Review Sheet for Test 4 - Biology 1107                         Dr. Adams

Gene Expression - Transcription and Translation
     Genes work by having information that ultimately codes for the structure of a protein; so . . .
        genes code for proteins which in turn make YOU.  Needs an intermediary between the DNA in 
        the nucleus and the making of proteins at the ribosomes in the cytoplasm.

RNA (ribonucleic acid): compared to DNA: ribose sugar, uracil instead of thymine, single
         nucleotide strand
1.  messenger (mRNA) - the transcript (made from the DNA template)
     2.  ribosomal (rRNA) - part of ribosomes (site of protein synthesis)
     3.  transfer (tRNA) - different types for carrying different amino acids to the ribosome

Transcription - making mRNA from DNA template; made in 5' - 3' direction from the sense strand. 
            Non-transcribed side of the DNA double helix is called antisense strand.
            Involves the enzymes helicase and RNA polymerase, which binds to DNA to begin
    transcription at the Promoter sequence (a sequence of DNA that says begin transcription here)

Translation - takes place at ribosomes; ribosomes have two binding sites (P and A) for tRNA=s.
     tRNA=s bring amino acids to ribosome, based on codon sequence of the mRNA. 
=s match up using appropriate anticodons.
Codons/Anticodons - three nitrogenous base sequences    
    Each transcript has Start (AUG) and Stop (3 different ones) codons, because transcript 
        also has:
            1.  A Leader sequence (part of transcript that is not translated; allows ribosome to 
                latch onto the transcript to line it up for appropriate translation)            and 
            2.  A Trailing sequence beyond end of what is translated.

Posttranscriptional modification and processing (covered much more thoroughly in Chap. 14)
1.  Cap/poly-A tail (in eukaryotes) for apparent added stability
2.  Removal of Introns; reconnection of Exons - exons used to form cistron

Genetic code is virtually universal -- all organisms share the same coding mechanism; exceptions: 
            some single-celled organisms and
Gene - functional unit; what is actually translated may not be the entire gene but a cistron, which 
                consists of the connected exons (after introns have been removed)

Mutations: The ultimate "stuff" of evolution
I. Point mutations : Substitutions - Silent, missense, nonsense
II. Frameshift :  Deletions and additions - always change gene (functionally nonsense), if occur
within a gene. May be turned off, but may be silent if these occur in non-coding regions.

CONTROL of Gene Expression - Gene Regulation
      Jacob & Monod -- Experiments with E. coli bacteria (prokaryotes) discovered that . . .
          Prokaryotes: use operons -- groups of functionally related genes controlled by one promoter
          have regulatory genes for regulatory (repressor) proteins that bind to the operator region of
          the promoter to control transcription
     may involve additional (C.A.P.) proteins
    The lactose operon - inducible; only if lactose present and glucose absent.  Absence of glucose
         results in build-up of AMP, which activates C.A.P. to bind to the promoter and make it better.
    The tryptophan operon - repressible

In prokaryotes, transcription virtually always leads to immediate translation (no nuclear membrane
between DNA and ribosomes), so most control of prokaryotic gene expression is transcriptional.
However, there is a limited amount of translational and posttranslational control (see below).

Eukaryotes: Many more levels of control than prokaryotes; do not appear to use operons
    Pretranscriptional/Transcriptional - heterochromatinization (condensation) of specific DNA
        sequences in different cells, Euchromatin, gene-specific promoter sequences, enhancing proteins, 
        generalized promoters ("TATA" box); multiple copy DNA
Posttranscriptional (Pretranslational) - Splicing of introns/exons, connecting exons together
        into different potential cistrons (exon shuffling), adding caps and poly-A tail (for stability)
Translational - different rates of translation; has to do with "good" and "bad" leader sequences
Posttranslational - activation/inactivation of proteins; modification in rER, sER & golgi

Examples of eukaryotic regulatory mechanisms:
Hormones (Chap. 48): 1.  protein [posttranslational]; activate cytoplasmic enzymes through
            secondary messengers released from membrane receptors (pg. 1035)
     2.  steroid [transcriptional]; bind to cytoplasmic receptors which then activate transcription
Immune system (Chapt. 44): Antibody gene modification during embryological development
Barr bodies (Chapt. 11, pg. 251): one X chromosome condensed in homogametic sex
    Blood clotting -- proteins must be in blood for rapid clotting, just inactive until needed 
        (post-translational control)

GENETIC ENGINEERING (Chapter 15) -- Recombinant DNA and transgenic organisms 
Recombinant DNA - involves inserting gene (DNA) for a desired protein into DNA of an
        appropriate host
Made possible by discovery of restriction enzymes, normally bacterial enzymes that defend 
        against viral DNA by chopping it up.

Restriction enzymes cut DNA, leaving "sticky" ends on both DNA for "desired" gene and bacterial 
DNA; makes insertion of gene into plasmid possible. "Give" plasmid back to bacteria 
        and bacteria then make desired protein from inserted gene (remember, in prokaryotes, virtually 
        all DNA transcribed and, if transcribed, translated.)

If want to "give" a eukaryotic gene to a prokaryote, as described above, have two problems:
        1.  Must have a prokaryotic promoter on the gene
        2.  Must get rid of introns in eukaryotic gene.  Made possible by discovery of . . .

Reverse transcriptase, used by retroviruses to turn their injected RNA into DNA in the host cell. 
So, to isolate a desired eukaryotic gene without introns: create copy (complementary) DNA,
called cDNA, from mRNA using
reverse transcriptase. Provides cDNA for cistron, not original
DNA, which means all
introns removed. This cDNA then inserted into plasmids, ultimately into the
which can then make many copies of desired proteins.

These problems are often not problems when sticking a eukaryotic gene into another eukaryote,
particularly if the "donor" and "host" are closely related.  This is because the regulatory mechanisms
for the gene are shared -- SO, not only do organisms share the same coding mechanism but apparently
the regulatory mechanisms as well.

Uses: monoclonial antibodies, oil-eating bacteria (genes for metabolism of unusual food sources),
resistant crops, hormone manufacture (eg., insulin)

EVOLUTION (Chapter 17) -- for FINAL EXAM
     Change in the genetic makeup (allele frequencies) of populations of species from one generation 
            to the
next. Requires time.

Evolutionary Theory: Important historical figures

For natural selection to occur:
     1. Must be overproduction of offspring.
     2. Variation (through sexual reproduction and mutation, the ultimate source)
     3. Limits on population growth -- Competition for resources, predation, etc.
     4. Differential reproductive success -- Survival to reproductive age, followed by reproduction

                                            "Survival of the fittest"

Fitness - the success an organism has at getting its genes into the next generation.

The evidence for evolution
   1.  Artificial Selection
   2.  Fossils (there are some intermediates ["missing links"] in the fossil record)
   3.  Comparative Anatomy - must use Homologous structures for analysis
        analogous structures indicate convergent evolution
   4.  Comparative Embryology/Development (eg., humans have tails/gill slits in the embryo)
   5.  Comparative Biochemistry - Molecular (DNA, proteins) similarities suggest close relationships
        (eg., chimpanzee and human DNA=s are >99% identical
   6.  Biogeography - Distribution of organisms of the earth

Phylogeny - trees of relationships between species indicates close relationships based on recent
common ancestors; more distantly related species share a more distant common ancestor