Chapter 16. Molecular Basis for Inheritance and
Chapter 17. Gene to Protein
16: The Molecular Basis for Inheritance.
as the Genetic Material.
for genetic material led to DNA.
Crick Discovered the double Helix by building models to confirm X-ray data.
Replication and Repair.
Replication base pairing enables existing DNA strands to serve as templates for
new complementary strands.
A large team
of enzymes and other proteins carries out DNA replication.
proofread DNA during its replication and repair damage in existing DNA.
mechanism is used to replicate the ends of DNA.
17: From Gene to Protein.
Connection between Genes and Proteins
The study of
metabolic defects provided evidence that genes specify proteins.
and translation overview.
triplets specify amino acids.
early in the history of life.
Synthesis and Processing of RNA.
is the DNA-directed synthesis of RNA.
cells modify RNA after transcription.
Synthesis of Protein.
is the RNA-directed synthesis of a protein.
multiple roles in the cell.
prokaryotic and eukaryotic translation.
mutations can affect protein structure and function.
DNA is the Genetic Material.
can be the genetic material of a virus and can often functions structurally or
as an information intermediate.
Nucleic Acid Structure.
Levels of structure:
are linked together to form a strand of DNA or RNA this linear sequence is the primary
structure is the formation of the double helix; two complementary
strands wound around one another.
double helix is bent around itself and proteins to form the tertiary
structure (chromosomes or chromatids).
the building blocks (subunits) of nucleic acids.
components make up a nucleotide: sugar, phosphate and nitrogenous
categories of nucleotides: purines and pyrimidines.
Purines: adenine (A) and guanine (G) (double-ring base structure).
Pyrimidines: cytosine (C), thymine (T) and uracil (U) (single-ring base structure).
distinguish DNA from RNA.
Thymine used in DNA, while Uracil is used in RNA.
and Crick discovered the double helix by building models to confirm X-ray data
and sugars make the backbone of DNA or RNA and the phosphate group is
connecting the sugar of one nucleotide to the sugar of the next nucleotide,
this is a phosphodiester bond.
direction and sequence specificity; for example the sequence TAACCG has
the direction 5 à
cannot be shuffled and maintain there position this is what can give individual
genes their specific sequences.
has a double helical structure (Fig 11.6 & 11.7).
Crick proposed this double helical structure with the help of findings from
Wilkins, Franklin and Chargaff.
strands of DNA are antiparallel and complementary.
Meaning each strand goes in an opposite direction (one
strand 5à3 other 3à5) and that individual base pairs have a complement on
the other strand.
base pairs with Thymine (A-T) and Guanine with cytosine (G-C) (Fig. 16.6).
There are ten bases per 360o turn of
minor groves along DNA.
Additional folding and proteins needed for chromatin
or chromosome structure.
RNA can also
form complex structures.
RNA is single stranded
which allows for interactions between base pairs within a strand or between
strands this can give RNA secondary structures like: Bulges, internal loops,
multibranched junctions and stem loops (hairpins).
DNA Replication and Repair.
replication is the copying of the genetic material of a cell.
and Stahl were the first to identify replication as semiconservative (Fig
DNA strands are used for making the new strands to make two complete sets of
DNA replication, base pairing enables existing DNA strands to serve as
templates for new complementary strands.
The DNA only
fits together because A bonds with T and G bonds with C (must retain
Two new strands are made complementary to each of the
DNA strand actually comes apart and is used as the template for building the
This makes two double helices both of which have one
old strand and one new strand this is semiconservative replication.
large team of enzymes carries out DNA replication.
research on replication focused on replication in the bacteria E. coli
so we know more about it than we do about eukaryotic DNA replication.
chromosomes contain a single origin of replication (Ori or ARS,
autonomous replication sequence) and replication proceeds bidirectionally (Fig
16.10) eukaryotic chromosomes have multiple origins.
Bidirectional replication involves two replication
forks moving in opposite directions outward from the origin of replication,
this also happens in eukaryotic cells.
Proteins are involved in recognizing the origin and
opening the DNA strands for replication.
polymerases are the enzymes responsible for generating the new DNA strands
by adding nucleotides one at a time.
Polymerases can not add nucleotides de novo
they must add new nucleotides onto a free 3 OH (Fig. 16.11).
This fact and the antiparallel nature of DNA results
in both template strands being replicated differently.
strand may be replicated continuously (leading strand) while the other
is synthesized in small fragments (lagging strand) (Fig 16.13).
These fragments are called Okazaki fragments
and are only about 100-200 bases in eukaryotes.
These short segments
each must be attached to one another in order to make a complete DNA strand, DNA
ligase is the enzyme responsible for joining the sugar-phosphate backbones
of these fragments.
Polymerases can only elongate strands from the 3-OH so they need a primer to
start from (RNA primer).
Primase is the enzyme that provides an RNA primer for the leading strand and
primers for the lagging strand (Fig 16.14).
Primers are removed replaced with DNA and ligated
machinery does not move it reels in parent DNA and extrudes new daughter DNA (Fig
proofread DNA during its replication.
polymerase makes errors about once every 10,000 base pairs, however it
proofreads every nucleotide and can correct these errors.
When an error slips through special enzymes
can carry out nucleotide excision repair.
Thymine cross-linking due to UV exposure from the sun (Fig 16.17).
The ends of DNA
molecules are replicated by a special mechanism (Fig. 16.19).
A primer at
each end of the chromosome (for replication) leaves a blank space with no way
to fill in the DNA.
is a special enzyme that lengthens the ends of the chromosomes (telomeres).
This slows the rate of telomere shortening because the
lengthened telomere can then be used for primer placement.
May be an important cancer drug target.
From Gene to Protein (Chapter 17).
know that genes hold the hereditary information encoding for proteins that give
cells and organisms their traits.
connection between genes and proteins.
expression: DNA à RNA à Protein (Central Dogma); uses the processes: transcription
and Translation are the two main processes linking gene to protein (overview) (Fig
1) The first
stage involves copying the gene sequence (DNA) into messenger RNA (mRNA)
this is transcription.
pre-mRNA must be processed to mature mRNA.
ribosome uses the mRNA, ribosome and transfer RNA (tRNA) to build
proteins one amino acid at a time (translation).
recognizes sites on the mRNA and brings in the corresponding amino acids.
the genetic code nucleotide triplets specify amino acids.
code allows for mRNA to be translated into a specific amino acid sequence.
The mRNA is
read in three nucleotide chunks called codons, each of which encodes for
a specific amino acid (Fig. 17.13).
Some codons indicate the start (AUG)or termination
of translation (UGA).
are four nucleotides (A, G, U and C) and three nucleotides per codon there are
64 (43) different codons.
are only 20 amino acids some codons are used more than once for a specific
amino acid, this is the degenerate code (Fig. 17.4).
base of a codon is sometimes called the wobble base since it may differ
but still encode for the same amino acid.
Ex: codon GGU, GGC, GGA and GGG encode for the amino
code must have evolved early in the history of life.
Ex: UGA is
stop except in mammalian mitochondria where it encodes for tryptophan.
synthesis and processing of RNA.
Transcription is the
DNA-directed synthesis of RNA.
Gene at the
molecular level is a relatively short segment of DNA located within a larger
A gene has
many important sections to it that play different roles during gene expression.
Promoter sequence provides a signal for the start of transcription.
Regulatory sequences are important because they bind proteins that control the speed of the
The stretch of DNA that is transcribed into an RNA
molecule is called a transcription unit.
of transcription (Fig. 17.6):
Initiation: The promoter sequence binds general transcription factors (Ex: TFIID
& TFIIB) in order to load the RNA polymerase holoenzyme (Fig
TATA Box in promoter is bound by TFIID, this is the
start of transcription
Elongation: RNA polymerase slides down the DNA within the open
complex synthesizing RNA (Fig 17.6).
RNA polymerase reaches termination signal and it and RNA transcript fall off.
of mRNA ends (Fig. 17.8).
Unlike prokaryotic mRNA in eukaryotes RNA must be
matured into mRNA.
A cap (7-methyl guanosine) is placed on the 5
end and poly-A tail on the 3 end.
A cap on the mRNA acts
as a recognition site for the ribosome.
The poly A tail adds
stability to the mRNA.
and RNA splicing.
Another important modification is splicing
which includes removing certain pieces of RNA and covalently linking the
remaining pieces together.
pieces that are spliced out are called introns, these are noncoding regions.
Believed some may
contain transcription regulatory sequences and allows for one gene to become
more than one protein.
spliced back together and hold the information coding for protein synthesis.
This makes the mature
mRNA, that leaves the nucleus to find a ribosome.
Synthesis of Protein (Fig 17.12).
is the RNA directed synthesis of a polypeptide.
In order for
translation of mRNA: ribosomes, tRNAs, protein factors and small
molecules (energy) are also necessary.
eukaryotes the ribosome binds to the mRNA and scans for a start codon
(often AUG, encodes for the a.a methionine).
slides in a 5 à
3 direction on the mRNA.
As a codon
is read the corresponding tRNA with the complementary sequence to the codon (anticodon)
brings in the specific amino acid for that codon.
continues until the stop codon (Ex:UAA, UAG or UGA) is reached.
the end of translation and then the complex (ribosome, tRNAs and mRNA)
dissociates from the polypeptide.
have two subunits, large (50S or 60S) and small (30S or 40S), made of proteins
and ribosomal RNA (rRNA).
have three important sites: Aminoacyl site (A), peptidyl site (P) and exit site
(E) (Fig. 17.15).
stages of translation: Initiation, elongation and termination.
The mRNA, tRNAmet and ribosome are involved with translation
initiation factors; loading of the small subunit occurs onto (5-cap in
eukaryotes or Shine-Delgarno sequence of prokaryotes) the mRNA, then loading of
the tRNAmet into the P site and finally the large subunit (Fig 17.7).
Polypeptide synthesis occurs; a new tRNA brings in an amino acid to the A
site and attaches it to the growing chain with the help of an enzyme (Fig.
The complex in the A site is then translocated into
the P site while the empty tRNA is ejected from the E site.
Occurs when a termination codon is reached.
Each termination codon is recognized by a release
factor (RF1 or RF2 in prokaryotes (eRF in eukaryotes)).
When a termination codon is located in the A site The
RF will bind this site releasing the finished primary protein, mRNA and tRNA (Fig.
are strings of ribosomes on a single mRNA and allow for quick translation of an
mRNA (Fig 17.20).
polypeptide to functional protein.
The amino acid sequence of a protein or its primary
structure indicates all further structure of the polypeptide and the
This includes secondary
and tertiary structures and even the proteins ability to interact with other
proteins (quaternary structure).
mutations can affect protein structure and function.
mutations are chemical changes in a single base pair of a gene.
mutation happens in germ cells or gametes then it may be passed on to
mutation has an adverse effect then it is a genetic disorder.
Sickle-cell anemia is due to a single nucleotide change leading to a single
amino acid change in the protein hemoglobin (Fig 17.23).
point mutations (Fig 17.24):
Base-pair Substitutions are the replacement of one nucleotide and its
Can lead to missense
(changes codon to encode for a new amino acid) or nonesense (introduces
a stop codon) mutations.
or deletions add in extra bases or remove bases changing the codons.
Alters the reading frame
during translation, frameshift mutation.