Chapter 8 Flashcards
what is the central dogma
the overall flow of genetic information within the cell
3 steps of the overall flow of information (central dogma)
DNA –> RNA –> Protein
mutations can be caused by
base substitutions or frameshift mutations
genetics
the study of genes, how they carry information, how information is expressed, and ow genes are replicated
chromosome
structures containing DNA that physically carry hereditary information; the chromosome contain genes
Genes
segments of DNA that encode functional products, usually proteins
Genome
all the genetic information in a cell
genetic code
set of rules that determines how a nucleotide sequence is converted to an amino acid sequence of a protein
genotype
the genetic make up of an organism
genotype represents _______ expression
potential
phenotype represents ________ expression
actual
bacteria usually have a _______ circular chromosome made of ____ and associated _________
single, DNA, protein
the chromosome is _______ and ________ and attached at one or several points to the _________ ________
looped, folded, plasma membrane
how much volume does the chromosome take up
10%
why does a chromosome only take up 10% volume
decays the DNA is supercoiled
the entire genome does not consist of __________
back-to-back genes
short tandem repeats
repeating sequences of noncoding DNA
short tandem repeats can be used in
DNA fingerprinting
Genomics
the sequencing and molecular characterization of genomes
computers are used to search for opening reading frames
regions of DNA likely to encode a protein
vertical gene transfer
flow of genetic information from one generation to the next
DNA is _________ into mRNA and then __________ into protein
transcribed, translated
DNA is the blueprint for a cells _______
proteins
DNA is obtained
from another cell in the same generation
or
from a parent cell during cell division
DNA can be expressed within a cell or transferred to another cell through __________ and ___________
recombination and replication
expression
genetic information is used within a cell to produce the proteins needed for the cell to function
recombination
genetic information can be transferred horizontally between cells of the same generation
replication
genetic information can be transferred vertically to the next generation of cells
DNA backbone consists of
deoxyribose-phosphate
DNA strands are
antiparallel
in DNA order of nitrogen containing bases forms the
genetic instructions of the organism
DNA replication one strand serves as a template for _________ of a second strand
production
in DNA replication one parental double stranded DNA molecule is converted to
two identical offspring moleules
in DNA replication _______ and ________ relax the strand
topoisomerase, gyrase
in DNA replication _________ separated the strands
helicase
in DNA replication a __________ ____ is created
replication fork
in DNA replication DNA _________ adds _________ to the growing DNA strand
polymerase, nucleotides
DNA replication works in the __ to __ direction
5’, 3’
DNA replication adding nucleotides is initiated by
RNA primer
DNA replication leading strand is synthesized
continuously
DNA replication lagging strand is synthesized discontinuously creating a
Okazaki fragment
DNA replication DNA polymerase removes ___________; Okazaki fragments are joined by the DNA polymerase and _________
RNA primers, DNa ligase
Events at the DNA replication fork step 1:
enzyme unwind the parental _______ _____
double helix
Events at the DNA replication fork step 2:
proteins ______ the unwound parental DNA
stabilize
Events at the DNA replication fork step 3:
the leading strand is synthesized _________ by ___ ________
continuously, DNA polymerase
Events at the DNA replication fork step 4:
the lagging strand is synthesized ___________. ______, an RNA polymerase, synthesizes a short ____ ________ which is then extended by ____ ________
discontinuously, Primase, RNA primer, DNA polymerase
Events at the DNA replication fork step 5:
DNA polymerase digests ____ _______ and replaces it with ___
RNA primer, DNA
Events at the DNA replication fork step 6:
____ _______ joins the discontinuous fragments of the lagoon strand
DNA ligase
most bacterial DNA replication is
bidirectional
replication is highly accurate due to the proofreading capability of
DNA polymerase
DNA replication is the process of
copying DNA
rRNA
integral part of ribosomes
tRNA
transports amino acids during protein synthesis
mRNA
carriers coded information from DNA to ribosomes
Prokaryote Transcription begins when
RNA polymerase binds to the promoter sequence on DNA
prokaryote transcription proceeds in the ______ direction
5’–>3’
prokaryotes are both DNA strands or just one transcribed
only one
prokaryotes transcription stops when it reaches the
terminator sequence
transcription step 1:
RNA polymerase binds to the _____, and DNA unwinds at the beginning of the ______
promoter, gene
transcription step 2:
RNA is synthesized by complementary base paring of free ________ with the nucleotide bases on the template strand of DNA
nucelotides
transcription step 3:
the site of synthesis moves along ____; DNA that has been transcribed ______
DNA, rewinds
transcription step 4:
transcription reaches the ________
terminator
transcription step 5:
RNA and RNA polymerase are _____ and the DNA helix ______
released, reforms
3 phases of transcription
Initiation, elongation, termination
initiation step 1:
RNA polymerase binds to the DNA and recognizes a site called a ________ at the end of ___
promoter, 3’
initiation step 2:
when RNA polymerase finds a promoter it breaks the ________ _____ holding the DNA strands together at the site of the _________
hydrogen bonds, promoter
RNA polymerase does not bind to all promoters with
equal affinity
the difference in promoter strength is one way that cells can control
gene expression
the more strongly RNA polymerase binds to a particular promoter the more likely the gene is to be
transcribed
increase levels of transcription leads to increase levels of _________ leads to increased concentrations of that ___________
translation, polypeptide
elongation step 1:
one strand of DNA serves as a template strand. The RNA transcript is copied from this strand of the gene and therfor has an _____________ complementary to this strand
RNA sequence
elongation step 2:
RNA polymerase moves along the ___, opening up a bubble in the DNA
DNA
elongation step 3:
as it moves RNA polymerase adds bases to the __ end of the growing RNA transcript
3’
elongation step 4:
this continues until RNA polymerase reaches a site on the DNA called the ________
terminator
termination step 1:
at this side RNA polymerase and the newly synthesized RNA transcript are _______ from the DNA
released
termination can occur in 2 ways
self terminator and enzyme dependent termination
self termination:
the RNA sequence transcribed at the terminator causes the RNA to ________ ____ with it self forming a ____ ____ ______ which essentially pulls the RNA polymerase off the DNA
hydrogen bond, stem loop structure
enzyme dependent termination:
a termination _____ binds to the terminator and pushes RNA polymerase off the DNA
protein
codons
groups of three mRNA nucelotides that code for a particular amino acid
61 sense codons encode the
20 amino acids
degeneracy
each amino acids is coded by several codons
AUG stands for
start
UAA stands for
stop
UAG stands for
stop
UGA stands for
stop
_______ molecules transport the required amino acid to the ribosomes
tRNA
amino acids are joined by
peptide bonds
translation step 1:
on the assembled ribosomes, a tRNA carrying the first ______ ____ is paired with the start codon on the ______. the place where this first tRNA sits is called the ______.
amino acid, mRNA, P site
translation step 2:
the second codon of the mRNA pairs with a tRNA carrying the second amino acid at the ______. the first amino acid joins to the second by a ______ bond, this attaches the polypeptide to the tRNA in the _______
A site, peptide, P site
translation step 3:
the ribosome moves along the mRNA until the second tRNA is in the _______. the next codon to be translated is brought to the A site, the first tRNA now occupies the _______
P site, E site
translation step 4:
the second amino acid joins to the third by another peptide bond, and the first tRNA is ________ from the _____
released, E site
translation step 5:
the ribosome continues to move along the _____ and new amino acids are added to the polypeptide
mRNA
translation step 6:
when the ribosome reaches a stop codon the ________ is ________
polypeptide, released
translation step 7: the last tRNA is released and the ribosome comes apart. The released polypeptide forms a new
protein
in eukaryotes where does transcription occur
nucleus
exons (transcription in eukaryotes)
regions of the DNA that code for proteins
introns (transcription in eukaryotes)
are regions of DNA that do not code for proteins
small nuclear ribonucleoproteins AKA snRNPs (transcription in eukaryotes)
removed introns and splice exons together
repression inhibits ____ ______ and decreases _______ ________
gene expression, enzyme synthesis
repression is always on until repressor protein binds and then is able to block
transcription
repression is mediated by _______, proteins that block transcription
repressors
default position of a repressible gene is
on
induction
turns on gene expression
induction is initiated by an
inducer
default position of an inducible gene is
off
when a inducer binds to a repressor protein it
inactivates it
repression and induction are 2 genetic __ _________ control mechanisms that regulate the transcription of mRNA, and this regulates the synthesis of enzymes
pre transcription
promoter
segment of DNA where DNA polymerase imitates transcription of structural genes
operator
segment of DNA that controls transcription of structural genes
operon
set of operator and promoter sites and the structural genes they control
inducible operon
structural genes are not transcribed unless an inducer is present
example of inducible operon:
in the absences of lactose, the repressor binds to the operator preventing
transcription
example of inducible operon:
in the presence of lactose, metabolite of lactose (allolactose) binds to the repressor; the repressor cannot bind to the operator and
transcription occurs
operon consists of ______ (P) site and _______ (operator) site
promoter, operator
operon is regulated by the product of the
regulatory gene (I)
in repressible operons structural genes are transcribed until they are
turned off
catabolite repression inhibits cells from using _____ sources other than glucose
carbon
cAMP is
cyclic AMP
cAMP builds up in the cell when glucose is
not avaliable
cAMP binds to the _________ _______ ______ (CAP) that in turn binds the lac promoter, imitating transcription and allowing the cell to use ________
catabolic activator protein (CAP)
methylating nucleotides turns genes
off
can methylated genes be passed to offspring cells
yes
is methylated nucleotides permeant
no, can be turned back on
how can you methylate a nucelotide
add a methyl group, CH3
riboswitch
part of an mRNA molecule that binds to a substrate and changes the mRNA structure
post transcriptional control stops protein synthesis after
transcription has occured
both eukaryotes and prokaryotes use riboswitches to control expression of certain
proteins
microRNAs (miRNAs)
base pair with mRNA to make it double stranded
miRNAs affect protein _____ and play many regulatory roles
expression
mutation
permanent change in the base sequence of DNA
mutations may be
neutral, beneficial or harmful
mutagens
agents that cause mutations
spontaneous mutations
occur in the absence of a mutagen
base substation (point mutation)
change in one base in DNA
frameshift mutation
insertion or deletion of one of more nucleotide pairs
frameshift is called frameshift because
shifts the reading frame so the correct nucleotides do not line up
missence mutation
base substitutions result in change in amino acid
nonsense mutation
base substitution results in nonsense (stop) codon
silent base substitution affects the phenotype or genotype?
genotype
frameshift leads to non functioning
protein
two types of radiation
ionizing and nonionizing
ionizing consists of what rays
gamma and x
ionizing with X and gamma rays cause cells to lose electrons leading to
free radicals
non ionizing radiation is caused by
UV light
non ionizing radiation causes thymine dimers, what are those?
when 2 thymines next to each other get covalently bonded to one another
thymine dimers prevent
replication and transcription
ionizing radiation causes the formation of ions that can _________ nucleotides and break the deoxyribose phosphate backbone
oxidize
2 types that can fix thymine dimers
photolyases and nucleotide excision repair
photolyases separate the thymine dimers by using ________ _____
visible light
nucleotide excision repair
enzymes cut out incorrect bases and fill in correct bases
excision repair enzymes is called ______ ____, it can occur with or without light
dark repair
mismatch repair enzymes scan newly synthesized DNA for mismatches and if they find one they repair it. The lack of ___________ to identify newly synthesized DNA and removed the new mutation before it can become _______
methylation, methylated
in mismatch repair enzymes if the mutation is already methylated can the repair enzyme fix it or not?
no it cannot fix it once it is methylated
positive (direct) selection
detects mutant cells because they grow or appear different than unmated cells
negative (indirect) selection
detects mutant cells that cannot grow or preform a certain function
auxtotroph
mutant that has a nutritional requirement absent in the parent
what is the technique to identify auxtotroph
use of replica plating
replica plating:
1. sterile velvet is pressed on the grown colonies on the master plate
2. cells from each colony are transferred from the velvet to the new plates (containing histidine, lacking histamine)
3. plates are incubated
4. a colony that grows on the medium _____ __________ but could not grow on the medium _____ ________ is auxotrophic
with histidine, without histidine
Ames test exposed mutant bacteria to mutagenic substances to measure
the rate of reversal of the mutation
Ames test indicates the degree to which a substance is
mutagenic
genetic recombination
exchange of genes between two DNA molecules; creates diversity
crossing over
two chromosomes break and rejoin, resulting in the insertion of foreign DNA into the chromosome
crossing over:
1. DNA from one cell aligns with DNA in the recipient cell
2. DNA from the donor aligns with complementary base pair in the recipient chromosome
3. RecA protein catalyzes the joining of the two strands
4. the results is that the recipients chromosome contains new DNA. Complementary base pairs between the two strands will be resolved by ___ _________ and ________. The donor DNA will be _________. The recipient may now have one or more new genes
DNA polymerase, ligase, destroyed
vertical gene transfer
transfer of gene from an organism to its offspring
horizontal gene transfer
transfer of gene between cells of the same generation
3 types of horizontal
transformation
transduction
conjucation
plasmids and transposons are mobile genetic elements
move from one chromosome to another or from one cell to another
plasmids
self replicating circular pieces of DNA
plasmids take up __-__% of a bacterial chromosome
1,5
plasmids often code for proteins that enhance the
pathogenicity of a bacterium
plasmids can confer ability to resist
antibiotics
3 types of plasmid
conjugative plasmid
dissimilation plasmids
resistance factors (R factor)
conjugative plasmid
carriers genes for sex pili and transfer of the plasmid
dissimilation plasmid
encode enzymes for the catabolism of unusual componds
resistance factors (R factor)
encode antibiotic resistance
2 things that make up R factor
RTF and R-determinant
transposons
segments of DNA that can move from one region of DNA to another
transposons contain insertion sequences (IS) that code for ___________ that cut and reseals DNA
transposase
complex transposons carry other _____
genes
simple transposons
only contain the essential elements needed for transportation
inverted repeat
region of DNA in which the sequence of nucleotides is identical to an inverted sequence in the complementary strand
transposons move through 1 of 2 mechanisms
1. cut and paste:
2. replicative:
cut and paste: the entire transposon moves to another location
Replicative: transposons is copied to a new location
complex transposons consist of 2 simple transposons with another sequence of DNA between them, other DNA is often a gene that gives some selective
advantage to the organism for containing the transposons
transformation in bacteria
gene transferred from one bacterium to another as “naked” DNA
transformation bacteria are capable of
taking up fragments of DNA from their surroundings and integrating the fragments into their own chromosome by recombination
competent
cells capable of taking up DNA from their environment
what is a competent bacteria
streptococcus pneumoniae
conjugation
plasmids transferred from one bacterium to another
conjugation requires
cell to cell contact via sex pili
donor cells carry the plasmid (F factor) and are called
F+ cells
Her (high frequency of recombination) cells contain the F factor on the
chromosome
cells lacking the F factor are called
F- cells
F- cells serve as
DNA recipients
start of conjugation F factor: conjugation pills extends from __ cell to the __ cell, and pulls the cells together. The cells come together and stabilize. Transfer of DNA begins. Single stranded copy of the F factor is transferred from F+ to F-. each cell synthesizes a __________ strand of plasmid resulting in a complete copy of the plasmid in each cell. After conjugation, both cells contain _____________
F+, F-, complementary, a copy of the F factor
start of conjugation Hfr: cells come together and stabilize. Transfer of DNA begins. DNA transfer begins in the middle of the F factor with in 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 receive a complete copy of the F factor, it remains F-. The DNA from the donor can recombine with recipient chromosome, giving the recipient new chromosomal genes
conjugation can be used to map the location of
gene on a chromosome
DNA is transferred from a donor cell to a recipient via a
bacteriophage
generalized transduction
random bacterial DNA is packaged inside a phage and transferred to a recipient cell
specialized transduction
specific bacterial gene are packaged inside a phage and transferred to a recipient cell
mutations are recombination create
diversity
natural selection acts on populations of organisms to ensure the
survival of organisms within a particular environment
