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Chapter 16 &17 (DNA is the genetic material (Double-helical…
Chapter 16 &17
DNA
is the genetic material
Double-helical structure composed of nitrogenous bases
adenine
Guanine
Thymine
Cytosine
Double Helix is the presence of two strands
this shape was modeled to a conform to the X-ray measurements and what was known about the chemistry about the DNA
it was discovered that there were sugar phosphate groups that covered the outside of the DNA molecule
there were also negatively charged phosphate groups facing the aqueous surrounding while the relatively hydrophobic nitrogenous bases were in the interior
two sugar-phosphate backbones are antiparallel which means that their subunits run in opposite directions
the sugar phosphates are represented as "ribbons"
when these four bases are arranged in a specific segment it is called a gene. When the segments are coiled in a form that can be easily duplicated they are known as
chromosomes
there are 23 pairs of chromosomes and each set has a chromosome given from each of their parents
Chromosomes are a chain of DNA that is compacted in order to fit within a cell
stands for deoxyribonucleic acid
the genetic material came form studies of viruses that infect bacteria. These viruses are known as bacteriophage
Bacteriophage means "bacteria-eaters" and are also called phages for short
A virus is a DNA or sometimes RNA enclosed by a protective coat of proteins
Viruses reproduce more viruses by infecting a cell and taking over its metabolic machinery
Chromatin
complex of DNA and protein that forms the nucleus of the eukaryotic cell
consists of small beads known as nucleosomes
nucleosomes are composed of DNA wrapped around eight proteins called histones
each histone contains about contains only about 100 amino acids where the total mass of the histones are almost equivalent to the mass of DNA
Heterochromatin
when the centromeres and telomeres of chromosomes exist in highly condensed state similar to that seen in a metaphase chromosome
euchromatin
means true chromatin
less compacted and more dispersed
The DNA Replication Complex
primase slows down the progress of the replication fork and coordinates the placement of primers and the rates of replication on the leading and lagging strands
Instead of moving along the complex, DNA may move through the complex during the replication
the Nuclear matrix
a framework of fibers extending through the interior of the nucleus
Proteins required during the Bacterial DNA replication
DNA pol III
uses parental DNA as a template
synthesises new DNA stands by adding on nucleotides to and RNA primer or 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 fragments
DNA ligase
joins Okazaki fragments of lagging strand on the leading strand, join 3' end of DNA that replaces primer to rest of leading strand DNA
Proofreading and Repairing DNA
when an error is found in an incorrectly paired nucleotide the polymerase removes the nucloetide and then resumes synthesis
mismatch repair
mismatched nucleotides pair up evading proofreading by a DNA polymerase
somes enzymes remove and replace incorrectly paired nucleotides that have resulted from replication errors
mutations
permanent changes to a DNA sequence error
uses a mechanism that takes advantage of the base-paired structure of DNA
nucleotide excision repair
repair genetic damage caused by ultraviolet rays of sunlight
RNA translation
(17.4) Translation is the RNA-directed synthesis of a polypeptide
molecular components of translation
a cell "reads" a genetic message and builds a polypeptide accordingly . The message is a series of codons along an mRNA molecule and the translator is called a transfer RNA (tRNA)
the function is to transfer an amino acid from the cytoplasmic pool of amino acids growing polypeptide in a ribosome
a cell keeps its cytoplasm stocked with all 20 amino acids by synthesizing them from other compounds or by taking them up from the surrounding solution
tRNA must carry a specific amino acid to the ribosome
the correct matching up of tRNA and amino acid is carried out by a family of related enzymes that are aptly named aminoacyl-tRNA synthetases
there are 20 different synthetases
a synthetases joins to a given amino acid to an appropriate tRNA one synthetases is able to bind to all different tRNAs for a particular amino acid
the synthetases catalyzes the covalently attachments of the amino acid to its tRNA in a process driven by hydrolysis of ATP
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mRNA is made in the nucleus and then travels to the cytoplasm
The Structure and Functions of Transfer RNA
tRNA bears a specfic amino acid at one end of its three-dimensional structure
at some ends of amino acids there is a nucleotide triplet that can base-pair with the complementary codon on mRNA
wobble
the flexible base pairing at the codon position
a tRNA with the anticodon 3'-UCU-5' can base pair with either the mRNA codon 5'-AGA-3' or 5'-AGG-3', both of which code for arginine
a tRNA molecule consists of a single RNA strand that is only about 80 nucleotides long
therefore nucleotide bases can hydrogen bond to each other which can fold back on itself and form a molecule with three-dimensional structure
it is roughly L shaped
a loop extending from the L includes the anticodon
the particular nucleotide triplet that base-pairs to a specific mRNA codon
anticodons are written as 3'-->5' to align properly with codons written 5'-->3'
The structure and function of Ribosomes
ribosomes facilitate the specific coupling of tRNA anti codons with mRNA codons during protein synthesis
a ribosome consists of a large subunit and a small subunit, each made up of proteins and one or more ribosomal RNAs (rRNAs)
in eukaryotic cells the subunits are made of nucleolus
is the most abundant type of cellular RNA .
binding sites of the tRNA
P site
peptidyl-tRNA binding site
holds the tRNA carrying the growing polypeptide chain
A site
aminoacyl-tRNA binding site
holds the tRNA carrying the next amino acid to be added to the chain
E site
exit site
discharged tRNA leaves the ribosome
the ribosome holds the tRNA and the mRNA in close proximity so that it can be added to the carboxyl end of the growing polypeptide
it then catalyzes the formation of the peptide bond and then passes through the exit tunnel as it becomes longer
Elongation of the polypeptide chain
amino acids are added one by one to the previous amino acid at the C-terminus of the growing chain
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Termination of Translation
Stage 1.
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Stage 2.
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Stage 3.
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(16.2) Proteins that work together in DNA replication and repair
Before duplication the hydrogen bonds are broken and the two chains unwind and separate
the chains then acts as a template for the formation on to itself of a new companion chain
then nucleotides complementary to the parental strand are connected to form the sugar-phosphate backbones of the new "daughter" strands
semiconservative model can be distinguished from a conservative model of replication in which two parental strands somehow comeback together after the process
these "daughter" strands are now each composed of an old strand
The Dispersive Model
all four strands of DNA following replication have a mixture of old and new DNA
Origins of Replication
the replication of chromosomal DNA begins at this particular site
The E. Coli. chromosome is circular and has a single origin
protein s that intiiate DNA replication recognize this sequence and attach to the DNA replication, separating the two strands and opening up a replication "bubble"
Replication bubble
at the end of each replication bubble is a replication fork
a Y-shaped region where the parental strands of DNA are being unwound by several different types of enzymes
Helicases
are enzymes that untwist the double helix at the replication forks, separating the two parental strands and making them available as template strands
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Topoisomerase
an enzyme that helps relieve this strain by breaking, swiveling, and rejoining DNA strands
the untwisting of the double helix causes tighter twisting and strain ahead of the replication fork
DNA pol III remains in the replication fork on that template strand and continuously adds nucleotides to the new complementary strand as the fork progresses
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DNA polymerases
catalyze the synthesis of new DNA by adding nucleotides to the 3' end of a pre-exisiting chain
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catalyzes the addition of each monomer via dehydration reaction
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Replication of DNA in a eukaryotic cell
multiple replication bubbles form and eventually fuse, thus speeding up the copying of the very long DNA molecules
DNA replication proceeds in both directions from each origin
(17.3) Eukaryotic Cells modify RNA
RNA processing
both ends of the primary transcript are altered
certain interior sections of the RNA molecule are cut out and the remaining parts spliced together
RNA splicing
large portions of the RNA molecules are removed and the remaining portions are reconnected
the removal of introns is accomplished by a large complex made of proteind and small RNAs called a spliceosome
this complex binds to several short nucleotide sequences along an intron, including key sequences at each end
Ribozymes
RNA molecules that function as enzymes
proteins often have a modular architecture consisting of discrete structural and functional regions called domains
a domain may include an active site that allows substrates to pair
some domains may allow the enzyme to bind to a cellular membrane
different exons code for different domains of a protein
Alternative RNA splicing
genes are known to give rise to two or more different polypeptides
noncoding segments of nucleic acid that lies between coding regions are called intervening sequences, or introns
exon shuffling
introns increase the probability of crossing over between the exons of alleles of a gene by providing more terrain for cross overs without interrupting coding sequences
can lead to new proteins with novel combinations of functions
other regions are called exons because they are expressed, usually by being translated into amino acid sequence
Alteration of mRNA Ends
The 5' end receives a 5' cap
5' cap is a modified form of guanine nucleotide added onto the 5' end after transcription of the first 20-40 nucleotides
(17.2) Transcription is the DNA-directed synthesis of RNA
The molecular components of transcriptase
Messenger RNA
the carrier of information from DNA to the cell's protein-synthesizing machinery
information is transcribed from the template strand of a gene where an enzyme called RNA polymerase pries the two strands of DNA apart and joins together RNA nucleotides
RNA polymerase
The DNA sequence where RNA polymerase attaches and initiates transcription known as promoter
the promoter is said to be the upstream from the terminator
In bacteria, the sequence that signals the end of transcription is called the terminator
the stretch of DNA downstream from the promoter that is transcribed into an RNA molecule called a transcription unit
Trancription factors
a collection of proteins that mediate the binding of RNA polymerase and the initiation of transcription
the complex of transcription factors and RNA polymerase is called the Transcription initiation complex
There are three stages in the the process of transcription
Stage 1. Initiation
After RNA polymerase binds to the promoter, the DNA strands unwind, and the polymerase initiates RNA synthesis at the start point on the template strand
At a eukaryotic promotor
A eukaryotic promotor
commonly includes a TATA box (a nucleotide sequence containing TATA) about 25 nucleotides upstream from the transcriptional start point
Several transcription factors
one recognizing the TATA box, must bind to the DNA before RNA polymerase II can bind in the correct position and orientation
Additional transcription factors
bind ti the DNA along with RNA polymerase II, forming the transcription initiation complex. RNA polymerase II then unwinds the DNA double helix, and RNA synthesis begins at the start on the template strand
Stage 2: Elongation
the polymerase moves downstream , unwinding the DNA and elongating the RNA transcript 5'-3'
the DNA strands re-form a double helix
Stage 3: Termination
the RNA transcript is released and the polymerase detaches from the DNA
(17.5) Mutations of one or a few nucleotides can affect protein structure and function
mutations
changes in the sequence of the DNA
chromosomal rearrangements that affect long segments of DNA
point mutations
changes in a single nucleotide pair of a gene
if it occurs in a gamete or in a cell that gives rise to gametes, it may be transmitted to offspring and to future generations
the mutant condition is referred to as a genetic disorder or hereditary disease
silent mutation
a change in a nucleotide pair may transform one codon into another that is translated into the same amino acid
has no observable effects on the phenotype
are able to occur outside of the genes as well
results from nucleotide-pair substitution
the replacement of one nucleotide and its partner with another pair of nucleotides
Insertions and deletions
Insertions and deletions are addition s or losses of nucleotide pairs in a gene
these mutations have disastrous effect on the resulting protein more often than substitutions do
may alter the reading frame of the genetic message, the triplet grouping of nucleotides on the mRNA that is read during translation
frameshift mutation
occurs whenever the number of nucleotides inserted or deleted is not a multiple of three
Missense mutations
substitutions that change one amino acid to another one
may have a little effect on phenotype
nonsense mutation
effect depends on how close the new stop codon is to the beginning of the coding sequence
a point mutation can change a codon for an amino acid into a stop codon
causes translation to be terminated prematurely
the resulting polypeptide will be shorter than the polypeptide encoded by the normal gene
spontaneous mutations
an incorrect base being used as a template in the next round of replication
a number of physical and chemical agents are called mutagens
mutagens interact with DNA that causes mutations
Nucleotide analogs
chemicals similar to normal DNA nucleotides but that pair incorrectly during DNA replication
some mutagens interfere with the correct DNA replication by inserting themselves into the DNA and distorting the double helix
(17.1) Genes specify protein via transcription and translation
Gene expression
the process by which DNA directs the synthesis of proteins
the expression of genes includes two stages : Transcription and translation
Transcription
the synthesis of RNA using information in the DNA
uses messenger RNA to carry genetic information from the DNA to the protein-synthesizing machinery of the cell
two nucleic acids are written in different forms of the same language, and the information is transcribed "rewritten" from DNA to RNA
Translation
the synthesis of a polypeptide using the information in the mRNA
there is a change in language, the cell must translate the nucleotide sequence of an mRNA molecule into the amino acid sequence of a polypeptide
the site of translation are ribosomes
molecular complexes that facilitate the ordely linking of amino acids into polypeptide chains
In bacteria, it lacks a nucleus mRNA produced by transcription is immediately translated without additional processing
In a eukaryotic cell, the nucleus provides a separate compartment for transcription. The original RNA transcript, called pre-mRNA, is processed in various ways before leaving the nucles as mRNA