Microbial Genetics Flashcards
Manifestation of the genotype; actual expressed properties.
Phenotype
Genetic makeup of an organism.
Genotype
The science of heredity; includes the study of what genes are, how they are replicated, how they are passed between generations/organisms.
Genetics
Genetic information in a cell (includes it’s chromosomes and plasmids).
Genome
Structures containing DNA that physically carry hereditary information.
Contains the genes.
Chromosomes
Segments of DNA (in some viruses - RNA) that code for functional products.
Genes
Repeating macromolecule units composing DNA; consists of a nucleobase (adenine, thymine, cystosine, guanine), deoxyribose (pentose sugar), and a phosphate group.
Each strand of the double helix has string of alternating sugar & phosphate groups with a nitrogenous base attached to a sugar.
Nucleotides
Nitrogenous bases held together by H bonds.
Base pairs
Set of rules that determines how a nucleotide sequence is converted into the amino acid sequence of a protein.
Genetic code
The resulting molecule produced from gene code.
Expression
Collection of genes.
Genotype
Collection of proteins.
Phenotype
Twisted DNA
Supercoiled
Number of base pairs in DNA of E. coli.
4.6 million
Length of DNA of one E. coli cell
1mm (1000 times longer than entire cell)
Repeating sequences of two- to five-base sequences; used in DNA fingerprinting.
Short tandem repeats (STRs)
Regions of DNA that are likely to encode a protein; base sequences between start and stop codons.
Open-reading frames.
The sequencing and molecular characterization of genomes.
Genomics
Blueprint for a cell’s proteins.
DNA
Genetic information transferred between generations of cells.
Replication
Genetic information transferred between cells of same generation.
Recombination
Genetic information used within a cell to produce the proteins needed for the cell to function.
Expression
The enzyme that relaxes the supercoiling when replication begins.
Topoisomerase or gyrase
Enzyme that unwindsdouble-stranded DNA.
Helicase
Enzyme that synthesizes DNA; proofreads and repairs DNA.
DNA Polymerase
The point at which replication occurs:
Replication fork
Each new double-stranded DNA molecule contains one original (conserved) strand and one new strand:
Semiconservative replication
Relaxes supercoiling ahead of the replication fork.
DNA Gyrase
Makes covalent bonds to join DNA strands; joins Okazaki fragments and new segments in excision repair.
(Bonds between phosphates and sugars)
DNA Ligase
Cut DNA backbone in a strand of DNA; facilitate repair and insertions.
Endonucleases
Cut DNA from an exposed end of DNA; facilitate repair.
Exonucleases
Adds methyl group to selected bases in newly made DNA.
Methylase
Uses visible light energy to separate UV-induced pyrimidine dimers.
Photolyase
RNA enzyme that removes introns and splices exons together.
Ribozyme
Copies RNA from a DNA template.
RNA Polymerase
An RNA polymerase that makes RNA primers from a DNA template.
RNA Primase
RNA-protein complex that removes introns and splices exons together.
snRNP
Relaxes supercoiling ahead of the replication fork; separates DNA circles at the end of DNA replication.
Topoisomerase
Cuts DNA backbone, leaving single-stranded “sticky ends.”
Transposase
Which end can DNA polymerases add new nucteotidesto?
3’
What is attached to the 3’ end of the DNA strand?
Hydroxyl
What is attached to the 5’ end of the DNA strand?
Phosphate
Where is the great deal of energy required for DNA replication supplied from?
Nucleotides (which are actually nucleoside triphosphates)
What is the only difference between ATP and the adenine nucleotide in DNA?
The sugar component
What is the sugar in the nucleoside used to synthesize DNA?
Deoxyribose
How many phosphate groups are removed to add the nucleotide to a growing strand of DNA?
Two
Process that is exergonic and provides energy to make the new bonds in the DNA strand.
Hydrolysis
Eukaryotic chromosomes are linear whereas prokaryotic chromosomes are ________.
Circular
Movement of the two replication forks in opposite directions away from the origin of replication.
Bidirectional
The separation of the two loops in a prokaryotic chromosome must be separated by ___________.
Topoisomerase
The rate of mistakes in DNA replication.
1 in every 10 to the 10th power bases incorporated.
Enzyme responsible for high accuracy due to the proofreading capability is:
DNA Polymerase
The three “STOP” codons:
UAA, UAG, UGA
Start codon:
AUG
Process where genetic information is copied, or transcribed, into a complementary base sequence of RNA:
Transcription
Information encoded in RNA used to synthesize specific proteins.
Translation
Synthesis of a complementary strand of RNA from a DNA template.
Transcription
The cellular machinery for protein synthesis; forms an integral part of ribosomes.
Ribosomal RNA (rRNA)
RNA that carries the coded information for making specific proteins from DNA to ribosomes, where proteins are synthesized.
Messenger RNA (mRNA)
A strand of mRNA is synthesized using a specific portion of the cell’s DNA as a template during:
Transcription
The process of transcription requires both:
RNA Polymerase and a supply of RNA nucleotides
Transcription begins when RNA polymerase binds to the DNA at a site called the:
Promoter
DNA and RNA are synthesized in the direction:
5’—->3’
RNA synthesis continues until RNA polymerase reaches a site on the DNA called the :
Terminator
The nitrogenous base that is an analog of thymine and plays well (doesn’t bond too much like thymine) in RNA:
Uracil
Code redundancy is useful for:
Silent mutation
Each codon codes for one amino acid; in contrast:
Each amino acid is coded by more than one codon.
We have the same evolutionary ancestors as bacteria. Our genetic code always starts with:
AUG (Methionine)
Protein synthesis
Translation
Decoding the “language” of nucleic acids and converting that information into the “language” of proteins.
Translation
Groups of three nucleotides.
Codons
Written in terms of their base sequence in mRNA.
Codons
Total number of amino acids.
20
Number of possible codons.
64
Most amino acids are signaled by several alternative codons:
Allows for certain amount of change, or mutation, in the DNA without affecting the protein ultimately produced.
Degeneracy of the code
Codons that code for amino acids (61).
Sense codons
Codons that do not code for amino acids (3).
Nonsense codons (stop codons)
Site of translation
ribosome
Type of RNA molectules that recognize the specific codons and transport the required amino acids
Transfer RNA (tRNA)
Process of translation (8 steps):
Components needed to begin translation come together.
Step 1 (Process of translation)
Process of translation (8 steps):
On the assembled ribosome, a tRNA carrying the first amino acid is paired with the start codon on the mRNA. The place where this first tRNA sits is called the P site. A tRNA carrying the second amino acid approaches.
Step 2 (Process of translation)
Process of translation (8 steps):
The second codon of the mRNA pairs with a tRNA carrying the second amino acid at the A site. The first amino acid joins to the second by a peptide bond. This attaches the poypeptide to the tRNA in the P site.
Step 3 (Process of translation)
Process of translation (8 steps):
The ribosome moves along the mRNA until the second tRNA is in the P site. The next codon to be translated is brought into the A site. The first tRNA now occupies the E site.
Step 4 (Process of translation)
Process of translation (8 steps):
The second amino acid joins to the third by another peptide bond, and the first tRNA is released from the E site.
Step 5 (Process of translation)
Process of translation (8 steps):
The ribosome continues to move along the mRNA and new amino acids are added to the polypeptide.
Step 6 (Process of translation)
Process of translation (8 steps):
When the ribosome reaches a stop codon, the polypeptide is released.
Step 7 (Process of translation)
Process of translation (8 steps):
Finally, the last tRNA is released, and the ribosome comes apart. The released polypeptide forms a new protein.
Step 8 (Process of translation)
Three parts of translation:
1) Chain initiation
2) Chain elongation
3) Chain termination
(ESSAY QUESTION!!!)
Sequence of three bases that is complementary to a codon
anticodon
In prokaryotic cells, the translation of mRNA into protein can begin even before transcription is complete. This is due to :
mRNA is produced in the cytoplasm; the start codons of an mRNA being transcribed are available to ribosomes before the entire mRNA molecule is even made.
In eukaryotic cells, transcription takes place in the:
Nucleus
Regions of expressed DNA.
Exons
Intervening regions of DNA that do not encode protein.
Introns
Particles that remove the introns and splice the exons together.
small nuclear ribonucleoproteins, or snRNPs (snurps)
In some organisms, the introns act as ________to catalyze their own removal.
Ribozymes
In the nucleus, __________ synthesizes a molecule called an RNA transcript that contains copies of the introns.
RNA polymerase
Many genes, perhaps 60-80%, are not regulated but are instead ______________, meaning that their products are constantly produced at a fixed rate.
Constitutive
Example of constitutive genes:
Enzymes of glycolysis
Protozoan parasite that causes African sleeping sickness
Trypanosoma
The two genetic control mechanisms (pre-transcriptional control)
Repression and Induction
Regulatory mechanism that inhibits gene expression and decreases the synthesis of enzymes
Repression
The type of regulatory mechanism that is usually a response to the overabundance of an end-product of a metabolic pathway
Repression
The type of regulatory mechanism that causes a decrease in the rate of synthesis of the enzymes leading to the formation of that product
Repression
Repression is mediated by regulatory proteins called:
Repressors
Regulatory proteins that block the ability of RNA polymerase to initiate transcription from the repressed genes.
Repressors
The default position of a repressible gene:
On
Bacteria control expression in a positive or negative manner?
Negative (most of their genes are turned on and need turned off)
Constitutive genes are also known as:
“housekeeping” genes needed for metabolic activity; they replicate ~15 minutes - makes no sense to turn them off
The process that turns on the transcription of a gene or genes is:
Induction
A substance that acts to induce transcription of a gene is called an:
inducer
Enzymes that are synthesized in the presence of inducers are:
Inducible enzymes
A well-known example of an inducible system are the genes required for lactose metabolism in what bacteria:
E. coli
One of the genes required for lactose metabolism in E. coli codes for _____________________, which splits the substrate lactose into two simple sugars, glucose and galactose.
B-galactosidase
B-glactosidase splits substrate lactose in lactose metabolism in E. Coli into the following:
two simple sugars, glucose, and galactose
_____ refers to the type of linkage that joins the glucose and galactose
B
What happens when E. coli is placed into a medium in which no lactose is present?
The organisms contain almost no B-galactosidase.
When lactose is added to a medium that E. coli is placed in, the bacterial cells produce a large quantity of:
B-galactosidase
Lactose is converted in the cell for lactose metabolism to the related compound:
allolactose
_____________ is an inducer for the genes that are required for lactose metabolism.
Allolactose
The presence of _______________ thus indirectly induces the cells to synthesize more enzyme.
lactose
Default position of an inducible gene:
Off
Francois Jacob and Jacques Monod formulated this general model in 1961 to account for the regulation of protein synthesis.
The Operon Model
In addition to B-galactosidase, the following enzymes that are involved with the induction of lactose catabolism in E. coli:
Lac permease
Transacetylase
Involved in the transport of lactose into the cell (enzyme)
Lac permease
Enzyme that metabolizes certain disaccharides other than lactose
transacetylase
Genes which determine the structures of proteins and distinguish them from an adjoining control region on the DNA
structural proteins
Short segment of DNA which is like a traffic light that acts as a go or stop signal for transcription of the structural genes.
Operator
The other short segment of DNA in the control region of the lac operon (besides the operator)
promoter
The region of DNA in the lac operon where RNA polymerase initiates transcription
promoter
A set of operator and promoter sites and the structural genes they control:
Operon
The combination of the three lac structural genes and the adjoining control regions is called:
Lac operon
A regulatory gene called the ___________ encodes a repressor protein that switches inducible and repressible operons on or off.
I gene
A protein that switches inducible and repressible operons on or off
repressor
The lac operon is an ___________operon.
Inducible
In _______________ operons, the structural genes are transcribed until they are turned off, or repressed.
repressible
The genes for the enzymes involved in the synthesis of tryptophan are regulated by:
repressible operons
Example: Tryptophan synthesis/Operon
The structural genes are transcribed and translated leading to tryptophan synthesis. When excess tryptophan is present, the tryptophan acts as a ______________, binding to the repressor protein. The repressor protein can now bind to the operator, stopping further tryptophan synthesis.
corepressor
Regulation of the lactose operon also depends on the level of the glucose in the medium, which in turn controls the intracellular level of the small molecule:
cyclic AMP (cAMP)
A substance derived from ATP that serves as a cellular alarm signal.
cyclic AMP (cAMP)
Enzymes that metabolize glucose are ___________ , and cells grow at their maximal rate with glucose as their carbon source because they can use it most efficiently.
constitutive
When glucose is no longer available, ____________ accumulates in the cell.
cAMP
cAMP binds to the allosteric site of ________________.
catabolic activator protein (CAP)
CAP binds to the lac promoter, which ____________________ by making it easier for RNA polymerase to bind to the promoter.
initiates transcription
Transcription of the lac operon requires both the presence of ______________ and the absence of ____________________.
lactose; glucose
Cyclic AMP is an example of an ______________, a chemical alarm signal that promotes a cell’s response to environmental or nutritional stress.
alarmone
for example, the lack of glucose
The operon consists of:
Promoter
Operator
Structural genes that code for the protein
The operon is regulated by the:
product of the regulatory gene
When the repressor is inactive, the operon is:
On
When the repressor is active, the operon is:
Off
Inhibition of the metabolism of alternative carbon sources by glucose is termed:
Catabolite Repression
When glucose is available, the level of cAMP in the cell is low, and consequently ____________ is not bound.
CAP
Eukaryotic and bacterial cells can turn genes off by methylating certain nucleotides.
Epigenetic control
The methylated genes are in the on or off position?
Off
Single-stranded RNA molecules of approximately 22 nucleotides that inhibit protein production in eukaryotic cells.
microRNA’s (miRNAs)
A permanent change in the base sequence of DNA is:
Mutation
The change in DNA base sequence causes no change in the activity of the product encoded by the gene.
Silent mutations
Silent mutations commonly occur when one nucleotide is substituted for another in the DNA, especially at a location corresponding to the third position of the:
mRNA codon
What are the three parts of a nucleotide?
Nucleobase (adenine, thymine, cystosine, guanine)
Deoxyribose (pentose sugar)
Phosphate group
Which part of the nucleotide forms the backbone of DNA?
Phosphate (sugar-phosphate backbone).
What type of bonds are formed between the complementary base pairs?
H bonds
How are the two strands of DNA aligned?
5’ opposite 3’ direction (antiparallel)
Define semi-conservative replication:
Each new double-stranded DNA molecule contains one original (conserved) strand and one new strand.
What enzymes are involved in DNA replication?
DNA gyrase DNA Ligase DNA polymerase endonucleases exonucleases helicase methylase photlyase ribozyme RNA polymerase RNA primase snRNP topoisomerase transposase
How does DNA polymerase minimize mutations?
Proofreading - evaluates for proper complimentary base-pairing structure
Also replaces with correct complimentary base is mutation is found.
What are structural genes?
They determine the structures of proteins.
What class of molecules does RNA belong to?
Nucleic acids
What are the three types of RNA?
Ribosomal - rRNA
Messenger - mRNA
Transfer - tRNA
What is meant by gene expression?
A gene is expressed if a protein is produced.
Phenotype.
How does RNA differ from DNA?
Uracil
Define transcription:
The copying or synthesis of RNA from a DNA template.
Define translation:
Protein synthesis.
What is a codon?
The language of mRNA.
Groups of three nucleotides.
Sequence of codons on mRNA determines sequence of amino acids = genetic code.
What is the start codon on mRNA?
AUG - methionine
What protein is involved in mRNA synthesis?
RNA polymerase (binds to the promoter region)
How many strands of DNA are copied into RNA?
One
What are the two binding sites of tRNA?
anticodon
What is an anticodon?
Sequence of three bases that is complementary to a codon.
Describe ribosomes
cellular machinery for protein synthesis
Describe the three steps of translation:
1) Chain initiation (steps 1-3 of 8)
2) Chain elongation (4-6)
3) Chain termination (7-8)
What are the two binding sites on the large ribosomal subunit called?
A site
P site
Where do the incoming tRNA molecules bind?
1st at P site
Thereafter @ A site
What type of bond is formed between amino acids?
peptide bond
What process forms a peptide bond?
hydrolysis
What is gene mutation?
permanent change in the base sequence of DNA
What are the three types of point mutations?
Missense mutation
Nonsense mutation
Frameshift mutation
What are frameshift mutations?
One or a few nucleotide pairs are deleted or inserted in the DNA, shifting “translational reading frame” (three by three grouping of nucleotides)
What is the relationship between gene and proteins?
Genes map the genetic code that produces the proteins. The genotype leads to the phenotype via translation.
How is the gene regulation controlled in prokaryotic cells?
Negative manner - most of their genes are turned on and need turned off
Describe the lac operon model:
The combination of the 3 lac structural genes and the adjoining control regions is called the lac operon. Inducible.
Repressor
switches inducible and repressible operons on or off
Inducer
substance that acts to induce transcription of a gene
Promoter region
region of DNA where RNA polymerase initiates transcription
Operon
set of operator, promoter sites, and the structural genes they control
Structural gene
determine structures of genes
Crossing over
Process by which a portion of one chromosome is exchanged with a portion of another chromosome
Vertical gene transfer
transfer of genes from an organism or cell to its offspring
Horizontal gene transfer
transfer of genes between two organisms in the same generation
Donor cell
cell that gives DNA to a recipient cell during genetic recombination
Recipient Cell
cell that receives DNA from a donor cell during genetic recombination
Transformation
the process in which genes are transferred from one bacterium to another as “naked” DNA in solution
Conjugation
transfer of genetic material from one cell to another involving cell to cell contact (pili)
Plasmid
small, circular DNA molecule that replicates independently of the chromosome
R factor
(resistance) bacterial plasmid carrying genes that determine resistance to antibiotics
F factor
(fertility) plasmid found in the donor cell in bacterial conjugation
base substitution
point mutation
single base in DNA sequence is replaced with a different base
base substitution
If the base substitution results in an amino acid substitution in the synthesized protein, the change in the DNA is known as a:
Missense mutation
Caused by a single change in the gene for globin. A change from A to a T at a specific site, results in the change from glutamic acid to valine in the protein. The effect of this change is that the shape of the hemoglobin molecule changes under conditions of low oxygen, altered the shape of the red blood cells such that movement of the cells through small capillaries is greatly impeded.
Sick cell disease
A stop codon created in the middle of an mRNA molecule, causing prevention of the synthesis of a complete functional protein; only a fragment is synthesized.
Nonsense mutation (nonsense codon)
One or a few nucleotide pairs are deleted or inserted in the DNA and can cause a shift in the “translational reading frame”.
Frameshift mutations
Three-by-three grouping of nucleotides recognized as codons by the tRNAs during translation
Transitional Reading Frame
Progressive Neurological disorder caused by extra bases inserted into a particular gene.
Huntington’s disease
Occasional mistakes made during DNA replication; occur without any mutation-causing agents
spontaneous mutations
Agents in the environment, such as certain chemicals and radiation, that directly or indirectly bring about mutations:
Mutagens
Name the three types of chemical mutagens:
Oxidation of nucleotides
Nucleoside analogs
Deletions/insertions (frameshift)
Altered adenine from exposure to nitrous acid can cause pairing with cytosine in daughter DNA, and then granddaughter DNA.
Oxidation of nucleotides (chemical mutagen)
Structurally similar molecules to normal nitrogenous bases, but have slightly altered base-pairing properties.
When given to growing cells, they are randomly incorporated into cellular DNA in place of the normal bases. During replication, they cause mistakes in base pairing.
Nucleoside analogs
What type of mutagen is nitrous acid?
Oxidative
What type of mutagens are antiviral and antitumor drugs?
Nucleoside analogs
What type of mutagen is AZT (azidothymidine)?
Nucleoside analog
What is one of the primary drugs used to treat HIV?
AZT (azidothymidine)
What type of mutagen is benzopyrene?
found in smoke and soot
frameshift mutagen
What type of mutagen is Aflatoxin (produced by Apergillus flavus)?
(mold that grows on peanuts and grain)
frameshift mutagen
Potent mutagens because of their ability to ionize atoms and molecules.
Xrays and gamma rays (radiation)
Penetrating rays of ionizing radiation cause electrons to pop out of their usual shells; then bombard other molecules and cause more damage; many of resulting ions and free radicals are very reactive.
Radiation
Causes ions to oxidize bases in DNA, resulting in errors in DNA replication and repair that cause mutations.
Radiation
An even more serious outcome of _______________ is the breakage of covalent bonds in the sugar-phosphate backbone of DNA, which causes physical breaks in chromosomes.
Radiation
A nonionizing component of ordinary sunlight that is another form of mutagenic radiation.
UV light
The most important effect of direct UV light on DNA is the formation of harmful covalent bonds between certain bases. Adjacent thymines in a DNA strand can cross-link to form:
thymine dimers
Thymine dimers can cause serious damage or death to the cell because it cannot:
properly transcribe or replicate DNA
light-repair enzymes
photolyases
Enzymes that can repair UV-induced damage
photolyases
Use visible light energy to separate the dimer back to the original two thymines
photolyases
Enzymes cut out the incorrect base and fill in the gap with newly synthesized DNA that is complementary to the correct strand.
Nucleotide excision repair
Enzymes that add a methyl group to selected bases soon after a DNA strand is made.
Methlylases
The enzyme that recognizes a methylated base in order to carry out nucleotide excision repair.
repair endonuclease
Two thymines read as one cause:
frameshift
Probability that a gene will mutate when a cell divides. Usually stated as a power of 10, and because rare, exponent is always a negative number.
Mutation rate
The spontaneous rate of mutations is about one in
one million replicated genes
Involves the detection of mutant cells by rejection of the unmutated parent cells.
Positive (direct) selection
Process that selects a cell that cannot perform a certain function.
Negative (indirect) selection
Method of inoculating a number of solid minimal culture media from an original plate to produce the same pattern of colonies on each plate.
Replica plating
Any mutant microorganism having a nutritional requirement that is absent in the parent is known as an:
auxotroph
Substances that cause cancer in animals, including humans.
Carcinogens
The use of bacteria as carcinogen indicators.
Ames test
New mutations that reverse the effect (the change in phenotype) of the original mutation.
Reversions
Test that measures the reversion of histidine auxotrophs of Salmonella (his- cells, mutants that have lost the ability to synthesize histidine) to histidine-synthesizing cells (his+) after treatment with a mutagen.
Ames test
If a reversion of his- bacteria is made to his+ bacteria, the substance being tested is:
mutagenic
Exchange of genes between two DNA moluces to form new combination of genes on a chromosome.
Genetic recombination
The recipient cell that incorporates donor DNA into its own DNA is called:
recombinant
