microbio exam 2

The genotype of bacteria can change through either

mutation or horizontal gene transfer.

Bacteria are _______, so any changes in DNA can easily alter the ________.

haploid

phenotype

A mutant that requires a growth factor ;

auxotroph;

in contrast, a _______ does not require growth factors.

prototroph

Spontaneous mutations

occur as a result of normal cell processes.

are stable but occasionally revert back to the non-mutant form.

Spontaneous mutations

The chance that two given spontaneous mutations will occur within the same cell is the
product of

the individual mutation rates

Base substitutions occur during ____________

DNA synthesis

_____result in synonymous, missense, and nonsense mutations

Base substitutions

frameshift mutation

Deleting or adding one or two nucleotides

,changing the reading frame of the encoded protein.

________results in a shortened non-functional protein.

frameshift mutation

Transposons

can move from one location to another in a cell’s genome.

The gene into which the transposon jumps is

insertionally inactivated by the event

Induced mutations

are caused by mutagen

Some chemicals modify nucleobases, altering their

hydrogen-bonding propertie

Base analogs can be mistakenly incorporated in place of the usual _______, and they have different hydrogen-bonding properties.

nucleobases

Intercalating agents insert between

adjacent bases in the double helix and push nucleotides apart,
resulting in frameshift mutations

Transposons can be introduced intentionally into a cell in order to

inactivate genes.

thymine dimer formation cause by

Exposure to ultraviolet light

The repair mechanism can cause mutations.

thymine dimer formation

X rays cause

single- and double-strand breaks

Repair of Errors in Nucleotide Incorporation
DNA polymerases have a.

proofreading function.

Mismatch repair

removes a portion of the strand that has a
misincorporated nucleotide.

As a result of Mismatch repair

A new DNA strand is then synthesized

Base excision repair

uses specific DNA glycosylases to remove damaged nucleobases in DNA

photoreactivation

an enzyme uses the energy of light to break the bonds of the thymine dimer.

In nucleotide excision repair

the damaged single-stranded segment is removed and replaced.

SOS repair

is a last-effort repair mechanism that uses a special DNA polymerase that has no proofreading
ability but can bypass the damaged DNA.

SOS repair results in DNA that

has many mutations

Genes can be transferred by

bacterial transformation, transduction, and conjugatio

For newly acquired DNA to replicate in a cell, it must either be a

replicon or integrate into the cell’s genome

Bacterial transformation

transfers “naked” DNA

A cell must be competent to

take up DNA, and only certain species naturally become competent.

The Process of Natural Transformation:
Short strands of double-stranded DNA

bind to cells, but only one strand enters

Transduction.

is the transfer of bacterial DNA by a bacteriophage

Two types of Transduction

generalized transduction and specialized transduction

Conjugation requires

cell-to-cell contact

___ cells synthesize an____,

F+

F pilus

F pilus encoded on an

F plasmid

the F plasmid is transferred from an ______ to an _____

F+ cel

F− cell.

Hfr cells have the ______ integrated into the chromosome.

F plasmid

When the F plasmid is transferred, __________ moves into a recipient cell along with it.

chromosomal DNA

An F′ donor carries

a modified F plasmid

An F′ donor carries a modified F plasmid that contains

piece of chromosomal DNA

pan-genome.

The sum total of genes encoded by the various strains of a given species is the

What make up the core genome

Genes common to all strains of the species

What are significant contributors to genome variability

Mobile genetic elements (MGEs), including plasmids, transposons, genomic islands, and phage DNA,

Restriction-modification systems

allow bacterial cells to quickly distinguish and destroy invading DNA.

Restriction enzymes ;

recognize and cut specific DNA sequence

modification enzymes

protect the hosts’ DNA from the action of the restriction enzymes by adding methyl groups to certain nucleobases.

CRISPR systems .

allow bacterial cells to destroy invading DNA that has been encountered previously

CRISPR array contains

; processing of the transcript generates RNA fragments that bind to a Cas nuclease, allowing it to recognize and
destroy that DNA

The cell transcribes a chromosomal region

CRISPR array contains

contains fragments captured from invading DNA;

The cell transcribes a chromosomal region called a CRISPR array that contains fragments captured from invading DNA;processing of the transcript generates

DNA fragments that bind to a Cas nuclease, allowing it to recognize and
destroy that DNA.

Most viruses are approximately

100-fold to 1,000-fold smaller than the cells they infect

Virion (viral particle) .

consists of nucleic acid surrounded by a protein capsid

Capsids are composed of .

capsomeres

Some viruses have an envelope surrounding the ________; other viruses are non-
enveloped or naked. Viruses contain either RNA or DNA, but never both. The shape of a virus is generally
icosahedral, helical, or complex

nucleocapsid

Viruses contain either

RNA or DNA, but never both.

The shape of a virus is generally

icosahedral, helical, or complex

Viruses are classified primarily

on the basis of their genome structure and hosts they infect.

The names of virus families end in _____.

-viridae

Viruses are also given informal names and are sometimes grouped based on their

routes of transmission.

Lytic or virulent phages exit

the host at the end of the cycle by lysing the host, resulting in a productive
infection.

Lytic or virulent phages exit the host at the end of the cycle by lysing the host resulting in

productive infection

The infection proceeds through five steps

attachment, genome entry, synthesis of phage proteins and
genome, assembly (maturation), and release.

Temperate phages have the option of either

directing a productive infection or initiating a lysogenic infection(lysogen)

A repressor

.

maintains the prophage in an integrated state, but the prophage can
be excised to initiate a lytic infection.

Lysogens are immune to

superinfection

Lysogenic conversion occurs if

a prophage carries genes that change the phenotype of the host cell

Filamentous phages cause ,

productive infections

Generalized transduction results from .

a packaging error during phage assembly

Generalized transducting particles can

transfer any gene of a donor cell to a recipient cell

Specialized transduction results from

.

an excision mistake made by a temperate phage during its transition from a lysogenic cycle to a lytic cycle

Only genes located near the site at which the temperate phage integrates are

transduced

The generalized infection cycle of animal viruses can be viewed as a five-step process

Attachment
Entry and Uncoating

Synthesis of Viral Proteins and Replication of the Genome
Assembly (Maturation)
Release

Attachment

Attachment proteins or spikes on the viral particle attach to specific receptors on the cell surface.

Entry and Uncoating: Enveloped viruses

fuse with the host membrane or are taken in by receptor-mediated endocytosis.

Entry and Uncoating - animal viruses

the entire virion enters the cell.

Entry and Uncoating: Non-enveloped

Non-enveloped virions enter by receptor-mediated endocytosis.

Entry and Uncoating

releases the nucleic acid from the protein coat

Synthesis of Viral Proteins and Replication of the Genome

DNA viruses generally replicate in _______ and use the _____________ as well as
_________, although they often encode their own DNA polymerase.

the nucleus

host cell machinery for DNA synthesis

gene expression

Synthesis of Viral Proteins and Replication of the Genome

Replication requires a _______________ to ____________________. This enzyme lacks ___________ and makes more mistakes in replication than DNA polymerases do.

virally encoded replicase
synthesize the complementary RNA strand.

proofreading ability

Synthesis of Viral Proteins and Replication of the Genome

Reverse-transcribing viruses encode _________, which
synthesizes _____________. As with replicases, these enzymes are ________.

reverse transcriptase

DNA from an RNA template

error prone

Assembly (Maturation)

_______are formed, and then the genome and any necessary proteins are packaged within it.

The process may take place in the _______, ___________, ___________

Capsids

cytoplasm, in the nucleus, or in a variety of organelles

Release
Enveloped virions most often exit by ________. Non-enveloped virions are released when _________

budding

the host cell dies

Acute infections are characterized by

the sudden onset of symptoms of relatively short duration.

Persistent infections can

continue for the lifetime of the host, with or without symptoms

Acute Infections

On a cellular level, acute infections can be compared to _________________, but even
though the cells often die, the host may survive because of ____________

productive lytic infections by bacteriophages

the immune response

Chronic infections are characterized by the

continuous production of low levels of viral particles

latent infections are similar to lysogeny in bacteriophages in that the virus genome

remains in the host cell but is not active, so no new virus particles are formed

Oncoviruses

are viruses that can cause cancer

Oncoviruses carry ________ that interfere with the
___________________

oncogenes

ability of the cell to control growth.

Most virus-induced tumors are caused by .

certain DNA viruses

A vaccine against human papillomaviruses (HPVs) prevents

many cervical cancers.

Oncolytic viruses target and destroy

cancer cells and have significant therapeutic potential.

Catabolism

is the set of processes that capture and store energy by breaking down complex
molecules.

Anabolism includes processes that

use energy to make and assemble the building blocks of a cell

Photosynthetic organisms harvest the

energy of sunligh

Photosynthetic organisms harvest the energy of sunlight, using it to

power the synthesis of organic compounds.