MICROBIAL GENETICS Flashcards by VILLANUEVA, PAULA CHARMIANNE M.

is the study of the mechanisms of heritable information in microorganisms (bacteria, archaea, viruses and some protozoa and fungi).

Microbial Genetics

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also involves the study of the genotype of microbial species and also the expression system in the form of phenotypes.

Microbial Genetics

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This mainly involves the conversion of DNA encoded information into RNA, that is then essential to form proteins.

The Central Dogma of Molecular Biology

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The Central Dogma of Molecular Biology is therefore divided into three major events:

DNA replication, mRNA Transcription, and protein Translation

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is any heritable alteration in the base sequence of the genetic material

Mutation

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(TRANSFER MECHANISM) can either be via vertical gene transfer (movement of genetic material by descent) or horizontal gene transfer (movement of genes between cells that are not direct descendants of one another).

 Gene transfer mechanisms in prokaryotes

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(movement of genetic material by descent)

vertical gene transfer

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(movement of genes between cells that are not direct descendants of one another).

horizontal gene transfer

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 Each nucleotide has 3 parts:

-> a nitrogen-containing base
- [adenine (A), thymine (T), cytosine (C), guanine (G), and uracil (U).]

-> Purines - A and G
- Pyrimidines - C, T, and U

-> a pentose (five-carbon) sugar
o DNA - deoxyribose
o RNA - ribose
- a phosphate group (phosphoric acid).

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[STRUCTURE OF DNA]

consists of two strands that form a double helix structure.

A molecule of DNA

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Each DNA strand is composed of

nucleotides

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—units made up of a sugar (deoxyribose), a phosphate group, and a nitrogenous base.

nucleotides

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 The nitrogenous base pairs are joined by

hydrogen bonds.

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 The two strands of DNA are

antiparallel

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[STRUCTURE OF RNA ]

RNA, like DNA, is made up of nucleotide consisting of a

5-carbon sugar ribose,
phosphate group, and
a nitrogenous base.

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three main differences between DNA and RNA:

 RNA uses the sugar ribose instead of deoxyribose.
 RNA is generally single-stranded.
 RNA contains uracil in place of thymine.

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RNA has 3 types:

 mRNA (messenger RNA) – type of RNA generated from transcribing DNA. Carries information for the translation of a particular protein.

 rRNA (ribosomal RNA) – structural component of ribosomes.

 tRNA (transfer RNA) – carries amino acids to the ribosome during translation to help build an amino acid chain.

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[Central Dogma of Molecular Biology ]

contains the complete genetic information that defines the structure and function of an organism.

 DNA

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[Central Dogma of Molecular Biology ] are formed using the genetic code of the DNA.

 Proteins

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 Thus, within most cells, the genetic information flows from –

DNA > RNA > PROTEIN

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the organism’s genetic makeup - all its DNA—the information that codes for all the particular characteristics of the organism.

 Genotype –

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refers to actual, expressed properties (proteins).

 Phenotype –

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DNA REPLICATION -

Universal Features of DNA replication

a.) semi-conservative mode
 resulting daughter molecules each have one parental (old) strand and
one newly synthesized strand

b.) Watson and Crick base pairing maintained

c.) DNA is synthesized in the 5’ to 3’ direction

d.) A primer is needed for initiation
 stretch of DNA or RNA nucleotides that provide 3’ OH end

e.) A complex process involving several enzymes and proteins

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[STAGES IN DNA REPLICATION]

sequence of DNA at which replication is initiated on a chromosome, plasmid or virus.

 Origin of Replication -

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[INITIATION]  relaxes supercoiling ahead of the replication fork.

DNA gyrase and topoisomerases

[INITIATION] - The point at which replication actively occurs.

Replication fork

[INITIATION] The two strands of parental DNA are unwound by

 The two strands of parental DNA are unwound by helicase.

[INITIATION]  signal the starting point of DNA replication, synthesized by _____

 Primers signal the starting point of DNA replication  Synthesized by primase

[Elongation] _______ parental strands serve as template for the DNA replication.

 Both parental strands serve as template for the DNA replication.

[Elongation] _______ synthesizes only at the 5’ to 3’ direction.

 DNA polymerase synthesizes only at the 5’ to 3’ direction.

[Elongation] DNA polymerase synthesizes only at the ____________

 DNA polymerase synthesizes only at the 5’ to 3’ direction.

[Elongation] DNA replication is ____________ (direction)

DNA replication is biredirectional.

[Elongation] Leading strand is __________

 Leading strand- continuous

[Elongation] _________________ synthesized opposite to the fork movement; discontinuous

 Lagging strand –synthesized opposite to the fork movement; discontinuous

[Elongation]  one primer  DNA polymerase ; 5' to 3’

 Leading strand

[Elongation]  several primers  DNA polymerase; 5' to 3'  Okazaki fragments

 Lagging strand

________________ occurs when two replication forks meet on the same stretch of DNA, during which the following events occur, although not necessarily in this order:

 Termination of DNA replication occurs when two replication forks meet on the same stretch of DNA, during which the following events occur, although not necessarily in this order:  forks converge until all intervening DNA is unwound  any remaining gaps are filled and ligated (DNA ligase) - replication proteins are unloaded

 the synthesis of a complementary strand of RNA from a DNA template.

TRANSCRIPTION

[TRANSCRIPTION] __________ is synthesized using a specific portion of the cell’s DNA as a template.

 a strand of mRNA is synthesized using a specific portion of the cell’s DNA as a template.

STEPS IN TRANSCRIPTION

1. RNA polymerase binds to the DNA at a site called the promoter.  Only one of the two DNA strands serves as the template for RNA synthesis for a given gene. 2. RNA polymerase synthesize mRNA in the 5’ – 3’ direction 3. RNA synthesis continues until RNA polymerase reaches a site on the

[TRANSCRIPTION] DNA called the ___________

 DNA called the terminator

[TRANSCRIPTION]  The language of mRNA is in the form of _________  groups of 3 nucleotides, such as ____________________

 The language of mRNA is in the form of codons.  groups of 3 nucleotides, such as AUG, GGC, or AAA

[TRANSCRIPTION] _________________________ determines the sequence of amino acids that will be in the protein being synthesized.

 The sequence of codons on an mRNA molecule determines the sequence of amino acids that will be in the protein being synthesized.

[TRANSCRIPTION]  Also known as ______________

Also known as protein synthesis.

[The Genetic Code]  there are #________ possible codons but only #______ amino acids.  This means that most amino acids are signaled by several alternative codons.

 there are 61 possible codons but only 20 amino acids.  This means that most amino acids are signaled by several alternative codons.

[The Genetic Code] Codons for same amino acid usually differ in __________ position only

 Codons for same amino acid usually differ in 3rd position only

[The Genetic Code] HYPOTHESIS FOR: Codons for same amino acid usually differ in 3rd position only

 Third Base Degeneracy / Wobble Hypothesis

are attached to a single mRNA, all at various stages of protein synthesis.

[The Genetic Code]  usually a number of ribosomes are attached to a single mRNA, all at various stages of protein synthesis.

[The Genetic Code]  In prokaryotic cells, the translation of mRNA into protein can begin ____________________

 In prokaryotic cells, the translation of mRNA into protein can begin even before transcription is complete.

[The Genetic Code]  In prokaryotic cells, the translation of mRNA into protein can begin even before transcription is complete.

 Co-transcription translation

STEPS IN TRANSLATION

1. The ribosome binds to mRNA at a specific area. 2. The ribosome starts matching tRNA anticodon sequences to the mRNA codon sequence. 3. Each time a new tRNA comes into the ribosome, the amino acid that it was carrying gets added to the elongating polypeptide chain. 4. The ribosome continues until it hits a stop sequence, then it releases the polypeptide and the mRNA. 5. The polypeptide forms into its native shape and starts acting as a functional protein in the cell.

 any heritable alteration in the base sequence of the genetic material

MUTATION

 appear suddenly without any transitional stage between the initial and final states of the organisms.

MUTATION

 when established, mutation may be permanently present whether or not the conditions of development of the mutated organism allow their detection

MUTATION

________________ Can either be spontaneous or induced.

MUTATION Can either be spontaneous or induced.

[TYPE OF MUTATION]  occur without external intervention, and most result from occasional errors in the pairing of bases by DNA polymerase during DNA replication

 Spontaneous mutation -> occur without external intervention, and most result from occasional errors in the pairing of bases by DNA polymerase during DNA replication

[TYPE OF MUTATION]  caused by agents in the environment and include mutations made deliberately by humans.

 Induced mutation -> caused by agents in the environment and include mutations made deliberately by humans.

[TYPE OF MUTATION]  result from exposure to natural radiation that alters the structure of bases in the DNA, or from a variety of chemicals that chemically modify DNA

 Induced mutation -> result from exposure to natural radiation that alters the structure of bases in the DNA, or from a variety of chemicals that chemically modify DNA

[TYPES OF MUTATION]  a single base at one point in the DNA sequence is replaced with a different base during replication.

A. Base Substitution / Point Mutation

A. Base Substitution / Point Mutation can either be: ____________

Can either be:  Transition * Purine to purine or pyrimidine to pyrimidine  Transversion * Purine to pyrimidine or vice versa

[A. Base Substitution / Point Mutation] * Purine to purine or pyrimidine to pyrimidine

Transition * Purine to purine or pyrimidine to pyrimidine

[A. Base Substitution / Point Mutation] * Purine to pyrimidine or vice versa

Transversion * Purine to pyrimidine or vice versa

[TYPES OF MUTATION] Consequences of Base Pair changes [1&2]

1. Missense mutation  changes a codon for one amino acid to a codon for another amino acid  results in an amino acid substitution in the protein product. 2. Nonsense mutation  changes a codon for an amino acid with a codon for chain termination (UAG, UAA, UGA)

[TYPES OF MUTATION - Consequences of Base Pair changes]  changes a codon for one amino acid to a codon for another amino acid

1. Missense mutation

[TYPES OF MUTATION - Consequences of Base Pair changes]  results in an amino acid substitution in the protein product.

1. Missense mutation

[TYPES OF MUTATION - Consequences of Base Pair changes]  changes a codon for an amino acid with a codon for chain termination (UAG, UAA, UGA)

2. Nonsense mutation

[TYPES OF MUTATION - Consequences of Base Pair changes]  a change in codon composition that has no effect on the resulting polypeptide

3. Silent mutation

[TYPES OF MUTATION]  adds or deletes one or two bases (or any non-multiple of 3) from a coding sequence in a DNA, so that the genetic code is read out-of-phase

4. Frameshift Mutation

[TYPES OF MUTATION] Frameshift Mutation - CONSEQUENCE

 incorrect amino acid or premature termination  severe phenotypic effects

[TYPES OF MUTATION]  mutation in which a region of the DNA has been eliminated.

5. Deletion

[TYPES OF MUTATION]  occurs when new bases are added to the DNA

6. Insertion

 physical or chemical agents that changes the genetic material.

MUTAGENS

[MUTAGENS]  high energy radiations  penetrate living cells

 Physical Mutagens

[MUTAGENS] 2 types of Physical Mutagens

 2 types: Electromagnetic radiations and Particulate radiations

[PHYSICAL MUTAGENS] * Gamma rays, X-rays and ultraviolet rays * penetration power is inversely proportional to their wavelength

1. Electromagnetic radiations

[PHYSICAL MUTAGENS - Electromagnetic radiations] RESULT #1 Gamma Rays and X-rays (ionizing radiation) - DIRECT & INDIRECT EFFECT

Gamma Rays and X-rays (ionizing radiation) -> Direct effect: single or double stranded breaks in the DNA molecules. -> Indirect effect: free radicals created  form compounds, hydrogen peroxide - initiate harmful chemical reactions within the cells.  Can lead to cell death

[PHYSICAL MUTAGENS - Electromagnetic radiations ] RESULT #2  Ultraviolet rays (non-ionizing radiation)

 Formation of pyrimidine dimers  Most are immediately repaired, but some escape repair and

[PHYSICAL MUTAGENS]  are in the form of sub-atomic particles emitted from the atoms with high energy

2. Particulate radiations

[PHYSICAL MUTAGENS] penetrating power : Beta particles > alpha particles because of its smaller size

 Alpha particles, beta particles and neutrons

[PHYSICAL MUTAGENS] extremely penetrant, and can cause severe damage to the living tissues as well as genetic material

 Neutrons: extremely penetrant, and can cause severe damage to the living tissues as well as genetic material

_____________________ breaks in the DNA

 single strand or double-strand breaks in the DNA

[Chemical Mutagens]

[Chemical Mutagens]  classified into 4 major groups: on the basis of their specific reaction with DNA.

1. Deaminating agents 2. Base Analogs 3. Alkylating Agents 4. Intercalating Agents

[Chemical Mutagens] - cause the loss of the amino group. e.g. nitric oxide, nitrous acid, or N-nitrosoindoles

1. Deaminating agents - cause the loss of the amino group. e.g. nitric oxide, nitrous acid, or N-nitrosoindoles

[Chemical Mutagens] ________ structurally resemble purines and pyrimidines and may be incorporated into DNA in place of the normal bases during DNA replication. They induce mutations because they often have different base-pairing rules than the bases they replace.

2. Base Analogs - structurally resemble purines and pyrimidines and may be incorporated into DNA in place of the normal bases during DNA replication. They induce mutations because they often have different base-pairing rules than the bases they replace.

[Chemical Mutagens] __________________ chemicals that donate alkly groups (methyl, ethyl) to other molecules. The alkylated base may then degrade to yield a baseless site, which is mutagenic and recombinogenic, or mispair to result in mutations upon DNA replication.  e.g. methylmethane sulphonate (MMS), ethyl methane sulfonate (EMS),N-methyl-N’-nitro-N-nitrosoguanidine (MNNG)

3. Alkylating Agents - chemicals that donate alkly groups (methyl, ethyl) to other molecules. The alkylated base may then degrade to yield a baseless site, which is mutagenic and recombinogenic, or mispair to result in mutations upon DNA replication.  e.g. methylmethane sulphonate (MMS), ethyl methane sulfonate (EMS),N-methyl-N’-nitro-N-nitrosoguanidine (MNNG)

[Chemical Mutagens] __________________ molecules that may insert between bases in DNA, causing frameshift mutation during replication.  E.g. acridine derivatives (acridine orange, proflavine, acriflavine), nitrogen mustards ethidium bromide

4. Intercalating Agents- molecules that may insert between bases in DNA, causing frameshift mutation during replication.  E.g. acridine derivatives (acridine orange, proflavine, acriflavine), nitrogen mustards ethidium bromide

[Gene Transfer Mechanisms in Prokaryotes]  movement of genetic material by descent where information travels through the generations as the cell divides.  e.g. antibiotic resistance due to spontaneous mutation transferred directly to all the bacteria's progeny during DNA replication

Vertical Gene Transfer

[Gene Transfer Mechanisms in Prokaryotes]  movement of genes between cells that are not direct descendants of one another.  3 mechanisms: Transformation, Conjugation, and Transduction

Horizontal Gene Transfer (HGT)

[Gene Transfer Mechanisms in Prokaryotes]  “10,000 unique genes flowing via HGT among 2,235 bacterial genomes," providing the bacteria with genetic information they didn't inherit from their parent cells.  multiple drug resistance

Horizontal Gene Transfer (HGT)

[Gene Transfer Mechanisms in Prokaryotes] -> the physical exchange of DNA between genetic elements

Recombination

[Gene Transfer Mechanisms in Prokaryotes] -> Horizontally-transferred DNA from a donor should undergo recombination with the recipient’s DNA in order to be retained in the recipient.

Recombination

[Gene Transfer Mechanisms in Prokaryotes] -> Not necessarily for plasmids

[Gene Transfer Mechanisms in Prokaryotes] -> Can replicate itself

Recombination

[Gene Transfer Mechanisms in Prokaryotes]

[Gene Transfer Mechanisms in Prokaryotes]  the uptake of exogenous DNA from the environment.  involves recombination and integration in the recipient’s genome.  sources of exogenous DNA: - native bacterial chromosome fragments - plasmid - bacteriophage DNA  cell-cell contact is not required

Transformation

[Gene Transfer Mechanisms in Prokaryotes]  sources of exogenous DNA:

- native bacterial chromosome fragments - plasmid - bacteriophage DNA

[Gene Transfer Mechanisms in Prokaryotes - Conjugation]  F plasmid (“F” stands for ___________)

 F plasmid (“F” stands for Fertility)

[Gene Transfer Mechanisms in Prokaryotes]  plasmid-encoded mechanism that can mediate DNA transfer between bacterial cells.  requires cell-to-cell contact (mating)  Occurs via a conjugal/membrane pore  DNA transfer occurs in one direction - from donor (contains F plasmid) to recipient not vice versa.  Found in donor cells which are designated as F+ cells.  Encode genes that allow conjugative transfer of genes.  F - encoded (sex) pilus  Allow specific pairing of donor (F+) and recipient cells (F-)

Conjugation

[Gene Transfer Mechanisms in Prokaryotes]  the transfer of genetic information between cells through the mediation of a virus (phage) particle  does not require cell to cell contact.

Transduction

[Gene Transfer Mechanisms in Prokaryotes]  common tool used by molecular biologists to stably introduce a foreign gene into a host cell’s genome on both bacterial and mammalian cells.

Transduction

 Transduction Two ways:

1. Generalized transduction 2. Specialized transduction

[Transduction Two ways]  DNA derived from virtually any portion of the host genome is packaged inside the mature virion in place of the virus genome  the bacterial donor genes cannot replicate independently and are not part of a viral genome

1. Generalized transduction

[Transduction Two ways]  DNA from a specific region of the host chromosome is integrated directly into the virus genome— usually replacing some of the virus genes.

2. Specialized transduction

MICROBIAL GENETICS Flashcards

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