Microbiology Exam 3 Riggs

What is a genome?

All the genetic information that defines an organism in one cell

What are genetics?

The study of genes

What are chromosomes?

Structures containing DNA, the chromosomes contain genes

What is a structural gene?

Produces a functional RNA which usually encodes a protein

Has a function to make a protein

What is a DN control sequence?

regulates the expression of a structural gene

Either allows or hinders the protein from being made

Includes promoters and binding sites for regulatory proteins

What are the two types of gene transfer?

vertical transmission and horizontal transmission

What is vertical transmission?

gene transfer from parent to child

What is horizontal transmission?

the transfer of small pieces of DNA from one cell to another

What is the genetic code?

a set of rules that determines how DNA is converted to an amino acid sequence

What are the steps in the central dogma?

replication, transcription, translation

What are the 4 types of mutations?

Missense, nonsense, silent, wild

What is extrachromosomal DNA?

plasmids

What % of eukaryotic genomes are noncoding DNA?

>90%

what % of prokaryotic genomes are noncoding DNA?

<15%

What is a gene?

The basic physical and functional unit of heredity

Can operate independently of others

What is an operon?

a unit made up of linked genes that is thought to regulate other genes responsible for protein synthesis.

What is a polymer of nucleotides?

DNA

What are the three parts of a nucleotide?

Nitrogen base

2-deoxyribose sugar

phosphate

Purine nitrogen base

Adenine and Guanine

pyrimindine bases

thymine and cytosine

What are nucleotides connected together by?

5'-3' phosphodiester bonds

What does the 5' end have?

phosphate group

What does the 3' end have?

OH group

How can you tell the difference between DNA and RNA

DNA has thymine and RNA has uracil

What does it mean to denature?

change of shape

This happens at a high temp hydrogen bonds in DNA break and the duplex changes into two single strands

What are the 3 main differences RNA has from DNA?

Usually single-stranded

Contains ribose sugar

Uracil replaces thymine

What is a nucleoid?

Where bacteria pack their DNA into

a series of loops

What are the loops of the nucleoid anchored by?

histone-like proteins (HU and H-NS)

Positive supercoils

DNA is overwound

Negative supercoils

DNA is underwound

Is most DNA positively or negatively supercoiled?

negatively supercoiled

What does supercoiling change in DNA?

topology

What are toposiomerases

Enzymes that change DNA supercoiling

Type I topoisomerases

Cleave one strand of DNA and relieve or unwind supercoils

Type II topoisomerases

have multiple subunits of GyrA and B

Cleaves both strands of DNA

Introduce negative supercoils

Needs ATP

What is targeted by quinolone antibiotics?

the introduction of negative supercoils

What two kinds of extrachromosomal DNA interact with bacterial genomes?

Horizontally transferred plasmids

The genomes of bacteriophages

What are bacteriophages?

viruses that infect bacterial cells

What do plasmids carry?

information that contribute to the physiology of the cell which is only used as an advantage to improve survival

What is conjugation?

horizontal gene transfer mechanism requiring cell-to-cell contact, which could transfer large segments of some bacterial chromosomes

What is recombination?

which the donor DNA fragment replaces the recipient DNA fragment.

the rebuilding of the 2nd strand of the DNA material

What is the process of bacterial genomes?

allowed genes to be mapped relative to one another according to time of transfer

What are histones?

where eukaryotic cells pack their DNA using proteins

What are introns?

non-coding regions

What are pseudogenes?

former genes that have accumulated mutations and are nonfunctional

Like bacteria, archaeal genomes have...

Polygenic operons

Cells lacking a nuclear membrane

A single circular chromosome

How is archaeal genomes similar to eukaryotes?

their DNA replication, transcription, and translation

What did Frederick Griffith do?

Discovered bacterial tranformation.

What did Oswald Avery do?

showed that the transforming substance is DNA

What did Rosalind Franklin do?

use X-Ray diffraction to get information about the structure of DNA discovering the double helix

What did James Watson, Francis Crick and Maurice Wilkins do?

discovered the complementary bases and antiparallel nature of DNA

What is DNA-Mediated transformation?

the transfer of naked DNA from one bacterium to another

What was Fredrick Griffith working with when he discovered transformation?

Streptococcus pneumoniae

Replication of cellular DNA in most cases is ________

semiconservative which means daughter cells receives one parental and one enwly synthesized strand

Replication is _____

bidirectional; start at a fixed origin and progress in opposite directions

What is DNA Pol III

Primary replication enzyme

What is DNA Pol I

replaces RNA primer with DNA

has RNAase activity

DnaA

Initiator protein; binds at ori C and opens up the double helix

DnaB

DNA helicase

DnaC

helicase loader

DNA primase

synthesis of RNA primer

DNA gyrase

relieves DNA supercoiling

DNA ligase

joins Okazaki fragments

7 steps in initiating replication

1. DnaA-ATP proteins bind to the repeated 9-mer sequences within oriC

2.Binding of DnaA leads to strand separation at the 13-mer repeats

3.DNA helicase (DnaB) and DNA helicase loader (DnaC) associate with the DnaA-bound origin

4.DNA helicase loaders open the DNA helicase protein ring and place the ring around the single0stranded (ss) DNA at the origin (13-mer region). Loading of the DNA helicase leads to release of the helicase loader

5.DNA helicases recruit DNA primase (orange) to make RNA primers (blue). Top strand primer starts rightward replication; bottom strand primer starts leftward replication. These primers initiate continuous or leading-strand DNA synthesis at each fork

6.A clamp loader carrying two DNA polymerase III enzymes loads a sliding clamp onto each leading-strand DNA at an RNA primer. Meanwhile, the Helicase-primase moves laterally at each fork to unwind the DNA and synthesize lagging stand primers

7. DNA polymerase binds to the clamp. Leading-strand synthesis begins and continues at the end of the template. At each lagging strand, a sliding clamp is then loaded

What is a leading strand?

is replicated continuously in the 5'-3' direction

What is a lagging strand?

replicated discontinuously in stages, each producing an Okazaki fragment

What eventually happens to Okazaki fragments found on the lagging strand?

they are progressively stitched together to make a continuous unbroken strand

The cell coordinated the activity of _________ enzymes in one complex

2 DNA Pol III

2 DNA Pol III enzymes together with DNA primase and helicase form what?

the replisome

What does the replisome do?

ensures that the leading and lagging strands are synthesized simultaneously in the 5' to 3' direction

What is energy for replication supplied by?

nucleotides

_____ proteins binds to ____ and acts as a counter-helicase

tus (terminus utilization substance)

ter

What are ringed catenanes?

formed at the completion of replication

What are ringed catenates separated by?

topoisomerase IV and XerCD proteins

What ways can plasmid-encoded functions contribute to the physiology of the cell?

Antibiotic resistance

Pathogenesis

Symbiosis

Describe Plasmids

Found in archaea, bacteria, and eukaryotic microbes

Usually circular

Need host proteins to replicate

Need host proteins to replicate

How can plasmids replicate?

through rolling circle mechanism or bidirectional replication

What tricks do plasmids have to ensure their inheritance?

Low-copy-number plasmids segregate equally to daughter cells

High-copy-number plasmids segregate randomly to daughter cells

Conjugation

What are some techniques used to extract DNA from bacterial cells?

Cells are lysed with lysozyme and detergents to dissolve the cell wall and membranes

Protein removed in a high-salt solution

The cleared lysate containing DNA is passed through a column containing a silica resin that specifically binds DNA

The extracted DNA can be examined with a variety of analytical tools

What is restriction endonucleases?

they cleave DNA at specific recognition sires, which are usually 4 to 6 bp and palindromes

What are Genome libraries

Containing all the genes in an organism were routinely made for many years

What is polymerase chain reaction (PCR)?

can produce over a million-fold copy of target DNA within a few hours

What is special about Thermus aquaticus

bacteria that can tolerate high temps

What is Taq DNA polymerase?

heat resistant enzyme

What are entire genomes are sequenced by?

fragmenting chromosomal DNA, amplifying the fragments in clusters, and sequencing each cluster

What is Metagenomics?

uses modern genomic techniques to study microbial communities directly in nature

bypasses the need for isolating and cultivating individual species in the laboratory

Where are codons found and what is their function?

in mRNA and code for single amino acids

What direction is the template strand of RNA synthesis read in?

3'-5' direction

What direction is the template strand of RNA synthesis synthesized in?

5'-3' direction

What is the complementary DNA strand?

same nucleotide sequence as mRNA (except in DNA bases)

Where is the promoter located for transcription?

the start of the gene

it is the recognition/binding sire for RNA polymerase

Leader sequence is transcribed into ____ but it is not translated into ____ ____

mRNA; amino acids

What is important for the initiation of translation?

Shine-Dalgarno sequence

Protein coding genes begins with what DNA sequence?

3'-TAC-5'

produces codon AUG

Genes coding for tRNA

may code for more than a single tRNA molecule or type of tRNA

Genes coding for rRNA

transcribed as single, large precursor

Spacers between the coding regions of both rRNA and tRNA

both are removed after transcription, some by the use of special ribonucleases called ribozymes

What are ribozymes?

RNA molecules that form peptide bonds and perform cellular work and replication

DNA template is used to create what?

a complimentary RNA sequence

What are the three types of RNA that are produced through transcription?

mRNA

tRNA

rRNA