Genetics exam 2

Single base substitution, causes the replacement of a single base nucleotide. This term also includes insertions or deletions

code for a stop, which can truncate the protein

code for a different amino acid.

Most proteins can withstand one or two point mutations before their function changes

Diff nucleotide but same amino acid

Also sometimes called a synonymous change, possible bc 64 codons specify only 20 amino acids

the substitutuion of a purine for a pyrimidine or vice versa

Can be drastic bc it changes the structure dramatically

changes a purine nucleotide to another purine

A, C, G, T

U

• Adenine and Guanine
• Cytosine, Thymine and Uracil

A sugar, a phosphate and a nitrogen base. (Either a purine or pyrimidine)

The sugar is iehter a Ribose sugar (in RNA) or a deoxyribose sugar (in DNA)

Mice- IIIS killed and injected with IIR (non-virulent) and the mice died. Also, these bacteria retained thier type IIIS characteristics through several generations.

Experiment-provided compelling evidence that the transforming principle (and genetic info) reside in DNA.  They keat-kill IIIS (virulent) strain->treate each of the 3 samples with enxymes that destroy proteins, DNA or RNA (Protease, RNase, or DNase). Then add eaxch of these samples to a culture of IIR bacteria. The culture treated with DNase was the only one out of the three to not contain the transformed IIIS bacteria.

nucleotides, sugar, phosphate and a nitrogen base

Macromolecule

used radioactive isotopes to follow the proteins and DNA separately.  DNA contains Phosphorus, so they used P-32 to follow the protein. Protein contains Sulfur but not Phosphorus, so they used S-35 to follow the protein. They grew a large batch of E.coli in a medium of either S-35 or P-32, then infected each T2 phage. Then they infected the E.coli iwth these T2 phage. Many of the phages progeny emitted radioactivity from P-32.

Discovered the 3-D structure of DNA-using x-ray diffraction and showed it as 2 strands of nucleotides wound around each other to form a right handed helix with sugars and phosphates on the outside with bases on the interior.

refers to its nucleotide structure and how the nucleotides are joined together. Like the ladder

refers to the stable 3-D helix. The 2 polynucleotide strands run in opposite directions.

the complex packing arrangements of double stranded DNA in chromosomes.

more reactive and less chemically stable


This is one reason DNA is better suited as a long term repositor of genetic info.

• 
• 4 Oxygen atoms.  Frequently carries a negative charge which makes DNA acidic. The phospate group is always bonded to the 5' Carbon atom of the sugar

A series of nucleotides linked by phosphodiester linkages (strong covalent bonds between the 5' phosphate group of one nucleotide to the 3' Carbon atom of the next).

the backbone of the strand is composed of alternating sugars and phosphates.

proteins, metals or other molecules.

They are anti-parallel, and A pairs with T through 2 H bonds; C pairs with G through 3 H bonds (therefore G-C pairing is stronger)

meaning it has a right handed or clockwise spiral. This spiraling of nucleotide strands creates major and minor grooves in the helix. These features are important for the binding of some proteins that regulate the expression of genetic info.

the process of DNA expressing its genetic instruction by 1st transferrin its info to an RNA molecule. The info remains in the language of nucleic acids.

the RNA molecule then transfers the genetic info to a protein by specifying its amino acid sequence.  (the info is translated, from the language of nucleotides into the language of amino acids)

• 1. Replication- info passes from DNA to another DNA molecule
• 2. Transcription- DNA or RNA
• 3. Translation- info passes from RNA to protein

creating the exact same thing

same language but different format

it's a copy of one gene made from a DNA template (through transcription or RNA synthesis), it's a template for making protein

transfers RNA - helps asseble the protein by reading (or attaching to) the mRNA, brings the amino acid to the mRNA

Each amino acid is attached to a tRNA. the old gets ejected and the new deposits another amino acid and all continues until a stop codon is encountered. You now have a polypeptide.

single base substitution, but the resulting amino acids are the same

to copy and deliver information outside the nucleus of the cell.

'unzips DNA', breaks H bonds

It's read from 3 to 5, and synthesizes complement from 5 to 3.

Replication, transcription and translation

both block a hypostatic gene.

in Rec., bb blocks A or a, but in Dom. Bb or BB blocks A or a.

• So : if A is the hypostatic, B is epistatic (in this case blocking the expression of color)
• Rec:                    Dom:
• 9:      A_B_ Black   12:
• 3:      aaB_ brown 
• 4: 3:  A_bb yellow  3:   
•     1:  aabb yellow  1:

• Griffith=like the dog=animals=mice
• Hershey-Chase=chocolate-food-blender
• Avery, McLeod, McCarty= 3ppl, 3 test tubes

5' end has the phosphate group and 3' has the hydroxyl group

The Watson Crick model of DNA structure implies a simple mechanism for replication involving a series of enzymes: the DNA unwinds and separates (with the help of helicase), RNA primers are laid down (primase), the primers are elongated (DNA polymerase) and individual pieces are linked together with DNA ligase. Although the enzymes are slightly different, the mechanism is very much the same in both prokaryotes and eukaryotes.

• 1. Initiation
• 2. Unwinding (followed by priming)
• 3. Elongation - in both priming and elongation, bases are added according to the base pairing rules previously established, always main a double stranded molecule that is anti-parallel.
• 4. Termination

origin of replication -> mechanism is the smae for E.coli, cows, humans, etc.

'replication bubble'

Helicase unwinds, SSBPs (single strand binding proteins) keep DNA from re-annealing, and gyrase reduces supercoil ahead of the fork (reduces torsional strain) to allow for continued unwinding.

Catalyze phosphodiester bond between 3'OH and 5'P04

• direction is always 5' to 3'
• Can only add to existing  3' end, cannot initiate de novo

Primase synthesizes short stretches of RNA to provide a 3'OH for DNA polymerase to add on to.

It's only job is at the beginning of synthesis, lays down a short stretch of RNA. Many don't have proofreading step though.

backspacing or proofreading

pol 1- slow, abundant, not processive enough (falls off soon, after processing only up to 200) Pol 1 replaces the RNA nucleotides of the primer with DNA nucleotides. ( This is where the nicks are left behind in the backbone, and DNA ligase  seals this nick with a phosphodiester bond between the 5'P group of the initial nucleotide added by DNA pol 3 and the 3'OH group of the final nucleotide added by pol 1)

pol 2-used in repair?

pol 3- highest processivity , DNA is synthesized by this polymerase.

• Helicase, then Gyrase
• then Primase, then pol 3.

discontinuous DNA synthesis on the lagging strand during replication

leading strand is being made 5' to 3' in the same direction as the movement of the replication fork. only needs a single primer.

lagging strand is also being made in the 5' to 3' but in the opposite direction as the movement of the replication fork. series of primers required creating "okazaki fragments"

Termination can occur in different ways. 

E.coli- termination protein called Tus binds to specific sequences (called ter)

others- meeting of replication forks

replaces RNA primer with DNA

• -multiple origins of replication "replicons" (due to greater size of genome)
• -more types of DNA polymerases
• -nucleosome assembly following DNA replication

yeast origins? ARS=autonomously replicating sequences

Each chromosome contains numerous origins. At each origin, the DNA unwinds, producing a replication bubble. Synthesis takes place on both strands at each end of the bubble as the replication forks proceed outward. Eventually the forks of adjacent bubbles run into each other and the segments of DNA fuse...producing to identical linear DNA molecules.

the entire genome must be replicated ONLY ONCE in each cell cycle

• ANS: 2 distinct steps in initiation
• -origins are "licensed" to replicate in G1 with a replication licensing factor
• -initiator proteins cause the separation of DNA strands

at least 13 DNA polymerases

-pol alpha = primase activity and begins DNA synthesis, no 3' to 5' exonuclease

-pol gamma? = completes replication on lagging strands, has 3' to 5' exonuclease

-pol beta = DNA repair

Ends of chromosomes, are special repetitive DNA sequences (humans = TTAGGG repeated 250-1500 times)

• Telomerase extends the DNA, filling in the gap due to the removal of the RNA primer.
• -protein + RNA (CCCUAA)
• -RNA serves as template to extend 3' end
• -NOT active in somatic cells
• -active in bone marrow, stem cells, germline cells

there is no adjacent 3'OH to which DNA nucleotides can be attached. When the primer at the end of a chromosome is removed, there is no 3'OH group to which DNA nucleotides can be attached, producing a gap.

the original two strands of the double helix serve as templates for new strands of DNA. When replication is complete, two double stranded DNA molecules will be present. Each will consist of one original template strand and one newly synthesized strand that is complementary to the template.

downstream, progressively adding nucleotides to the RNA molecule according to the sequences on the template.

an inverted repeat followed by a Poly-A region. When the inverted repeat has been transcribed, it forms an RNA hairpin, which causes RNA Polymerase to pause. The stretch of AU base pairs is unstable and causes the RNA strand to separate from the template  during the pause.

The rho-independent terminator is typically encoded in the genome and is positioned downstream from the stop codon. There is definitely a difference in structure between the two terminators; rho-independent terminators contain an inverted and repeated sequence which is able to form a hairpin structure. The sequence within the loop in the rho-independent terminator is partly species specific.

The elongation phase of transcription refers to the process through which nucleotides are added to the growing RNA chain. As the RNA polymerase moves down the DNA template strand, the open complex bubble moves also. The bubble is of a fixed number of nucleotides, meaning that at the leading end of the bubble the DNA helix is being unwound, while at its trailing end the single strands are being rejoined. Whereas separation of the DNA helix is permanent in replication, it is only temporary in transcription. depicts the beginning steps in transcription up to elongation and the relative positions of the bubble and the polymerase holoenzyme.Figure %: Steps in TranscriptionAs the figure shows, within the open complex bubble the DNA and RNA form a hybrid or joint complex. The exact length of this region is unknown, but it is thought to be between 3 and 12 base pairs long and is found at the growing 3' end of the RNA. The figure also illustrates how the 5' tail end of the RNA chain is separate from, as opposed to base paired to, the DNA template strand. This is another difference between DNA replication and DNA transcription; in replication, the newly synthesized DNA strand remains bound in a helix to the strand with which it has base paired. After the initial stretch of approximately 8 base pairs has been synthesized, the sigma unit, which is responsible for recognition and binding to the promoter region, is released. The core enzyme is left to polymerize the growing RNA chain alone. This leads to the continuous extrusion of the 5' end of the RNA from the enzyme complex. At normal room temperature, the rate of transcription in prokaryotes is 40 nucleotides per second.

RNA synthesis will continue along the DNA template strand until the polymerase encounters a signal that tells it to stop, or terminate, transcription. In prokaryotes, this signal can take two forms, rho-independent and rho-dependent.

The rho-dependent terminator received its name because it is dependent on a specific protein called a rho factor. The rho factor is thought to bind to the end of the RNA chain and slide along the strand towards the open complex bubble. When the factor catches the polymerase, it causes the termination of transcription. The mechanism of this termination is unclear, but the rho factor could in some way pull the polymerase complex off of the DNA strand.

The rho-independent terminator is the more simple of the two systems and as a result is also called simple termination. The rho-independent signal is found on the DNA template strand and consists of a region that contains a section that is then repeated a few base pairs away in the inverted sequence.Figure %: Rho-Independent TerminatorAs is shown in the figure, the patch is followed by a short string of adenines. When this stretch is transcribed into an RNA sequence, the RNA can fold back and base pair with itself forming a hairpin loop.As you can see, the string of adenines in the DNA sequence are transcribed into uracils in the RNA sequence. Because the uracil bases will only pair weakly with the adenines, the RNA chain can easily be released from the DNA template, terminating transcription.

the core enzyme and the sigma subunit (the two main segments of the RNA polymerase molecule)

is responsible for carrying out the polymerization or synthesis of RNA

• Initiation
• Unwinding (followed by priming)
• Elongation 
• Termination

• Initiation: Origin of replication, bidirectional startpoint
• Unwinding: after initiator proteins, helicase unwinds (binding to the Lagging strand template), SSBP's keep DNA from re-annealing, and gyrase reduces supercoil ahead of the fork. 
• polymerases in prokaryotes: catalyze phosphodiester bond between 3'OH and 5'PO4. Direction is always 5'to3', cannot initiate de novo. can only add to existing 3' end.
• Primase synthesizes short stretches of RNA because they can start de novo.

exonuclease activity = backspace or proofreading.

3' to 5' AND 5' to 3' 

3' to 5' (no backing up)

dnaA- binds oriC to initiate replication

Helicase-unwinds DNA

SSBP-prevents unwound strands from reannealing

• Gyrase-
• creates nicks in DNA to prevent supercoiling

• Primase-adds
• RNA primers for DNA pol III to add to

• DNA
• pol I-removes RNA primers, replaces with DNA

DNA pol III-main synthesis polymerase

Ligase-seal okazaki fragments together

• a)Both are found in prokaryotic DNA replication, have 3’ to 5’ exonuclease activity. DNA pol I is used for
• replacing RNA primers with DNA while DNA pol III is used for actual
• polymerization. DNA pol I also has 5’ to 3’ exonuclease activity, while DNA pol III does
• not.

b)Prokaryotic... Eukaryotic DNA polymerases would be denoted with greek letters (ex. DNA pol α, DNA pol δ, etc)