Unit 3.1: Bacterial Genetics Flashcards
briefly describe the chain of events of central dogma
DNA > mRNA > Protein > Function
briefly describe how mutations change the chain of events of central dogma
mutated DNA > altered mRNA > altered protein > altered function
name the two types of mutations to DNA
- base substitution
- frameshift mutation
briefly describe a base substitution mutation
a single DNA pair is altered
briefly describe a frameshift mutation
DNA base pairs are added or removed from the sequence (causing a shift in the sequence reading)
briefly describe an inducible operon
- with repressor bound to the DNA
- genes that are in the “off” mode, turned “on” by the environmental inducer
briefly describe a repressible operon
- without the repressor bound to the DNA
- genes that are in the “on” mode, turned “off” by the environmental corepressor and repressor
give example results of the alteration of bacterial genes or their expression
(disease) toxic proteins cause damage
(prevents treatment) biofilms, antibiotic resistance
(human benefit) biotechology such as making insulin
describe genetics
the study of genes, how they carry information, how information is expressed, and how genes are replicated
describe chromosomes
structure that physically carries hereditary information as DNA, they contain genes
describe genes
segments of DNA that encode functional products, usually proteins
describe genome
all the genetic information in a cell
what is the genetic code
a set of rules that determines how a nucleotide sequence is converted into an amino acid sequence of a protein
describe genotype
the genetic makeup of an organism
describe phynotype
expression of the genes
briefly describe the structure of chromosomes found in bacteria
bacteria usually have a single circular chromosome made of DNA and associated proteins
name or phrase for:
the repeating sequences of noncoding DNA
Short Tandem Repeats
aka STRs
the name or phrase for:
the flow of genetic information from one generation to the next
vertical gene transfer
DNA is the blueprint for what?
a cell’s proteins, including enzymes
from what sources is DNA obtained?
either from
* another cell of the same generation
* a parent cell during cell division
describe gene expression
genetic information is used within a cell to produce the proteins needed for the cell to function
describe gene recombination
genetic information transferred between cells of the same generation
(aka horizontally)
describe gene replication
genetic information transferred to the next generation of cells
(aka vertically)
DNA can be (blank) within a cell,
or transferred to another cell through (blank) and (blank)
expressed within a cellor transferred through recombination and replication
What is the form/structure of DNA?
double helix
Of what does the “backbone” of DNA consist?
deoxyribose-phosphate
The two strands of nucleotides of DNA are held together by what (between the A-T, C-G)?
hydrogen bonds
Describe the orientation of the two strands of DNA to each other.
antiparallel,
the sugar-phosphate backbone of one strand is upside down relative to the other strand
During DNA replication, each strand serves as a template for what?
for the production of a second strand
Name the two proteins that relax the strands of DNA for replication.
- topoisomerase
- gyrase
Name the protein that separates the strands.
Helicase
Describe the functions of DNA polymerase.
DNA polymerase adds nucleotides to the growing DNA strand
* removes RNA primers,
* joins Okazaki fragments (DNA ligase participates)
Other things to know about DNA polymerase (in addition to its functions).
DNA polymerase adds nucleotides to the growing DNA strand
– In the 5‘ 3’ direction
– Initiated by an RNA primer
– Leading strand is synthesized continuously
– Lagging strand is synthesized discontinuously, creating Okazaki fragments
Describe the energy needs of DNA replication.
– Energy for replication is supplied by nucleotides
– Hydrolysis of two phosphate groups on ATP provides energy
Regarding the energy source for adding a nucleotide to DNA, when a nucleotide triphosphate bonds to the sugar, what happens?
- it loses two phosphates
- hydrolysis of the phosphate bonds provides the energy for the reaction.
Which direction does DNA replication proceed in bacteria?
Most bacterial DNA replication is bi-directional
How many copies of the DNA is made for offspring cells?
Each offspring cell receives one copy of the DNA molecule
What is the source of accuracy for DNA replication?
Replication is highly accurate due to the proofreading capability of DNA polymerase
Describe some features of
Ribonucleic acid
– Single-stranded nucleotide
– 5-carbon ribose sugar
– Contains uracil (U) instead of thymine (T)
name the RNA integral to ribosomes
Ribosomal RNA
aka rRNA
name the RNA that transports amino acids during protein synthesis
Transfer RNA
aka tRNA
name the RNA that carries coded information from DNA to ribosomes
Messenger RNA
aka mRNA
describe the process of transcription
genetic information in DNA is copied into a complementary base sequence of RNA
what indicates the beginning of transcription?
RNA polymerase binds to
the promoter sequence on DNA
In what direction is DNA transcribed in prokaryotes?
Transcription proceeds in the 5‘ -> 3’ direction
Regarding transcription in prokaryotes, how many strands are involved?
only one of the two strands of DNA is transcribed
what indicates the end of transcription?
transcription stops when it reaches the terminator sequence on DNA
Why is protein synthesis called “translation?”
because it involves decoding the “language” of nucleic acids and converting it into the “language” of proteins.
describe codons
groups of three mRNA nucleotides that
code for a particular amino acid
describe sense codons
codons involved in making amino acids
describe nonsense codons
codons involved in stopping protein synthesis, aka stop codons
number of sense codons and the number of possible amino acids
61 codons make 20 amino acids
as it relates to DNA and codons, briefly describe degeneracy
redundancy of the genetic code, each amino acid is coded by several codons
What is the three letter code for the codon that starts translation of mRNA
AUG
What are the three letter codes for the codons that end translation of mRNA.
UAA, UAG, UGA
In what order are the codons of mRNA “read?”
codons of mRNA are read sequentially
What is the function of tRNA molecules?
these transport the required amino acids to the ribosome
In tRNA molecules, what base-pairs with the codon?
an anticodon
Regarding translation, what joins amino acids?
peptide bonds
Regarding the process of translation, the place where the first tRNA is paired with the start codon is called what?
the P site
Regarding the process of translation, the place where the next tRNA is paired is called what?
The next codon to be
translated is brought into the A site.
Regarding the process of translation, the tRNA moves from the A site, to the P site, to what area before it is released?
The tRNA is released from the E site.
Regarding the process of translation, when the ribosome reaches a stop codon, what happens next?
the polypeptide is released, it then forms a new protein!
In bacteria, when can translation begin.
In bacteria, translation can begin before transcription
is complete
Contrast the location of transcription and translation in eukaryotes.
transcription occurs in the nucleus, whereas translation occurs in the cytoplasm
What are exons?
Exons are regions of DNA that code for proteins.
What are introns?
Introns are regions of DNA that do not code for proteins.
What is responsible for removing introns and splicing exons together?
Small nuclear ribonucleoproteins (snRNPs)
After RNA transcription, what happens with the mRNA?
After further modification, the mature mRNA leaves the nucleus to the cytoplasm, where it directs protein synthesis.
What are the stages of transcription?
There are three.
initiation
elongation
termination
Regarding transcription, what kicks off the initiation stage?
RNA polymerase recognizes and binds to a site called a promoter at the 3’ end of the template.
Regarding transcription, how does the promoter help control gene expression?
differences in promotor strength - the affinity for RNA polymerase to bind to that promoter
Regarding transcription, describe the elongation step.
During elongation, RNA polymerase moves along the template strand, adding bases to the growing RNA transcript.
Regarding transcription, describe the termination step.
When the RNA reaches the site called a terminator, the RNA polymerase is released from the DNA strand. (and the newly synthesized RNA transcript goes with it)
Regarding transcription, identify the mechanisms through which termination can occur.
There are two.
* self-termination
* enzyme-dependent termination
Regarding transcription, describe self-termination.
the RNA sequence transcribed causes the RNA to bind with itself, pulling it off the DNA strand.
Regarding transcription, describe enzyme-dependent termination.
a termination protein binds to the terminator and pushes the RNA polymerase away from the DNA strand
Name the term for genes produced at a fixed rate.
Constitutive genes
Name the terms for the genes regulated by mechanisms that limit transcription.
There are two.
* Inducible genes
* Repressible genes
(The two pre-transcription genetic control mechanisms are known as repression and induction.)
Identify the mechanism that regulates gene expression in response to the amount of carbon sources present.
Catabolite repression
(Example: cyclic AMP (cAMP), a substance derived from ATP that serves as a “cellular alarm signal” to regulate the lactose operon.)
Regarding gene expression, briefly describe repression.
inhibits gene expression and decreases
enzyme synthesis
Regarding gene expression, briefly describe repressors.
proteins that block transcription (during repression)
True or false:
The default expression of a repressible gene is on.
True.
The default expression of a repressible gene is on.
True or false:
The default expression of a repressible gene is off.
False
The default expression of a repressible gene is on.
Regarding gene expression, briefly describe induction.
Induction turns gene expression on.
Regarding gene expression, briefly describe inducer.
initiates gene expression (during induction)
True or false:
The default expression of an inducible gene is off.
True.
The default expression of an inducible gene is off.
True or false:
The default expression of an inducible gene is on.
False.
The default expression of an inducible gene is off.
Regarding the operon model, briefly describe promoter.
segment of DNA where RNA polymerase
initiates transcription of structural genes
Regarding the operon model, briefly describe operator.
segment of DNA that controls transcription of structural genes
Regarding the operon model, briefly describe operon.
set of operator and promoter sites and the structural genes they control
Briefly describe what happens in the absence of lactose for an inducible gene.
the repressor binds to
the operator, structural genes are not transcribed
Briefly describe what happens in the presence of lactose for an inducible gene.
the inducer, allolactose, binds to the repressor, the repressor cannot bind to the operator, transcription occurs
Regarding an inducible (or repressible) operon, what gene sits right before the operon and what does it do?
the regulatory gene
the product of the regulatory gene regulates the operon.
Excess tryptophan acts as a what when it binds and activates the repressor to bind to the operator, stopping tryptophan synthesis.
a corepressor
Briefly describe the effect of catabolite repression on cellular metabolism.
inhibits cells from using carbon sources other than glucose
Regarding catabolite repression, what builds up when glucose is not availabe?
Cyclic AMP (cAMP)
Regarding catabolite repression, what happens after enough cAMP builds up?
cAMP binds to the catabolic activator protein (CAP)
that in turn binds the lac promoter, initiating transcription and allowing the cell to use lactose
Bacteria growing in a medium containing glucose and lactose first consume the glucose and then, after
a short lag time, the lactose.
What happens during the lag time?
During the lag time,
* intra-cellular cAMP increases,
* the lac operon is transcribed
Describe the phrase epigenetic inheritance.
Changes in gene expression passed to offspring.
Briefly describe the function of methylating nucleotides.
turn genes off
True or false:
Methylated genes of offspring will always match those of their parents.
False.
Unlike mutations, this isn’t permanent, and the genes can be turned on in a later generation.
True or false:
Methylated genes of offspring can differ from those of their parents.
True.
Unlike mutations, this isn’t permanent, and the genes can be turned on in a later generation.
Regarding gene expression, describe the riboswitch.
A part of an mRNA molecule that, when bound to a substrate, can initiate or stop translation.
Regarding gene expression, describe microRNAs.
An RNA molecule that base-pairs with mRNA to inhibit protein production.
What happens to the mRNA once combined with microRNA?
Double-stranded RNA is enzymatically destroyed, preventing production of a protein
Briefly define mutation.
a permanent change in the base sequence of DNA
True or false:
Mutations may be neutral, beneficial, or harmful.
True.
Mutations may be neutral, beneficial, or harmful.
True or false:
Mutations will always be either beneficial or harmful.
False.
Mutations may be beneficial, harmful, or neutral (aka silent).
The word or phrase for agents that cause mutations.
mutagen
The word or phrase for mutations that occur in the absence of agents that might cause them.
Spontaneous mutations
Regarding genetic material, briefly describe base substitution.
a single base at one point in the DNA sequence is replaced with a different base
(aka point mutation)
Regarding genetic material, briefly describe point mutation.
a single base at one point in the DNA sequence is replaced with a different base
(aka base substitution)
The word or phrase for when base substitution results in a different amino acid.
missense mutation
The word or phrase for when a base substitution results in a stop codon.
nonsense mutation
The word of phrase for the insertion or deletion of one or more nucleotide
pairs.
frameshift mutation
(Shifts the translational “reading frame.”)
Regarding chemical mutagens, describe the effect of nitrous acid.
causes adenine to bind with cytosine instead of thymine
Describe nucleoside analogs.
These molecules are structurally similar to normal nitrogenous bases, but they have slightly altered base-pairing properties.
* incorporates into DNA in place of a normal base
* causes mistakes in base pairing
Regarding genetic material, describe the effects of ionizing radiation.
Ionizing radiation causes the formation of ions that can
* oxidize nucleotides
* break the deoxyribose-phosphate backbone
Name the types of ionizing radiation.
There are two.
* X-rays
* Gamma rays
Regarding genetic material, describe the effects of UV radiation.
UV radiation causes thymine dimers
* the formation of harmful covalent bonds between pyrimidine bases.
* Adjacent thymines in a DNA strand can cross-link to form thymine dimers.
Why is photolyase also known as light-repair enzymes?
it uses visible light energy to separate the dimer back to the original two thymines.
Briefly describe nucleotide excision repair.
Enzymes cut out
incorrect bases and fill in correct bases
Briefly describe the function of photolyases.
repair UV-induced damage, separate thymine dimers.
Name or phrase for:
enzymes cutting out incorrect bases to fill in correctr bases
nucleotide excision repair
Regarding DNA repair, a (blank) cuts the DNA, and a (blank) removes the damage.
an endonuclease cuts, and a exonuclease removes
Regarding DNA repair, what uses the intact strand as a template to fill in the correct bases?
DNA polymerase fills in the gap by synthesizing new DNA
Regarding DNA repair, after the correct bases are filled in, what happens next?
DNA ligase bridges the gap between the old an new DNA
What are the frequencies of mutation with and without mutagens.
Spontaneous mutation rate =
* 1 in 10^9 replicated base pairs or
* 1 in 10^6 replicated genes
Mutagens increase the mutation rate to * per 10^-5 or
* 10^-3 replicated gene
Regarding mutant cells, describe positive (direct) selection.
detects mutant cells because they grow or appear different than unmutated cells
Regarding mutant cells, describe negative (indirect) selection
Negative (indirect) selection detects mutant cells that cannot grow or perform a certain function
Describe Auxtotroph
mutant that has a nutritional requirement absent in the parent
Briefly describe replica plating and its use.
- transfer of colonies into petri dishes of different mediums
- to identify auxtotrophic colonies
Briefly describe the Ames test and its use.
- exposes mutant bacteria to mutagenic substances
- to measure the rate of reversal of the mutation
- Indicates degree to which a substance is mutagenic
Briefly describe genetic recombination.
exchange of genes between two DNA molecules; creates genetic diversity
Regarding gene transfer, describe crossing over.
two chromosomes break and rejoin, resulting in the insertion of foreign DNA into the chromosome
Regarding genetic recombination by crossing over, what joins the donor DNA strand?
RecA protein catalyzes the joining of the two strands.
Regarding genetic recombination by crossing over, how are the mismatched DNA strands resolved?
Complementary base pairs between the two strands will be resolved by DNA polymerase and ligase. The donor DNA will be destroyed. The recipient may now have one or more new genes.
Describe mobile genetic elements.
Segments of DNA that can move between chromosomes and between cells.
Which structure is the one that often encodes for proteins that enhance the pathogenicity of a bacterium?
plasmids
Describe R Factory type of plasmids.
Plasmids that carry genes for resistance of antibiotics and other cell toxins.
Describe Conjugative plasmid.
carries genes for sex pili and transfer of the plasmid
Describe Dissimilation plasmids.
encode enzymes for the catabolism of unusual compounds.
Describe Transposons
are segments of DNA that can move from one region of DNA to another
Regarding transposons, describe insertion sequences.
encodes for transposase that cuts and reseals DNA
Regarding transposons, the name or phrase for one that carries additional genes?
Complex transposons also carry other genes not connected with the transposition process.
Regarding gene transfer, briefly describe transformation.
genes are transferred from one bacterium to another as “naked” DNA in solution.
Regarding genetic transformation, briefly describe the results of Griffith’s experiment.
Hereditary material (genes) from the dead bacteria had entered the live cells and changed them genetically so that their progeny were encapsulated and therefore virulent
Regarding gene transfer, briefly describe conjugation.
plasmids transferred from one bacterium to another
Regarding gene transfer, describe the physical requirements for bacterial conjugation.
- Requires cell-to-cell contact via sex pili
Regarding bacterial conjugation, donor cells carry the plasmid (F factor) are said to be what?
are called F+ cells
In some bacteria carrying F factors, the factor integrates into the chromosome, converting it to what?
an Hrf cell
(high frequency of recombination)
When an F factor (a plasmid) is transferred from a donor (F+) to a recipient (F–), the F– cell is converted to what?
an F+ cell.
When an F factor becomes integrated into the chromosome of an F+ cell, it makes the cell a what?
a high frequency of recombination (Hfr) cell.
When an Hfr donor passes a portion of its chromosome into an F– recipient, what is the result?
a recombinant F– cell results.
Observing conjugation in bacteria is useful for what purpose?
A map of gene locations can be made by observing recombinant cells after conjugation.
Regarding transduction in bacteria, what transfers the DNA?
DNA is transferred from a donor cell to a recipient via
a bacteriophage
Briefly describe generalized transduction in bacteria.
Random bacterial DNA is packaged inside a phage and transferred to a recipient cell
Briefly describe Specialized transduction.
Specific bacterial genes are packaged inside a phage and transferred to a recipient cell
Regarding evolution, what is the noteworthy effect of mutations and recombination?
- Mutations and recombination create cell diversity
- Natural selection results in organisms best fit for a particular environment
Regarding bacterial transduction, bacterial DNA are packaged inside of what?
a phage capsid
Regarding bacterial transduction, after bacterial DNA are packaged, what happens next?
The donor cell lyses, releasing the phage particles.
