Exam #3 Study Guide Flashcards
central dogma
overall flow of genetic information
genetics
study of genes, how they carry information, how information is expressed and how they are replicated
gemine
all the genetic information
chromosome
structures containing DNA that physically carry hereditary information, contains genes
gene
segment of DNA that encode functional products
genetic code
set of rules that determines how a nucleotide sequence is converted to an amino acid sequence in a protein
geneotype
genetic makeup of an organism and represents potential expression
pheotype
expression of actual genes, represents actual expression
genomics
the sequencing and molecular characterization of genomes
DNA gyrase
relaxes supercoiling ahead of the replication fork
DNA ligase
makes covalent bonds to join new strands, Okazaki fragments and new segments in excision repair
DNA polymerase
synthesize DNA, proofreading and facilitating DNA repair
topoisomerase
relaxes supercoiling ahead of the replication fork and separates DNA circles at the end of DNA replication
helicase
separates stands
replication fork
The point at which the two strands of DNA are separated to allow replication of each strand.
top stand is the
3’-5’
the lagging stand is
5’-3’
top strand is the
leading strand
primase places
RNA primers
transcription
transcribe the DNA in to a message
transcription occurs in the _________ in eukaryotic cells
nucelus
RNA polymerase transcription role
copies RNA from a DNA template
transcription begins when RNA polymerase binds to the
promoter sequence
in transcription only
one strand is transcribed
3 stages of transcription
initiation, elongation, termination
initation
RNA polymerase binds to the DNA and recognizes a site called _________ at the end of 3’ end of the template strand of the target gene. When RNA polymerase finds a promoter it breaks ___________ ______ holding the DNA strands together at the site of the promoter and __________ begins
promoter, hydrogen bond, transcription
RNA polymerase does not bind to all promoters with equal __________
affinity
the difference in promoter strength is one way that cells can control _______ __________. The more strongly RNA polymerase binds to a particular promoter the more likely the gene is to be ___________
gene expression, transcribed
in elongation one strand of the DNA serves as the _______ ________ and the RNA is transcribed from this
template strand
elongation continues until it reaches the
Terminator
at the termination site the
RNA polymerase and the newly synthesized RNA transcript are released
termination can occur in 2 mechanisms
self termination and enzyme dependent termination
self termination
RNA sequence transcribed at the terminator causes the RNA to hydrogen bond with itself forming a stem loop structure which essentially pulls the RNA polymerase off
enzyme dependent termination
termination protein binds to the terminator and pushes RNA polymerase off the DNA
codons
groups of 3 mRNA nucleotides the code for a particular amino aicd
degeneracy
each amino acid is coded by several codons
START
AUG
STOP
UAA, UAG, UGA
what components are needed for translation
ribosome, tRNA, mRNA
translation step 1
on the assembled ribosome a tRNA carrying the first amino acid isa pried with the ______ ______ on the mRNA. The place where this first tRNA sits is called the _______ site
start codon, P site
translation step 2
the second codon of the mRNA pairs with a tRNA carrying the second amino acid at the ___ site. The first amino acid joins to the second by a _______________ bond. this attaches the polypeptide to the tRNA in the __ site
A site, polypeptide, P site
translation step 3
the ribosome moves along the mRNA until the second tRNA is in the __ site. The next codon to be translated is brought into the ___ site. The first codon now occupies the ___ site
P, A, E
translation step 4
the second amino acid joins to the third by another ________ _______ and the first tRNA is _______ from the E site
peptide bond, released
translation step 5
when the ribosome reaches a stop codon
the polypeptide is released
prokaryotes transcription location
cytoplasm
eukaryotes transcription location
nucelus
prokaryotes: can translation begin BEFORE transcription is complete
YES
eukaryotes: can translation begin BEFORE transcription is complete
NO
prokaryote translation location
cytoplasm
eukaryote translation location
cytoplasm
3 things that are unique to just eukaryotic cells
exons, introns, snRNPs
exons
regions of DNA that code for proteins
introns
regions of DNA that do NOT code for proteins
snRNPs (small nuclear ribonucleoprotein)
remove introns and splice exons together
mutation
permanent change in the base sequence of DNA
mutagens
agents that cause mutations
Ames test
exposes mutant bacteria to mutagenic substances to measure the rate of reversal of the mutagen
indicates the degree to which substance is mutagenic
2 types of repairs to fix mutagens
photolyases
nucleotide excision repair
photolyses use what to break apart what
use visible light to break apart thymine dimers
nucleotide excision reapir
enzymes cut out incorrect bases and fill in correct
nucleotide excision repair are also called
dark reactions
but can occur with or with out lighr
2 ways to identify mutagens
positive (direct) selection
negative (indirect) selection
positive (direct) selection
detects mutant cells because they grow/appear different than unmuated cells
negative (indirect) selection
detects mutant cells that cannot grow or preform a certain function
auxotroph
mutant that has a nutritional requirement absent in the parent
how to identify a auxotroph
replica plating
constitutive genes
expressed at a fixed rate (not regulated but constantly produced at this rate)
operons
segment of DNA where RNA polymerase imitates transcription of structural genes
operon consists of
promoter and operator
promoter
segment of DNA where RNA polymerase imitates transcription of structural genes
operator
segment of DNA that controls transcription of structural genes
all of the structural genes of an operon are transcribed into a single _____ which is then translated into this entire set of _________
mRNA, proteins
pre transcriptional contro;
epigenetic control, repression, induction
epigenetic control, how do you turn nucleotides off
methylating them
methylated genes can be or cannot be passed to offspring
can
is epigenetic control permeant or not
not permanent
repression
inhibits gene expression and decrease enzyme synthesis
repressor is mediated by
repressors
repressors are
proteins that block transcription
the default position for repression is
on
repressible operons
are always transcribed unless deactivates by a repressor
induction
turns genes on
induction is initiated by an
inducer
default position of induction is
off
inducible operons
not transcribed unless they are activated by an inducer
example of inducible operon
lac operon of E. coli
3 parts of lac operon
promoter, operator, 3 structural genes
the 3 structural genes of lac operon encode for proteins involved in
catabolism of lactose
when lactose is available to the cell the operon is _______________ to produce the proteins of lactose catbolism
induced/stimulated
e.coli has a regulator gene near lac operon and this gene is constantly transcribed and translated to produce
repressor protein
the repressor protein binds to the operator DNA at lac operon physically preventing
RNA polymerase from moving beyond the promotor
when a repressor protein is bound the genes for lactose catabolism can to cannot be transcribed
cannot
when lactose is present in the cell some of it is converted to
allolactose
allolactose binds to the repressor proteins and
inactivates them which prevents them from binding to the operator
once the repressor proteins are inactivates the structural genes are now transcribed resulting in the production
of the enzyme needed to catabolize lactose
in lac operon the inducer is ____________ because it stimulates transcription of lac operon
alloactose
an example of a repressible operon is
trp operon in e.coli
3 parts of tap operon
promoter, operon and 5 structural genes
5 structural genes encode for proteins involved in the biosynthesis fo
tryptophan
when excess tryptophan is available to the cell the operon is ___________ ending the production of the proteins of tryptophan biosynthesis
repressed
e coli contains a regulatory gene near the trp operon and this gene constantly transcribed and translated to produce
repressor proteins
repressor proteins of trp operon are inactive unless
excess tryptophan is avaibale
the repressor proteins of trp operon can be activated by
tryptophan
once the repressor protein is activated by tryptophan it can bind to the trp operon preventing
RNA polymerase from moving beyond the promotor
when a repressor protein is bound to trp operon the genes for tryptophan biosynthesis cannot be transcribed into
mRNA
post transcriptional control
riboswitch
microRNAs
riboswitch
part of an mRNA molecule that binds to a substrate and changes the mRNA structure
translation is initiated or stopped
mircoRNAs
base pair with mRNA to make it double stranded
double stranded RNA is enzymatically destroyed preventing production of a protein
positive regulation
catabolite repressoin inhibits cells from using carbon sources other than glucose
cAMP
builds up in the cell when glucose is not available
cAMP binds to
CAP
CAP binds to
lac promotor
lac promotor
imitates transcription allowing the cell to use lactose
genetic recombination
exchange of genes between two DNA moleules; creates genetic diversity
crossing over
two chromosomes break and rejoin resulting in there insertion of foregin DNA into the chromosome
vertical gene transfer
transfer of genes from an organism to its offspring
horizontal gene transfer
transfer of genes between cells of the same generation
2 types of mobile genetic elements
plasmids and transposons
mobile genetic elements
move from one chromosome to another or from one cell to another
are plasmids self replicating or not
self repliating
plasmids are what shape
circular
plasmids often code for proteins that enhance the
pathogenicity
3 types of plamsids
conjugative plasmid, dissimilation plasmids, resistance factors
conjugative plasmids
carries genes for sex villi and transfer of the plasmid
dissimilation plasmid
encode enzymes for catabolism of unusual compunds
resistance factors
encode antibiotic resistance
two groups of resistance factor genes
RTF, and r determinant
transposons
segments of DNA that can move from one region of DNA to another
transposons contain
insertion sequences
insertion sequences code for
transposes that cuts and reseals DNA
2 types of transposons
simple and complex
simple transposons
only contain the essential elements needed for trans positioning
simple transposons are compose of
transposes gene flanked by an inverted repeat
simple transposons are complete units capable of effecting their own movement from
one location to another
inverted repeat sequin is a region of DNA in which the sequence of nucleotides is
identical to an inverted sequence in the complementary strand
the transposase enzyme recognizes this inverted repeat in a target site and
inserts the transposon or a copy into the DNA moleules at such target site
the transposase gene codes for the enzyme that
facilitates the movement of the transposon
transposase cuts the DNA so the transposon can
leave its original position
transposase also cuts the DNA in new positions where the
transposon inserts itself and creates the covalent bond between the transposon and its new host DNA
simple transposons move through 2 types of mechanisms
cut and paste and replicative
cut and paste
the entire transposon moves to another location
replicative
transposon is copied to a new location
complex transposons
carry other genes and transposase gene
complex transposons consist of
two simple transposons with another sequence of DNA between them
in a complex transposon the other gene is often something that gives
select advantage to the organism containing the transposon
ends of complex transposons are
insertion sequences
the insertion sequences are capable of
moving/coping themselves independent of the rest of the complex transposons
the element in the middle of the complex transposon can or cannot move on its own
cannot
3 types of horizontal gene transfer
transformation, conjugation, transduction
transformation
genes transferred from one bacterium to another as ‘naked’ DNA
transformation
some bacteria are capable of taking up fragments of DNA from
their surroundings and integrating the fragments into their own chromosome by recombiniation
competent
cells capable of taking up DNA from their environment
species that is naturally compenent
streptococcus pneumoniae
species that can be MADE compenent
e. coli
conjucation
plasmids transferred from one bacterium to another
conjugation requires cell to cell contact via
sex pilli
2 types of conjucation
f factor and Hfr
F factor F+ cells
cells containing an F factor and serve as DNA donors during conjucation
F factor F- cells
cells lacking F factor and serve as DNA recipients during conjucation
conjucation F factor
Conjucation pills extends from an _____ cell to an ____ cell and pulls the cells together, the cells come together and stabiliz. Transfer of DNA begins. A _________ stranded copy of the F factor is transferred from F+ to F-. each cell synthesizes a complementary strand of plasmid resulting in a __________ copy of the plasmid in each cell.
F+, F-, single, complete
Hfr conjugation contains the F factor on the
chromosome
Hfr conjucation
Occasionally an F factor integrates into the E.coli __________ converting the F+ cell to an ________ cell. Hfr form conjucation pili and cells come together and stabilize. Transfer of DNA. DNA transfer begins in the _________ of the F factor within the HFr cells chromosome, the result is the F- cell does not receive a full copy of the F factor since the recipient cell does not revieice a full copy of the F factor it is still ___. However the DNA from the donor can recombine with recipient chromosome giving the recipient new chromosomal ________
chromosome, Hfr, middle, F-, genes
transduction
DNA is transferred from donor cell to recipient via bacteriophage
2 types of transduction
general and specialized
general transduction
random bacterial DNA is packaged inside a phage and transferred to a recipient cell
specialized transdcution
specific bacterial genes are packaged inside a phage and transferred to a recipient cell
mutations and recombination create
diverity
natural selection
acts on populations of organisms to ensure the survival of organisms within a particular environment
biotechnology
use of microorganisms, cells or cell components to make a product
example of products from biotechnology
foods, antibiotics, vitamins, enzymes
biotechnology selection
selecting for a naturally occurring microbe the produces a desired product
biotechnology mutation
mutagens cause mutations that might result in a microbe with desirable trait
biotechnology site directed mutagensis
a targeted and specific change in a gene
recombinant DNA (rDNA) technology
insertion or modification of genes to produce desired proteins
examples of rDNA
gene encoding for a protein for pest resistance
gene encoding segregative enzyme to clean up toxic waste
human growth hormone
amylase, cellulase and other enzymes prepare for clothing manufacture
vector
self replicating DNA molecule used to transport foregin DNA into a cell
vector can carry new DNA to
desired ell
a vector MUST
BE ABLE TO SELF REPLICATE
what can be used as a vector
plasmids and viruses
shuttle vectors
exist in several different species and can move cloned sequences among various organisms
clone
population of genetically identical cells arising from one cell; each carries the vector
restriction enzymes
cut specific sequences of DNA
restriction enzymes ____________ phosphodiester bonds between individual nucleotides at specific recognition sequences on both strands of DNA and they are able to ____ or ______ the DNA sequence the same way everytime
hydrolyze, cut, digest
restriction enzymes occur naturally in bacterial cells and are able to destroy
invading DNA
restriction enzymes create blunt ends or staggered cuts known as sticky ends. what one is better for cloning
sticky ends
polymerase chain reaction (PCR)
process of increasing samll quants of DNA for analysis
PCR is used diagnostic tests for
genetic diseases and detecting pathogens
3 steps of PCR
denaturation
priming
extension
denaturation
DNA is incubated at high temps which causes strands to separate by breaking the hydrogen bonds between each base pair
priming
DNA is incubated at a relatively low temp allowing primers to attach to the single stranded target DNA
extension
DNA is incubated at an intermediate temp at which the DNA polymerase rapidly replicates DNA
PCR occurs in what machine
thermocylcer
target DNA
piece of DNA being amplified in the PCR reaction
Reverse transcriptase PCR
uses mRNA as template and reverses the normal flow of genetic information utilizing the enzyme reverse transcriptase, mRNA is used to create cDNA
ways DNA can be incorporated into the cell
transformation, electroporation, protoplast fusion, gene gun, microinjection
transformation
cells take up DNA from the surrounding environment
electroporation
electrical current forms pores in plasma membrane
protoplast fusion
removing cell walls from 2 bacteria allows them to fuse
gene gun is used in
plant
microinjection
technique that uses a glass micropipette with a diameter much smaller than that of the cell and is able to puncture the plasma membrane so that DNA can be injected through it
genomic libraries are collection of
clones containing different DNA fragments
complementary DNA is made from mRNA by
reverse transcriptase
cDNA is used for obtaining eukaryotic genes because eukaryotic genes have
introns
synthetic DNA
builds genes using DNA synthesis machine
selecting a clone
blue white screening, colony hibridization
blue white screening uses a plasmid vector containing
amplicllin resistance gene and b-galactpsidease
blue white screening
bacteria is grown in media containing amplicllin and X gal only the bacteria that have picked up the plasmid will grow because they are now ampicillin reistance
white colonies
bacteria that have picked up the recombinant plasmid will not hydrolyze lactose
blue colones
bacteria with the intact lacZ gene will hydrolyze the x-gal
colony hybridization
common method of identifying cells that cary a specific gene
colony hybridization uses
DNA probes
DNA probes are
short segments of single stranded DNA complementary to the desired gene
gene produces are frequently the reason for
genetic modifcation
E. coli advantages
easily grown
genomics are known
E. coli disadvantages
produces endotoxins
saccharomyces cerevisaiae
easily grown and larger genome
express eukaryotic genes easily
likely to continuously secrete product
plant cells
express eukaryotic genes easily
easily grown
large scale
low cost
mammalian cells
express eukaryotic genes easily
can make products for medical use
harder to grow
2 ways to silence genes
siRNAs
RNAi
siRNA
bind to mRNA which is then destroyed by RNA induced silencing complex
RNAi
inserts DNA encoding siRNA into a plasmid and transferred into a cell`
viruses are obligatory intracellular parasites meaning
require living host cells to multiply
viruses contain
DNA/RNA
viruses have a _________ coat
protein
viruses have no
ribosomes and ATP-generating mechanisms
viruses are sensitive to
interferon
host range
spectrum of host cell a virus can infect
most viruses infect only specific types of cells in one
host
bacteriophages
viruses that infect bacteria
genus
-virus
family
-viridae
order
-ales
subspecies are designates by a
number
viral species
a group of viruses sharing the same genetic information and ecological niche (host)
viruses must be grown in
living cells
bacteriophages are grown in
bacteria
bacteriophages form
plaques
plaques are
clearings on lawn of bacteria on the surface of agar
each plaque corresponds to a single
virus
plaques can be expressed as
plaque forming units
growing animal viruses
in living animals
embryonate cells
cell cultures
embryonated eggs
virus injected into the eggs
viral growth is signaled by changes or death
what is the most convientiet way
cell cultures
cell cultures
tissues are treated with enzymes to separate cells
in cell cultures _______ cell lines are used
continuous
normal cells grow in __________ across the container
monolayer
transformed cells
do not grow in monolayer
viral identification
cytopathic effects
serological tests
nucleic acids
seroglical test example
western blotting
western blotting
reaction of the virus with antibodies
nucleic acids example
RFLPs
PCR
for a virus to multiply it must
invade host cell and take over hosts machinery
bacteriophage 2 cycles
lytic and lysogenic
lytic cycle causes
death of host
what bacteria go through lytic cycle
T-even
lytic cycle steps
attachment
phage attaches by the tail fibers to host cell
lytic cycle steps
penetration
phage lysozyme opens the cell wall; tail sheath contracts to force the tail core and DNA into cell
lytic cycle steps
biosynthesis
production of phage DNA and proteins
lytic cycle steps
maturation
assembly of phage particles
lytic cycle steps
release
phage lysozyme breaks cell wall
lysogenic cycle
phage DNA is incorporated in the host DNA
lytic cycle uses what transduction
general
lysogenic cycle uses what transduction
specialized
what cycle does bacteriophage lambda use
lysogenic
lysogeny
phage remains latent
during lysogenic cycle phage DNA incorporates into
host cell DNA
prophage
inserted phage DNA
during lysogenic cycle when the host cell replicates its chromosome
it also replicates prophage DNA
lysogenic cycle results in
phage conversion
phage conversion
host cell exhibits new properties
in temperate bacteriophages the phage DNA forms a ______ which can either replicate and be transcribed to produce phage components in the lytic cycle or proceed to __________ ______
circle, lysogenic cycle
multiplication of animal viruses steps
attachment, biosynthesis, maturation
attachment of animal viruses
viruses attach to the cell membrane
entry of animal viruses by
receptor mediated endocytosis or fusion
biosynthesis of animal virsues
production of nucleic acids and proteins
maturation of animal viruses
nucleic acid and capsid proteins assemble
animal viruses vary based on
nucleic acids, naked or enveloped
naked viruses
without an envelope
bind to surface of host cell and inject their DNA
membrane fusion
infect their host by binding to receptors on host cell
envelope of the virus merges with the host membrane and then capsid enters the cell, the capsid opens and released the viral genetic material into cytoplasm
phagocytosis
host cell envoploes the viral envelope and absorbs the virus and once it has entered the host the outer and inner part of the envelope merge together and the capsid is released into the cytoplasm
biosynthesis of DNA viruses, they replicate their DNA in ____________ of the host using ______ ____________
nucleus, viral enzymes
adenovirus strands
double
adenovirus envelope
no
adenovirus diease
respiratory infection
poxviridae strands
double
poxviridae envelope
yes
poxviridae diease
skin lesions, smallpox
herpesvirdae strands
double
herpesvirdae envelope
yes
herpesvirdae diease
cold sores, chickenpox, mononucleosis, kaposis sarcoma
papoviridae strands
double
papoviridae enveloped
no
papoviridae diease
warts and cancer
hepadenaviridae strands
double
hepadenaviridae enveloped
yes
hepadenaviridae diease
Hep B
biosynthesis of RNA virsues
virus multiples in the host cells cytoplasm using RNA dependent RNA polymerase
biosynthesis of RNA virsues
ssRNA +(sense) strand
viral RNA serves as mRNA for protein
biosynthesis of RNA virsues
ssRNA- (antisense) strand
viral RNA is transcribed to a + strand to serve as mRNA for protein synthesis
picornaviridae strand
single
picornaviridae envolpoed
non
picornaviridae disease
enterovirus: poliovirus and coxsackievirus
rhinovirus: common cold
togaviridae strand
single
togaviridae enveloped
yes
togaviridae disease
alphavirus
rubivirus: rubella
rhabdovirdae strand
single
rhabdovirdae diease
lyssgavirus: rabies
reoviridae strand
double
reoviridae envoloped
no
reoviridae diease
reovirus, rotavirus
biosynthesis of RNA to produce DNA
use reverse transcriptase to produce DNA from viral genome
oncogenesis
transform normal cells into cancerous cells
oncogenic virus
become integrated into host cells DNA and induce tumors
transformed cell
harbors a tumor specific transplantation antigen on surface and a T antigen in the nucelus
why would viral cancer go without detection
most of the particles of certain viruses may infect cells without inducing cancer
may develop after long viral infection
cancers caused by viruses are not contagious
2 types of viral cancers
sarcoma and adenocarcinoma
sarcoma
cancer of connective tissue
adenocarcinoma
cancer of glandular epithelial tissue
DNA oncogenic viruses non cancer
adenovirus, herpesvirdae, poxvirdiae
herpesviridae
epstein barr
DNA oncogenic viruses cancer
papovaviridae, hepadnaviridae
papovaviridae leads to
cervical and anal cancer
hepadnaviridae leads to
hep b which leads to liver cancer
RNA oncogenic viruses
retroviridae
retroviridae
viral RNA is transcribed to DNA (using reverse transcriptase) which can integrate into host DNA
retroviridae can lead to HTLV1 and 2 and lead to adult T cell
leukemia and lymphoma
provirus
viral DNA that is integrated into the host cells DNA
oncolytic viruses
1900-1920, able to selectively infect and kill tumor cells or induce an immune response genetically modified to removed virulence genes and add CSF genes that promote WBS
oncolytic viruses can treat
melenoma
latent virus
remains asymptomatic in host cell for long periods
latent virus may reactivate due to change in
immunity
persistent virus
occurs gradually over long periods of time
examples of latent
cold sores, leukemia, shingles
examples of persistent
cervical and liver cancer, HIV/AIDS
plant viruses enter how
through wounds caused by insects
plant viruses normally are protected from disease by
cell wall
viroids
short pieces of naked DNA
virusoids
viriods enclosed in protein coat
prions are
proteinaceous infectious particles
prions are inherited via
ingestion, transplant, surgical instruments
example of transmissible spongiform encephalopathies
mad cow diease
sheep scrapie
creutzfeldt-jakob diease
GSS diease
fatal familial insomnia
PrP c
normal cellular prion protein on cell surface
PrP sc
scrapie protein, accumulates in brain cell forming plaques
normally PcP folds into a functional form with several
a helices
prion protein is capable of forming
B pleated sheets
infectious prions convert normal prions into more infectious ones by folding into
beta pleated sheet
infectious prions group into multimers which are very stable and resistance to
protease
