Microbiology 351 - Exam 2 - lecture 10 - 21

From Lecture 8–11: Molecular Microbiology, slide 27: what are the key points about DNA replication is extremely accurate?

Proofreading helps to ensure high fidelity; Mutation rates in cells are 10–8 to 10–11 errors per base; inserted; Polymerase can detect mismatch through incorrect hydrogen; bonding; Proofreading occurs in prokaryotes, eukaryotes, and viral

From Lecture 8–11: Molecular Microbiology, slide 28: what are the key points about III. RNA Synthesis: Transcription?

Transcription (DNA to RNA) is carried out by RNA polymerase; RNA polymerase uses DNA as template; RNA precursors are ATP, GTP, CTP, and UTP (not dATP, dTTP, dCTP; and dGTP); Chain growth is 5′ to 3′ just as in DNA replication; Only one of the two strands of DNA is transcribed by RNA

What is Promoter?

site of initiation of transcription

What is Pribnow box?

located 10 bases before the start of transcription (–10 region)

What is –35 region?

located ~35 bases upstream of transcription

From Lecture 8–11: Molecular Microbiology, slide 29: what are the key points about Promoter?

Promoter: site of initiation of transcription; Recognized by sigma factor of RNA polymerase; Transcription stops at specific sites called transcription terminators; Unlike DNA replication, transcription involves smaller units of DNA; Often as small as a single gene; Allows cell to transcribe different genes at different rates

From Lecture 8–11: Molecular Microbiology, slide 30: what are the key points about C?

Sigma; mRNA start; –35 region; Consensus; Pribnow box; Promoter sequence

From Lecture 8–11: Molecular Microbiology, slide 31: what are the key points about 5′?

Transcription begins;; sigma released. RNA; chain grows.; Sigma recognizes; promoter and; initiation site.

What is Rho-dependent termination?

Rho protein recognizes

What is Intrinsic (Rho-independent) termination?

stem-loops

From Lecture 8–11: Molecular Microbiology, slide 33: what are the key points about Termination?

Termination of RNA synthesis is governed by a specific; DNA sequence; Rho-dependent termination: Rho protein recognizes; specific DNA sequences and causes a pause in the; RNA polymerase; Intrinsic (Rho-independent) termination: stem-loops

From Lecture 8–11: Molecular Microbiology, slide 34: what are the key points about Transcription of light?

green (lower) strand; RNA forms secondary; structure.; Stem–loop in RNA; immediately upstream; from a run of uracils

What is Unit of transcription?

unit of chromosome bounded by sites

What is Three types of rRNA?

16S, 23S, and 5S

From Lecture 8–11: Molecular Microbiology, slide 35: what are the key points about The Unit of Transcription?

Unit of transcription: unit of chromosome bounded by sites; where transcription of DNA to RNA is initiated and terminated; Most genes encode proteins, but some RNAs are not; translated (i.e., rRNA, tRNA); Three types of rRNA: 16S, 23S, and 5S; rRNA and tRNA are very stable

What is Operon?

a group of related genes co-transcribed to a

From Lecture 8–11: Molecular Microbiology, slide 37: what are the key points about 5′ leader?

Operon; Poly-; cistronic; ORF 1; ORF 2; ORF 3

From Lecture 8–11: Molecular Microbiology, slide 38: what are the key points about Transcription in Archaea and Eukarya?

The Archaea contain only a single RNA polymerase; Resembles eukaryotic polymerase II; Archaea have a simplified version of eukaryotic transcription; apparatus; Promoters and RNA polymerase similar to eukaryotes; Regulation of transcription has major similarities with Bacteria

From Lecture 8–11: Molecular Microbiology, slide 40: what are the key points about Binding of?

TBP and TFB; Start of; transcription; Binding of RNA; polymerase; Promoter

What is Eukaryotic RNA processing?

many RNA molecules are

From Lecture 8–11: Molecular Microbiology, slide 41: what are the key points about Eukaryotic RNA processing?

Eukaryotic RNA processing: many RNA molecules are; altered before they carry out their role in the cell; RNA splicing; Removes introns from RNA transcripts; Performed by the spliceosome; RNA capping

From Lecture 8–11: Molecular Microbiology, slide 42: what are the key points about Addition of 5′-Cap and?

3′-polyadenylation; [poly(A) tail]; Introns excised; Export to cytoplasm; and translation; 5′-Cap

From Lecture 8–11: Molecular Microbiology, slide 43: what are the key points about IV. Protein Synthesis?

Polypeptides, Amino Acids, and the Peptide Bond; Proteins play a major role in cell function; Catalytic proteins (enzymes); Structural proteins; Proteins are polymers of amino acids; Amino acids are linked by peptide bonds to form a

What is (Note?

Because proline lacks a free amino group,

From Lecture 8–11: Molecular Microbiology, slide 44: what are the key points about General structure of an amino acid?

Amino group; Structure of the amino acid "R" groups; Carboxylic; acid group; α-Carbon; Ser Serine (S)

What is Translation?

the synthesis of proteins from RNA

What is Genetic code?

a triplet of nucleic acid bases (codon) encodes

What is Degenerate code?

multiple codons encode a single amino acid

What is Wobble?

irregular base pairing allowed at third position of tRNA

What is Stop codons?

terminate translation (UAA, UAG, and UGA)

What is Start codon?

translation begins with AUG (sometimes GUG)

What is Ribosome-binding site (RBS)?

ensures proper reading frame

From Lecture 8–11: Molecular Microbiology, slide 45: what are the key points about Translation and the Genetic Code?

Translation: the synthesis of proteins from RNA; Genetic code: a triplet of nucleic acid bases (codon) encodes; a single amino acid; Degenerate code: multiple codons encode a single amino acid; Anticodon on tRNA recognizes codon; Wobble: irregular base pairing allowed at third position of tRNA

From Lecture 8–11: Molecular Microbiology, slide 47: what are the key points about Alanine?

Key bases in codon:; anticodon pairing; C G G; G C U; Anticodon; Codon

From Lecture 8–11: Molecular Microbiology, slide 48: what are the key points about Open reading frame (ORF): AUG followed by a number of?

codons and a stop codon in the same reading frame; The definition of an open reading frame

What is Codon bias?

multiple codons for the same amino acid are not

From Lecture 8–11: Molecular Microbiology, slide 49: what are the key points about Codon bias?

Codon bias: multiple codons for the same amino acid are not; used equally; Varies with organism; Correlated with tRNA availability; Cloned genes from one organism may not be translated by recipient; organism because of codon bias

What is Transfer RNA?

at least one tRNA per amino acid

What is Anticodon?

three bases of tRNA that recognize three

From Lecture 8–11: Molecular Microbiology, slide 50: what are the key points about Transfer RNA?

Transfer RNA: at least one tRNA per amino acid; Bacterial cells have 60 different tRNAs; Mammalian cells have 100–110 different tRNAs; Specific for both a codon and its cognate amino acid; tRNA and amino acid brought together by aminoacyl-tRNA; synthetases

From Lecture 8–11: Molecular Microbiology, slide 51: what are the key points about phe?

Acceptor; D loop; Acceptor; D loop; Anticodon; TΨC loop

From Lecture 8–11: Molecular Microbiology, slide 52: what are the key points about Uncharged?

tRNA specific; for valine (tRNAVal); Anticodon; region; Charged valyl; tRNA, ready for

What is Ribosomes?

sites of protein synthesis

What is 1. Initiation?

two ribosomal subunits assemble with mRNA

What is 2. Elongation?

amino acids are brought to the ribosome and are added

What is Translocation?

movement of the tRNA holding the polypeptide from the A to the

What is 3. Termination?

occurs when ribosome reaches a stop codon

What is Release factors (RF)?

recognize stop codon and cleave polypeptide from tRNA

From Lecture 8–11: Molecular Microbiology, slide 53: what are the key points about Protein Synthesis?

Ribosomes: sites of protein synthesis; Thousands of ribosomes per cell; Composed of two subunits (30S and 50S in prokaryotes, S = Svedberg units); Combination of rRNA and protein; E. coli has 52 distinct ribosomal proteins; Translation is broken down into three main steps:

From Lecture 8–11: Molecular Microbiology, slide 54: what are the key points about A site = acceptor site?

P site = peptide site; E site = exit site; Use GTP as energy; Ribosomes move along mRNA; A loaded tRNA enters the A site of a chromosome

From Lecture 8–11: Molecular Microbiology, slide 55: what are the key points about Formation of peptide?

bonds is catalyzed; by 23S rRNA; atch?v=5bLEDd-PSTQ; Caption available @ youtube; The cycle of peptide elongation by a ribosome

What is Polysomes?

a complex formed by ribosomes

From Lecture 8–11: Molecular Microbiology, slide 57: what are the key points about Ribosome?

Growing polypeptide; Nearly finished; polypeptide; subunit; subunit; Polysomes: a complex formed by ribosomes

From Lecture 8–11: Molecular Microbiology, slide 58: what are the key points about Protein Folding and Secretion?

Once formed, a polypeptide folds to form a more stable; structure.; Secondary structure; Interactions of the R groups force the molecule to twist; and fold in a certain way; Tertiary structure

From Lecture 8–11: Molecular Microbiology, slide 59: what are the key points about Amino?

terminus; Hydrogen bonds; between nearby; amino acids; Hydrogen bonds; between distant

From Lecture 8–11: Molecular Microbiology, slide 60: what are the key points about A chain?

α-Helix; B chain; β-Sheet; Insulin; Ribonuclease; Tertiary structure of polypeptides

From Lecture 8–11: Molecular Microbiology, slide 61: what are the key points about Protein Folding and chaprones?

Chaprones help protein to fold

What is Signal sequences?

found on proteins requiring transport

From Lecture 8–11: Molecular Microbiology, slide 62: what are the key points about Protein secretion?

Signal sequences: found on proteins requiring transport; from cell; 15–20 residues long; Found at the beginning of the protein molecule; Prevent protein from completely folding

What is Secretion of unfolded protein?

Sec system

From Lecture 8–11: Molecular Microbiology, slide 63: what are the key points about Translational?

apparatus; Protein; Cytoplasmic; membrane; Periplasm; Proteins with

What is Secretion of folded proteins?

the Tat (twin-arginine

What is Secretion of folded protein?

Tat system

From Lecture 8–11: Molecular Microbiology, slide 64: what are the key points about translocation) system?

Secretion of folded proteins: the Tat (twin-arginine; Proteins that fold in the cytoplasm are exported by a transport; system distinct from Sec, called the Tat protein export system; Tat system recognize a signal sequence containing a pair of; arginines.; Secretion of folded protein: Tat system

What is Secretion of proteins?

types I through IX

From Lecture 8–11: Molecular Microbiology, slide 65: what are the key points about Other Secretion Systems?

Secretion of proteins: types I through IX; All are a large complex of proteins that form channels through; membranes; Types II and V depend on Sec or Tat; Types I, III, IV, and VI do not require Sec or Tat; Other secretion machineries

From Lecture 12–15: Microbial Genetics, slide 1: what are the key points about LECTURE 12-15?

MICROBIAL GENETICS

From Lecture 12–15: Microbial Genetics, slide 2: what are the key points about phenotype (observable properties of an organism)?

Mutation; Heritable change in DNA sequence that can lead to a change in; Mutant; A strain of any cell or virus differing from parental strain in; genotype (nucleotide sequence of genome); Wild-type strain

From Lecture 12–15: Microbial Genetics, slide 3: what are the key points about Mutations and Mutants?

Selectable mutations; Those that give the mutant a growth advantage; under certain conditions or a distinguishable; phenotype; Useful in genetic research; Nonselectable mutations

What is Example?

replica plating

From Lecture 12–15: Microbial Genetics, slide 4: what are the key points about Master plate; growth?

on complete medium; 1. Pick and transfer colonies; to fresh medium.; Complete medium; Selective medium; Sterile toothpick

From Lecture 12–15: Microbial Genetics, slide 5: what are the key points about Molecular Basis of Mutation?

Induced mutations; Those made environmentally or deliberately; Can result from exposure to natural radiation or oxygen radicals; Spontaneous mutations; Those that occur without external intervention; Point mutations

From Lecture 12–15: Microbial Genetics, slide 6: what are the key points about Type of Mutation?

Silent mutation; Does not affect amino acid; sequence; Missense mutation; Amino acid changed;; polypeptide altered

From Lecture 12–15: Microbial Genetics, slide 7: what are the key points about Frameshift mutation?

Deletions and insertions cause more dramatic changes in DNA; Frameshift mutations; Deletions or insertions that result in a shift in the reading frame; Often result in complete loss of gene function; …GTGCCCTGTT …; …CACGGGACAA…

What is from G?

A transition

What is Same-site revertant?

mutation is at the

What is Second-site revertant?

mutation is at a

What is Suppressor?

mutation that

From Lecture 12–15: Microbial Genetics, slide 8: what are the key points about …GTC…?

Nonsense mutation; from G:A transition; …ATC…; Transcription of; mutated DNA; …UAG…

From Lecture 12–15: Microbial Genetics, slide 9: what are the key points about Ames test?

For most microorganisms, errors in DNA replication occur at; a frequency of 106 -107/kb (per gene); The Ames test makes practical use of bacterial mutations to; detect for potentially hazardous chemicals; Looks for an increase in mutation of bacteria in the presence; of suspected mutagen

What is Mutagens?

chemical, physical, or

What is Nucleotide base analogs?

resemble nucleotides,

From Lecture 12–15: Microbial Genetics, slide 10: what are the key points about Mutagenesis?

Mutagens: chemical, physical, or; biological agents that increase mutation; rates; Several classes of chemical mutagens exist:; Nucleotide base analogs: resemble nucleotides,; directly incorporated into DNA, introduce

From Lecture 12–15: Microbial Genetics, slide 11: what are the key points about Several forms of radiation?

Two main categories of mutagenic; electromagnetic radiation; Nonionizing (i.e., UV radiation); Purines and pyrimidines strongly absorb UV; Pyrimidine dimer is one effect of UV; radiation

What is Direct reversal?

mutated base is still recognizable and can be repaired

What is Repair of single-strand damage?

damaged DNA is removed and

What is Repair of double-strand damage?

a break in the DNA

What is Mutator (hypermutable) strains?

bacteria that benefit from increased

From Lecture 12–15: Microbial Genetics, slide 12: what are the key points about DNA repair systems?

Three types of DNA repair systems; Direct reversal: mutated base is still recognizable and can be repaired; without referring to other strand; Repair of single-strand damage: damaged DNA is removed and; repaired using opposite strand as template; Repair of double-strand damage: a break in the DNA

From Lecture 12–15: Microbial Genetics, slide 13: what are the key points about RecA?

protein; DNA damage; activates RecA.; Active; RecA activates LexA; protease activity.

From Lecture 12–15: Microbial Genetics, slide 14: what are the key points about Three mechanisms?

of genetic exchange; Transformation; Transduction; Conjugation; Three possible fates of; horizontal gene transfer

From Lecture 12–15: Microbial Genetics, slide 15: what are the key points about Genetic Recombination?

Recombination; Physical exchange of DNA between genetic elements; Homologous recombination; Process that results in genetic exchange between homologous DNA; from two different sources. RecA is essential.; Selective medium can be used to detect rare genetic

From Lecture 12–15: Microbial Genetics, slide 16: what are the key points about Holliday intermediate?

(heteroduplex); ?v=3qgBKrAZCLg; A simplified version of homologous recombination

What is Competent cells?

cells are capable of taking up DNA and

From Lecture 12–15: Microbial Genetics, slide 17: what are the key points about Transformation?

Transformation; Genetic transfer process by which DNA is incorporated into a recipient; cell and brings about genetic change; Competent cells: cells are capable of taking up DNA and; being transformed; Many G+ bacterial are naturally competent

From Lecture 12–15: Microbial Genetics, slide 18: what are the key points about 1. Binding DNA?

2. Uptake of single-; stranded DNA; 3. RecA-mediated homologous; recombination; Transforming DNA from donor cell; Bacterial

What is Two modes?

Generalized transduction and Specialized transduction

What is Generalized transduction?

DNA derived from virtually any portion of

From Lecture 12–15: Microbial Genetics, slide 19: what are the key points about Lytic cycle?

Phage; Donor; Normal lytic; events; Recipient is; infected by

From Lecture 12–15: Microbial Genetics, slide 20: what are the key points about from a specific region of the host?

Specialized transduction: DNA; chromosome is integrated; directly in the virus genome; DNA of temperate virus excises; incorrectly and takes adjacent host; genes along with it