genetics exam 3

requirements of genetic material

1. must have complex information in stable form

2. must accurately reproduce and transit info

3. must be expressed to produce other molecules (must have the capacity to encode phenotypic traits)

4. must have the capacity to vary

johann friedrich miescher

discovered DNA (nuclein) in 1869

• realization that the nucleus was the physical basis of heredity

• isolated DNA from pus of wounds

mitosis and meiosis

chromosomes became focus of interest because of movements in what

protein theory

1. chromosomes found to be proteins and DNA

2. DNA is chemically simple

3. proteins are chemically complex

proteins and DNA

major components of chromatin

4 nitrogenous bases and 1 sugar

what is DNA made up of

proteins

in the original idea what was the most likely source of genetic material

• being more chemically complex

frederick griffith

discovered principle of transformation in 1928

• injected mice with different strains of bacterial pneumonia

• some unknown component of dead virulent IIIS pneumonia cells “transformed” live nonvirulent IIR cells into live IIIS

  • (IIR- do not cause disease)

  • (IIIS- cause disease)

conclusion: a substance in the heat-killed virulent bacteria genetically transformed the type IIR bacteria into live, virulent type IIIS bacteria

avery, macleod, and mccarty

repeated griffiths work in test tubes cultures rather than live mice

• found that purified IIS DNA from dead cells transforms live IIR into live IIIS

• treating dead IIIS with DNase stops the transformation, but treating dead cells with protease or RNase does not

conclusion: because only DNase destroyed the transforming substance, the transforming substance is DNA

hershey and chase

used bacteriophage T2 to demonstrated that DNA, not protein, is the genetic material that viruses inject into bacteria to produce new viruses

• labeled virus DNA with ³²P- radioactive isotope of phosphate

• labeled virus proteins with ³⁵S- radioactive isotope of sulfur

  • labeled virus DNA with ³²P

  • labeled virus protein with ³⁵S

  • allowed labeled phages to attack separate batches of bacteria, then washed away leftover phages and “ghosts”

conclusion: found ³²P inside bacteria and in progeny phages and found ³⁵S only in ghosts

albrecht kossel

discovered 4 bases (A,C,G,T) in late 1800s

phoebus aaron

worked out the structure of the nucleotide

sugar, base, PO4

structure of the nucleotide

phoebus levene

proposed the tetranucleotide theory 1910

• boring structure- A = C = G = T

• they are all connected in a square like structure

erwin chargaff

has a rule

• A=T and G=C but A+T does not equal G+C in 1948 (disproved the tetranucleotide theory)

rosalind franklin

used X-ray diffraction data to suggest helix form with with of 3.4 angstroms

OH in 2’

what makes RNA less stable than DNA

draw structure of ribose

draw structure of deoxyribose

purine

adenine

guanine

pyrimidine

cytosine

thymine

uracil

watson and crick

early information on structure of DNA

discovered the double helix model in 1953

• antiparallel

antiparallel B form

form of DNA that is 10 bases per turn

• obey chargaffs rules, bases on the inside, sugat PO4 on outside

features of double helix model

• two sugar PO4 backbones with strong covalent bonds

• base-pairing due to weak H bonding

  • G:C has 3 bonds

  • A:T has 2 bonds

• distance between base pairs is even, about 3.4 A

• major and minor grooves, right-handed twist

• chains are polar, must go in opposite directions

CG

content of __ ___ in double stranded DNA is related to its stability

dsDNA molecules with higher GC content have correspondingly higher melting temperatures

more recent evidence suggests that this is due to base stacking interactions rather than the number of hydrogen bonds between base pairs

antiparallel

chains are polar and must go in opposite directions

polarity

given by 5’ and 3’ C,s of sugar

requirements of genetic material

1. must have complex information in stable form

2. must accurately reproduce and transmit info

3. must be expressed to produce other molecules (must have the capacity to encode phenotypic traits)

4. must have the capacity to vary

DH model

1. stable storage of complex info- bases can go in many orders (coding) but stay fixed once ordered

2. replicable- one chain determines other

3. expressible- linear code system can work for other polymers

4. changes in bases- (order or composition) create mutations that fuel variation

B-DNA

standard double helix

• 10 bases per turn

• most stable configuration

• most common

• right handed helix

A-DNA

tight wound double helix

• 11 bases per turn

• has been found in some DNA-protein complexes in spores and bacteria

• right handed helix

Z-DNA

has left-handed twists

• 12 bases per turn

• found in regions of heavy transcription

viruses

some of these use RNA as their genetic material

fraenkel conrat and singer

used tobacco to determine RNA carries genetic material in tabacco mosiac virus

• degrade both types of TMV to yield RNA and coat proteins

• mix RNA of one type with protein of the other to create hybrind viruses

• infect tobacco with the hybrids

mRNA, rRNA, tRNA

large forms of RNA

mRNA

transmits info from DNA

3% of RNA

more of an intermediate

rRNA

translation machinery

• majority of RNA in a cell

tRNA

interpreters of translation

inverted repeats

in RNA (sometimes DNA) can lead to self-pairing structures

• hairpin structures

secondary structure

extensive structure of this in RNA is thought to serve important regulatory function

• sometimes U pairs with G in RNA

primary structure

simply nucleotide sequence

secondary structure

DNA: double helix

RNA: stems and loops in RNA

methylation in prokaryotes

commonly methyl A or C often used to distinguish bacteria chromosome from foreign (viral) DNA

• restriction enzyme defense

• innate immunity

• defense against its own restriction enzymes

methylation in eukaryotes

epigenetic phenomenon

• methyl group added to base, usually C

• changes how proteins interact with DNA

• major eukaryotic gene regulation method

  • used to regulate gene expression (chromatin structure)

genomes of viruses

very small (1kb-340kb) nucleic acid

genetic material varies with species

• DNA or RNA

• single or double

Short genes (100-8000bp) without introns

• genes can overlap

very little non-gene sequence

fred sanger

first sequenced viral genome

• used 5386 bp circular ssDNA

• found gene B lies entirely within gene A

retroviruses

are always RNA viruses that must convert their genome into DNA before integrating into the host genome as a provirus

• include at least 3 genes

  • gag, pol, env

must be reverse transcribed into double stranded DNA, then infect

gag

gene in retroviruses that encodes viral capsid proteins

pol

gene in retroviruses that encodes the reverse transcriptase and integrase

env

gene in retroviruses that encodes glycoproteins that surround the capsid

virus chromosomes

chromosomes are packaged almost naked

• no attached structural proteins

• retroviruses have reverse transcriptase packaged with the viral RNA

retrovirus

retrovirus infection

1. virus attaches to host cell at receptors in the membrane

2. the viral core enters the host cell

3. viral RNA uses reverse transcriptase to make complementary DNA, and viral RNA degrades

4. reverse transcriptase synthesizes the second DNA strand

5. the viral DNA enters the nucleus and is integrated into the host chromosome, forming a provirus

6. on activation, proviral DNA transcribes viral RNA, which is exported to the cytoplasm

7. in the cytoplasm, the viral RNA is translated

8. viral RNA, proteins, new capsids, and envelopes are assembled

9. an assembled virus buds from the cell membrane

once virus is in chromosome, never comes out

HTLV I

human retrovirus

leukemia after long latency

HTLV II

human retrovirus

possible leukemia

HIV1

human retrovirus

AIDS

derived from recombined SIV from red capped mangabey and spot nosed monkey that subsequently infected chimpanzees

HIV2

human retrovirus

AIDS

derived from SIV from sooty mangabeys

viral species

non-retroviral ssRNA genomes can be either positive or negative strand depending on the viral species

• influenza (-)

• common cold (+)

• polio (+)

• SARS (+)

• hep C (+)

rotavirus

double stranded RNA viruses

gemini and parvo

single stranded DNA viruses

T2, T4, phage, HPV

single stranded DNA viruses

positive

RNA _____ strand

• RNA genome directly codes for protein

• viral genome can be used right away for protein synthesis

negative

RNA _____ strand

• RNA genome is complimentary to the protein coding strand

• have to make copy then can code for protein

influenza

• rapid changes occur through genetic recombination

• three main types: A, B, and C

• most cases are A: divided into subtypes based upon expression of hemagglutinin (HA) and neuraminidase (NA)

H1N1

spanish flu

• influenza pandemic

• 1918

• 50,000,000 dead

H2N2

asian flu

• influenza pandemic

• 1957

• 2,000,000 dead

H3N2

hong kong flu

• influenza pandemic

• 1968

• 1,000,000

H1N1

swine flu

• influenza pandemic

• 2009

• 280,000

antigenic drift

small genetic changes resulting from mutations during viral replication

• slow change

antigenic shift

reassortment of genetic material from different viruses

• rapid change and lots of change

low

RNA has ____ fidelity

• makes more mistakes

bacteria and archaea genomes

genomes that has double stranded DNA

usually one main circular chromosome

can have small supplemental chromosomes (plasmids)

bacteria and archaea plasmids

circular with range of sizes (3kb-400kb)

optional- not present in all individuals

encode a few supplemental genes

often multiple copies per cell

replicate separately from main chromosome

• optional under ideal conditions- take work by cell to be maintained so if not beneficial they are usually lost

main chromosome in bacteria and archaea

single, usually circular

defined sizes range from 0.2Mb- 8.7Mb

moderate number of genes: 800-5000

short genes without introns

very little non-gene sequence

packaging problem

• if stretched out straight, the E coli genome of 4.6 × 10⁶ would be 1000X the length of the cell

  • has to package genome

supercoiling

represents a way to conserve space in circular DNA

• the ends must not be free to rotate

• DNA in cells tends to be negatively supercoiled

• accomplished by topoisomerase

topoisomerases

accomplishes supercoiling (create kinks in molecule so they take up less space)

• cut one or both strands

prokaryotic main chromosome

negative supercoiling

most common supercoiling

• easier to unwind strands during replication and transcription

• supercoiled DNA uses less space than relaxed DNA

second level packaging

tight coiling based on proteins and RNAs

1. basic proteins bind to acidic DNA

2. short RNA “twist ties” hold loops

• positive charged proteins to negative charged DNA

organelle genome

in eukaryotes (chloroplasts and mitochondria)

• small circular double stranded chromosome

• short genes (1000-5000bp) with few introns

• few genes

• very little non-gene sequence

• multiple copies per cell, maternal inheritance

mitochondria and chloroplasts

contain DNA

encodes some polypeptides used by the organelle, rRNA, and some tRNAs

protein function stays in these 2 organelle

• encoding is in chromosomal DNA

endosymbiotic theory

proposes that mitochondria and chloroplasts were once free-living bacteria

• both organelles are similar to eubacteria, and DNA sequences found within them are also similar to eubacteria

present day cell

1. approximately 1 billion to 1.5 billion years ago, an anaerobic eukaryotic cell engulfed an aerobic eubacterial call through endocytosis

2. the aerobic endosymbiont evolved into mitochondria

3. likewise, endocytosis of a photosynthesizing eubacterium

4. led to the evolution of modern eukaryotic cells with mitochondria and chloroplasts

evidence of endosymbiotic theory

• mitochondria and chloroplasts have double membrane

• mitochondria and chloroplasts have their own DNA with a circular genome

• mitochondria and chloroplasts have their own ribosomes which exhibit sensitivity to antibiotics directed at prokaryotic protein synthesis

• currently, several single cell eukaryotes harbor symbiotic bacteria

• mitochondria and chloroplasts DNA sequences are more closely related to eubacterial genes than eukaryotic genes

nuclear genome

part of eukaryotic chromosome:

has multiple linear double stranded DNA chromosomes

• total size extremely variable

• many genes that are spaced apart

• elaborate condensation around proteins

  • usually by histone proteins

size

____ of eukaryotic chromosome

• variable within organism

• variable between closely related species

centromere

______ of eukaryotic chromosome

• special sequences in DNA bind special proteins

• essential for segregation of chromosomes in mitosis or meiosis

• can be point or regional

• no universal specific sequence requirement but tend to be very A-T rich

  • contains a special variant histone CenH3 that replaces H3

• made up of heterochromatin

euchromatin

• less condensed chromatin

• located on chromosome arms

• unique types of sequences

• many genes present

• replicated throughout the S phase

• transcription occurs often

• crossing over is common

heterochromatin

• more condensed chromatin

• located at centromeres, telomeres, and other specific places

• repeated sequences

• few genes present

• replicated in late S phase

• infrequent transcription

• crossing over is uncommon

centromere

special sequences in DNA bind special kineticore proteins

• point of attachment for spindle fibers

  • fibers bind to proteins, not DNA itself

• position varies widely between chromosomes

  • telocentric, acrocentric, metacentric

without one there is no mechanism for a piece of DNA to be retained in the nucleus after cell division

acentric pieces of DNA are lost during cell division

telomeres

caps that stabilize ends of linear chromosomes

• made up of heterochromatin

• necessary to prevent degradation

• special repetitive sequences

  • same sequence on every chromosome in genome

  • very similar between species

mammals: TTAGGG

tetrahymena: TTGGGG

G rich

shelterin

multisubunit protein complex that protect the ends of telomeres

banding patterns

characteristics of chromosomes used to identify

• numbering system for human chromosomes

relates to chromosome composition

• euchromatin

• heterochromatin

euchromatin

light staining, decondenses, actively transcribed

heterochromatin

dark staining, stays condensed, not transcribed

constitutive heterochromatin

is always condensed

facultative heterochromatin

can convert to euchromatin depending on conditions