Microbiology - molecular biology

Question 0

human DNA structure
how many BP
how many proteins

Answer 0

23 linear chromos
diploid
3x10^9 BP’s
25,000 proteins

Question 1

structure of bacterial DNA
how many BP
how many proteins

Answer 1

circular
haploid
5 x 10^6 BP
2000 proteins

Question 2

main enzyme that mediates DNA replication

Answer 2

DNA dependent DNA polymerase

Question 3

main constituents of DNA

Answer 3

5C sugar (deoxyribose) (RNA = ribose)
phosphate (along with sugar make the backbone)
nitrogenous base
purines (Guanine Adenine)
pyrimidines (Cytoine Uracil Thymine) (uracil in RNA)

Question 4

what do bacteria use restriction enzymes for? can they be used clinically for analytical techniques?

Answer 4

Restriction enzymes:
are used by bacteria to delete foreign nucleotides from their genome.
REs cleave double stranded DNA at specific sequences.
REs are also used clinically to analyze/characterize bacterial and viral DNA

Question 5

bacterial DNA replication process highlights

Answer 5

initiation of replication occurs at the replication bubble/replication fork.
Bidirectional DNA synthesis at the replication fork creates a replication bubble
Two replication forks meet at a termination site.
Semiconservative replication = Each daughter cell receives a parent strand and a new strand.

Question 6

transcription highlights

Answer 6

uses RNA  polymerase
only one strand of DNA is read
no primer required
5' --> 3'
initiation, elongation, termination

Question 7

mRNA

Answer 7

only RNA that is translated into protein

Question 8

rRNA

Answer 8

complexes with proteins to form the ribosome

note: the bacterial ribosome = 30S + 50S = 70S
(remember bacteria are “odd” so the ribosome “numbers” start with odd numbers 3, 5, 7)

Question 9

tRNA

Answer 9

adapts info from mRNA to protein

Question 10

where is the “anticodon” located

Answer 10

on tRNA

Question 11

2 “enzymes” used by the ribosome to assemble the protein

Answer 11

aminoacyl-tRNA sythetase

peptidyl transferase

Question 12

the transfer of genetic information can occur by 4 different processes (according to the text)

Answer 12

conjugation
transduction
transformation
transposition

Question 13

conjugation

Answer 13

mating of 2 bacteria
controlled by an F (fertility) plasmid (which carries the genes for the proteins required for mating)
this includes the sex pilus protein, pilin
male = F+ (attaches the pilius to a receptor on the “female” F- bacteria)
cells brought into direct contact and reeled in together by pilus
F factor DNA cleaved by enzymes
one strand transferred across bridge to female
after synthesis of a complementary strand, there is now a double-stranded F plasmid in both donor and recipient cell
this new DNA becomes a stable part of the recipients DNA and the female is now a “male”

Question 14

transduction

Answer 14

DNA transfer by means of a bacteriophage (phage). when phage replicates, a piece of bacterial DNA gets incorporated accidentally into the virus’ (phage) particle and is carried into the recipient bacteria cell at the time of infection
2 types:
generalized transduction - phage carries (“steals”) any random piece of bacterial chromosome and incorporates it into the viral (phage) DNA
specialized transduction - occurs when the phage DNA already integrated into the bacteria DNA is excised and carries with it an adjacent part of the bacterial DNA. only genes next to insertion site are incorporated.

note: Plasmid DNA can also be transferred to another bacterium by transduction

Question 15

transformation

Answer 15

transfer of exogenous DNA that is floating around after dying bacteria release their DNA and it is taken up and incorporated into a neighboring bacterial cell’s DNA

note: does not appear to play sig. role in disease

Question 16

transposition

Answer 16

occurs when transposons move from one DNA site to another within the genome of same organism
“insertion sequences” = the simplest transposable elements that encode enzymes (transposase) required for “jumping” from one site to another.

Question 17

what are transposons

Answer 17

also called “jumping genes”
pieces of DNA that move from one site to another either within or between the DNA’s of bacteria, plasmids, and bacteriophages
transposons:
- can code for metabolic or drug resistance enzymes and toxins
- cannot replicate independently (like a plasmid or bacterial virus can)
- can jump from:
host genomic DNA to plasmid
plasmid to plasmid
plasmid to genomic DNA

Question 18

2 type of recombination

Answer 18

homologous - exchange of pieces that have extensive homo regions - exchange by breakage and reunion
non-homologous - little homology required for recombination to occur - enzymes such as endonucleases and ligases are involved

Question 19

plasmids

Answer 19

extrachromosomal double stranded circular DNA
can replicate independently of the bacterial chromo (i.e. they are “replicons”)
occur in G+ and G- bacs
several diff plasmids can exist in one cell

Question 20

transmissible plasmids
vs.
non-transmissible plasmids

Answer 20

transmissible = can be transferred from cell to cell by conjugation (contain the sex genes)

non-transmissible = do not contain the transfer sex genes however they can be mobilized by co-resident plasmids that DO contain the transfer gene

Question 21

clinical relevance of plasmids (what do they code for)

Answer 21

code for the following:
antibiotic resistance
the production of toxins that are produced by enterobacteria (“colicins”) and are lethal for other bacteria
resistance to heavy metals
pili (fimbriae) - mediate adherance to epithelial cells
exotoxins

Question 22

2 different “paths” that a cell can take after transduction occurs

Answer 22

lytic - causes lysis of the host cell and releases viral progeny
lysogeny - viral genome integrated into the bacterial chromosome

Question 23

according to our slides (#27):

when toxins are produced due to a phage - what is this process called?

Answer 23

lysogenic conversion
or
phage conversion

Question 24

mutations:

2 main types

Answer 24

base substitution
&
framshift

Question 25

3 types of base substitution mutation

Answer 25

mis-sense = (AA change) = when the base substitution results in a codon for a different AA

non-sense = when mutation codes for a stop codon

silent = no change in AA

Question 26

frameshift mutation

definition and types

Answer 26

frameshift occurs when one or more BPs are added or deleted which shifts the reading frame on the ribosome and results inthe incorporation of the wrong AA’s downstream form the mutation and produces an inactive protein.

can be:
insertion (like transposons) or deletion

Question 27

transition mutation

Answer 27

replace purine with purine or pyrimidine with pyrimidine

Question 28

transversion mutation

Answer 28

replace purine with pyrimidine or vice versa

Question 29

restriction enzymes

Answer 29

recognizes 4-8bp sequences and creates complimentary ends

originally a defense against bacteriophage (i.e. methylase protects bacterial DNA from phages)

Question 30

PCR

Answer 30

used to amplify DNA from a source that is available in limited quantity.
uses primers and heat stable Taq polymerase

Question 31

southern blot

Answer 31

what is transferred to the gel = DNA
probe = oligonucleotide
why use??? = you want to know whether a certain gene is present

Question 32

Northern blot

Answer 32

what is transferred to gel? = mRNA
probe = oligonucleotide
why use? want to know if a gene is expressed

Question 33

Western

Answer 33

.

Question 34

Array hybridization

Answer 34

.