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Chapter 16 Molecular Basis of Inheritance, Euchromatin image loosely…
Chapter 16 Molecular Basis of Inheritance
DNA Replication
Proteins work together in
DNA Replication and Repair
relationship btw structure and function is evident in the double helix:
the specific complementary pairing of nitrogenous bases in DNA is functional significance (DNA Replication)
Prior to duplication the Hydrogen bonds are broken, & two chains unwind and separate. Each chain then acts as a template for the formation on to itself of a new companion chain, resulting in 2 exactly duplicated pairs of chains
Model for DNA Replication: Basic concept
Proteins involved in the initiaion of DNA Replication:
Origins of DNA replication
the replication of chromosomal DNA begins at particular sites, short stretches of DNA that have a specific sequence of nucleotides
DNA Replications: three alternative models
Semiconservative model:
watson and crick's model predicts that when a double helix replicates, each of the two daughter molecules will have one old strand, from the parental molecule, and one newly made strand.
Conservative model:
predicts the two parental strands somehow come back together after the process
Dispersive model:
all four strands of DNA following replication have a mixture of old and new DNA
Origins of Replication
the particular site where replication of chromosomal DNA begins
short stretches of DNA that have a specific sequence of nucleotides
proteins that initiate DNA replication recognize the sequence and attach to the DNA, separating the two strands and opening up a replication "bubble"
Origins of replication in E. coli and eukaryotes
Summary of bacterial DNA replication
Helicase unwinds the parental double helix.
Molecules of single-strand binding protein stabilize the unwound template strands
The leading strand is synthesized continuously in the 5' to 3' direction by DNA pol III.
Primase begins synthesis of the RNA primer for the fifth okazaki fragment.
DNA pol IIIis completing synthesis of fragment 4. When it reaches the RNA primer on fragment 3, it will detach and begin adding DNA nucleotides to the 3' end of the fragment 5 primer in the replication fork.
DNA pol I removes the primer from the 5' end of fragment 2, replacing it with DNA nucleotides added one by one to the 3' end of fragment 3. After the last addition, the backbone is left with a free 3' end.
DNA ligase joins the 3' end of fragment 2 to the 5' end of fragment 1.
Bacterial DNA Replication Proteins and their functions
Helicase
- Unwinds parental double helix at replication forks
Single-strand binding protein
- Binds to and stabilizes single-stranded DNA until it is used as a template
Topoismerase
- Relieves overwinding strain ahead of replication forks by breaking, swiveling, and rejoining DNA strands
Primase
- Synthesizes an RNA primer at 5' end of leading strand and at 5' end of each Okazaki fragment of lagging strand
DNA pol III
- Using parental DNA as a template, synthesizes new DNA strand by adding nucleotides to an RNA primer or a pre-existing DNA strand
DNA Pol I
- removes RNA nucleotides of primer from 5' end and replaces them with DNA nucleotides added to 3' end of adjacent fragment
DNA ligase
- Joins Okazaki fragments of lagging strand; on leading strand, joins 3' end of DNA that replaces primer to rest of leading strand DNA
Synthesizing a new DNA strand:
Replication Fork:
the ends of a replication bubble, Y-shaped region where the parental strands of DNA are being unwound
Helicases:
enzymes that untwist the double helix at the replication forks, separating the two parental strands and making them available as template strands.
Single-strand binding proteins:
these bind to the unpaired DNA strands, keeping them from re-pairing, the untwisting of the double helix causes tighter twisting and strain ahead of the replication fork.
Topoisomerase:
enzyme that helps relieve this strain by breaking, swiveling, and rejoining DNA strands.
Primer:
the RNA Chain
Primase:
the enzyme that synthesizes the RNA Chain, primer
DNA Polymerase:
enzyme that catalyze the synthesis of new DNA by adding nucleotides to the 3' end of a preexisting chain
Proteins involved in the initiation of DNA replication
New Strand from Template Strand
Antiparallel arrangement of double helix w/constraint of function of DNA Polymerase
ensure DNA polymerase can add nucleotides ONLY to the free 3' end of a primer or growing DNA Strand, never the 5' end.
New DNA strands can elongate only in the 5' to 3' direction
Leading strand
- the new complementary strand made as the fork progresses
Synthesis of the Leading Strand
Lagging Strand
- DNA Pol III must work along the other template DNA strand in the mandatory 5' -> 3' direction away from the replication fork, elongating
Okazaki fragments
lagging strands synthesize discontinuously as a series of segments
after Reiji Okazaki, Japanese scientist who discovered them
-100-200 long in eukaryotes
each fragment requires its own primer separately
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Nitrogenous Bases Pair off:
Adenine (A) with thymine (T)
Guanine (G) with cytosine (C)
Purine (A/G) with Pyrimidine (C/T) is only combination that results in a uniform diameter for a double helix
Base Pairing in DNA
DNA - The genetic material
Structure of a DNA Strand
Chargraff identified
regularity in the ratios of nucleotide bases
A-T / G-C are approximately equaled in their percentages
Chargraff's Rule:
1)
DNA base composition caries between species
2)
for each species, the percentages of A and T are roughly equal, as are those of Gand C bases.
Watson-Crick model
:
yielded that the only combination that worked with X-ray data was Pairing Purine with Pyrimidine that results in a uniform diameter for the double helix
General Definitions
:
Pathogenic:
disease-causing
Nonpathogenic:
harmless
Transformation:
change in genotype and phenotype due to the assimilation of external DNA by a cell.
Bacteriophages:
bacteria eaters, viruses that attack bacteria
Virus:
DNA enclosed by a protective coat often simply protein
Double Helix:
the presence of two strands
Antiparallel:
their subunits run (or oriented in) opposite directions to each other
Purine:
Adenine and Guanine (Nitrogenous bases w/2 organic rings), Ex: two sides of a street
Pyrimidine:
Cytosine and thymine (nitrogenous bases with single ring)
DNA Replication
: the copying of DNA
A virus infecting a baterial cell
Components of Virus:
Phage Head
DNA
Tail Sheath
Tail Fiber
Genetic material
DNA Replication Complex -
The trombone model
Mismatch repair -
other enzymes remove and replace incorrectly paired nucleotides that have resulted from replication errors.
Nuclease
- DNA-cutting enzyme, that cut out (Excised) a segment of the strand containing the damage, the resulting gap is then filled in with nucleotides, using the undamaged strand as a template
Nucleotide excision repair
- DNA repair systems, enzymes involved in filling the gap are a DNA polymerase and DNA ligase
Shortening of the ends of linear DNA molecules
for linear DNA the usual replication machinery cannot complete the 5' ends of daughter DNA Strands because there is no 3' end of a preexisting polynucleotide for DNA polymerase to add onto.
consequence of the enzyme's requirements
once a primer is removed, it cannot be replaced with DNA because there is no 3' end available for nucleotide addition
-
repeated rounds of replication produce shorter and shorter molecules with uneven (staggered) ends
Telomeres
eukaryotic chromosomal DNA molecules have special nucleotide sequences at their ends
do not contain genes
consists of multiple repetitions of one short nucleotide sequence.
EX: TTAGGG repeated btw 100 & 1,000 times
2 protective functions:
1) specific proteins associated with telomeric DNA prevent the staggered ends of the daughter molecule from activating the cell's systems for monitoring DNA damage,
Ex: staggered ends can cause cell death
2) telomeric DNA acts as a kind of buffer zone that provides some protection against the organism's genes shortening (telomeres do not prevent erosion just postpone it.
Telomeres become shorter during every round of replication
Shortening telomeres is connected to the aging process of certain tissues and even to aging of organism as a whole
Telomeres
Links to Cancer
Telomerase activity is abnormally high in cancerous somatic cells, suggesting that its ability to stabilize telomere length may allow these cancer cells to persist.
Many cancer cells do seem capable of unlimited cell division
A Chromosome
consists of DNA molecule packed together with proteins
each eukaryotic chromosome contains a single linear DNA double helix that, in humans, averages about 1.5 x 10^8 nucleotide pairs (4 cm long).
Chromatin
The exact way in which this complex of DNA and protein fits into the nucleus
DNA, the Double Helix
Nucleosomes in a 10-nm Fiber, under an electron micrograph
Each "bead" is a nucleosome, basic unit of DNA packing; the "string" between beads is called
linker
DNA
linker DNA wound twice around a protein core of 8 histones, tails outward
The basic constituent of interphase chromatin
Euchromatic/
Heterochromatin
This organization is dynamic but disappears once mitosis begins
Histones
proteins responsible for the main level of DNA packing in interphase chromatin
more than a 1/5th of histone;s amino acids are Lys and Arg and therefore bind tightly to the negatively charged DNA
4 Types of histones
Prophase
Chromosomes consist of two sister chromatids
the chromatin of each sister chromatid begins to condense
Condesin II (red) bind to 10-nm fiber of DNA and form DNA loops that get larger and larger; Condensin I a central scaffold from which the loops extend and grow,
chromosome get wider and shorter, by the end of prophase they are half as long
Prometaphase
Condensin I (Green) proteins bind to DNA outside the central scaffold, making smaller loops out of the larger loops generated by condensin II
process continues, w/more and more loops extending outward, and the chromosome getting denser, shorter, and wider
the scaffold begins to twist into a helix allowing even more loops per given length of chromosome.
Metaphase
the chromosome is at its most dense, w/most loops per turn, and therefore is at its shortest length
two sister chromatids are fully condensed
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Interphase
Euchromatin
loosely arranged 10-nm fiber
Heterochromatin
densely arranged 10-nm fiber
because its so compacted, it is largely inaccessible to the proteins responsible for transcribing the genetic information
the less compacted, more dispersed interphase chromatin
-
true chromatin
