translation and HGT (in person)

what happens during translation

protein synthesis
mRNA--> protein

what is needed for translation

small and large ribosomal subunits, tRNA, mRNA

what does tRNA carry

has an anticodon that will pair with the codon on mRNA which is associated with a given AA also carried by tRNA

what are 3 steps of translation


describe initiation

tRNA brings 1st AA (Met) in china w antibody to bind to start codon (AUG) on mRNA

describe elongation

polypeptide chain grows from the P site
-peptide bonds form between AAs by ribosomal RNA

what are 3 sites in ribosome for translation

E (exit), P, A (attachment)

what happens in termination

stop codon recognized and polypeptide released
-folds to become protein after

where do tRNAs enter

enter A site, drop AA at P site, and leave via E site

how is ribosomal structure and rRNAs similar in prokaryotes and eukaryotes

-both have small subunit (SSU) and LSU
-both have ribosomal RNAs that interact w each subunit

what does SSU rRNA do

helps w mRNA binding

what does LSU rRNA do

catalyzes peptide bond formation

how to pro and eukaryotes differ in ribosome structure

pro: 50s and 30s--> 70s ribosome
eukaryote: 60s and 40s--> 80s ribosome

how do codons differ in pro and eu

same codons BUT pro has different AA codes for by start codon
-use altered form of Met called n-formyl methionine (fMet)

what its he 3rd letter in a codon calld

wobble positin
-multiple codons code for same AA

what does tRNA have that makes it more stable

hairpin loops

how does initiation differ in pro vs eukaryotes

in eukaryotes, ribosome recognizes 5' cap of mRNA to start translation
-in pro, ribosome recognizes ribosome binding site--> Shine-Delgarno sequence (AGGAGG) that rRNA binds to

when does transcription and translation occur in pro

ribosomes bind immediately bc mRNA is unstable

what types of ribosomes do prokaryotes use that we do not

polyribosomes-- many ribosomes acting on single mRNA transcript
**allows bacteria to respond quickly (make multiple of the same protein)

what is bacterial molecular bio geared towards? give ex

fast response!
1. operons (multiple genes on same transcript)
2. polyribosomes
3. no transcript editing
4. shorter 1/2 life of transcript (so protein production starts immediately)
5. smaller genome

what are 2 types of gene transfer

1. vertical: parent to child (all living things do this)--> making a clone of yourself, mutation occurs at slow rate
2. horizontal: parent to parent or child to child (ppl can NOT do this--only bacteria)
-HGT is bacterial sex--move DNA from one cell to an

what does HGT allow for

quickly adapting to environment by acquiring large chunks of new DNA
-gains antibiotic resistance genes and virulence factors

what are obstacles to HGT

1. getting DNA into cell
2. getting DNA to recombine onto the genome

what does adding genes onto a chromose require

homologous regions (similar )
-happens in ppl during meiosis! crossing over (causes genetic diversity)
higher match=more likely to recombine

what catalyzes the joining of 2 strands in recombination

RecA protein
**dononr DNA is destroyed

what can recombination occur between

2 plasmids
fragment and genome
plasmid and genome

why is recombination a complicated process

involves >30 proteins
-mediated by major group of proteins called Rec (recombination)
-includes helices, nuclease, etc
*requires alignment of homologous regions

what do all successful HGT events require


what are 3 forms of HGT


who conducted a transformation experiment
describe it

Griffith in 1928
injected virulent bacteria into mice and they died
-injected avirulent bacteria and they lived
-injected heat killed virulent bacteria and they lived
-injected heat killed virulent and live avirulent and they died
**genes were transferred

what does transformation consist of

picking up DNA form environment

what is competence

ability to perform transformation (take up DNA from the environment)

what are 2 types of competence


describe natural competence

-not many bacteria can do this (needs a lot of specific genes
requires pili
-highly regulated!

what is pili

hairlike structure coming out of bacteria
-allows them to stick to DNA in environment and pull it inside

why is natural competence highly regulated

requires a lot of energy (don't want to do it unless it will pay off)
-only turned on during high cell density or as a stress response
*dependent on quorum sensing! don't want to turn it on if nothing is around

how is artificial competence made

treat cells with CaCl2--> makes holes in membrane/walls
-manipulated in lab conditions

what are 2 ways to make artificial competence

1. electroporation--electroshock cells which destabilizes membrane (can take up DNA)
2. heat shock--switch form cold to hot (temporarily disrupts membrane)

does only DNA from related species enter the cell

no! all types can make it in but we only see ones that recombine so they have to have related DNA!!
-need homologous regions

what happens during transduction

viruses transfer DNA to bacteria

what are 2 types of transduction


what is general transduction

host bacterial genome can be fragmented during viral replication
-pieces of host DNA can then incorporate into phage and get transferred

what occurs in both transformation and transduction

cell has to lyse

describe specialized transduction

viral genes get incorporated into host genome during lytic cycle
-when phage separates from bacterial genome it can sometimes accidentally take host genes w it and transfer these to another bacteria (HGT!)
**bacteriophage acts as delivery system

what happens to virus if it takes up host genome

is unable to replicate and dies

what is an example of transduction

vibrio cholerae
-prob w water in 3rd world countries
-has toxin that was given by a virus that causes diarrhea

how can we use transduction as a tool since viruses infect ppl too

1. use phage as delivery system (give it something that will kill bacteria)
2. gene therapy--gene editing w CRISPR
3. vaccine delivery
4. phage therapy

what is CRISPR

came from prokaryotes and functions as their immune system against viruses
- bacterial system that bacteria use to fight viruses. It consists of an enzyme called Cas9 and a guiding RNA.
-they keep a piece of the bacteriophage DNA so when it tries to infec

what does Cas9 do

enzyme that degrades what the guide RNA binds to

how can we use CRIPSR

put guide RNA and Cas9 system into phage
-the guide RNA will bind to the specific sequence we want to remove

what have we hijacked CRISPR to do

edit genes
-can cut out unwanted genes and replace them using guide RNA

what is guide RNA

Guide RNA is a strand of RNA that helps the bacteria know what part of the genomic DNA to cut.
Guide RNA contains complementary sequences to the target DNA you want to cut/get rid of/ or change. The complementary DNA replaces what you get rid of with a ne

describe conjugation

transfer DNA by directly connecting to other bacteria
-plasmid mediated transfer
donor donates plasmid
recipient receives plasmid

what must the plasmid be for conjugation

transmissible (capable of transfer)

what is an F plasmid

example of transmissible plasmid
-codes for proteins, has orin and omit sites

what is necessary for donor to have in conjugation

sex pilus
-protein filament that attaches to recipient cell and uses to transfer plasmid
*this is encoded on the plasmid that will be transferred

what does relaxase do in conjugation

nicks and unrolls the plasmid DNA
-helps direct plasmid to the pore in the sex pilus

what is the pore in the sex pili

tunnel for DNA transfer

what does conjugation require
what is this called

requires one cell to have plasmid and other to not
**called different matin types
**also requires direct contact btwn 2 cells

how does the plasmid replicate in conjugation

rolling circle

what does F factor integrating on chromosome make

Hfr cell (high frequency of recombination)

what happens when F factor gets transferred form an Hfr cell

takes some of the donor genome with it
-accidentally grabs part of chr, so makes new recombinant F- cell during recombination because entire F factor is not transferred

what can conjugation be used to do

map out bacterial genome
-depending on how long it takes for genes to transfer, can determine where in chromosome these genes are

what else can bacteria inject DNA into via conjugation
give ex

plant cells
ex. Agrobacterium
-conjugation causes overgrowth/tumor in plants

what can injecting DNA be used to do

genetically engineered plants (GMOs)

what can be done w GMOs

-resistance to disease
-add extra nutrients
-higher yield (decreases food shortages)