chap 15 midterm Flashcards
Capsid
exterior protein coat that gets
left behind on the outside of the cell
capsid is the protein shell of a virus, enclosing its genetic material(DNA)
DNA
is packed in the Capsid and subunits (protein) called promoters
primary structure of DNA strand
backbone made up of sugar and phosphate groups of deoxyribonucleotides
nitrogen containing bases that project from backbone.
*DNA directionality
5 end: start (phosphate)
3 end: finish (OH) (sugar end of DNA)
The 3’ end has an exposed hydroxyl group attached to the 3’ carbon of deoxyribose.
The 5’ end has an exposed phosphate group attached to a 5’ carbon.
*structure of deoxyribonucleotide
-Phosphate group attached to 5’ carbon of the sugar
-Hydroxyl group on 3’ carbon of the sugar
-Base could be (A, T, G, C) Adenine, thymine, guanine, cytosine
code of DNA is determined by
the base, A T G C
PROTEIN
contains sulfur but not phosphorus
DNA
contains phosphorus but not sulfur
T2 infects bacterium
virus injects its genes into the cell
The genes direct production of new virus particles
*complementary base pairing
pairing of the nitorgenous bases
2 DNA STRANDS ARE ANTIPARALLEL,
line up in opposite direction
A WITH T, C WITH G
5’ links with 3’ at top
bottom 3 with 5
*DNA’s secondary structure
2 polynucleotides twists to form double helix
Rosalid franklin
Laboratory technician
provided photographic evidence
DNA as templates
strands of DNA served as templates for production of new strands
*Alternative hypotheses for DNA replication
Semiconservative
Conservative
Dispersive
*Semiconservative
Parental DNA separate and each strand is used as a template for daughter strand
1 old copy stand and 1 new copy strand
old copy makes new copy
*Conservative
Parental DNA is template for synthesis for new molecule
both parental strands are copied and end up with 2 strands of DNA (one original parental DNA and one copy of the DNA of the parental double strand
*Dispersive
stretches of old DNA would be interspersed with new DNA down the length of each daughter cell.
Daughter molecules old DNA interspersed with newly synthesized DNA.
combination of parental DNA and daughter DNA.
*determine how replication occurs
grew ‘heavy” nitrogen (15N) after generations moved back to ‘normal” nitrogen medium (14N)
separated DNA by density
*DNA POLYMERASE
enzyme responsible forming new copies of DNA
DNA synthesis only works in 5–3 direction on a single stranded template, in one direction. Requires a 3′ end to extend from
DNA IS READ LIKE A BOOK, FRONT TO BACK
it polymerizes deoxyribonucleotide monomers into DNA !!!
Replication Bubbles
DNA is replicated in replication bubbles in the chromosome
synthesis proceeds in two diff directions.
since replication is 5–3 antiparallel synthesis occurs in both directions
Bacteria has a single origin of replication!!
Eukaryotes have multiple origins of replication!!!
Initiation of replication
(synthesis of leading strand)!
4 steps; Helicase opens double helix–stabilize single strands–topoisomerase–primase RNA primer
-Helix is opened, Helicase, an enzyme that opens double helix (bonds b/n DNA strands)
-Single Strand DNA-binding proteins (SSBPs) stabilize single strands
-Topoisomerase, relieves twisting forces, Helix is stabilized by single strand DNA-binding proteins
-Unwinding of helix creates tension, then cuts and rejoins DNA downstream of replication fork.
-DNA polymerase is primed
provides 3 hydroxyl (OH) group that can combine with a nucleotide.
Now ready to replicate
deoxyribonucleotide
a nucleotide that contains deoxyribose.
deoxyribomnucleoside triphosphates
monomers
high potential energy bc their three closely packed phosphate groups
they have enough poteinal energy to make formation of phosphoiester
origin replication
When DNA is being synthesized it forms specific sequence..
-Bacteria have one and form one replication bubble
-Eukaryotic cells have many on each chromosome
(replication bubble!! its sequence inside )
replication forks
Y shape where the parental DNA double helix is seperated
each replication bubble has…
TWO replication forks
because synthesis is bidirectional
replication bubbles grow in two directions (5—3)
genome
bacterial cells copy their entire complement of DNA
-genetic material in organism, is made up of DNA
-entire set of DNA instructions found in a cell.
intermediate density DNA
hybrid dna n ot jus N14 or N15
(low density- (14N)
high density- (15N)
REPLISOME
contains enzymes responsible for carrying out replication of DNA (DNA synthesis around the replication fork)
Large Macromolecular machine.
composed of 2 DNA polymerase complexes synthesis the
(leading strand) with other (lagging strand)
Leading strand (go back to initiation of replication)
strand of DNA being replicated continuously and continuously polymerized toward the replication fork !
5—3 prime continuously synthesizes in direction of the moving fork
*1) DNA is opened, unwound and primed)
2)synthesis of leading strand begins
Lagging Strand
MOVES IN DIRECTION THAT RUNS AWAY FROM THE MOVING REPLICATION FORK
synthesized away from strand and lags behind the fork, slowing down the process. Okazaki Fragments are then linked into a continuous strand
Okazaki Fragments
Short DNA fragments attached to RNA’s primersDNA polymerase I removes the RNA primers and replaces them with DNA
The enzyme DNA ligase joins the Okazaki fragments (15.10)
DNA helicase
breaks hydrogen bonds between the two DNA strands to separate them
Single-strand DNA-binding proteins (SSBPs)
attach to the separated strands to prevent them from closing
Topoisomerase (unwinding DNA helix creates tension)
Topoisomerase cuts and rejoins the DNA to relieve this tension
DNA polymerase has two parts:
A sliding clamp that forms a ring around the DNA
A part that grips the DNA strand
primer
An RNA strand about a dozen nucleotides long
Forms complementary base-pairs with the DNA template strand
Provides a 3′ hydroxyl (OH) group that can combine with a dNTP to form a phosphodiester bond
Primase
Primers are made by enzyme called (Primase)
A type of RNA polymerase
Does not require a free 3′ end to begin synthesis
(one type of RNA polymerase)
RNA polymerase
enzymes that catalyze the polymerization of ribonucleotides into RNA
don’t require primer like DNA polymerase
leading strand synthesis (vocab words)
-primase- catalyzes synthesis of RNA primer on an Okazaki fragment
-DNA polymerase III- Extends the leading strand
-Sliding clamp- holds DNA polymerase in place during strand extension.
Lagging strand synthesis (vocab words)
Primase- catalyzes the synthesis of the RNA primer on an okazaki fragment
DNA polymerase III- Extends an okazaki fragment
Sliding clamp-holds DNA polymerase in place during strand extension.
DNA polymerase I- Removes the RNA primer and replaces it with DNA
DNA ligase- Catalyzes the joining of Okazaki fragments into a continuous strand.
Telomeres
the end of eukaryotic chromosome can be problematic
(when the primer is lost it shortens chromosome bc cant be replaced with DNA), left as a single strand.
dosent contain genes, just stretches of bases
Telomerase
catalyzes the synthesis of DNA and from an RNA template that it contains.
It fixes the “telomeres” it adds DNA to the end of a chromosome to prevent it from getting shorter. on lagging strand
somatic cells
lack telomerase (chromosomes of somatic cells progressively shorten) occurs in diff ages.
ANY CELL NOT INVOLVED IN GAMETE FORMATION (TELOMERASE) Don”t produce gametes
# of cell division is limited by length of a cells telomere
Proofreading DNA
If DNA polymerase adds a mismatched deoxyriboonucleotide such as ( C pairing with A) DNA polymerase can recognize and remove the mismatched deoxyribonucleotide and start over to add correct deoxyribonucelotide.
(accuracy for DNA synthesis)
Mismatch repair
occurs when mismatched bases are corrected after DNA synthesis is done,DNA polymerase sometimes leaves a mismatched pair behind in a newly synthesized strand
once DNA synthesis moves beyon a mismatched base pair proofread is no longer possible so
Mismatch repair enzymes, Recognize the mismatched pair
Remove a section of the newly synthesized strand that contains the incorrect base
Fill in the correct bases
Repairing Damaged DNA
DNA can be damaged by sunlight, X-rays, and many chemicals
Organisms have DNA damage-repair systems
For example, UV light and some chemicals can cause thymine dimers to form
These dimers produce a kink in the DNA strand
This blocks DNA replication
UV light damages DNA
WHEN UV light is absorbed by a section if DNA that has adjacent thymines, the energy can lead to the formation of bonds between them. Thymine dimer that is produced causes Kink in the DNA Strand.
nucleotide excision repair system
recognizes such types of damage
A protein complex recognizes the kink
Removes the damaged single-stranded DNA
Uses the intact strand as a template for new DNA
DNA ligase links the repaired strand to the original undamaged DNA
Xeroderma pigmentosum (XP)
A rare autosomal recessive disease in humans
extremely sensitive to UV light
Increases chance of skin cancer by 1000−2000 times
XP is caused by mutations in nucleotide excision repair systems
The cells of people with XP cannot repair DNA damaged by ultraviolet radiation
Can result from mutations in any of eight genes
Xeroderma Pigmentosum: A Case Study
If mutations in the genes involved go unrepaired
The cell may begin to grow in an uncontrolled manner
This growth can result in the formation of a tumor
If the overall mutation rate in a cell is elevated
Because of defects in DNA repair genes
Then the mutations that trigger cancer become more likely
