Genetics Exam 3

Central Dogma of Biology

how information flows through cells, dna, transcription, mrna, translation, protein

genetic material characteristics

replicable, stores and expresses information, variation via mutation

frederick griffith

1927, infected mice with rough and smooth bacteria, smooth virulent and lethal, rough plus smooth heat inactivated dna mice would kill the mouse, isolated bacteria would then show live smooth cells, shows that rough cells could be transformed into smooth

B DNA

discovered by watson, crick, and franklin, most stable conformation in aqueous, low salt environments (human body)A

A DNA

can form in high salt environments, right handed double helix but thicker, more compact, unlikely in vivo

Z DNA

only forms when DNA is only composed of G and C base pairs, left handed double helix, may form in vivo (in certain sections of DNA)

avery, maclead, mccarthy

1944, identified dna as a transforming agent, took heat inactivated smooth cells and added protease, rnase, dnase plus rough cells, the mouse died when dnase was present therefore dna likely carries genetic information

herschey and chase

1952, used bacteriophage and radioactive labelling to support that it wasn’t proteins carrying genetic information

dna structure

composed of nucleotides each with three parts, a nitrogenous base, 5 carbon sugar, and phosphate group

nitrogenous base

purines and pyrimidines

pyrimidine

single ring, cytosine, thymine, uracil

purine

double ring, guanine, adenine

pentose sugar

oh group on carbons two, three, and five, one less oxygen on dna than on rna

phosphate group

negatively charged, bonds between phosphates are very high energy, alpha phosphate directly connects to 5’ carbon, then the beta phosphate, then the gamma phosphate

nucleoside

sugar and nitrogenous base but no phosphate

abbreviating nucleotides

sugar (nothing-ribose, d-deoxy, dd-dideoxyribose); nitrogenous base (a, t, c, g, u); number of phosphates, P (eg-dADP- deoxyribose adenine two phosphates)

linking nucelotides

linked with a 3’ to 5’ phosphodiester linkage, forms sugar phosphate backbone

oligonucleotides

less than twenty nucleotides

polynucleotides

greater than twenty nucleotides

Hints Chargaff

1949-53, base composition- amount of a is equal to the amount of t and amount of g is equal to the amount of c therefore the amount of purines is equal to the amount of pyrimidines

Watson, crick, franklin

1950-53, paper by watson and crick hypothesized the 3d structure of dna

dna structure

two long chains coiled around a central axis, right hand double helix, the two chains are antiparalell with nitrogenous bases perpendicular to the chain, base pairs form between the chain, alternates major and minor grooves

one complete turn around the double helix

34 angstroms

distance betwen base pairs

3.4 angstroms

diameter of dna

7.2 angstroms

rna structural differences from dna

ribose as the pentose sugar, uracil as a nitrogenous base instead of thymine, usually single stranded

rna functions

messenger, ribosomal, transer, many other non coding rna functions (micro, circular, short interfering, etc)

noncoding rna

often help to regulate gene expression, one common way is to alter the half life of specific mrna, can target specific sequences with complementary base pairing

three possibilities for dna replication

conservative, semiconservative, dispersive

conservative dna replication

one strand of dna is all the new and one is all origninal

semi conservative dna replication

one side of each strand is new and one is original

dispersive dna replication

both sides of both strand contain new and original dna

dna replication experiment

let bacteria grow in 15N media, transfer to 14N media and wait 20 mins (one doubling), extract the dna, centrifuge, showed it’s not conservative model, then do the same thing waiting fourty mins (two doublings), showed it’s semi conservative model

origin of replication

a specific dna sequence where replication begins/initiates, variable between and within species and not all are identical

ori

bacterial origin of replication

ars

autonomous replicating sequence, origin of replication in yeast

canonical sequence

the sequence that the protein factor will preferentially bind to, therefore early origin of replication, then after the factor will bind to alterations

dna polymerase

the enzymes which create new dna, requires a single stranded dna template, new nucleotides are complementary and anti parallelko

kornberg et al

1957, first work on dna polymerase, isolated dna polymerase one from e coli, made dna polymerase one deletions in e coli cells and the cells still grew but had a high mutagenesis rate therefore there must be multiple versions of dna polymerase (five in e coli)

dnaa, dnab, dnac, dnad

bind to the origin of replication and recruit/bind dna helicase

dna helicase

breaks the hydrogen bonds between the base pairs and unzips the dna

single stranded binding proteins

bind to the single stranded (unzipped) dna and prevent it from rezipping

dna gyrase

a topoisomerase thats found upstream from the replication fork, releases the torque caused by unzipping a helical molecule, nicks the double stranded dna to allow free rotation, then will reconnect it

dna polymerase 3

binds at the replication fork, primary enzyme for de novo dna synthesis, a huge enzyme complex (holoenzyme), 5-3 polymerase activity, 3-5 exonuclease, NOT 5-3 exonuclease

primase

creates a short complementary rna primer because dna polymerase 3 can only extend from regions of double strandedness

leading v lagging strand synthesis

leading-continuous lagging-discontinuous

mitochondrial and chloroplast dna

inherited through maternal cytoplasm, variable in size and copy number per species and cell

mtdna

one circular piece of ds dna, no introns, no histonesm

mitochondria

contain 70S (50s/30s) ribosomes, inner and outer membrane

cpdna

similar to mitochondrial, contains genes for photosynthesis, 100-225 kb, triple membrane structure

endosymbiont theory

mitochondria and chloroplasts are derived from free living prokaryotic cells which were engulfed by another cell, over time the cells became interdependent

eukaryotic cellular genomes

double stranded dna, multiple linear chromosomes, use introngs, package/compact dna using histone proteins

chromatin

genomic eukaryotic dna and histone proteins (h1, h2a, h2b, h3, h4) and non histone proteins, can compact dna up to 10000x

heterochromatin

tightly compacted dna even during interphase, stains darkly, transcriptionally inactive, commonly repeated dna sequences (telomeres, centromeres, others)

euchromatin

less compacted, stain darkly, transcriptionally active

viruses

acellular, composed of nucleic acid genome (ds/ss dna or rna, circ or linear), a protein coat (capsid), envelope (phospholipid bilayer) often containing glycoprotein spikes

virion

extracellular form of virfus

viral genome

tightly packed inside the capsid, functionally inert, only able to be read when inside of host

bacterial genome

composed of double stranded dna, usually one circular chromosome, located in the nucleoid region, no histones and introns and therefore no chromatin, not very compact

telomeres

repeated dna sequence found at the linear ends of dna, “junk” dna which is non coding, acts as a buffer for the loss of dna during replicagtion, usually enough for about fifty rounds of replication

telomeres as expiration

most cells have picked up many mutations by the time they have replicated 50 times, so running out of telomere length and therefore cell death is helpful. certain cells have a lower mutation rate due to better dna repair mechanisms, they can express telomerase

telomerase

an enzyme which adds telomere repeats to the ends of a chromosome, expressed most often in stem and cancerous cells

non reciprocal translation viability

often result in chromosomes which don’t have telomeres, which results in the important info during dna replication, making cells inviable

dna replication in eukaryotes

chromosome arrangement is different, have telomeres, deal with nucleosomes (need to be disassembled), all enzymes have different names and sometimes slightly different functions