overview of transcription

DNA -> RNA

- The strand that is copied is called the template strand.  The RNA transcipt's sequence is complementary to this strand.  The DNA strand not used as a template is the coding strand.

- The RNA transcript created is mRNA.

- Has three parts: initiation, elongation, and termination.

- During initiation, promoters provide attachment sites for RNA polymerase.

- During elongation, the RNA transcript is synthesized. Nucleotide triphosphates are joined in the 5' to 3' direction by RNA poly.  As this continues, DNA is unwound by RNA poly and rewound behind it.  The region that is unwound is the transcription bubble.

-During termination, terminators cause RNA poly to stop and release the DNA when it reaches a stop sequence.  The RNA transcript dissociates from the DNA and the DNA rewinds.

codons

a series of blocks of information, each corresponding to an amino acid in the encoded protein.

-the information in one codon is a sequence of 3 nucleotides.

reading frame / frameshift mutation

the reading frame is established by the first codon in the sequence and determines how all subsequent codons are read.

-frameshift mutations alter the reading frame of the genetic message.

- takes place on the ribosome.

-Initiation: initiation complex is formed and initiator tRNA bound to methionine.

-Elongation: polypeptide grows as tRNA intermediaries bring amino acids to the ribosome complex.  tRNA molecule carrying an amino acid = charged tRNA.  Ribosome moves along mRNA strand and bind to charged tRNAs so their anticodon can hydrogen bond to codons in mRNA.  The enzyme peptidyl transferase catalyzes formation of peptide bond between each new amino acid and the growing chain.

-Termination: stop codon is encountered, release factors recognize this and cause dissociation of the peptide chain, releasing the last tRNA from the ribosome complex.

intermediate between mRNA and amino acids.  Have amino acids covalently attached to one end and an anticodon that can base-bair with an mRNA codon at the other.

genetic maps: abstract maps that place the relative location of genes on chromosomes based on recombin. frequency.

physical maps: use landmarks within DNA sequences

1. restriction maps - created by cutting DNA with different restriction enzymes and analyzing the patterns of fragments.  When the process is repeated and used to put the pieces back together based on size and overlap, a contig is created.

2. chromosome banding patterns - flourescent in sito hybridization

3. radiation hybrid maps - radiation fragments the chromosomes and then the fragments are recovered by fusing the irradiated cell to another cell

common language used during the Human Genome Project.

-site is a small stretch of DNA that only occurs once in a genome.  The boundary is defined by PCR primers

-uses BACs.

-construct a physical map first and then use it to place the site of BAC clones for later sequencing.  Aligning large portions of the chromosome requires identifying regions that overlap between clones. If two BAC clones have the same STS, they must overlap.

-alignment of BAC clones creates a contig and the individual clones can be sequencing 500 bp at a time to produce the sequence of the contig

DNA is randomly cut into small fragments, the cloned fragments are sequenced, and then a computer is used to put together all the overlaps.

the coding region of a genome.  begins with a start codon and has no stop codons for a distance long enough to encode a protein.

-the addition of information like ORFs to a sequence is called annotation

using computer programs to search for genes, compare genomes, and assemble genomes.

-example: BLAST algorithm searches for sequences that are homologous to known genes in other species

1. single copy genes

2. segmental duplications

3. multigene families

4. tandem clusters

1. introns

2. structural DNA - constitutive heterochromatin, highly condensed and tightly coiled

3. simple sequence repeats - repeated thousands or times, arise from DNA repliation errors

4. segmental duplications

5. pseudogenes - inactive genes that lost function as the result of a mutation

6. transposable elements - some code for proteins, some do not. can move from one location on a chromosome to another

-types of transposable elements

-Long Interspersed Elements: creates a double stranded segment that can reinsert into the genome rather than undergo translation into a protein

-Short Interspersed Elements: cannot transpose w/o using transposition machinery of LINEs.  Alu SINE.

-Long Terminal Repeats: similar to LINEs.

-single-base differences between individuals.  to be a polymorphism but be present in less than 1% of the population.

-many SNPs are in linkage disequilibrium (tendency of genes not to be randomized) -> idea of haplotypes (regions of chromosomes not being exchanged by recombination)

the study of the function of genes and their products

"gene chips" - a representation of a genome that can be manipulated experimentally.

-prepared by depositing DNA fragments onto either a microscope slide or silicon chips.

-has been used in cancer research

1. help identify infectious diseases (ex. anthrax attacks)

2. help improve agricultural crops

1. growth/cell division

2. differentiation

3. pattern formation - cells in embryo become oriented to body plan of organism the embryo will become.

4. morphogenesis - development of organs and anatomical features

-divisions are controlled by cyclins and cdks.

-begins with cleavage, which divides the zygote into blastomeres which form a blastocyst.

-stem cells divide and can form multiple kinds of tissue.  they divide while staying undifferentiated.

-plant growth occurs in specific areas called meristems, which contain groups of stem cells.

-cell is committed to a particular developmental pathway.

-takes place in stages - cells becomes partially committed, acquires positional labels that reflect its location in the embry.

-become differentiated in two ways

1. via differential inheritance of cytoplasmic determination

2. via cell-to-cell interactions (induction)

change in cell fate due to interaction with an adjacent cell.  example is the formation of the notochord and mesenchyme

-induction uses the fibroblast growth factor family of signaling molecules

reversal of cell determination

-For Dolly, mammary cells and egg cells were surgically combined via somatic cell nuclear transfer

-Implanted into reproductive tracts of surrogate mothers

-suffers from low success rate and age-associated diseases due to genomic imprinting (genes are expressed differently depending on parental origin)

- gain info about their relative locations in the body.

-polarity: the acquisition of axial differences in developing structures.

-anterior-posterior and dorsal-ventral axes are created.

-prefertilization: nurse cells move some maternally encoded mRNA into the oocyte. Transcribed into proteins at fertilization

-postfertilization: syncytial blastoderm --> cellular blastoderm

-morphogen gradients provide the basic body axes (Bicoid and Nanos and Hunchback and Caudal)

-body plan is then produced by sequential activation of genes (segmentation genes - gap, pair-rule, and segment polarity)

-segment identify arises from the action of homeotic genes

* genes in which mutants occur that cause normal body parts to appear in inappropriate places.

* bithorax complex = mutations affect thoracic and abdominal segments

* Antennapedia complex = mutations affect anterior end

* Hox genes

- ex: in jack pines seed dispersal can only occur after a fire, thalidomid causes limb defects

- the environment affects normal development (ex larvae do not metmorphose into adults until they find a substance to settle down on, temperature dependent sex determination)

- endocrine-disrupting chemicals interefere w/ the production, transport, or receptor binding of endogenous hormones. Ex DES