2) Chemical Composition and
Structure of DNA & RNA
Pentose Sugar (Fig 10.9)
*deoxyribose DNA (hydrogen attached to the 2' carbon)
*ribose RNA (hydroxyl group
attached to the 2' carbon)
Nitrogenous Base (Fig 10.10)
Thymidine (T) ONLY in DNA
Uracil (U) ONLY in RNA
Base linked to sugar by 1 carbon of pentose sugar (Fig
dGMP dAMP dCMP cTMP = DNA
GMP AMP CMP UMP = RNA
-Polynucleotides- (Fig 10.11)
Linked by covalent bonds between a phosphate group of one nucleotide and the 3'
carbon of the pentose sugar of the next nucleotide (a 5' - 3' linkage).
The bonds between the nucleotides are phosphodiester bonds.
The two ends of the polynucleotide chain are not the same. The 5' end has a phosphate
group attached to the 5' carbon of the pentose sugar. The 3' end has a hydroxyl group (OH)
attached to the sugar's 3' carbon. Thus the chain has polarity.
-Pairing of Complementary Bases (Fig 10.15)
3) Forms of DNA & RNA
-Watson & Crick put the puzzle together.
-The polynucleotide strands are antiparallel and hydrogen
bonds form between complementary base pairs (A and T; C and G). The strands are twisted in
a helical configuration, with 10 base pairs between each turn of the helix (Fig 10.14,
-Mainly the B form of DNA is found in the
Which species has RNA? DNA?
Which is double stranded? Single stranded?
Take Home Messages & You Had Better Know
-Genetic material must contain all the information for the
cell structure and function of an organism.
-Genetic material must also replicate accurately so the progeny cells have the same
genetic information as the parent cell.
-Genetic material must be capable of variation.
-Know the structure of A, T, C, G & U.
-Know the difference between DNA and RNA.
Organization of DNA into Chromosomes
1) Bacteria DNA Packaging
-One circular supercoiled
chromosome. (Fig 11.1) Circular double stranded DNA molecule that is compacted
-Same principle in eukaryotic chromosomes.
(Positive and Negative supercoiling controlled by Topoisomerases)
-Some proteins similar to histones are in
-Genetic material may be single-
or double-stranded RNA or DNA, linear or circular.
-Chromosome consists of Protein and DNA
3) Structure of Eukaryotic
-Karyotype-Largest is usually
labeled #1. Pairs of chromosomes; 1 from each parent. (Fig 11.11 & 13).
-G and Q banding identify the same regions of chromosomes (A and T
-Fluorescence in situ hybridization (FISH), identifies specific
regions of a chromosome, e.g. A specific probe for growth hormone will bind the gene
on the chromosome #1 in cattle. Binding is mediated after removing the protein and
allowing the base pairs to match-up.
-Amount of DNA
C value is the haploid amount of DNA for any
given species, i.e. the amount of DNA in a sperm.
Humans 94 cm, ~3 feet.
Humans have ~2.7X107 base pairs
4) Chromatin = Protein + DNA
Stains lightly, uncoiled during interphase, but
condensed during mitosis.
Stains darkly, more condensed, genetically
Found near centromeres, telomeres and
*Constitutive heterochromatin, centromeres
*Facultative heterochromatin, has the potential
to become condensed, e.g. X chromosome inactivation.
Histones- Sequences are very similar in all
*Very rich in arginine and lysine
*Have a net positive charge, thus bind to
negatively charged DNA.
*Histones associate to form nucleosomes,
Nucleosomes fold into chromatin fibers.
These chromatin fibers are attached to a
protein scaffold (Fig 11.23).
Two copies of H2B, H4, H3, H2Athus an
H1 is a linker between nueleosomes.
*Scaffolds, DNA- and RNA polymerases,
Chromosomes are composed of DNA, histone and
non-histone chromosomal proteins.
Each chromosome consists of one linear,
unbroken, double stranded DNA molecule, with coils and folds.
Histones are fairly constant from cell to cell,
but the non-histone protein vary considerably.
5) Centromeres & Telomeres
Sites at which chromosomes attach to the
mitotic and meiotic spindle (Fig. 11.25).
Responsible for accurate segregation of the replicated
chromosome to the progeny cells during meiosis and mitosis.
Without a centromere the chromosomes will
Non-disjunction results from mistakes in
segregation during meiosis (Fig 3.27).
Generally seen as a constriction on the
chromosome where unique sequences are located.
Located at the ends of the chromosomes.
Often associated with the nuclear envelope.
Short tandemly repeated sequences and other
repeated sequences further in from the ends.
required for replication and stability of the
They are not 'sticky', so individual
chromosomes do not stick together.
Take Home Messages & You Had Better Know
What is a Karyotype.
What is Banding.
Describe the amount of DNA in an organism.
What is Euchromatin versus Heterochromatin.
How do Histones package DNA.
What is the function of Centromeres & Telomeres.
Topoisomerase II induces negative supercoils
Matrix Attachment Regions (MARs)
Chapter 12 & pg 47-66
DNA Replication, Mitosis & Meiosis
1) DNA replication occurs by a
semiconservative mechanism (Meselson-Stahl Exp. (Fig 12.1)
2) Enzymes involved in DNA synthesis.
-DNA polymerase I
takes dNTPs (dATP, dCTP,dTTP, dGTP), Mg2+ ions, a fragment of DNA
and makes a copy, by catalyzing the formation of phosphodiester bonds between the 3'-OH
group of the deoxyribose on the last nucleotide and the incoming 5'-phosphate of the dNTP
precursor. Each incoming dNTP is selected by the DNA polymerase I according to the order
of bases on the template strand (Fig 12.3). First dNTP binding acts as a primer to
get the reaction started. Synthesizes 5' to 3'.
3 subunits constitute the catalytic core (alpha, episilon, theta [a , e , f ]).
Polymerases also have 3'-5' exonuclease activity to correct
errors in polymerization (Tbl 12.2).
-Telomerase to replicate telomeres.
3) DNA replication in Eukaryotes
-Occurs in the nucleus during S phase of the
-Is initiated by RNA primers, occurs in the 5'
to 3' direction, is catalyzed by DNA polymerases,
requires a large number of other enzymes and proteins (Fig 12.6, 12.8, 12.9, 12.12).
-Is semiconservative and continuous,
discontinuous, and bidirectional. Replication is
initiated at the same time at many points (origins of replication) along the chromosome
-Heterochromatin replicates later in S than
-In Eukaryotes DNA polymerases are classified
as in Tbl 12.4.
4) Packaging of newly replicated DNA.
-Histone synthesis is coordinated with DNA synthesis. Note
that these histones must disassemble for
DNA synthesis to occur. Segregation of
the histones is not clear.
Take Home and You Had Better Know
*DNA replication is semi-conservative.
*A large number of enzymes are involved in DNA replication, and each has a different
function; primase, polymerase, ligase, etc..
*Histones must disassemble and then reassemble during replication.
5) Cell Cycle
*G1, In G1 phase, the morphology of the chromosomes changes from
condensed to a dispersed state.
This is a result of a change in the coiling of the fibers. The cell also prepares for S by
producing RNA and protein.
*G0, Is a quiescent phase of neither growing or progressing to S. It is usually
induced by starvation of some nutrient.
*During G1 there is a period called the 'restriction point'. Once the cell
passes this point
(completes certain biochemical events), then it must enter S phase.
*S, The untwisting of the DNA and replication as previously described.
*G2, This phase is generally short, the DNA begins to condense
Chromosomes are characterized as highly condensed and
segregate to the two daughter cells (Fig 3.5, 3.7).
Sister chromatids become detectable.
Mitotic spindle assembles outside the nucleus.
Microtubules (tubulin) and a centrosome (in
animals centrioles are present).
Kinetochores form on the centromere and the
Nuclear envelope breakdown begins.
Begins when the nuclear envelop is completely
Centromeres become aligned.
Sister chromatids separate at the centromere
(disjunction). Pac-Man model.
Migration is complete and chromosomes begin to
The nuclear envelop reforms.
Division of the cell (animals) or formation of
the wall (plants).
No G1 or G2
Meiotic cell cycle with no DNA synthesis
No G1, but tissue specific G2.
DNA synthesis without mitosis- polytenization
6) Cell Growth Cycle
-Double everything in the cell
Turn on or off gene
Cell Size regulates entry into S
Little or no cell growth in early embryos
7) Measurement of DNA
Sperm = 1C. In G1 then 2C. In G2 then 4C
Sperm = 1N.
G1, S, or G2 = 2N.
Haploid = 1 complete set of chromosomes
Diploid = 2 complete sets of chromosomes (each pair are homologous chromosomes).
Areas of homology will
recombine (Fig 12.21).
Occurs during prophase I.
One homologue from the father and one from the
Homologues duplicate and remain together as
Homologous Chromosome Pairing & Crossing
On average 2-3 crossover events occur per pair
Here sister chromatids go to the same spindle
-Synapsis (tight associations) Pachytene
-Synaptonemal complex is complete
-Chiasmata become visible (results of the crossover).
-Can be very long stage, in human females arrest occurs from the 7th month of fetal
development until ovulation.
-Chiasmata often terminalize, i.e. joined region moves to the telomeres.
Here sister chromatids remain attached.
Here sister chromatids go to the same spindle pole.
Stage of arrest form most female mammals.
Centromeres split (similar to mitosis)
Nuclear envelop reforms.
Meiosis generates 4 halpoid sets of chromosomes. (Fig 3.15 & 3.17).
SEX Determination Pg 77-84
1) Genotypic & Phenotypic Sex
Genotype is usually X or Y chromosomes. If a Y is present then it is male. If no Y
is present then individual develops into a female.
XO are female and sterile "Turner syndrome" 1:10,000 females
XXY are males "Klinefelter syndrome" 1:1,000
Dosage compensation & X chromosome inactivation (Tbl 3.2)
Sry, Testis Determining Factor (TDF) and Tdf region
of the Y chromosome. Some XX appear to be males, & some XY appear to be
2) Birds, butterflies, moths and some fish
the male is the homogametic sex, i.e. ZZ; females are ZW.
Dioecious, Male plants
& Female plants (cedar trees).
Monoecious, Male organs
and Female organs in different flowers on the same plant (corn).
-if free swimming
settles alone, it becomes female;
-if it attaches to a
female, then it becomes male.
Egg incubation >32 C, then female, <28 C, then male.
Snapping turtles are
female if <20 or >30C, otherwise mainly males.
Take Home & You had Better Know
*Understand the difference between 'C' and 'N'.
*Understand why the products of first meiosis are not 1N or 2N.
*Understand what determines the 'sex' of a mammal.
Chapter 13 & 14
Transcription and Translation,
or "DNA makes RNA makes Protein"
1) Transfer of genetic information from DNA to RNA.
*RNA polymerase acts like DNA polymerase and catalyzes the production of RNA (A,U,C,G).
*DNA unwinds at the promoter region and makes RNA 5' to 3, using the 3' to 5' strand
of DNA (Fig 13.1, 13.2, 13.3).
*messenger RNA (mRNA)
*transfer RNA (tRNA)
*small nuclear RNA (snRNA)
*Only mRNA codes for protein.
*RNA polymerases in eukaryotes (Tbl 13.1)
RNA polymerase I
transcribes genes for rRNAs.
RNA polymerase II " "for mRNA .RNA polymerase III " "for 55 rRNAs,
tRNAs & snRNAs.
*Regulatory regions determine if transcription occurs.
regulation (Fig 13.6, 13.7). Transcription factors and regulatory factors.
Enhancer- distant regulation. Regulatory factors.
2) mRNA (structural genes)
mRNA vary in length due
to length of the gene and protein.
mRNA has a 5' cap (Fig 13.11)
and a 3' poly (A) tail.
mRNA must have introns
spliced out before translation. This occurs with snRNPs
(small nuclear ribonucleoproteins) in a spliceosome (Fig 13.13).
The eukaryotic ribosome
has a size of 80S, and the subunits are 60S and 40S.
The large subunit
contains 50 proteins, and 28S, 5.8S and 5S rRNA.
The small subunit
contains 35 proteins and 18S rRNA.
rRNAs made by RNA
polymerase I (18S, 5.8S and 28S rRNA are made as a single transcript
and then processed in the nucleolus (Fig 13.20).
5S rRNA is imported
into the nucleolus where the ribosome is assembled.
tRNA is 4S
in size, and the leader and trailer are removed.
Molecules of tRNA bring
amino acids to the ribosome.
The sequence 5'-CCA-3'
is found at the 3' end of all tRNAs.
individual amino acids linked by peptide bonds (Fig 14.1, 14.2, 14.3).
sequence of amino acids.
Secondary and tertiary
structures after folding (Fig 14.4).
Function is determined
by 3-dimensional structure.
Sequence of nucleotides
(triplet code) in the mRNA specify the amino acid sequence.
Triplet code is (Fig 14.9):
-degenerate, i.e. more than one codon for each amino acid.
-AUG is the start codon & codes for methionine
-Three stop codons (UAG, UAA, & UGA).
Protein synthesis occurs on the ribosomes
First aminoacyl tRNA enters the P site
Second tRNA enters the A site (Fig 14.12).
Peptide bond is formed.
The chain moves down and a new tRNA enters the A site (Fig 14.17).
Ribosome recognizes a stop codon and disengages from the
reading frame of the mRNA (Fig 14.19).
Take Home & You had Better Know
DNA makes RNA makes Protein.
RNA synthesis is very similar to DNA synthesis.
Know the subclasses of RNA and their function.
Know what regulates RNA synthesis (promoter, enhancer, etc.).
Know what RNA's are processed.
Ribosomes contain rRNA and proteins.
Know what determines the amino acid sequence in a protein.
Know how a polypeptide is elongated and terminated.