labeled at virus' DNa in one, and protein in another, it was inserted into a blender with bacteria. 

RESULTS: found that the virus in which the DNA was labeled had pellet with infected bacteria. Virus with protein just had supernatant and virus seperate

Double helix, antiparallel, double stranded

base (ATCG) + sugar + phosphate= nucleotide

Bases are complimentary to each other

A=T, C=G

Watson and Crick = two strands twisted together, complimentary base pairs hold strands together

Describe the key features that define DNA structure?

-double-stranded helix

-antiparallel

-right handed

-deoxyribose

How is DNA replicated?  Describe the steps involved.

1. unwinding- double helix unwinds to separate the two strands, expose the base, and make them available for new base paring

2. Pairing & Joining- new nucleotides pair with complimentary nucleotides expose on each strand.

 In what direction does DNA replication progress?

Where on the DNA strand does DNA replication begin?

Since DNA polymerase cannot add new nucleotides to a template strand, how is able to ever replicate the template strand.   What must first be added to the template strand before DNA polymerase can lay down new DNA.  What enzyme is responsible for this the addition?

Primer (a short piece of RNA that is complimentary to the DNA template strand)

Added by enzyme primase

DNA helicase- unwinds DNA and separates strands

Single-strand binding proteins- bind to unwound strands and keep them for re-associating into a double helix

Replication fork – where the double helix is opened up by DNA helicase to expose the two DNA strands, unzips in one direction; the two strands are antiparallel and since DNA polymerization can only go from 5’ to 3’, polymerization occurs in opposite directions

Leading strand - the newly replicating strand that is oriented so that it can grow continuously at its 3’ end as the fork opens up

 Lagging strand – the other new strand oriented so that as the fork opens up, the 3’ end gets farther and farther away from the fork; requires synthesis of small, discontinuous pieces going in the opposite direction of the replication fork – short fragments called Okazaki fragments

DNA ligase- joins DNA pieces

Sliding DNA clamp- increases efficiency of DNA repliaction

1.After DNA replication in typical eukaryotic cells of multicellular organisms, the chromosomes shorten with each division, eventually leading to their demise.  How do stem cells and cancer cells repair the ends of it chromosomes so that the can continue dividing?

1.     DNA proofreading – an incorrect base may be added to the growing chain; proteins of replication complex immediately excise the incorrect base; DNA polymerase adds the correct base

2.     Mismatch repair – during replication a base was mispaired and missed in proofreading; the mismatch repair proteins excise the mismatched base and some adjacent bases; DNA polymerase adds the correct bases; DNA ligase repairs the remaining nick

3.     Excision repair – a base in DNA is damaged and not functional; section is removed; DNA polymerase adds the correct bases; DNA ligase repairs nick

1 gene= 1 protein = 1 enzyme

If one gene is defective, the enzyme will be wrong

ex: albinism ( can't make melanin)

What is the “Central Dogma.” Discuss the flow of genetic information.  In your answer be sure to explain in detail the process of transcription and translation.

Central dogma = the process of genetic flow

DNA –transcriptionà RNA –translationà protein

Transcription – DNA into RNA – the info in a DNA sequence (a gene) is copied into a complimentary RNA sequence

Translation – RNA into protein – the RNA sequence is used to create the amino acid sequence of a polypeptide

What is the difference between DNA and RNA?

1.     Initiation – binding of RNA polymerase to promoter site of gene (gene activiation). Within the promoter is an initiation site, which is the site where transcription actually begins

2.     Elongation – unwinding DNA to expose nucleotide bases; joining of RNA nucleotides by RNA polymerase to form single strand RNA; separation of the RNA strand from DNA and closure of DNA helix

3.     Termination – certain base sequences on DNA specify termination of the process

1.     mRNA – messenger RNA, actual copy of gene, contains the info for making the protein

2.     tRNA – transfer RNA, carries amino acid to mRNA for making protein

3.     rRNA – ribosomal RNA, key component of ribosomes > serve as scaffolding, ribosomes have catalytic activity

How does the structure of eukaryotic genes compare with that of prokaryotic genes?

- prokaryotic = continuous gene

- eukaryotic = introns and exons

Both introns and exons appear in the pre-mRNA, mRNA only contains exons

Through hybridization studies and visualized with electron microscopy

1.     At 5’ end – G Cap; it facilitates the binding of mRNA to the ribosome for translation and protects the mRNA from being digested by ribonucleases

2.     At 3’ end – poly A tail; addition of adenine nucleotides which assists in the export of mRNA from the nucleus and is important for mRNA stability

3.     Splicing to remove introns – introns must be removed before it leaves the nucleus or we would get a different kid of protein

snRNPs bind to consensu regions at the boundary between introns and exons through complimentary base paring

snRNPs at either end of an intron come together to form the splicesome. In this, the ends of the exons are brought together and the intron is cut out while the exons are joined together

If the base sequence of the DNA strand used as a template for messenger RNA synthesis is TACGTT, then what would be the sequence of bases in the corresponding mRNA?

RNA to protein

Genetic code = 3 nucleotide bases constitutes a codon; one codon = one amino acid

The codon sequence determines amino acids sequence

How are tRNAs connected with the correct amino acid?

-        codon is found on mRNA

-        anticodon is found on tRNA

-        complimentary to eachother

1.     initiation – the anticodon of first tRNA/amino acid aligns with start codon (AUG) on mRNA

2.     ribosome complex formation – the ribosome forms around the mRNA

3.     chain elongation – according to the codon sequence of the mRNA, tRNAs deliver the correct amino acids to a growing polypeptide chain

4.     termination – stop codon on mRNA ends the process.  A protein release factor binds to the stop codon and promotes the release of the last tRNA and the subsequent release of the newly formed protein from the ribosomal complex

knows when to stop bc termination

- A protein release factor binds to the stop codon and promotes the release of the last tRNA and the subsequent release of the newly formed protein from the ribosomal complex

-Signal sequences bind to specific receptor proteins on the outer membranes of the organelles to which they are addressed

- the amino acid sequence at the N terminus directs the protein to the nucleus.  Docking proteins bind the sequence and direct the proteins to enter

1.     Proteolysis – the polypeptide chain may be cut with enzymes

2.     Glycosylation – sugar groups may be added to the polypeptide chain

3.     Phosphorylation – added phosphate groups alter the shape of the protein

-        somatic mutations – those that occur in somatic body cells. Mutations are passed onto daughter cells during mitosis, not passed onto sexually produced offspring. Most cancers are a result of this mutation

-        germ line mutations – those that occur in the germ line, which gives rise to gametes. This are passed onto sexually produced offspring

Mutations have what four possible phenotypic effects?

1.     silent mutations – do not effect protein function (functional protein)

2.     loss of function mutations – affect protein function (nonfunctional protein)

3.     gain of function mutations – leads to protein with altered function (new function)

4.     conditional mutations – alter the phenotypes only under certain restrictive conditions (change in environment brings out mutation) – bunny ears and toes!

1.All mutation are alterations of in the nucleotide sequence of DNA.  At the molecular level, mutations can be divided into what two categories?

1.     point mutation – results from gain, loss, or substitution of a single nucleotide

2.     chromosomal mutation – results from dramatic changes to a chromosome usually happening during meiosis, in which a whole piece of DNA molecules (choromsomes) break and rejoin during synapsis in abnormal ways, grossly disrupting the sequence of genetic material

What are the four possible point mutations?  What type has no effect on amino acid sequence?  Which type are more likely to result in the expression of nonfunctional proteins, why?

1.     silent mutation – no effect on amino acid sequence

2.     nonsense mutation – a base substitution that causes a stop codon to form somewhere in the mRNA. non functional protein

3.     missense mutation – some base substitutions change the genetic code such that one amino acid substitutes for another in a protein (can have either positive or negative effect)

4.     frame shift mutations – single or double bases inserted or deleted from DNA. Alters the coding sequences from that point on (most lethal). nonfunctional protein

-       sickle cell anemia > missense point mutation changes one base that changes the entire protein

1.     deletion – loss of part of the genetic material.

2.     duplication – presence of a chromosomal segment more than once in the same chromosome. Double amount of DNA.

3.     inversion – piece of chromosome breaks loose and then rejoins in a flipped direction

4.     translocation – movement of a chromosome segment from one chromosome to another, nonhomologous chromosome 

1.With regards to causes of mutation, what are the two general categories?

1.     spontaneous mutations – permanent changes in the genetic material that occur without any outside influence

2.     induced mutations – when some agent (mutagen) from outside the cell causes a permanent change in DNA

1.     nucleotide base tautomers - nucleotide bases exist in alternate forms that have different properties that can enable them to sometimes base pair with the wrong base;

2.     chemical reactions – may change bases bases in DNA; Ex: deamination of cytosine will create a uracil, which will now pair with adenine

3.     DNA polymerase errors – during replication, mismatched bases can occur

4.     Meiosis is not perfect – nondysjunction – failure of homologous chromosomes to separate during meiosis; Ex: trisomy of chromosome #21 results in down syndrome

-        Euploidy – the correct number of chromosomes in a species

-        Aneuplody – change in chromosomal numbers

- trisomy of chromosome #21 results in down syndrome – extra chromosome 21

- caused by nondysjunction 

1.     chemicals alter nucleotide bases; Ex: nitrous acid can react with cytosine and convert it to uracil by deamination

2.     chemicals add groups to the bases; Ex: benzopyrene, from cigarette smoke, adds a lorge chemical group to guanine, making it unavailable for pairing

3.     radiation damages the genetic maerial; Ex: ionizing radiation (X-rays, etc) produce highly reactive molecules called free radicals which damage bases or break the sugar phosphate backbone of DNA

5-methylcytosine – an especially vulnerable base found in DNA. If it is deaminated, it becomes thymine, which can now pair with adenine (instead of C > G)

1.     amniocentesis – extract amniotic fluid, centrifuge, grow cell in culture, test

2.     chorionic villi sampling – go through vagina

3.     pre-implantation genetic diagnosis – harvest eggs and test them, then do artificial insemination with good eggs

When and why is amniocentesis used?

To test wither a child is a carrier or will express a genetic disease. Used while child is in womb.

- if there is a history in the family

What are restriction enzymes and how are they used in genetic testing?

- restriction enzymes come from bacteria

- Used for the specific cutting of DNA so that it can be worked with.

Restriction enzymes cut DNA either into double-stranded “blunt” ends (example, HaeIII) or short single-stranded “sticky” ends (example, EcoR1). Sticky-ended cuts are useful for inserting and splicing new genes into DNA genomes.

The first DNA marker to be used in the identification of people was Restriction-Fragment Length Polymorphisms (RFLPs).

- Human DNA contains noncodeing regions that vary in length from one individual to another. Short sequences of nucleotides, repeat over and over anywhere from 20 to 100 times. These are called short tandem repeats.  When DNA containing tandem repeats is cut with restriction enzymes, fragments of DNA of various lengths are produced. Variations (polymorphisms) in lengths of the fragments produced with restriction enzymes are known as RFLPs. Each person has a unique profile of RFLPs.

1) Cutting DNA with restriction enzymes generates DNA fragments of varying lengths (polymorphisms)

2) Separation of DNA fragments from each other using electrophoresis

 3) Detection of DNA fragments (bands in gel) using a fluorescent probe specific for tandem repeats

How do defective proteins lead to diseases?

-        certain key enzymes are requires. without them can result in a build up of disease

-        No - Albinism – cannot make melanin

What is the molecular basis for phenylketonuria? Is this mutation a recessive or dominant autosomal disorder?  Does its inheritance follow simple Mendelian genetics?

-        cannot properly process excessive amounts of phenylalanine, results in the build up of the toxic metabolite, phenylpyruvate

-        recessive autosomal disorder

-        YES

1.     Restricting the substrate; Less substrate results in less severe disease symptoms Phenylketonuria

2.     Metabolic inhibitors to block the harmful effects of accumulated substrate

3.     Supplying the missing protein; Hemophilia - clotting factors

- Goal: Introduce genes or genetically engineered cells containing the genes into an individual for therapeutic purposes.

- Example: Treatment of Severe Combined Immune Deficiency Syndrome (SCIDS) - A rare homozygous recessive condition inherited defect in enzyme adenosine deaminase (ADA)

- cut out normal gene from healthy genome, insert into virus that will bind to white blood cells, take out DNA, add viral DNA to blood with disease…

Where you regulate the actual transcription. Many are blockers, but also have enhancers that speed up the rate

epigenetics- changes in expression of genes without changing DNA sequence. 

silencing transcription, chromatin remodeling

Eu-true (contains sections of DNA that are exposed) genetically expressed

Hetero- more tightly compacted (dark patches) locked up

Barbody- inactivation of the x chromosome. Cat coat pattern, one x chromosome had orange color, other x had black

proteosomes- break down proteins

proteins are targeted for break down, recognized by proteosome, bound to ubiquitin and proteasome rids protein