Bacterial Genetics Flashcards
1
Q
What are the functions of DNA
A
- Inheritance: Genetic material is responsible for inheritance, passed from parent to offspring
- Replication: Great accuracy with minimal errors that introduce changes to DNA sequence, preserves integrity of genetic information
- Genome: Contains full complement of DNA within a cell and is organised into smaller, discrete units called genes that are arranged on chromosomes and plasmids
- Protein Synthesis: Directs and regulates the construction of proteins necessary to a cell for growth and reproduction in a particular cellular environment
2
Q
What is the central dogma and gene expression
A
- Central Dogma: Process of DNA being transcribes to mRNA which is translated to a protein
- Each stages includes initiation, elongation, termination
- Gene Expression: Processes of transcription and translation, synthesis of a specific protein with a sequence of AA that is encoded in the gene
3
Q
What is a genotype
A
- Genetic makeup, all its DNA, the information that codes for all the particular characteristics of the organism, potential properties
- Although a cell’s genotype remains constant, not all genes are used to direct the production of their proteins simultaneously
4
Q
What is a phenotype
A
- Observable / expressed properties, manifestation of genes, product of an array of proteins produced by a cell at a given time, influenced by genotype and interactions with environment
- Genes code for proteins that have functions in the cell
- Production of a specific protein encoded by an individual gene results in a distinct phenotype
- Cells carefully regulate expression of their genes, only using genes to make specific proteins when those proteins are needed
5
Q
Define genes, genetics and chromosomes
A
- Gene: A segment of DNA that encodes a functional product, transcribed to produce an RNA molecule during the process of transcription and eventually a functional product (protein)
- Genetics: The study of what genes are, how they carry information, how information is expressed, and how genes are replicated
- Chromosome: Structure containing DNA that physically carries hereditary information, contain genes
- Bacterial Chromosome: Singular circular model of DNA and associated proteins, looped, folded and attached at one of several points to cell membrane
6
Q
What are the 3 different replication models
A
- Semiconservative: Two strands of DNA separate, each serves as a template from which a new strand is copied
- Conservative: Two parental strands remain together after replication
- Dispersive: Strands broken into segments, even after second replication parental strand is somewhat present
7
Q
What is DNA vs RNA
A
DNA:
- Long antiparallel strands of nucleotides twisted together in pairs to form a double helix
- Strands held together by H bonds
- Each strand has a string of alternating sugar and phosphate groups (sugar-phosphate backbone), and a nitrogenous base is attached to each sugar in the backbone
- Nucleotide: 3 parts, nitrogen base (AT and CG), deoxyribose pentose sugar and phosphate
RNA
- Long strands of nucleotides, single stranded, nitrogenous bases (AU and CG), ribose sugar
8
Q
How does the flow of genetic information occur
A
- Vertical: Transfer of genes from an organism to its offspring, between generations of cells (replication)
- Horizontal: Transfer of genes laterally, to other microbes of same generation (recombination)
9
Q
Provide an overview of DNA replication
A
- “Parental” double-stranded DNA molecule is converted to two identical molecules, one strand serves as a template for the production of a second strand
- Topoisomerase / Gyrase: Relaxes supercoiling ahead of replication fork
- Helicase: Unwinds double-strand, replication fork created
- DNA Polymerase: Synthesise DNA, proofread and facilitate repair of DNA, add nucleotides to the growing DNA strand, in 5’ 3’ direction, removes RNA primer and joins okazaki fragments with ligase
- Leading Strand: Continuously synthesised
- Lagging Strand: Synthesised discontinuously, creating okazaki fragments
10
Q
What are okazaki fragments
A
- Relatively short fragment of DNA (with an RNA primer at the 5’ terminus)
- Created on the lagging strand during DNA replication
11
Q
Describe the steps in DNA synthesis / replication
A
- Enzymes (topoisomerase / DNA gyrase) unwind parental double helix
- Proteins stabilise unwound parental DNA
- Leading strand synthesised continuously from primer by DNA polymerase
- The lagging strand is synthesised discontinuously, primase (RNA polymerase) synthesises a short RNA primer which is then extended by DNA polymerase
- DNA polymerase digests RNA primer and replaces it with DNA
- DNA ligase joins discontinuous fragments of lagging strand
12
Q
How does replication of bacterial DNA occur
A
- Bidirectionally
- Around the chromosome, two replication forks move in opposite directions away from the origin of replication
13
Q
What is transcription
A
- Synthesis of a complementary strand of RNA from a DNA template
- rRNA (ribosomal subunit, integral part of ribosomes)
- tRNA (transfer, transports AA during protein synthesis)
- mRNA (messenger, carries coded information from DNA to ribosomes)
14
Q
Describe the steps involved in transcription
A
- RNA polymerase binds to promoter and DNA unwinds at the beginning of the gene
- RNA is synthesised by complementary base pairing of free nucleotides with the nucleotide bases on the template strand of DNA
- The site of synthesis moves along DNA, DNA that has been transcribed rewinds
- Transcription reaches the terminator (complete RNA strand produced)
- RNA and RNA polymerase are released and the DNA helix reforms
15
Q
What is translation
A
- Protein synthesis, decoding the “language” of nucleic acids (mRNA) and converting it into the “language” of proteins (codons)
- Multiple ribosomes attached per mRNA molecule, all at various stages of protein synthesis
- Codon: Language of mRNA, groups of three mRNA nucleotides that code for a particular AA
- Start / Stop: Translation begins at start codon (AUG) and ends at stop codon (UAA, UAG, UGA)
16
Q
Describe the steps involved in translation
A
- Components needed to begin translation come together
- On the assembled ribosome, a tRNA carrying first AA is paired with start codon on mRNA (P site)
- Second codon of mRNA pairs with a tRNA carrying the second AA at A site
- First AA joins second AA via a peptide bond, this attaches the polypeptide to the tRNA in the P site
- Ribosome moves along mRNA so first tRNA is in E site, second tRNA is in P site and next codon to be translated is in A site
- Second AA joins third AA via another peptide bond and first tRNA is released from E site
- The ribosome continues to move along the mRNA and new AA are added to polypeptide
- When ribosome reaches a stop codon polypeptide is released
- Last tRNA is released and ribosome comes apart, released polypeptide forms a new protein
17
Q
What is simultaneous transcription / translation
A
- Transcription and translation take place in cytoplasm (no nucleus)
- Translation of mRNA into proteins can begin even before transcription is complete
- Occurs in bacteria
18
Q
What is genetic code
A
- Set of rules that determines how a nucleotide sequence is converted into AA sequence of a protein
- Complementary structure allows precise replication during cell division
- Each codon “codes” for a particular AA (genetic code)
- Degenerate (one AA is encoded by more than one codon)
- tRNA carries complimentary anticodon
- 61 sense sense codons on mRNA encode the 20 AA
19
Q
What is mutation, spontaneous mutation and mutation rate and the different types (4)
A
- Mutation: A permanent change in the base sequence of DNA, sometimes causes a change in the product encoded by that gene, may be beneficial, neutral or harmful
- Mutagen: Agent that causes mutations
- Spontaneous Mutation: Occur in absence of mutagen
- Mutation Rate: Probability that a gene will mutate when a cell divides, power of 10, exponent is always -ve
- Silent, point / missense, nonsense, frameshift
20
Q
What is a silent mutation
A
- Effect: Change in DNA base sequence causes no change in activity of product encoded by the gene
- Because of degeneracy / redundancy new codon might still code for the same AA
- Cause: One nucleotide is substituted for another in the DNA, often corresponding to third position of mRNA codon
21
Q
What is a point mutation (missense)
A
- Effect: Incorrect base may cause insertion of an incorrect AA in the protein
- Cause: A single base at one point in DNA sequence is replaced with a different base, resulting in AA substitution
- Sickle cell (change A to T in globin, changes protein, alters shape of RBC)
22
Q
What is a nonsense mutation
A
- Effect: Some base substitutions effectively prevent the synthesis of a complete functional protein; only a fragment is synthesised, result in a truncated and non functional protein
- Cause: A base substitution resulting in a nonsense codon and hence premature termination
23
Q
What is a frameshift mutation
A
- Effect: Deleting one nucleotide pair in the middle of a gene, cause changes in AA sequence downstream of original mutation site, inactive protein produced
- Cause: One or more nucleotide pairs are deleted or inserted in DNA, shifts translational reading frame (each codon is made up of 3 nucleotide bases)
24
Q
What are mutagens
A
- Mutagen: Agents in environment (chemicals and radiation), directly / indirectly bring about mutations
- Ionising Radiation: Potent mutagens, causes formation of ions that can react with nucleotides and deoxyribose-phosphate backbone (X rays and gamma rays)
- Non-Ionising Radiation: Mutagenic, non-ionising component of sunlight, formation of harmful covalent bonds between pyrimidine bases, adjacent thymines can cross-link to form thymine dimers (damage or death to cell, cannot properly transcribe or replicate DNA)
25
How are mutations fixed
- Photolyases: Light repair enzymes, use visible light energy to separate thymine dimers
- Nucleotide Excision Repair: Enzymes cut out incorrect bases and fill in correct bases
26
What is genetic recombination
- Exchange of genes between two DNA molecules to form new combinations of genes on a chromosome, more likely to be beneficial than mutation
- Effect: Contributes to a population’s genetic diversity (crossing over), bring together genes that enable an organism to carry out a valuable new function (virulence factor, antibiotic resistance)
27
What are the steps involved in genetic recombination
1. DNA from one cell aligns with DNA in the recipient cell
2. DNA from donor aligns with complementary base pairs in recipients chromosome
3. RecA protein catalyses the joining of the two strands
4. Recipients chromosome contains new DNA, complementary base pairs between strands are resolved by DNA polymerase and ligase, donor DNA is destroyed, recipient has one or more new genes
28
What are plasmids
- Mobile Genetic Elements: Move from one chromosome to another or from one cell to another, genetic elements that exist out- side chromosomes
- Plasmid: Self-replicating, gene-containing, circular pieces of DNA, occur outside of chromosomes
- F Factor: Conjugative plasmid, carries genes for sex pili and transfer of plasmid to another cell
- Dissimilation Plasmids: Code for enzymes that trigger catabolism of certain unusual sugars and hydrocarbons, crucial to the survival and growth of the cell
- R Factor: Resistance factor, significant importance, carry genes that confer upon their host cell resistance to antibiotics, heavy metals, or cellular toxins, preferential survival
29
What are transposons
- Mobile Genetic Elements: Move from one chromosome to another or from one cell to another, genetic elements that exist out- side chromosomes
- Transposons: Small segments of DNA that can move from one region of a DNA molecule to another
- Simple: Insertion sequences (IS), contain gene that codes for an enzyme and recognition site
- Complex: Carry genes not connected with transposition process (enterotoxins or antibiotic resistance)
30
What is bacterial conjugation
- Requires direct cell-cell contact and conjugating cells must generally be of opposite mating type (donor carry plasmid recipient does not)
- Gram -ve cells have plasmid encoded sex pillus genes
- Gram +ve bacteria have sticky surface molecules that attract cells together
31
Describe conjugation in E.coli
- When an F factor (plasmid) is transferred from a donor (F+) to a recipient (F-), the F- cell is converted to an F+ cell
- Alternatively, when an F factor becomes integrated into the chromosome of an F+ cell, it makes the cell a high frequency of recombination (Hfr) cell.
- When an Hfr donor passes a portion of its chromosome into an F- recipient, a recombinant F- cell results
32
What is transduction by a bacteriophage
- Bacterial DNA is transferred from a donor cell to a recipient cell inside a virus that infects bacteria (bacteriophage / phage)
- Generalised: Random bacterial DNA is packaged inside a phage and transferred to a recipient cell
- Specialised: Specific bacterial genes are packaged inside a phage and transferred to a recipient cell
33
What is the Ames test
- A procedure using bacteria to identify potential carcinogens
- Based on observation that exposure of mutant bacteria to mutagenic substances may cause new mutations that reverse effect of original mutation
34
What is genetic transformation
- Genes transferred from one bacterium to another as “naked” DNA in solution
- Occurs naturally among a few spp. of bacteria, works best with related donor and recipient cells
- Bacillus, staph, strep, haemophilus
- Competent Cell: Recipient cell that is in a physiological state to take up DNA, competence results from alterations in the cell wall that make it permeable to large DNA molecules
