Download 17.1 – Isolating the Genetic Material

Biology 3201 - Ch. 17- Molecular Genetics
17.1 – Isolating the Genetic Material
Scientists who contributed to the development of our modern understanding of DNA and
genomes:
1) Gregor Mendel – early studies on genetics
2) Sutton and Boveri – discovered the link between behavior of chromosomes during
meiosis and Mendel’s “factors”
3) Phoebus Levene – isolated DNA and RNA and studied their properties
4) Griffith – discovered the principle of transformation in bacteria (see fig 17.6, p. 570)
→ transforming principle: genetic information that can be transferred. In 1928, Fred Griffith
discovered that dead pathogenic (disease-causing) bacteria could pass on their pathogenic
properties to live non-pathogenic bacteria
→ Griffith died before discovering what the transforming factor was
5) MacLeod, McCarty, and Avery – isolated the transforming factor in bacteria as DNA.
This was the first evidence that DNA was the hereditary material (it was believed that
protein was the hereditary material at the time)
6) Hershey and Chase – finally demonstrated that DNA was the genetic material
→ used radioactively labeled DNA and protein phages (viruses that attack bacteria). Infected
bacteria with these phages and tracked whether it was the DNA or protein that entered the cell
and caused the viruses to reproduce. Found that only the DNA entered the cell while the protein
stayed outside. Therefore, DNA must be hereditary material. (see fig 17.8, p. 571)
7) Erwin Chargaff – studies DNA structure. Found several things:
→ the nucleotide composition of DNA varies from one species to another
→ the nucleotide composition of DNA specimens taken from different animals of the
same species is fairly constant
→ in DNA, the amount of adenine is always equal to the amount of thymine and the
amount of guanine is always equal to the amount of cytosine (Chargaff’s rule)
8) Rosalind Franklin and Maurice Wilkins – studied DNA structure
→ found two distinct but regular repeating patterns in the structure of DNA
→ also found that nitrogen bases must be located inside molecule because of how it
reacts with water
9) James Watson and Francis Crick – developed the current model of DNA structure
The Components of Nucleic Acids
Nucleotide – the monomers of nucleic acids. Each nucleotide is
composed of a five-carbon sugar, a phosphate group and one of four
nitrogen-containing bases
DNA – stands for deoxyribonucleic acid
→ consists of long chains of individual nucleotides, each of which is composed of a five
carbon sugar (deoxyribose), a phosphate group, and the nitrogen bases adenine, thymine,
guanine, and cytosine.
→ double-stranded (2 chains of nucleotides)
RNA – stands for ribonucleic acid
→ consists of long chains of nucleotides, each of which contains a phosphate group, a
five carbon sugar (ribose), and the nitrogen bases adenine, uracil, guanine, and cytosine
→ single-stranded (1 chain of nucleotides) (see fig 17.4, p. 569)
17.2 – The Structure of Nucleic Acids
DNA – The Double Helix (see fig 17.12 and 17.13, pp. 574-575)
Purines – nitrogenous compounds that have a double-ring structure. The nucleotide bases
adenine and guanine are derived from purines and always bind with pyrimidines in DNA
Pyrimidines – nitrogenous compounds that have a single-ring structure. The nucleotide bases
thymine, uracil, and cytosine are derived from pyrimidines and always bind with purines in DNA
If a DNA molecule was unwound, it would resemble a ladder. The sugar and phosphate groups
would form the outside while the paired nitrogen bases would form the rungs.
Complimentary base pairings – pairing of bases between nucleic acid strands. The two strands
of a DNA helix are complimentary with each other. Each purine base pairs with a pyrimidine
base on the other side.
A binds with T (2 hydrogen bonds)
C binds with G (3 hydrogen bonds)
Antiparallel – describes the property by which the 5’ to 3’ phosphate bridges run in opposite
directions on each DNA strand
In essence, one DNA strand is upside down compared to the other one. This is necessary to
allow the nitrogen bases to bind together correctly
Organization of Genetic Material
Prokaryotic cells
→ usually a single, double stranded DNA molecule
→ nucleoid: area within prokaryotic cells where the DNA is found
→ plasmid : small, self-replicating loop of DNA in a prokaryotic cell that is separate
from the main chromosome and contains from one to a few genes. Plasmids often carry
information that gives the cell resistance to certain antibiotics and heavy metals or the
ability to break down unusual compounds
Eukaryotic cells
→ each human cell has about 2 m of DNA, yet it is packaged into a relatively small area
→ histone: complex of small, very basic polypeptides that form the core of nucleosomes,
around which DNA is wrapped
→ nucleosome: the bead-like structural unit of chromosomes, composed of a short
segment of DNA (about 200 base pairs) wrapped twice around a cluster of eight histone
molecules.
Genes and Genomes
Gene – a specific sequence of DNA that governs the expression of a particular trait and can be
passed to an offspring
Genome – the sum of all the DNA in an organism’s cells
Exons – the coding region of a eukaryotic gene. Each gene is composed of one or more exons
Introns – intervening non-coding sequences in a eukaryotic gene
17.3 – DNA Replication
The process of replication follows a semi-conservative model; when a molecule of DNA is
copied, each new molecule contains one strand of parental DNA and one strand of new DNA
Replication machine – complex involving dozens of different enzymes and other proteins
working together in the process of DNA replication
Stages of Replication
1) Initiation (see fig 17.21, p. 583)
→ replication starts at specific parts of a DNA molecule called replication origins (could
be thousands at a time)
→ involves several enzymes and steps
→ primer – short strand of RNA that works as a starting point for the attachment of new
nucleotides during DNA replication
→ primase – in DNA replication, an enzyme that forms a small RNA primer that is
complimentary to the DNA sequence.
→ helicases – set of enzymes that cleave and unravel short segments of DNA just ahead
of the replicating fork during DNA replication
→ DNA polymerase – during DNA replication, an enzyme that slips into the space
between two strands, uses the parent strands as a template, and adds nucleotides to make
complimentary strands
→ replication fork – during DNA replication, point at which the DNA helix is unwound
and new strands develop
2) Elongation (see fig 17.22 and 17.23, pp. 584-585)
→ since the two strands are antiparallel, their replications occur differently
→ leading strand – in DNA replication, the strand that is replicated continuously in the 5’
to 3’ direction (in the same direction as the movement of the replication fork)
→ lagging strand – in DNA replication, the strand that is replicated by splicing together
Okazaki fragments in the 5’ to 3’ direction (moving opposite to the replication fork)
→ Okazaki fragments – short-nucleotide fragments used during DNA replication on the
lagging strand. They are made by DNA polymerase working in the direction opposite to
the movement of the replication fork, after which they are spliced together.
→ DNA ligase – enzyme that splices together Okazaki fragments during DNA replication
on the lagging strand. DNA ligase catalyses the formation of phosphate bonds between
nucleotides.
3) Termination (see fig 17.24, p. 585)
→ once the new strands are formed, the daughter DNA molecules rewind into helices
automatically (no enzymes required)
→ telomere – specialized non-transcribed structure typically rich in G nucleotides, at the
end of each chromosome. The use of telomeres protects us against the loss of genetic
material during replication
Proofreading and Correction
DNA polymerase checks to see if base pairs are paired correctly. If there is a mistake, DNA
polymerase will remove the incorrect base and insert the correct one.
17.4 – Protein Synthesis and Gene Expression
gene expression – the transfer of genetic information from DNA to protein
As described earlier, DNA is the genetic material in living things which gives the blueprint of
how an organism develops. This blueprint, however, has to be put into a useful or structural
form. In most living things, the main structural molecule is protein. Hence, DNA provides the
blueprint for all the different proteins found in living organisms
Examples of protein structures:
1) skeletal muscle tissue
2) smooth muscle tissue
3) hormones
4) enzymes
5) transporters in cell membranes
However, DNA is not directly used to make protein. Instead, DNA is copied to RNA, and RNA
is used to make protein. This leads us to the central dogma of gene expression, proposed by
Francis Crick:
DNA → RNA → protein
The use of DNA to produce RNA is called transcription. The use of RNA to make protein is
called translation.
The Genetic Code
Recall that in humans there are 20 amino acids (the basic units of proteins). However, there are
only 4 different nucleotides. Therefore, if it only took 1 nucleotide to code for 1 amino acid only
4 amino acids could be produced. If 2 nucleotides in a row coded for 1 amino acid, you still
could not code for all 20 amino acids (only 16 possible combinations). It takes combinations of
3 nucleotide sequences to code for 1 amino acid
Codon – the basic unit, or “word”, of the genetic code. It is a set of 3 adjacent nucleotides in
DNA or mRNA that codes for amino acid placement on polypeptides. (see table 17.2, p. 590)
Characteristics of the genetic code
→ more than one codon can code for an amino acid
ex. UCA, UCU, UCG, and UCC all code for serine
→ it is continuous (no spaces or overlap)
→ universal code – is almost the same in all living things
Transcription (see fig 17.28, p. 591)
The main job of transcription is to make a RNA copy of a small section of the organism’s DNA
(the particular gene needed to make a specific protein)
Messenger RNA (mRNA) – strand of RNA that carries genetic information from DNA to the
protein synthesis machinery of the cell during transcription
RNA polymerase – main enzyme that catalyses the formation of mRNA from a DNA template
Sense strand – strand of nucleotides containing the instructions that direct protein synthesis. It
is located within a stretch of DNA that includes a gene
Antisense strand – strand of nucleotides that is complimentary to the sense strand (not
transcribed)
Steps in Transcription
1) Initiation
→ RNA polymerase binds to a particular sequence of nucleotides in the sense strand
→ RNA polymerase opens up the double helix and begins inserting complimentary
nucleotides
2) Elongation
→ proceeds in the 5’ to 3’ direction (no Okazaki fragments)
→ as the polymerase molecule proceeds, the DNA helix reforms and the mRNA
molecule separates from the template DNA strand
3) Termination and processing
→ the RNA polymerase proceeds until it reaches a signal to stop and the RNA
polymerase and mRNA completely separate from the DNA molecule
→ a special sequence of nucleotides is added to the 5’ and 3’ ends
→ introns are spliced out (removed), leaving only the exons
→ the mRNA is transported out of the nucleus.
Translation (see fig 17.29, p. 593)
Translation occurs outside the nucleus in eukaryotic cells, and involves several elements in order
to occur.
Transfer RNA (tRNA) – RNA molecules that serve to link each codon along a mRNA strand
with its complimentary amino acid. Transfer RNA has an unusual structure. They have a
cloverleaf shape (single-stranded), and contain an anticodon.
Anticodon – specialized base triplet located at one lobe of a tRNA molecule that recognizes its
complimentary codon on an mRNA codon. At the 3’ end of a tRNA is an amino acid transport
site.
Ribosomes – tiny two part structures found in the cell’s cytoplasm and attaches to the rough
endoplasmic reticulum that helps to put together proteins. They bring together the mRNA
strand, tRNA molecules carrying amino acids, and the enzymes involved in building proteins.
Ribosomal RNA (rRNA) – most common class of RNA molecules. During protein synthesis,
these RNA molecules supply the site on the ribosome where the polypeptide is assembled.
The Translation Cycle
1. mRNA binds to an active ribosome in such a way to expose two adjacent codons.
2. The first tRNA molecule (carrying the amino acid methionine) binds to the codon AUG (start
codon).
3. A second tRNA molecule carrying an amino acid arrives at the codon adjacent to the first
tRNA.
4. Enzymes catalyze the formation of a peptide bond that joins the amino acid carried by the
first tRNA to that carried by the second tRNA. At the same time, the polypeptide chain is
transferred from the first tRNA to the second.
5. The ribosome moves a distance of one codon along the mRNA strand. The first tRNA
molecule detaches from the mRNA and goes to pick up another amino acid. The second tRNA
now holds a growing polypeptide chain. A third tRNA molecule arrives at the exposed codon
next to the second tRNA and the cycle repeats.
6. When a “stop” codon is reached (UAG, UGA, UAA), the completed protein is released and
the ribosome assembly comes apart.
Regulating Gene Expression
The rates of transcription and translation can be controlled to adjust to environmental conditions.
For example, artic foxes have white fur in winter, but brown in warmer temperatures.
Factors that affect transcription and translation in living cells:
1) changes in temp. or light
2) the presence or absence of nutrients in the environment
3) the presence of hormones in the body.
Mutations
Mutation – in cellular reproduction, permanent change in the DNA molecule that can change the
information of a gene, causing the gene to function improperly or not at all.
Germ cell mutation – permanent change in the genetic material in a reproductive cell of an
organism. They can be passed on to offspring
Somatic cell mutation – permanent change in the genetic material in a body cell. These
mutations are not passed on to offspring.
Types of mutations
Point mutation – chemical change that affects one or just a few nucleotides. Includes
substitutions and frame-shift mutations.
Chromosome mutation – change in the number or structure of a chromosome. Includes
nondisjunction, deletion, insertion, inversion, duplication, and translocation (see section 16.3 of
notes)
Point mutations:
1) substitution – one or more nucleotides are substituted for a different nucleotide (see f
ig 17.32, p. 597)
i. silent mutation – permanent change in the genetic material that has no effect on
the metabolism of the cell
ii. mis-sense mutation – permanent change in the genetic material of a cell that
results in slightly altered but still functional protein.
iii. nonsense mutation – permanent change in the genetic material of a cell that
renders a gene unable to code for any functional polypeptide product
2) frame-shift mutation – permanent change in the genetic material of a cell caused by the
insertion or deletion of one or two nucleotides within a sequence of codons. Usually, a
frame-shift causes a nonsense mutation (see fig 17.33, p. 597)
transposons – segments of DNA that move randomly throughout the cell’s genome. Also
called “jumping genes”. Discovered by Barbara McClintock.
Causes of Mutations
Spontaneous mutations – occur naturally within cells
Induced mutations – caused by a mutagen introduced into the cell
Mutagen – substance or event that increases the rate of mutation in an organism. May be
physical or chemical.
Physical mutagen – agent that forcibly breaks a nucleotide sequence and causes changes to one
or both strands of a DNA molecule
Ex. X-rays, UV radiation
Chemical mutagen – molecule that can enter the cell nucleus and induce a permanent change in
the genetic material of a cell.