Microbiology Ch. 9 - Genetics

Transcription of DNA

* more detail in our slides * cannot find better visual description *

DNA Translation

*look at notes taken on slide*

Horizontal Gene Transfer: General Transduction

- bacteriophage serves as a carrier for DNA between donor cell and recipient cell - random fragments of disintegrating host DNA are taken up by the bacteriophage - virtually any gene from the bacterium can be transmitted

Excision Repair

- enzymes break the bonds between the bases at the sugar-phosphate strand at the site of the error - an enzyme removes the defective bases one at a time - the remaining gap is filled in by DNA polymerase I and ligase

RNA involved in translation

- mRNA - tRNA - rRNA

Regulatory RNAs

- micro RNAs (miRNA) - anti-sense RNAs - riboswitches - small interfering RNAs (siRNA)

UV Damage Repair

- photoactivation/light repair through photolyase is effective for small numbers of mutations - rec pathways are successful in repair of larger numbers of UV mutations

Posttranslational Modifications

- some have the starting amino acid removed - cofactors must be added to make enzymes - some join other proteins to form quaternary structures

Horizontal Gene Transfer: Specialized Transduction

- specific part of the host genome is regularly incorporated into the phage - DNA moved by a temperate (lysogenic) prophage inserted in a fixed site on the bacterial chromosome - when activated the prophage DNA separates from the bacterial chromosome taking adjacent host genes with it - during the lytic cycle, these specific viral-host gene combinations are incorporated into the viral particles

Genetic Code

AUG = start UAA, UAG, UGA = stop

Nucleotides

DNA- made up of a phosphate group, a deoxyribose sugar, and a nitrogenous base (A, T, C, G) RNA- made up of a phosphate group, a ribose sugar, and a nitrogenous base (U, T, C, G) *nitrogenous base attached by covalent bonds at the 1' position of the sugar; phosphates attached at the 5'

5) Translation: formation of peptide bond 2

This releases tRNA 2, shifts mRNA to the next position, moves tRNA 3 to position P, and opens position A for the next tRNA (which will be called tRNA 4).

Viral Genomes

vary in size and organization: circular, linear, segmented (ex: influenza)

Polyribosomal Complex

mRNA is long enough to be fed through more than one ribosome, allowing for the synthesis of hundreds of protein copies from the same mRNA transcript *only in prokaryotes

Structural Locus (lac operon)

made up of three genes, each coding for a different enzyme needed to catabolize lactose

Genotype

the sum of all gene types; an organism's distinctive genetic makeup

Horizontal Gene Transfer: Transposons

these genetic elements are capable of moving from place to place in genome, can be transferred from a chromosome to a plasmid, can move adjacent DNA - involved in changes in traits such as colony morphology, pigmentation, and antigenic characteristics; replacement of damaged DNA; intermicrobial transfer of drug resistance (in bacteria) - not interdependent

Horizontal Gene Transfer

transfer of DNA from one organism to another that did not come directly from parental organisms; typically involves plasmids

Proofreading Mechanisms

used to repair mistakes in replication

Baltimore Classification

classifies DNA and RNA by how they become mRNA; 7 groups

Exons

coding regions that will be translated into proteins (eukaryotic cells)

Control Locus (lac operon)

composed of the promoter and the operator, a sequence that acts as an on/off switch

Genome

comprises all the genetic material that an organism possesses bacteria typically have a single (haploid) circular chromosome while eukaryotes have a complete set of nuclear chromosomes

Repressible Operons

contain genes for coding anabolic enzymes and are repressed by the product synthesized by the enzyme

Chromosomes

contain genetic material necessary to reproduce an organism; DNA + proteins

Operons

coordinated set of genes controlled by the same promotor(s), typically found in bacteria

Segmented Viral "Reassortment"

ex: influenza- one component accumulates mutation changes that the virus is no longer vaccinated for, creating a genometric shift (why we vaccinate every flu every year)

Genes that code for certain types of RNA's

examples: rRNA, snRNA, ...

Processing of mRNA

1) transcription of entire gene 2) a series of adenosines are added to the mRNA to protect it and direct it out of the nucleus for translation 3) spliceosome cuts through the intron-exon junctions 4) exon joined to the end 5) mRNA is then translated

Nonsense Mutation (Point)

changes a normal codon into a STOP codon; almost always results in a nonfunctional protein

High Frequency Recombination (Hfr) Donors

F plasmid becomes integrated into the F+ donor chromosome through conjugation Hfr transfer: involves transmission of chromosomal genes from a donor cell to a recipient cell, the plasmid jumps into the chromosome, and when the chromosome is duplicated the plasmid and part of the chromosome are transmitted to a new cell through conjugation; this plasmid/chromosome hybrid then incorporates into the recipient chromosome

Gram Negative Conjugation

Fertility (F' factor) allows synthesis of conjugative pilus, recipient cell has a recognition site on its surface F+ cell has the plasmid, F- cell lacks the plasmid contact is made when a pilus grows out from the F+ cell, attaches to the surface of the F- cell, contracts, and draws the two cells together the process: donor (F+) cell makes a copy of its F factor, transmits this to a recipient (F-) cell and turns it into an F+ cell capable of producing a pilus and conjugating with other cells

6) Translation: discharge of tRNA 2; second translocation; enter tRNA 4

From this point on, peptide elongation proceeds repetitively by this same series of actions out to the end of the mRNA.

Initiation of Transcription

RNA polymerase recognizes a segment of the DNA called the promoter region. This region consistsof two sequences of DNA just prior to the beginning of the gene to be transcribed. These promoter sequences provide the signal for RNApolymerase to bind to the DNA. Then there is a special codon called the initiation codon, which is where the RNA polymerase begins itstranscription. As the DNA helix unwinds, the polymerase first pulls the early parts of the DNA into itself, a process called "DNA scrunching,"and then, having acquired energy from the scrunching process, begins to advance down the DNA strand to continue synthesizing an RNAmolecule complementary to the template strand of DNA. The nucleotide sequence of promoters differs only slightly from gene to gene, withall promoters being rich in adenine and thymine.

2) Translation: formation of the peptide bond

Rules of pairing dictate that the anticodon of this tRNA must be complementary to the mRNA codon AUG; thus, the tRNA with anticodon UAC will first occupy site P. It happens that the amino acid carried by the initiator tRNA in bacteria is formyl methionine. The formyl group provides a special signal that this amino acid is not part of the translated protein because usually fMet does not remain a permanent part of the finished protein but instead is cleaved from the finished peptide. The ribosome shifts its "reading frame" to the right along the mRNA from one codon to the next. This brings the next codon into place on the ribosome and makes a space for the next tRNA to enter the A position. A peptide bond is formed between the amino acids on the adjacent tRNAs, and the polypeptide grows in length. Elongation begins with the filling of the A site by a second tRNA. The identity of this tRNA and its amino acid is dictated by the second mRNA codon.

3) Translation: discharge of tRNA 1 at E site

The entry of tRNA 2 into the A site brings the two adjacent tRNAs in favorable proximity for a peptide bond to form between the amino acids (aa) they carry. The fMet is transferred from the first tRNA to aa 2, resulting in two coupled amino acids called a dipeptide. For the next step to proceed, some room must be made on the ribosome, and the next codon in sequence must be brought into position for reading. This process is accomplished by translocation, the enzyme-directed shifting of the ribosome to the right along the mRNA strand, which causes the blank tRNA 1 to be discharged from the ribosome at the E site.

1) Translation: entrance of tRNAs 1 and 2

The mRNA molecule leaves the DNA transcription site and is transported to ribosomes in the cytoplasm. Ribosomal subunits come together and form sites to hold the mRNA and tRNAs. The ribosome begins to scan the mRNA by moving in the 5' to 3' direction along the mRNA. The first codon it encounters is called the START codon, which is almost always AUG (and, rarely, GUG). With the mRNA message in place on the assembled ribosome, the next step in translation involves entrance of tRNAs with their amino acids. The pool of cytoplasm contains a complete array of tRNAs, previously charged by having the correct amino acid attached. The step in which the complementary tRNA meets with the mRNA code is guided by the two sites on the large subunit of the ribosome called the P site (left) and the A site (right). The ribosome also has an exit or E site where used tRNAs are released. (P stands for peptide site; A stands for aminoacyl (amino acid) site; E stands for exit site.)

7) Translation: formation of peptide bond 3

The termination of protein synthesis is not simply a matter of reaching the last codon on mRNA. It is brought about by the presence of at least one special codon occurring just after the codon for the last amino acid. Termination codons—UAA, UAG, and UGA—are codons for which there is no corresponding tRNA. Although they are often called nonsense codons, they carry a necessary and useful message: Stop here. When this codon is reached, a special enzyme breaks the bond between the final tRNA and the finished polypeptide chain, releasing it from the ribosome.

4) Translation: first translocation

This also shifts the tRNA holding the dipeptide into P position. Site A is temporarily left empty. The tRNA that has been released is now free to drift off into the cytoplasm and become recharged with an amino acid for later additions to this or another protein. The stage is now set for the insertion of tRNA 3 at site A as directed by the third mRNA codon. This insertion is followed once again by peptide bond formation between the dipeptide and amino acid 3 (making a tripeptide), splitting of the peptide from tRNA 2, and translocation.

Wild Type

a microorganism that exhibits a "natural" characteristic

Causes of Mutations: Spontaneous Mutation

a random change in the DNA arising from errors in replication

Nucleiod

a region of a bacterial cell where the chromosome is found; not membrane bound

Lac Operon*

accounts for the regulation of lactose metabolism in E. Coli *original notes

Silent Mutation

alters the base but does not change the amino acid

Mutation

an accidental or unplanned change in a nucleotide sequence *a mutation in DNA that is copied into mRNA and translated can change the structure of the protein which can change morphology and physiology * majority are neutral, followed by harmful * permanent and passed down

Gram Positive Conjugation

an opening is created between two adjacent cells, replicated DNA passes across from one cell to another

DNA Polymerase III

can add nucleotides in the 5' to 3' direction; can identify a mismatched nucleotide and remove it from the daughter strand (working 3' to 5') *a proofreading mechanism

Competent Cells

cells that are capable of accepting genetic material

Regulators (lac operon)

gene that codes for a protein capable of repressing the operon (a repressor) and, distantly, a gene that codes for a protein capable of activating the operon (an activator)

Structural Genes

genes that code for proteins

Regulatory Genes

genes that control gene expression

Codon

groups of three nucleotides encode which amino acid is added to the peptide chain

Polyploid

having more than one complete genome copy per cell; the obligate human pathogen Neisseria Gonorrhoeae is ____

Primosome

in DNA replication, DNA helicase and primase are physically bound to each other to form a complex called the _____

Eukaryotic Transcription and Translation

in this type of cell, mRNAs code for just one protein, transcription takes place in the nucleus and translation in the cytoplasm

Prokaryotic Transcription and Translation

in this type of cell, the start codon AUG codes for a different form of methionine called formylmethionine

Inducible Operons

induced by the presence of a substrate, code for enzymes; only produced when needed

Introns

intervening sequence of bases that do not code for a protein (eukaryotic cells)

Horizontal Gene Transfer: Conjugation

mode of genetic exchange in which a plasmid or other genetic material is transferred by a donor to a recipient cell via direct contact conjugation is a conservative process in which the donor bacterium retains (conserves) a copy of the genetic material being transferred

Missense Mutation (Point)

mutation that leads to a different amino acid - creates a faulty, nonfunctional, or less functional protein - produces a protein that functions in a different manner or - causes no significant alteration in protein function

Frameshift Mutation

mutation that occurs when one or more bases are inserted into or deleted from a DNA strand putting the code out of frame - reading frame of mRNA has been changed - nearly always results in a nonfunctional protein - generally every amino acid after the mutation is different from what was coded for in the original DNA *addition or deletion of bases in multiples of 3 does not alter the reading frame

Conditional Lethal Mutations

mutations that are lethal under one condition but not under other conditions *example?

Wobble

only the first two nucleotides are required to encode the correct amino acid, the third does not change its sense; this is called ________

Primer RNAs

operative in both prokaryotic and eukaryotic cells

Elongation of Transcription

proceeds in the 5' to 3'direction (with regard to the growing RNA molecule), the mRNAis assembled by the addition of nucleotides that are complemen-tary to the DNA template. Remember that uracil (U) is placed asadenine's complement. As elongation continues, the part of DNAalready transcribed is rewound into its original helical form.

Neutral Mutations

produce neither adverse or helpful changes

Riboenzymes

remove unneeded sequences from other RNAs

Causes of Mutations: Induced Mutations

result from exposure to known mutagens, which are primarily physical or chemical agents that disrupt DNA - radiation: UV light, X rays - chemicals: nitrous acid, acridine orange, ...

Mutant Strain

shows variance in one or more of the following: - morphology - nutritional characteristics - Genetic control mechanisms - resistance to chemicals - temperature preference - enzymatic function - genomic sequence that is not found in the "wild type"

Termination of Transcription

the polymerases recognize anothercode that signals the separation and release of the mRNA strand,or transcript. The smallest mRNA might consist of 100 bases; anaverage-size mRNA might consist of 1,200 bases; and a large onemight consist of several thousand.

Replisome

the primosome is physically associated with two DNA polymerase III holoenzymes to form the ____

Molecular and Biochemistry

site on the chromosome that provides information for a cell to function

Point Mutations

small mutations that affect only a single base in a gene

Plasmids

small, circular pieces of DNA that contain their own origin of replication, can replicate independently of the bacterial chromosome, can contain genes that confer useful traits (like antibiotic resistance, virulence factors, ...)

Genetics

study of inheritance or heredity of living things, the transmission and expression of traits from parent to offspring, and the regulation of genes

Recombination

the breaking and rejoining of DNA strands to form new DNA sequences; new sequence is different from both the donor and the original; can provide resistance to drugs; new nutritional and metabolic capabilities; and virulence determinants

Phenotype

the expression of certain traits

Classical Genetics

the fundamental unit of heredity responsible for a given trait in an organism

Intergenic Regions

the nontranscribed DNA between adjacent genes in bacterial chromosomes

Semi-conservative

the overall replication process of DNA is ______ - strands of the existing DNA split, copy one strand and produce two complete daughter molecules; each daughter is identical to the parent in composition; neither strand is 100% new

Chargoff's Rule

the pairing of the bases; formed by H-bonds - Adenine always pairs with Thymine - Guanine always pairs with Cytosine *more stable

Horizontal Gene Transfer: Transformation

when a chromosome released by a lysed cell breaks into fragments small enough to be accpeted by a recipient cell and its DNA retains sequence, _____ is the "nonspecific" acceptance by a bacterial cell of those small fragments of DNA from the environment - facilitated by DNA-binding proteins on cell wall, DNA uptake sequence required in some cases - no special appendages required

Back Mutation

when a gene that has undergone mutation reverses to its original composition or a composition that restores function

Phase Variation

when bacteria turn on or off a complement of genes that leads to obvious phenotypic changes, managed by regulatory proteins; most often describes the ability of bacteria to change its surface for targeting the host's immune system and attach to surfaces examples: - Neisseria gonorrhoeae- production of attachment fimbriae/pili - Streptococcus pneumoniae- production of a capsule