Bact Gen - Chapter 1 Flashcards
Bacteria are ___ organisms.
relatively simple
Many types of bacteria are hard/easy to manipulate in the lab.
easy
____ have remained largely unchanged throughout evolution.
central cellular functuions
____ originally identified in bacteria are highly similar in
all organisms – cancer research
DNA repair responses
Bacteria are essential for ecology of the Earth by:
Nitrogen -fixation, degradation of recalcitrant natural polymers, detoxification of poisonous compounds, production of
greenhouse gases
Bacteria capable of surviving in extreme environments. Ex. high temperature, pressure, and osmolarity
extremophiles
Perform
functions which allow other
organisms to survive
symbiotic bacteria
Many bacteria are _____
of humans, plants, and
animals
pathogens
Of the 10^14 cells in a human, __% are human!
10
___ can be studied to learn about antibiotics, medicines, foods,
chemicals, & molecular biology
tools.
bacterial genetics
All organisms on Earth belong to one of three divisions:
Eubacteria, Archae, or Eukaryotes
- Familiar - E. coli, Staphylococcus aureus
- Most are single celled and rod shaped or spherical
- Some are multicellular with complicated developmental cycles
- Distinguished by biochemical criteria: ribosomal RNA sequence
Eubacteria
- Single celled organisms- differ biochemically from Eubacteria
- Majority are extremophiles- high temperature, pressure, osmolarity
- May be more closely related to eukaryotes than eubacteria
Archae
- Diverse organisms- plants, animals, and fungi
- Can be single or multicellular
- Very similar at the biochemical level (macromolecular synthesis)
Eukaryotes
the study/manipulation of DNA to characterize cellular
and organismal functions
genetics
mutants that are altered in the function being studied
are isolated. The changes in the DNA (mutations) are localized in the
chromosome by genetic crosses. Functions of the genes affected can
sometimes be deduced by the phenotype displayed.
Classical genetics
Individuals that differ from the normal, or wildtype,
members of the species by an observable attribute, or phenotype.
mutants
a gene is first cloned from an organism
and altered in a test tube before reintroducing it back
into cells to determine the effect of the alteration.
reverse genetics
____ is made possible by the development of modern molecular
genetic techniques
reverse genetics
Both ____ and ____ have strengths and
weaknesses and the two approaches often complement
each other
classical and reverse genetics
Bacteria are _________, one copy or allele of each gene
haploid
Most higher organisms are ____ (two copies of each gene).
diploid
With haploid organisms the effects of the mutation are ____.
immediate
all progeny are genetically identical to
parents (________)
clones
ability to isolate clones
colony formation
large numbers of bacteria can be
diluted to manageable numbers by ____.
serial dilution
Bacteria have short ____.
generation times
A major advantage that allows us to identify rare
individual mutants among billions of normal bacteria
selection
Some selective conditions include:
nutrients/nutrient limitation
temperature
antibiotics
Bacteria can be stored in a ____ state, which prevents the need to continuously propagate them.
dormant
Methods of storing bacteria:
dormant spores
frozen in glycerol
dried down
Storing stocks of bacteria can be useful for accumulating a variety of different ____ for genetic experiments.
clones
Includes transformation, conjugation, and transduction.
genetic exchange
In the early 1950’s who discovered that DNA was a double helical structure by X-ray diffraction?
Rosalind Franklin and Maurice Wilkins
in 1953 ___ proposed the now famous model for the structure of DNA.
Francis Crick and James Watson
DNA is a ____ handed helix.
right
DNA has a ____ backbone.
sugar-phosphate
Helices are connected by ____ between nucleobases (purines and pyrimidines)
hydrogen bonding
Spacing between helices result in ____.
major and minor grooves
1 helical turn is how many base pairs?
10 (3.4 nm in length)
Two ring bases, adenine and guanine.
purine
One ring bases, thymine cytosine and uracil.
pyrimidine
In DNA, all 4 bases are attached to the 5-carbon sugar ____.
deoxyribose
Deoxyribose lacks an oxygen at the ____ carbon.
2nd
base + sugar + one or more phosphates
deoxynucleotides (nucleotides)
base + sugar but no phosphate
deoxynucleosides
Collectively the four deoxynucleoside triphosphates are ____.
dNTPs
Deoxynucleotides are linked together by ____.
phosphodiester bonds
The phosphate attached to the ____ of one nucleotide is attached to the ____ of the next nucleotide.
5’ carbon of the deoxyribose sugar
3’ carbon of the deoxyribose sugar
DNA has ____ construction.
antiparallel
5’ end holds a free ____.
phosphate
3’ end holds a free ____.
hydroxyl group
____ says: no matter the source of DNA, the concentration of A = T and C = G.
Chargaff’s Rule
____ and ____ pair with 2 hydrogen bonds.
adenine and thymine
____ and ____ pair with 3 hydrogen bonds.
cytosine and guanine
DNA replication involves ____ using sequence of the opposite strand as a template.
polymerizing deoxynucleotides
Deoxynucleotides are ____ and must be synthesized by a series of enzymatic steps prior to being incorporated into DNA
precursors or DNA synthesis
removes oxygen
reductase
adds phosphates
kinase
removes phosphates
phosphatase
links together two molecules
synthetase
____ reduces ribose sugar to deoxyribose by changing the OH at the 2’ position to H.
ribonucleotide reductase
A kinase adds a phosphate to the deoxynucleotide diphosphate the make the ____.
dNTP precursor
____ removes 2 phosphates from dUTP to make dUMP.
phosphatase
dUMP is converted to dTMP by thymidylate synetase using ____ to donate a ____.
tetrahydrofolate
methyl group
DNA polymerization requires enzymes known as ____, that join deoxynucleotides together to make long chains.
DNA polymerases
____ attaches the 1st phosphate (alpha) of one dNTP to the 3’ carbon of the sugar of the dNTP previously added to the growing chain.
DNA polymerase
DNA polymerase releases the last 2 phosphates (beta and gamma) to produce _____.
the energy for the reaction
Two types of DNA polymerase
DNA polymerase III
DNA polymerase I
degrade DNA strands by breaking phosphodiester bonds
nucleases
initiate breaks in the middle of the DNA strand
endonucleases
Can remove nucleotides only from the ends of DNA
exonucleases
degrade DNA only from the 3’ end in the 3’-to-5’ direction
3’ endonucleases
degrade DNA only from the 5’ end in the 5’-to-3’ direction
5’ endonucleases
form phosphodiester bonds between the ends of two chains of DNA
ligases
make RNA primers to initiate synthesis of new strands of DNA
primases
DNA polymerases cannot initiate the synthesis of new strands of DNA, they can only attach ____ to ____.
dNTP’s
a free OH group
travel with DNA polymerase as part of the DNA replication complex (with the polymerase, they make up the ____.)
accessory proteins
DNA polymerase III holoenzyme
keep the DNA polymerase from falling off of the DNA
Beta clamp
Other proteins form a ____ to allow the polymerase to release when required (example, during lagging strand synthesis)
clamp loader
Additional proteins traveling with the DNA polymerase are ____ and serve editing functions to correct any mistakes made by the polymerase
exonucleases
The ___ experiment helps show semiconservative replication in DNA.
Meselson-Stahl Experiment
Replication begins at __ and moves in ___.
one point
both directions
Before replication can occur, the template strands must be ___.
separated
The structure where the strands are separated and new DNA is being synthesized.
replication fork
DNA stands are separted by proteins called ___.
DNA helicases
a doughnut shaped protein complex which surrounds the DNA ahead of the replication fork.
DnaB helicase
To keep the stands from coming back together _____ bind and prevent the premature formation of double stranded DNA.
single stranded binding proteins (SSB)
Antiparallel strands require different strategies since DNA polymerase III can only move in the _____ direction.
3’-to-5’
On one strand DNA Pol III initiated DNA
synthesis from an ___ and proceeds
in the 3′-to-5′ direction
RNA primer
This newly synthesized continuous strand is referred to as the ____.
leading strand
DNA Pol III polymerizes short pieces called
___ in the opposite direction to that in which the fork is moving
Okasaki fragments
___ is required for starting each Okasaki fragment
an RNA primer
___ produces the required primers at 3′-GTC-5′ sequences
DnaG primase
Pol III continues on the ___ until it encounters the previously synthesized piece
lagging strand
RNA primers are removed by ___ and ___.
Rnase H and DNA polymerase I
DNA polymerase I removes the RNA primer using ____ and replaces it with DNA using upstream Okazaki fragments as a primer
5’ exonuclease activity
Okazaki fragments are joined by ___
DNA ligase
A break or nick in the DNA exists between Okazaki fragment and RNA primer
“nick translation”
The trombone model of replication helps explain the replication of the ___ strand.
lagging
The lagging strand loops out as the ___ is synthesized
Okazaki fragment
The loop is relaxed as the ___ releases the lagging-strand polymerase which hops ahead to the next primer
sliding clamp
When replicating the lagging strand, DNA polymerase is released when it reaches a ____. By this time the next primer has been added and the polymerase hops ahead again.
nick
DNA must be faithfully replicated to prevent ___ (mutations).
changes in the DNA sequence
Sometimes the wrong base is inserted into the growing chain of DNA. Such mutations are called ____ (created distortion in the helix)
mismatch mutations
2 methods for correcting replication errors:
Editing functions and Methyl directed mismatch repair
___ check the newly replicated DNA for mistakes and removes the incorrectly paired bases.
Editing proteins
If an incorrect base is inserted the editing function ____ until the incorrect nucleotide is removed.
stops replication
Since the new DNA strand grows in the 5’-to-3’ direction, ____ is required to remove incorrectly inserted bases.
3’ exonuclease activity
DNA pol I possess 3’ exonuclease activity but DNA pol III requires accessory proteins (encoded by the ___ gene; also called ___)
dnaQ
mutD
mutD mutants, which have a mutation in the mutD gene have much ___ rates of ____ than do wild type cells.
higher
spontaneous mutations
____ have 3’ and 5’ exonuclease activity
DNA pol I
A way for the organism to tell which strand is correct and which is incorrect
methyl directed mismatch repair
E. coli uses the ___ of the DNA strands to distinguish between the new and old DNA.
methylation state
The enzyme ___ adds a methyl group to the A’s of the GATC/CTAG only after incorporation into the new DNA strand
deoxyadenosine methylase (Dam methylase)
DNA in the new strand is ___ and DNA at this site is said to be ___ (only methylated on one strand)
temporarily unmethylated
hemimethylated
The new strand is identified by the lack of ___.
methylation
Mutants that lack either functions or mismatch repair have unacceptably _________.
high mistake rates
Editing and mismatch repair are essential for ___.
maintaining replication fidelity and stability of the genome.
time in which a cell is born, grows larger, and divides into two progeny cells
cell division cycle
the process by which the larger cell splits into two new cells
cell division
time from the point when a cell is born until it divides
division time or generation time
the original cell before division
mother cell
the two progeny cells after division
daughter cells
the DNA molecule that carries most of the bacterium’s normal genes
chromosome
generally circular in contrast to eukaryotic chromosomes which are linear with free ends
bacterial chromosomes
bacterial chromosomes are much less structured than eukaryotic DNA which is wrapped around proteins called ___
histones
Replication begins at a unique site called the ___.
oriC (origin of chromosomal replication)
Replication is ___ with two replication forks proceeding in opposite directions away from the oriC
bi-directional
Sometimes the wrong base is inserted into the growing chain of DNA. Such mutations are called ____ (created distortion in the helix)
mismatch mutations
2 methods for correcting replication errors:
Editing functions and Methyl directed mismatch repair
___ check the newly replicated DNA for mistakes and removes the incorrectly paired bases.
Editing proteins
If an incorrect base is inserted the editing function ____ until the incorrect nucleotide is removed.
stops replication
Since the new DNA strand grows in the 5’-to-3’ direction, ____ is required to remove incorrectly inserted bases.
3’ exonuclease activity
DNA pol I possess 3’ exonuclease activity but DNA pol III requires accessory proteins (encoded by the ___ gene; also called ___)
dnaQ
mutD
mutD mutants, which have a mutation in the mutD gene have much ___ rates of ____ than do wild type cells.
higher
spontaneous mutations
____ have 3’ and 5’ exonuclease activity
DNA pol I
A way for the organism to tell which strand is correct and which is incorrect
methyl directed mismatch repair
E. coli uses the ___ of the DNA strands to distinguish between the new and old DNA.
methylation state
The enzyme ___ adds a methyl group to the A’s of the GATC/CTAG only after incorporation into the new DNA strand
deoxyadenosine methylase (Dam methylase)
DNA in the new strand is ___ and DNA at this site is said to be ___ (only methylated on one strand)
temporarily unmethylated
hemimethylated
The new strand is identified by the lack of ___.
methylation
Mutants that lack either functions or mismatch repair have unacceptably _________.
high mistake rates
Editing and mismatch repair are essential for ___.
maintaining replication fidelity and stability of the genome.
time in which a cell is born, grows larger, and divides into two progeny cells
cell division cycle
the process by which the larger cell splits into two new cells
cell division
time from the point when a cell is born until it divides
division time or generation time
the original cell before division
mother cell
the two progeny cells after division
daughter cells
the DNA molecule that carries most of the bacterium’s normal genes
chromosome
generally circular in contrast to eukaryotic chromosomes which are linear with free ends
bacterial chromosomes
bacterial chromosomes are much less structured than eukaryotic DNA which is wrapped around proteins called ___
histones
Replication begins at a unique site called the ___.
oriC (origin of chromosomal replication)
Replication is ___ with two replication forks proceeding in opposite directions away from the oriC
bi-directional
Sequences of DNA where proteins act to initiate replication are called ___ as opposed to the actual proteins that act on these sites which are called ____.
trans-acting proteins
