genetics exam

qualities of the bacterial genome

• unicellular, lacks a nuclear membrane

• single circular chromosome

plasmids

small extra chromosomal circular DNA

• replicate independently of the chromosome

• generally carry nonessential genes (promote mating, kill other bacteria)

three types of horizontal gene transfer

conjugation, transformation, transduction

conjugation 

direct gene transfer from one bacterium (donor) to another (recipient) 

transformation

gene uptake by a bacterium from the medium

transduction

gene transfer from a bacterium to another through a virus

• generalized and specialized 

different types of F factor, their characteristics, and role in conjugation

• F+, present as separate circular DNA, donor 

• F-, absent, recipient

• Hfr, present and integrated into bacterial chromosome, high frequency donor 

• F’, present as separate circular DNA and carrying some bacterial genes, donor 

result of F+ X F- conjugation

two F+ cells, F- becomes F+

results of Hfr X F- conjugation

one Hfr cell and one F-

results of F’ X F-

two F’ cells (F- becomes F’)

Natural gene transfer

transfer of plasmids is not restricted to bacteria of the same or even related species

• R plasmid: antibiotics resistance transferred by conjugation  

life cycle of virulent phages and temperate phages 

virulent and temperate undergo the lytic cycle but only temperate phages (prophages)  undergo the lysogenic cycle 

replication 

genetic information must be copied every time a cell divides

• replication is semiconservative 

modes of replication and descriptions 

• theta: common in circular DNA, single rep. origin, bidirectional 

• rolling circle: viral DNA & F factor, single rep. origin, unidirectional 

• linear: eukaryotic DNA, multiple replication origin, bidirectional 

function of single stranded binding protein 

attach to single stranded DNA and prevent secondary structures from forming 

DNA gyrase

moves ahead of the replication fork, making and resealing breaks in the double helical DNA to release the torque that builds up as a result of unwinding at the replication fork

DNA primase

synthesizes a short RNA primer to provide a 3 ‘OH group provided by the primer

DNA polymerase III

elongates a new nucleotide strand from the 3 OH group provided by the primer

DNA polymerase I

removes RNA primers and replaces them with DNA

DNA ligase backbone

joins Okazaki fragments by sealing nicks in the sugar-phosphate of newly synthesized DNA

equation of transcript

synthesis of RNA = transcription, transcribed RNA =transcript

structures of DNA 

composed of nucleotides joined by phosphodiester bonds , deoxyribose sugar, A+G+C+T, double stranded with a secondary structure of a double helix, stable 

structures of RNA

composed of nucleotides joined by phosphodiester bonds, ribose sugar, A+G+C+U, single stranded with many types of secondary structures, easily degraded

classes of RNA and their different types

• messenger RNA: intermediate necessary for synthesizing protein (funct. product)

• functional RNA:

• tRNA: bring correct amino acid to the mRNA

• , rRNA: major components of ribosomes

• , snRNAs: RNA processing components of spliceosome

• , miRNAs: regulating gene expression

• , siRNAs: genome defense

retrovirus

viruses with RNA as genetic material

• human: flu, common colds, polio, AIDS

• plant: almost all plant viruses

requirements of replication

• a template of single stranded DNA

• a growing nucleotide strand

• deoxyribonucleoside triphosphates, enzymes and other proteins

core enzymes function

• alpha: help assembly/promote interactions with regulatory proteins

• beta: active in catalysis

• beta prime: binding to DNA

• omega: enzyme assembly

holo-enzymes

all of the core enzymes with the addition of sigma

• binding to -35 & -10 → correct positioning the holoenzyme

• separating the DNA strands around the -10 region

• dissociate after transcription begins

• different sigma factors recognize different set of promoters

promoters of genes transcribed by RNA polymerase II

TFIIB recognition element (-35), TATA box (-25), initiator element (+1), downstream core promoter element (+30)

sequence found in prokaryotes only before the start codon

shine-dalgarno sequence

reasons for cotranscriptional processing of RNA

• protects RNA from degradation (increases stability)

• required for ribosome binding (translation)

Function of DNA polymerases in E. coli

1- removes and replaces primers

2- DNA repair, restarts replication after damaged DNA halts synthesis

3- elongates DNA

4- DNA repair

5- DNA repair, trans lesion DNA synthesis