End of Chapter 18 and the beginning of Chapter 19

Transcription initiation is another important control point in gene expression. At this stage, DNA control elements that bind transcription factors (needed to initiate transcription) are involved in regulation.

Gene control also occurs after transcriptionm and during RNA processing, in alternative RNA splicing
Some things to consider:
1.Why do so many inherited diseases involve splicing errors and why to they show up as human cancers?
Splicing errors are associated with 15% of inherited diseases. Many of these genetic mutations cause inappropriate exon skipping, which ultimately cause defects in protein expression. The unerlying mechanisms responsible are poorly sliced genes.
2. What types of problems or questions drive our current research efforts? Why are there far fewer protein coding genes than can account for the size of the human proteasomes?

The control of gene expression also occurs both prior to translation and just after translation, when proteins are processed. "blocking translation"
Protein processing and degradation by proteasomes are subject to regulation.

mRNA degradation: Each mRNA has a characteristic life span, determined in part by sequences in the 5' and 3' UTR's (prime ends) mRNA may last anywhere from hours to weeks.

(18.3) Genes make up only a small group of the genomes of most eukaryotes; only about 97% of the DNA does not code for proteins, These noncoding regions of DNA are made up of introns, repetitive sequences, and sequences whose function is not yet understood. Repetitive DNA is responsible for anumer of genetic disorders.

The molecular biology of cancer:
Oncogens are caner-causing genes; proto-oncogenes are genes that code for proteins that are responsible for normal cell growth. Protooncogenes become oncogens when a mutation occurs that causes an increase in the product of the protoonogene or that increases the activity of the protooncogene itself.
p53 gene "guardian angel of the genome":

1. activates gene 21 whose product halts the cell cycle by binging to cyclin-dependent
2. When DNA demage is irreversible p53 will activate suicide
3. p53 can also turn on genes dirctly involved in DNA repair
   
4. (*also see: http://en.wikipedia.org/wiki/P53)

Cancer can also be caused by amutation a gene whose products normally inhibit all divison. these genseaare called tumor-suppressor genes. The incidence of cancer inceases with age because multiple somatic mutations are required to produce a cancerous cell.

Chapter 19: Viruses
Researchers disovered viruses int he late 1800's by studying a plant disease, tobacco mosaic disease.

Chapter 19 Vocab:

Capsid: The protein shell that encloses a viral genome. It may be rod-shaped, polyhedral, or more complex in shape.

Viral envelopes: A membrane that cloaks the capsid that in turn encloses a viral genome.
Bacteriophages: A virus that infects bacteria

Host range: The limited range of host cells that each type of virus can infect.

Virulent phage: A phage that reproduces only by a lytic cycle.

Restriction enzymes: An endonuclease that recognizes and cuts DNA molecules foreign to a bacterium. The enzyme cuts at specific nucleotide sequences.

Lysogenic cycle: A type of phage reproductive cycle in which the viral genome becomes incorporated into the bacterial host chromosome as a prophage and does not kill the host.

Temperate phages: A phage that is capable of reproducing by either a lytic or lysogenic cycle.

Prophage: A phage genome that has been inserted into a specific site on a bacterial chromosome.

Retrovirus: An RNA virus that reproduces by transcribing its RNA into DA and then inserting the DNA into a cellular chromosome; an important class of cancer-causing viruses.

Reverse transcriptase: An enzyme encoded by certain viruses that uses RNA as a template for DNA synthesis.

Viroid: A plant pathogen consisting of a molecule of naked, circular RNA a few hundred nucleotides long.

Prion: An infectious agent that is a misfolded version of a normal cellular protein. Prions appear to increase in number by converting correctly folded versions of the protein to more prions.

Pretest for misconceptions:

Unlike viruses, viroids do not encode proteins: False
Unlike viruses, the genetic material for vioids is RNA: False
Unlike viruses, prions are infectious proteins: True
Unlike viruses, prions do not include nucleic acids: True

Classify as true or false:
Viruses are 2D rather than 3D: false
The viral genome can be single stranded or double stranded: true
Viruses are intracellular parasites: true
An isolated virus is unable to reproduce: true

The genetics of viruses and bacteria:
(19.1) Viruses: Smaller than ribosomes, viruses are about 20nm across. The genetic material of viruses can be double or single-stranded DNA, or single or double RNA. The viral genome is enclosed by a proteins shell called a capsid. Some viruses also have viral envelops tat surround the capsid and aid the viruses in infecting their hosts.
(19.2) Bacteriophages, which are also called phages are viruses that infect bacteria. Viruses use enzymes, ribosomes, and small molecules of host cells to synthesizing progeny viruses each type of virus has a chracteristic host range.
Pages (viruses that infect bacteria) can reproduce by two alternative mechaisms: the lytic cycle or lysogenic cyle
(http://www.youtube.com/watch?v=wVkCyU5aeeU&feature=related)


Viruses are energy parasites; they can only reproduce within a host, and each virus can only reproduce within a particular group of hosts.
Some viruses (called virulent phages) have a reproductive cycle that ends in the death of the host cell, and this is called the lytic cycle. In this course of the lytic cycle, the phage attaches to receptors on the cell surface, injects its DNA into the host, and directs the replication of its own DNA. New phages are assembled and then produce lysozyme, which disintegrates the cell wall so that the cell dies and new phages are released.

Multiple Choice:

1) The simplest infectious biological systems are
A) viroids. B) viruses. C) bacteria. D) A and B. E) B and C.

2) Which of the following is a true statement about viruses?
A) A single virus particle contains both DNA and RNA.
B) Viruses are classified below the cellular level of biological organization.
C) Even small virus particles are visible with light microscopes.
D) A and B only are true.
E) A, B, and C are true.

3) A researcher lyses a cell that contains nucleic acid molecules and capsid units of tobacco mosaic virus (TMV). The cell contents are left in a covered test tube overnight. The next day this mixture is sprayed on tobacco plants. Which of the following would be expected to occur?
A) The plants would develop some but not all of the symptoms of the TMV infection.
B) The plants would develop symptoms typically produced by viroids.
C) The plants would become infected, but the sap from these plants would be unable to infect other plants.
D) The plants would develop the typical symptoms of TMV infection.
E) The plants would not show any disease symptoms.

4) Which of the following is a characteristic of all viruses?
A) nucleic acid genome
B) a protein capsid
C) glycoprotein cell wall
D) A and B only
E) A, B, and C

1) Answer: A 2) Answer: B 3) Answer: D 4) Answer: D