Microbiology MCC Scott Quinton Exam 3

mRNA (messenger RNA)

"A riboswitch" that regulates translation. A type of RNA, synthesized from DNA, that attaches to ribosomes in the cytoplasm and specifies the primary structure of a protein.

transformation

"naked" DNA, in solution from the environment

Translation (RNA to protein)

*Initiation*: Initiation factors bind ribosome to 1st codon, AUG *Elongation*: EF-Ts, EF-Tu, EF-G bring GTP energy -Polymerization, movement of ribosome along mRNA *Termination*: Releasing factors undock ribosome from mRNA

Describe DNA replication

1) Unwinding of DNA molecule 2) Breaking parent strands apart hydrogen bonds broken 3) Assembly of new DNA strands DNA polymerase assembling new strands of DNA complementary deoxyribonucleotides paired e.g., AATCGATCG paired with TTAGCTAGC via hydrogen bonds 4) Restoration of DNA to coiled double helix

Transcription (DNA to RNA)

1. Initiation 2. Elongation 3. Termination Unit: stretch of DNA that codes for a polypeptide or RNA (tRNA, rRNA) RNA Polymerase II: Separates DNA strands and transcribes mRNA. Attaches to promoter (start of gene), stops at terminator (end). mRNA elongates in 5' - 3' Uracil replaces thymine when pairing to adenine

RNA processing in eukaryotes

1. initiation 2. elongation 3. termination *4. "tail step"-splice and dice*

DNA is synthesized in what direction?

5' to 3' at the replication fork, the leading strand is synthesized continuously and the lagging strand (3' to 5') discontinuously

Nucleic acids only grow in

5-->3-'OH

Gene

A segment of DNA on a chromosome that codes for a specific trait

terminator

A special sequence of nucleotides in DNA that marks the end of a gene. It signals RNA polymerase to release the newly made RNA molecule, which then departs from the gene

DNA polymerase

An enzyme that catalyzes the formation of the DNA molecule. proofreads new molecules of DNA and removes mismatched bases before continuing DNA synthesis

RNA polymerase

Binds to promoter; transcription begins at AUG; the region of DNA that is the end point of transcription is the terminator; synthesizes a strand of RNA from on strand of double-stranded DNA, which serves as a template

shuttle vectors

Can exist in several different species, plasmids and viruses can be used as vectors

chemical mutagens

Chemicals (nitrogen/nitrogenous bases)that cause genetic mutations

What is tryptophan?**

Corepressor because if there is too much trypt, made, it'll bind and help to repress the operator gene

Four tools of biotechnology that every technique uses

Cut, amplify, insert, grow

Define and describe: Transduction

DNA is passed from one bacterium to another in a bacteriophage and is then incorporated into the recipients DNA, generalized description: any bacterial gene can be transferred

How can mutations be repaired?

DNA polymerase, and photolyases(for uv radiation only)

describe the process of dna replication

DNA replication fork; DNA is copied; DNA unzips, one strand serves as the template and creates 2 new DNA molecules

central dogma

DNA-transcription-RNA-translation-protein

Southern Blotting uses

DNA; DNA probes detect specific DNA in fragments (RFLPs) searated by electrophoresis

restriction enzymes

Enzyme that cuts DNA at a specific sequence of nucleotides

Define and describe: Transformation

Genes are transferred from one bacterium to another as "naked" DNA in a solution

Describe how DNA serves as genetic information.

Genetic information is encoded by the sequence of bases along a strand of DNA.

What is the role of cAMP in catabolite repression?

Is a co-inducer, super promoter. Makes it go fast

inducible operon (lac operon)

Lac is always "off" uless lactose is present-active repressor binds to the operator -inducer (lactose) binds to and inactivates the repressor

How do you repair thymine dimers from UV radiation(nonionizing) ?

Photolyases; light repair mechanism to separate dimers

Four tools of biotech: step 2 amplify

Polymerase chain reaction (PCR)

Operon model of gene expression

Promoter: segment of DNA where RNA polymerase initiates transcription of structural genes Operator: segment of DNA that controls transcription of structural genes Operon: set of operator and promoter sites and the structural genes they control

Northern blotting uses

RNA

Define and describe: Transposons

Small segments of DNA that moves from one region to another of the same chromosome or to a different chromosome or plasmid. Complex versions can carry any type of gene; including antibiotic resistant genes

nonsense codons

Stop codons (UAA, UAG, and UGA)

What is CAP?

Super promoter for RNA polymerase

explain how mutant microorganisms can be used to detect chemical carcinogens

The Ames test is inexpensive and fast for identification of possible chemical carcinogens, test assumes the mutant cell can revert to a normal cell in presence of a mutagen and that many mutagens are carcinogens

non-coding strand (anti-sense strand)

The DNA strand that forms the template for the transcribed mRNA. This strand is the opposite strand of the coding strand. contains anticodons.

tRNA (transfer RNA)

The form of RNA that carries each amino acid to the ribsome to form the polypeptide chain (protein)

leading strand

The new continuous complementary DNA strand synthesized along the template strand in the mandatory 5' to 3' direction.

Genetic Recombination

The regrouping of genes in an offspring that results in a genetic makeup that is different from that of the parents.

lagging strand

The strand in replication that is copied 3' to 5' as Okazaki fragments and then joined up by DNA ligase

antiparallel strands

The structure of DNA, which means there are to strands parallel to each other going in opposite directions. (5 prime to 3 prime)

Differentiate of transcription and translation

Transcription: DNA-> RNA, double strand to single strand DNA, DNA polymerase, end up with mRNA Translation: mRNA--> polypeptide --> protein

horizontal(lateral) gene transfer of foreign DNA

Transformation, transduction, conjugation

How may viruses have evolved by?

Transposons

repressible operon (trp operon)

Trp is always "on" unless tryptophan is present

Hfr cell

a cell with the F plasmid integrated into the *chromosome*

Describe a DNA molecule

a double helix with nitrogenous bases as the "rungs" and phosphate groups as the "sides"

Lac operon

a gene system whose operator gene and three structural genes control lactose metabolism in E. coli; contains genes coding for proteins in charge of transporting lactose into the cytosol and digesting it into glucose

Exon

a segment of a DNA or RNA molecule containing information coding for a protein or peptide sequence. (messenger)

Intron

a segment of a DNA or RNA molecule that does not code for proteins and interrupts the sequence of genes.

coding strand (sense strand)

a strand of DNA that is not used as a template during transcription, protects from degradation, corresponds to the base sequence of the RNA transcript produced (although with thymine replaced by uracil)

DNA chips

all DNA/RNA turned on at one time

Why is redundancy important?

allows for mistakes to be not so serious

Mutation: Nucleotide

altering chemicals, alter bases to pair with something else, example: nitrogenous bases

rRNA (ribosomal RNA)

an organelle that contains most of the RNA in the cell and that is responsible for ribosome function

Western blotting uses

antibodies; "confirmation tests" (ex. pregnancy tests)

Conjugation

bacterial sex, requires F-plasmids "sex pilus"

Transduction

bacteriophage mediated transfer of bacterial DNA

Types of mutations in DNA

base/point substitution, missense/frameshift/nonsense

Reverse transcriptionase

cDNA <---mRNA; reverse transcription

Radiation mutation: Ionizing

causes lose of electrons and breaks in chromosome

mutation

change in a DNA sequence that affects genetic information

Compare and contrast Prokaryotic and Eukaryotic chromosomes: PROKARYOTIC

circular DNA Naked (no associated proteins) Plasmids often present one chromosome only

tRNA carries

complementary anticode. every single codon has tRNA for each amino acid

How does spreading happens?

conjugative plasmids, dissimilation plasmids, R-factors

Transposons (jumping genes)

contain insertion sequences for cutting and resealing DNA (transposase)

Four tools of biotech: step 4 Grow

creating a gene library

Selection

culture a naturallly occuring microbe that produces desired product

blunt ends

cuts are straight through both DNA strands at the line of symmetry

Chemical mutations cause

deletion frameshift mutations

Vector

delivery vehicle

Describe how a mutant organism can be identified

detected & selected by testing for an altered phenotype - replica plating used for negative selection - auxotrophs (require a specific nutrient for growth) can be selected by growing cells in media without the nutrient

R factors are

encode antibiotic resistance

Operons in eukaryotes

every gene is turned off/on by multiple switches

polymerase chain reaction (PCR)

every techinque uses, requires specialized DNA polymerase and a primer

Phenotype

expression of the genes/genotype

evolution occurs by

genetic change, diversity(mutations and recombination)

Genotype

genetic makeup, its compliment of DNA

The random shotgun method is used in

genome sequencing

Anticodon

group of three bases on a tRNA molecule that are complementary to an mRNA codon to form amino acid

how can mutations be beneficial?

help to adapt

DNA is held together by

hydrogen bonds between the base pairs AT and CG

Describe protein synthesis

include transcription, rna processeing and translation... mRNA copies the code for the gene from the DNA in the nucleus. mRNA then carries this code to the ribosomes in the cytoplasm. A sequence of three bases is the code for a particular amino acid. Carrier molecules (tRNA) bring the bases to the ribosomes in the correct order. When the protein chain is complete, it folds up to form a unique shape which helps the protein to carry out its function

rDNA rechnology

insertion or modification of genes to produce desired proteins

Possible causes of mutations

ionizing radiation, non-ionizing(UV) radiation, spontaneous

Four tools of biotech: step 1 Cut

isolate gene of interest using restriction enzymes

DNA ligase function

joins Okazaki (lagging strand) fragments

Transposons are

jumping genes

Compare and contrast Prokaryotic and Eukaryotic chromosomes: EUKARYOTIC

linear DNA Associated with histone proteins no plasmids 2 or more different chromosomes

Genetic transformation: crossover

living took up deads ability from environment, (mouse example)

auxotrophs

lost ability to synthesize one or more organic compound

operons for prokaryotes

lots of genes translated at once (one switch)

Importance of plasmids

many different purposes in biotechnology, can be used as a tool to insert genes into bacteria to encourage their production of therapeutic proteins such as human insulin

Mutations: nucleoside analogs cause

mismatching and base substitutions

vertical transmission

mother to daughter

What is the principle behind the AMES test?

mutating it back to lost ability -ability to cause cancer

**How do bacteria evolve?

mutations, transposons, transduction, antibiotic resistance

**Nanotechnology

nanospheres used in drug targeting +delivery

Where does transcription occur?

nucleus for eukaryotes, cytoplasm for prokaryotes

clone

population of cells arising from one cell; each carries the new gene

CRISPR

powerful gene editing technique

Radiation mutation: Nonionizing

produces thymine dimers- UV light prevents replication

How do operons work?

promoter genes bind to the operator to turn on/off gene by blocking RNA polymerase from bind b/c it "coils/twists" the DNA

Proteomics is the study of

proteins

restriction enzymes

recipient DNA is usually a plasmid, evolved as bacterial DNA

gene therapy

replace defective or issing genes

tryptophan operon

repressible operon---when trp is absent, the repressor is inactive-----when trp is present and there is enough of it, the trp binds to the repressor and activates it to stop producing

Define and describe: Conjugation (Mouse example in book)

requires contact between living cells one type of genetic donor is an F+, recipient is F-. F cells contain plasmids called F factors; these are transferred to the F- cells

riplets

restriction length polymorphism(shapes); what you see with electrophoresis

horizontal gene transfer vs vertical gene transfer

same generation vs reproduction between generations of cells

Vectors

self replicating DNA, delivery device to carry gene to new cell

Define and describe: Plasmids

self replicating, circular DNA, carries genes not usually essential for cells survival. Gives a "superpower" gene; ex. antibiotic resistance, toxin carrier, bacteriocins

typical genetic modification procedure

separate 2 DNA --> transformation --> rDNA

gel electrophoresis

separates our DNA according to size "DNA fingerprint"

RNA primer

short segment of RNA used to initiate synthesis of a new strand of DNA during replication

What kind of mutation is sickle cell anemia?

single base change mutation

Mutations: frameshift

some dyes for staining DNA causes a bulge in DNA which allows for insertion/deletions

Promoter

specific region of a gene where RNA polymerase can bind and begin transcription

sticky ends

staggered ends of DNA formed after a cut

Agrobacterium

take away nasty gene and ass gene we want (ex. herbicide resistance)

transgentic

term used to refer to an organism that contains genes from other organisms

sense codons

the 61 codons that specify amino acids

Crossing-over

the exchange of genes between homologous chromosomes, resulting in a mixture of parental characteristics in offspring.

Genetics

the study of genes, how they carry information, how information is expressed, and how genes are replicated and passed to generations

metagenomics

the study of genetic material recovered directly from environmental samples

biotechnology

the use of microorganisms, cells or cell components to make a product -- foods, antibiotics, vitamins and enzymes

Why are operons important?

they change their metabolism based on the environment

Why are stem cells important?

they have the potential to develop into other cells

codon

three-nucleotide sequence on messenger RNA that codes for a single amino acid

How did E. coli acquire genes from shigella?

transduction of virus

horizontal gene transfer

transfer of genes between cells of the same generation

What processes get into cells?

transofrmation, transduction, transcription/translation, conjugation

zenotransplantation

transplant of an organ from animals

The genetic code is:

universal and redundant

bioinformatics

use of computer databases to organize and analyze biological data

Inserting foreign DNA into cells: Transformation

uses electricity or something else to allow for pores

Inserting foreign DNA into cells: Electroporation

uses electricity to make "pores"; FORCED transformation

Four tools of biotech: step 3 insert

using plasmids to transfer DNA from one organism to another, GLUE with ligase

repressible enzymes

usually function in anabolic pathways; their synthesis is repressed by high levels of the end product

inducible enzymes

usually function in catabolic pathways; their synthesis is induced by a chemical signal

genetic code

ways codons translated to amino acids