Test 3 Microbiology Dr. Moore

Nucleotides

Basic units of DNA molecule, composed of a sugar, a phosphate, and one of 4 DNA bases

5' end

The free phosphate end of the sequence is the ____________

3' end

The free hydroxyl end of the sequence is termed ___________

deoxyribonucleotides

polymer of DNA

Double stranded

Conformation of DNA

Doexyribose

Sugar in DNA

Adanine and Guanine

Purine bases in DNA

Cytosine and Thymine

Pyrimidine bases in DNA

Adanine and Guanine

Purine bases in RNA

uracil and thymine

Pyrimidine bases in RNA

Antiparallel

The opposite arrangement of the sugar-phosphate backbones in a DNA double helix.

Genes

The entire DNA sequence necessary for the production of a functional RNA or Protein

One

Number of chromosomes in Prokaryotes

Haploid

Copy number of Prokaryotes

Circular

Conformation in DNA in Prokaryotes

No introns

Are there intervening sequences in Prokaryotes

Multiple

Number of chromosomes in Eukaryotes

Haploid/Diploid

Copy numbers in Eukaryotes

Linear

What is the conformation in DNA for Eukaryotes

Yes introns

Are there intervening sequences in DNA for Eukaryotes

Microbial genome

sum of all genetic material in a cell

-Chromosome

-Plasmid

-F plasmid

-R plasmid

- Virulence factor plasmid

-Bacteriophage

Fertility

What does "F" stand for in F plasmid

(contained by cell donor that allows the synthesis of a conjugation (sex) pilus.)

Resistant

What does the "R" stand for in R plasmid

(resistant to antibiotics)

semiconservation replication

replication where each daughter cell receives one original (parent strand) in the newly synthesized strand.

Plasmids

Small rings of DNA found naturally in some bacterial cells in addition to the main bacterial chromosome. Can contain genes for antibiotic resistance, or other "contingency" functions.

semiconservative DNA replication

Replication:

-requires a Template

-requires a Primer

-needs an Origin of replication

-replication always 5' to 3'

Okazaki fragments

Small fragments of DNA produced on the lagging strand during DNA replication, joined later by DNA ligase to form a complete strand.

Steps for DNA repliaction

1) unwind DNA

2) strand separation

3) stabilization of ssDNA

4) polymerization of leading and lagging strand

5) repair and ligation

ssDNA

single stranded DNA

ssDNA binding proteins

prevent unwound DNA strands from snapping back

RNA primer

short segment of RNA used to initiate synthesis of a new strand of DNA during replication

-needs a free OH group

One

Leading strands only need ___________ primer

Multiple

Lagging strands need __________ primer

5' to 3'

mRNA is synthesized in a _______ direction

3' to 5'

mRNA is read __________

Topoisomerase I

relaxes supercoiled DNA

Topoisomerase II

supercoils the DNA back together

Helicase

Melts the H2 bonds in DNA

Primase

An enzyme that joins RNA nucleotides to make the primer.

DNA polymerase I

removes the RNA primer and replaces it with DNA

DNA polymerase II

DNA repair

DNA polymerase III

synthesizes new DNA only in the 5' to 3' direction

DNA ligase

an enzyme that eventually joins the sugar-phosphate backbones of the Okazaki fragments

rolling circle replication

a DNA replication mechanism in which one strand is nicked and unrolled for use as a template to synthesize a complementary strand

OriC

origin of replication

polymerase chain reaction

A method to amplify DNA in vitro by using many cycles of DNA denaturation, primer annealing, and DNA polymerization with a heat-stable polymerase

(Offers a way to detect pathogens present in patients who have nor shown symptoms)

PCR

polymerase chain reaction

Taq polymerase

A DNA synthesis enzyme that can withstand the high temperatures of PCR

Thermus aquaticus

Taq polymerase

Electrophoresis

The movement of suspended particles through a fluid or gel under the action of an electromotive force applied to electrodes in contact with the suspension.

Top

In electrophoresis larger DNA is on the ________

Bottom

In electrophoresis smaller DNA is on the _____________

PCR buffer, MgCl2, Taq polymerase, DNA specific primer, original DNA, dioxynucleotides

List the materials necessary to achieve a successful PCR reaction

gene expression

process by which a gene produces its product and the product carries out its function

constitutive genes

genes that are expressed all the time

inducible genes

Genes that are expressed only when their products are needed.

Transcription

synthesis of an RNA molecule from a DNA template

mRNA

A type of RNA, synthesized from DNA, that attaches to ribosomes in the cytoplasm and specifies the primary structure of a protein.

tRNA

An RNA molecule that functions as an interpreter between nucleic acid and protein language by picking up specific amino acids and recognizing the appropriate codons in the mRNA

rRNA

type of RNA that combines with proteins to form ribosomes

miRNA

a class of functional RNA that inhibits the translation of mRNA

Sense strand

in viruses mRNA is called _____________

Translation

______________ can occur simultaneously as transcription

Translation

Process by which mRNA is decoded and a protein is produced

polyribosomal complex

assembly line for mass production of proteins

Transcriptome

the sum total of all the messenger RNA molecules expressed from the genes of an organism.

Shine-Dalgarno sequence

In prokaryotes, what is the name of the RNA sequence that ribosomes bind to so translation can occur?

Codons

A three-nucleotide sequence of DNA or mRNA that specifies a particular amino acid or termination signal; the basic unit of the genetic code.

degenerative code

When more than one series of three nucleotides codes for any amino acid.

AUG

start codon

UAA, UAG, UGA

stop codons

formylmethionine

first amino acid in protein synthesis in a bacteria

Operon

A unit of genetic function common in bacteria and phages, consisting of coordinately regulated clusters of genes with related functions.

-Consist of regulatory gene, control sites, and structural genes

Sponataneous mutations

NO outside influences, they are permanent, usually caused by errors in replication in DNA polymerase.

Mutations

Random errors in gene replication that lead to a change in the sequence of nucleotides. The source of all genetic diversity.

Inducible mutations

Changes in gene replication due from outside sources like Physical or Chemical.

physical mutagens

radiation-x-rays, UV light

frameshift mutation

mutation that shifts the "reading" frame of the genetic message by inserting or deleting a nucleotide

insertion mutation

a mutation in which one or more nucleotides are added to a gene

deletion mutation

a mutation in which one or more pairs of nucleotides are removed from a gene

substitution mutation

Mutation in which a single base is replaced, potentially altering the gene product.

inversion mutation

Mutation in which a chromosome piece reattaches to original chromosome but in reverse orientation

nonsense mutation

changes a normal codon into a stop codon

missense mutation

A base-pair substitution that results in a codon that codes for a different amino acid.

silent mutation

A mutation that changes a single nucleotide, but does not change the amino acid created.

Induced operon

Operon that turns on upon introduction of specific substrate

Repressed operon

Operon that gets turned off by products it has produced

Lac operon

a gene system whose operator gene and three structural genes control lactose metabolism

-governs catabolsim

-normally turned off

absense of lactose

Lac repressor binds to the operator region and blocks RNA polymerase from transcribing DNA

presence of lactose

Lactose binds to the repressor; the repressor cannot bid to the operator and transcription occurs

catabolite repression

System of gene control in some bacterial operons in which glucose is used preferentially and the metabolism of other sugars is repressed in the presence of glucose.

Glucose

In the presence of Lactose and Glucose the cell will metabolize ________________

cAMP

In the presence of Lactose and absence of glucose the cell will produce ____________

catabolic activator protein

CAP stands for

Alarmone

a chemical alarm signal that promotes a cell's response to environmental or nutritional stress

presence of lactose and absence of glucose

Transcription at high affinity due to the CAP-cAMP complex

Low glucose and High cAMP

Presence of lactose and glucose

Transcription at normal (low) affinity

High Glucose and low cAMP

Bends the DNA

CAP-cAMP complex binds before the Plac region, the complex then ________________ which increases the affinity for the RNA polymerase

trp operon

tryptophan binds to the repressor protein and enables it to repress gene transcription.

absence of tryptophan

Trp repressor is inactive so the RNA polymerase can transcribe and translate the mRNA