Molecular Basis of the Gene Flashcards
Transformation
change in genotype and phenotype due to assimilation of external DNA by a cell
Think: Griffith and Avery
Griffith did not know in 1928 what the transforming factor was made of!
Avery and team figured it out.
phage
Virus that attacks bacteria
Chargaff’s rules
DNA base composition varies between species
For each species. the % of A and T are roughly equal
The % of G and C bases are roughly equal.
photo 51
Confirmed DNA is a helix
2 strands (not 3)
uniform width (eliminating Watson’s idea that A could pair with A)
Antiparallel
subunits run in opposite directions
5’ to 3’ paired to a strand that is running 3’ to 5’
The 5’ end has a phosphate group, the 3’ a -OH
semiconservative model of replication
Proposed by Watson and Crick, proven by Meselson and Stahl.
origins of replication
sites where DNA replication begins
Replication fork
Y shaped region where the parental strands are being unwound by helicase (shown in yello)
single-strand binding proteins
bind to unpaired DNA strands to keep them from re-pairing
topoisomerase or gyrase
The untwisting of the DNA causes strain ahead of the fork.
Topoisomerase relieves the strain.
primer
short stretch of RNA (5 to 10 nucleotides long)
Made by primase.
The primer is shown in green.
DNA polymerase
catalyze the synthesis of new DNA by adding nucleotides to the 3’ end of the preexisting chain.
There are several polymerases in E.Coli but 2 you need to know.
DNA polymerase I and DNA polymerase III
There are 11 in eukaryotes!
DNA polymerase can add 500 nucleotides per second in prokaryotes and 50 per second in human cells.
dATP or dGTP, etc
a sugar, base, and three phosphates.
2 phosphates are released when a nucleotide is added.
exergonic reaction/helps drive polymerization
leading strand vs. lagging strand
leading: one primer, made continuously by DNA pol III
lagging: many primers, made discontinuously, series of segments called Okasaki fragments.
Fragments are 1000-2000 nucleotides in E. coli and 100-200 nucleotides in Eukaryotes
ligase
enzymes the joins the sugar-phosphate backbones of the Okasaki Fragments
We’ll see it again in figure 13.21 and 13.25
Anytime repairs must be made, ligase is used!
mismatch repair/change in base repair
Even though DNA polymerase is a great proofreader (there is one error per 10 billion nucleotides) it does happen.
Other enzymes remove (nuclease) and replace incorrectly paired nucleotides.
Ligase seals the backbone together.
One mismatch is associated with a form of colon cancer.
telomeres
As a result of many rounds of replication, DNA molecules get shorter.
telomeres protect the ends of DNA-contain no genes.
A buffer zone of repeated TTAGGG to protect genes.
Postpone erosion of genes
The telomerase enzyme lengthens telomeres but is not active in most human cells.
The shortening of telomeres is proposed to play a role in aging.
Short Video: https://www.youtube.com/watch?v=U0fRAr-ZHCo
https://www.healthline.com/health/telomeres#telomere-lengthening
purine
2 ring nitrogenous base
Includes A and G
pyrimidine
one ring nitrogenous base
includes cytosine, thymine and uracil
hydrogen bonds
hold DNA together
3 for G and C
2 for A and T
covalent bond
holds:
sugar to phosphate
sugar to nitrogenous base
semiconservative replication
one old strand and one new strand.
Meselson-Stahl
replication fork
Y shaped region where the parental strands are being unwound
primer
short strand of RNA made by primase
5-10 nucleotides long
uses parental strand
DNA polymerase
There are two you need to know:
I removes primer and replaces RNA with DNA
III adds a DNA nucleotide to the RNA primer and then keeps going until the end of the DNA strand
50/second in human cells
leading vs. lagging strand
Leading:DNA polymerase continuously adds nucleotides to the new strand as fork progresses.
Lagging: discontinuous, moving away from the fork, series of segments called Okasaki fragments
DNA ligase
The enzyme that glues the fragments into a continuous step.
Can glue a plasmid together or when a repair is made to the DNA
nuclease
DNA cutting enzyme.
Removes damaged DNA
telomeres and fertility
no genes
end of chromosomes
repetitions of TTAGGG
a buffer zone that protects genes
postpone erosion of genes
telomerase
an enzyme that elongates telomeres
active in germ cells, not somatic cells
may be overacitve in cancer cells
histone
100 amino acids
first level DNA packing
Four types of histones
nucleosome
DNA wound twice around a protein core of 8 histones
30-nm fiber
interaction between histone tails of one nucleosome and the linear DNA and nucleosomes on either side
Found in interphase
heterochromatin
10 nm, 30 nm and looped
not accessible to transcription (genes are not expressed or are off)
genetic engineering
direct manipulation of genes for practical purposes
agriculture
criminal law
medical research
plasmid
a circular molecule of DNA
recombinant DNA
a molecule of DNA containing two different sources often different species
restriction enzymes
cut up DNA at a specific site, called a restriction site
sticky ends vs. blunt ends
unpaired bases
PCR
polymerase chain reaction
This technique can make billions of copies of a specific target DNA
CRISPR Cas 9
bacterial protein that helps defend bacteriophage infections.
Cas9 works with guide RNA (homing device)
Cas9 cuts specific DNA.
Triggers DNA repair or the DNA can be knocked out
gene drive
altering genes in an insect (example) so that it can’t transmit disease
engineering the new allele so that it is much more highly favored for inheritance
reproduction drives the new allele through the population
