Chapters 13-14 Genomics

VirusesViruses are insidious pathogens, they attack cells from the inside.  They hijack your own DNA and use it against you.  A virus cannot be treated with antibiotics, it can only run its course until your immune system kicks it out.

..Even then, the virus may lay dormant within the cells and come back at a later date

Adenovirus - cause of the common cold

Properties of viruses• no membranes, cytoplasm, ribosomes, or other cellular

components• they cannot move or grow• they can only reproduce inside a host cell• they consist of 2 major parts - a protein coat, and hereditary

material (DNA or RNA)• they are extremely tiny, much smaller than a cell and only

visible with advanced electron microscopes

Structure of DNA (review)

Shape of a DOUBLE HELIX

Each side held together by weak HYDROGEN BONDS

Repeating units of NUCEOTIDES

Sides of "ladder" are deoxyribose and phosphates

Center is A, T, G, C

A -> TG -> C         *base pair rule

nucleotide

Virus Structure

Parasitic Nature Obligate intracellular parasites (they cannot exist independently)Specific to hosts (human, dog, some can cross species) Specific to cells , the common cold is a virus that specifically attacks cells of the respiratory track (hence the coughing and sneezing and sniffling). HIV specifically attacks white blood cells

This is a bacteriophage, a type of virus that attacks bacteria. It is recognizeable because it looks like the lunar landing spaceship.

See animation http://www.youtube.com/watch?v=41aqxcxsX2w&feature=related

Viral Reproduction 

Lytic cycle = reproduction occurs, cells burstLysogenic cycle = reproduction does not immediately occur (dormancy) 

Virulent = viruses that undergo both cycles

1. Attachment2. Penetration - the virus is engulfed by the cell                    (Cell can enter Lysogenic or Lytic Cycle)3. Biosynthesis - viral components are made                        (protein coat, capsid, DNA/RNA)4. Maturation - assembly of viral components5. Release - viruses leave host cell to infect new cells                     (often destroys host)

Viruses multiply, or replicate using their own genetic material and the host cell's machinery to create more viruses. Viruses cannot reproduce on their own, and must infect a host cell in order to create more viruses.

Lytic vs Lysogenic Pathways of viruses

Starring the phage named Lambda

See: http://highered.mcgraw-hill.com/sites/007352543x/student_view0/chapter20/lambda_phage_replication_cycle.html

Retroviruses -- RNA viruses that have a DNA stage • Human Immunodefiency Virus - causes AIDS • Retrovirus (RNA inside a protein coat) • Reverse Transcriptase makes DNA from the virus RNA • DNA inserts into host DNA • Proteins are assembled from the DNA code • Viruses assembled from the proteins • Viruses released from the cell

(Link) HIV Animation - how virus infects cells

Howard Hughes Medical Institute Video on HIV

Source: http://www.hhmi.org/biointeractive/disease/hiv_life_cycle.html

Developing a vaccine for AIDS is difficult because it is a RETROVIRUS.  RNA mutates easily and each individual virus can be slightly different from the others.  In fact, different viruses can exist within the same person.

See:  HIV coloring

• Emerging Viruses illnesses not previously known 

AIDS, West Nile Virus, SARS, Ebola, Bird Flu 

Could be mutations of known viruses Could be viruses exposed when new areas were developed Could have jumped species (avian flu, swine flu)

Related to Viruses 

Viroids - even smaller than viruses, consist of RNA strands that lack a protein coat

Prions - "rogue protein", believed to be the cause of Mad Cow Disease, also may cause Kuru in cannibal tribes

See:  http://highered.mcgraw-hill.com/sites/007352543x/student_view0/chapter20/how_prions_arise.html

How Do Vaccines Work?

1.  Once you have gotten a virus, such as chicken pox, your body develops the immunity to that virus.  

2. Vaccines are made by growing a weakened or killed form of the virus (often grown in eggs)

3.  This form of the virus is injected into a person's body, which causes an immune response, and immunity to the virus.

   - Remember Jenner's cowpox vaccine?

RV = rotovirus; DTaP = diptheria, tetanus, pertussis (whooping cough);  Hib = haemophilus influenza type B;  PCV = pneumococcal vaccine; IPV = inactivated polio virus;  MMR = measles, mumps, rubella,  

Some parents are opting out of immunizations due to fears about vaccine safety.  

In response, government agencies are producing commercials to encourage parents to get their child vaccinated.

Discuss:

1.  What are the risks of vaccines?  Are they safe?2.  Would you have your own child vaccinated?3.  Should the government force immunizations?

Consider that....Every cell of the body contains ALL the DNA for the organism.

Not all genes are necessary all the time

Cells must then have the ability to turn a gene on and off

 ENTER:  THE OPERON MODEL OF GENE EXPRESSION

Francois Jacob and Jacques MonodExperiments with E. Coli showed that it is capable of regulating the expression of its genes

An operon consists of the following elements

1.  Promoter   -  where RNA polymerase attaches, signalling the start of the gene

2.  Operator  -  where a repressor binds, stopping the transcription of that gene

3.  Structural Genes - genes coding for the enzyme, they are transcribed as a unit

The trp Operon It exists in the "on" state and controls the production of tryptophan. If tryptophan is already present, it binds to the repressor and prevents more tryptophan from being made

The lac Operon

This region is normally in the "off" position, it turns on when lactose is present

Repressors versus Inducers

The tryp operon is a repressible operon, it is normally on but can be turned off when tyrptophan is present

The lac operon is an inducible operon because it is normally off but can be turned on when lactose is present

Grammar Time

A woman is pregnant and the baby is later.  The doctor says they will "INDUCE" labor tomorrow.  What does he mean?

What does this shirt mean?

https://www.youtube.com/watch?v=3S3ZOmleAj0

Tying it All Together:  Lac Operon

In eukaryotes, a variety of mechanisms regulate gene expression

1.  chromatin structure2.  transcriptional control3. post transcriptional control4.  translational control5.  post translational control

BARR BODIESIn females, chromatin of one of the X chromosomes inactivates, this inactive chromosome is called a BARR BODY

Evidence for barr bodies

1.  Women who are heterozygous for duchenne muscular dystrophy have patches of muscle tissue that are degenerative

2.  Women who are heteroyzous for a condition that causes no sweat glands have patches of skin that are normal, and patches that lack sweat glands

Barr Body in Cats

The black patches are XB and the orange patches are XO, the cat is multicolored because not all X's are activated

Genotype:     XB XO

Gene Mutations

Point Mutations - single base changes, causing a change in the amino acid structure (protein)

Frameshift mutation

A base is added or deleted and changes the reading frame

G A T    C A T    A A A 

G A T    A  C A   T A A  A

What happens when you have a nonfunctional protein?

Hemophilia

PKU

Cystic Fibrosis

Androgen Insensitivity - caused by a faulty receptor for androgens, individual is a chromosomal male but appears female  (hermaphrodite)

Transposonshttp://www.thenakedscientists.com/HTML/articles/article/jamilcolumn1.htm/

Barbara McClintock studying maize corn found that controlling elements could move from one location to another on a chromosome

   --  Transposons or Jumping Genes

In maize corn a colorless kernel results from the inability to create purple pigment.

If the transposon jumps to another location, the cells regain the ability to make the pigment, this creates a speckled pattern on the kernel

Cancer and GeneticsGrowth of cancer often begins with the loss of the TUMOR SUPRESSOR GENE 

ONCOGENES activate, cell division occurs uncontrollably

Breast Cancer Gene

BRCA1  (brak-uh)

Introns versus Exons

Exons = parts of DNA that are transcribed and code for a protein

Introns = sections of DNA that are not transcribed, function unknown sometimes called "JUNK DNA"

What is epigenetics?

What is Junk DNA?