicate?

where to start transcription

Sigma factors are proteins that?

bind specific promoters and instruct RNA polymerase

How do promoter sequences affect rates of transcription in prokaryotes?

Determine the binding affinity of RNAP with more consensus sequences.

What is a consensus sequence?

Nucleotide or amino acid sequence derived from aligning multiple related sequences.

How do DNA and RNA polymerase differ?

DNA synthesizes dna from dna template, RNA synthesizes rna from DNA template.

How is transcription terminated most commonly in prokaryotes? Describe these ways in detail.

Rho independent termination: mRNA loop forms followed by poly u tract, knock rna polymerase off of dna template. Rho dependent: rho protein binds to untranslated mRNA, rolls along transcript and kncoks rna polymerase off.

What areas of a transcript are typically subject to Rho-dependent transcriptional termination?

mRNA with rut sites. C bases.

Transcription inition requires

: sigma factors to bring RNA polymerase and promoters together.

RNA polymerase polymerizes?

RNA

Transcription termination is either:

rho dependent or independent

Describe the role of rRNAs, tRNAs, and mRNAs during translation.
rRNAs:

forms structure of ribosome, recognizes mRNA transcript, catalyzes peptide bond formation

tRNAs:

activates amino acid monomer. Decodes mRNA

mRNAs:

contains all of the information for coding a particular proteins primary sequence. Ribosome binding site, start codon, reading frame, stop codon.

What are tRNA synthetases?

Facilitate addition of specific amino acid to specific tRNA.
What is a codon vs. anticodon?

Codon:

triplet of nucleotides encode one amino acid

Anticodon:

triplet of nucleotides that is contemplentarty to codon

Given a DNA template strand and a genetic code be able to determine the amino acid sequence of a protein produced from that template. AAATGCAAATCCG –

TTTACGTTTAGGC

Why is the genetic code degenerate, and why is this advantageous?

A particular codon always equals the same aa but more than one codon can equal a particular aa

What is codon bias? How can codon bias impact expression of genes?
Codon bias:

based on relative trna abundance.

Expression of genes?

Abundant tRNAs means higher expression levels and vice versa

What are the steps in initiation of translation? What are some of the important RNA sequences involved?
Initiation:

Ribosomes facilitate the coupling of codons in mRNA to anticodons in tRNA. Initiation starts with 30S subunit binding to mRNA

How does the 30S subunit know where to bind?

A AUG start codon preceded by the shine dalgarno sequence

Important RNA sequences involved?

IF1, IF2, IF3, GTP, Start codon, and Shine dalgarno

Shine dalgarno interacts with?

16S rRNA to line up on correct start codon

Be able to describe the steps involved in the elongation phase of translation. What is the energy source for translation during this stage?
Elongation phase:

EF proteins facilitate ribosomes function. Amino group of AA on charged tRNA in a site interacts with carboxyl group of P site charged tRNA. Uncharged trna exits.

Energy source during elongation?

GTP to orient incoming charge of tRNA in A site.

How is translation terminated?

When ribosome reaches a stop codon, release factors enter a site and cause release of peptide chain from tRNA.

What are polysomes?

Translation of a single mRNA by several ribosomes at the same time

What is the benefit of polysomes?

Makes proteins faster and makes more proteins.

Why is transcription and translation coupled in prokaryotes, but not eukaryotes. What is the significance of this then?

Because they are both in the cytoplasm of prokaryotes, translation starts before transcription so its faster and more efficient.

What are operons?

When multiple genes are expressed from a common promoter

Why are bacterial genes organized into operons?

For efficient and coordinated regulation.

Describe the difference between horizontal and vertical gene transfer.
Horizontal:

Genetic transfer requires two cells via transformation, conjugation, or transduction.

Vertical:

chromosomes/all genes passed from one generation to the next via reproduction

Describe the different types of horizontal gene transfer and how they occur, including any important enzyme complexes if present.
Transformation:

uptake of dna found free in the environment. Com machinery

Com machinery is?

Highly specialized dna import systems, naturally competent

Steps in transformation?

Dsdna binding, digested to single strand, single strand up take by competence system, recombination

Conjugation:

export of dna from one cell into another. . sex pilus, tra machinery, indepedent origon of replication.

Tra machinery:

channel for dna to be transferred

F factor:

plasmid with its own Origin of replication.

Generalized transduction –

mispackaged bacteria DNA can come from any location on the bacterial chromosome

Specialized transduction:

mispacked bacteria dna can only come from the part of the bacterial chromosome that is adjacent to the prophage integration site.

What is the main differences between generalized and specialized transduction?

Generalized transfers random fragments while specialized transfers specific.

What is an Hfr strain and how does that change conjugation relative to conjugation using an F factor plasmid?

A high frequency recombination is a bacterium where the f plamdi has become integrated into the chromosome.

What is the difference between passive and active gene regulation?
Passive gene regulation:

parents transmit both genes and a correlated environment to their children

Active gene regulation:

individuals select environments that match their genetic predispositons.

How are promoter/Shine Dalgarno sequences involved in passive gene regulation?

Their influence on translation initiation and mRNA stability.

What are sigma factors?

Proteins that bind specific promoters and instruct RNA polymerase.

How can sigma factors be used to regulate expression of genes?

Different sigma factors recognize different promoter sequences. Different genes can be expressed by changing sigma factors.

What is an activator versus a repressor when it comes to DNA binding proteins? What does each do and to what do they bind?
Activator:

dna binding protein that increase transcription rate of a gene, binds to operator.

Repressor:

dna binding protein that inhibits transcription of a gene, binds to operator sequence.

Be able to describe the two proteins that regulate the expression of the lac operon, how they impact expression, and what conditions would result in these proteins being active or inactive.
Two proteins?

CAP and LacI

CAP impact on expression?

Activate lac operon but requires cAMP to bind to its operator.

LacI impact on expression?

Repressor tha tbinds to the operator sequence and block expression of lac operon.

What conditions result in cap being active or inactive?

The presence of glucose deactivates cAMP and cap no longer activates the operon.

Operon is only expressed when?

only Lactose is present

Be able to determine if the lac operon would be on or off during different conditions.
When no sugar is in the media?

Gene expression off

When glucose is in the media?

Gene expression is off

When glucose + lactose are in the media?

Gene expression is off

When lactose is present in the media?

Gene expression is on.

What is the role of histidine protein kinases versus response regulators in two component systems?

HPK senses a signal and transmits that signal into the cell and a response is regulated. RR controls gene expression.

What functional group is added to activate these proteins?

Phosphate is added to the protein and hpk transfers it to the RR.

What is quorum sensing?

Cells sense population density.

How do cells accomplish quorum sensing?

Controlled by a signaling molecule called an autoinducer.

Why do autoinducers have to be membrane soluble?

To passively diffuse in and out of the cell.

Can one species detect another species’ autoinducer?

No each species of bacteria can only sense their own autoinducer, they are unique.

How is the trp operon regulated during anti-termination?

Transcription continues through the operon because low tryptophan levels stall a ribosome at the leader peptide region.

What is the role of the leader peptide in this scenario?

Acts as a primary sensor for tryptophan availability.

What is the role of Rho in this situation?

Rho has no role in this scenario because an antiterminating loop forms.

What is a riboswitch?

5’ mRNA leader sequence that acts as a regulator

Where are riboswitches located/encoded and how do they control gene expression?

5’ region of mRNA that blocks shine dalgarn sequence

How do sRNA’s control gene expression?

Interact with specific transcript and block the SD to inhibit translation

What chaperone protein is necessary for their function?

Hfq rna chaperone

What is a biofilm?

Multicellular aggregates of bacteria held together by an extracellular polysaccharide.

What signaling molecules control biofilm formation?

Quorum sensing and Cyclid di GMP.

What are the advantages of biofilm formation?

Many bacteria eating as one, persist in favorable environment, collaborative metabolism, high cell density, eps for defense.

What is disease?

Abnormal condition that effects and organism causing symptoms and signs.

What are signs?

Objective changes that can be observed

Examples of signs?

Lesions, swelling, fever

What are symptoms?

Subjective changes in bodily fucntions of patient, not readily apparent to observer

Examples of symptoms?

Malaise, fatigue, aches, pain

Be able to describe the difference and provide examples of internal vs external dysfunctions.
Internal dysfunctions and example?

Inherent part of body that is defective in some way. Autoimmune or cancer

External dysfunction and example?

Caused by an outside agent, pathogen.

What are symbiotic relationships?

An intimate interaction between two organisms

What are the different types of symbiotic relationships?

Mutalism, commensalism, and parasitism

Mutalism:

both partners benefit, gut flora

Commensalism:

one partner benefits, other is unharmed, microflora

Parasitism:

one partner benefits, other is harmed. pathogens

Be able to define the following terms, as well as use/apply them to scenarios/case studies:
Agent:

cause of disease

Pathogen:

a microorganism that causes disease

Virulence:

how a pathogen causes disease.

Infection:

entry and colonization of the host body by a pathogen.

Reservoir:

living or non living object that provide pathogen with conditions for survival, reproduction, and opportunity for transmission.