- 1.- duplications and deficiencies tend to have opposite phenotypic effects.
- 2.- duplications are more readily tolerated than deficiencies.
- 3.- the higher the level of polyploidy the better a species can tolerate lose of chromosomes.
- 4.- aneuploids tend to produce other aneuploids.
- presence of an extra copy on one chromosome. (2n+1)
- sources: nondisjunction, asynapsis resulting in malsegregation, desynapsis resulting in malsegregation, and translocation heterozygotes.
- loss of a single chromosome. (2n-1)
- this is a very sever conditions, remember loss is more sever than addition.
- arise through nondisjunction.
- loss of a pair of chromosomes. (2n-2)
- extremely sever in diploids.
- best studied in higher levels of poliploidy.
- produced by crossing two monosomies.
- generally infertile and very sickly.
- addition of a pair of chromosomes. (2n+2)
- also very sever, though not as bad as nullisomy.
- generally show reduced fertility.
- produced by crossing two trisomies.
USES OF ANEUPLOIDS.
useful if you have monosomics and nullisomics to use.
ANEUPLOIDY IN HUMANS
- Triplo X XXX
- Klinefelter's Syndrome XXY
- Turner's Syndrome X
- Jacob's Syndrome XYY
all of these are dealt with fairly well duel to the theory of dosage compensation.
TRISOMY 21: DOWN SYNDROME
- most common.
- pronounced maternal-age effect.
- mental retardation.
- mean life expectancy of 17 years.
- classic phenotype: short stature, obesity in adolescence, spontaneous behavior, premature aging, flat face, small head, extra folding skin on the eyelids, open mouth with a tendency of tongue protrusion, over folded ears, heart conditions, short fat neck, short broad hands, etc.
TRISOMY 18: EDWARD'S SYNDROME
- very rare.
- no evidence of maternal-age effect.
- sever mental retardation.
- generally die before the age of 6 months.
- classic phenotype: small head, elongated skull, growth retardation, small eyes, malformed ears, small jaw, small mouth, distinctively clenched fingers, and other congenital malformations.
TRISOMY 13: PATAU SYNDROME
- very rare.
- no evidence of maternal-age effect.
- death in early infancy, usually in days.
- classic phenotype: cleft lip, polydactyly, small head, rocker-bottom feet, small eyes, hernias, scalps defects, etc.
- extremely rare.
- occurs as a mosaic of both normal and trisomic cells.
- sever mental retardation.
- classic phenotype:
- *depends on the degree of mosaicism.
- arise through the breakage and reunion of chromosomes.
- small deletions are better tolerated.
- lethal in the homozygous state.
- the severity depends on the amount of material involved.
- the loss of material results in the hemizygous state which effect the ratios and phenotypes produced by a cross.
- unexpected expression of a recessive allele in the presence of a deletion.
- expression is due to hemizygous state rather than dominance.
- small deletion of 5p-.
- primary phenotype is the "cat-like" cry or mewing of the infants.
- mental retardation.
- difficult speaking-larynx problems.
- classic phenotype: low birth weight, hypotonia, microcephaly, growth retardation, round face with full cheeks, hypertelorism, epicanthal folds, down-slanting palpebral fissures, strabismus, flat nasal bridge, down-turned mouth, micrognathia, low-set ears, short fingers, single palmar creases, cardiac defects, etc.
- structural abnormalities of the brain.
- sever mental retardation.
- early death.
no response to social stimuli.
- profound mental retardation.
- fish mouth.
- repeats of a specific chromosome region.
- duplications are fairly well tolerated with larger duplications being more harmful.
- unequal crossing over.
- normal ABC
- tandem repeat ABCABC
- reverse tandem repeat ABCCBA
- transposition ABC ABC
- reverse transposition ABC CBA
- duplicated gene loci provide a source for the origin of new genes, which can acquire new functions through mutation without the harmful effects due to their presence in multiple copies.
- human hemoglobin series.
- results in a change of the linear arrangement of the genes on the chromosome. (reverses the order).
- arise from breakage and reunion of the chromosome sections.
- no addition or deletion of genetic material.
- problems arise in heterozygous state due to difficulty of synapsis in meiosis I.
- results in looped structures to produce maximal homologous pairing.
TYPES OF INVERSIONS
paracentric: the inverted segment of the chromosome does NOT include the centromere.
A D C B E . F G H I J
pericentric: the inverted segment of the chromosome does include the centromere.
PROBLEMS DUE TO INVERSIONS
- problems arise during meiosis in heterozygous individuals when crossing over occurs within the inverted segment.
- results in the production of nonfunctional gametes via deletions, duplications, and breakage of chromosomes.
- inversions are sometimes referred to a cross-over suppressors.
- cross-overs still occur, but are not recovered in the resulting progeny due to occurring in duplicated and deficient gametes.
- movement of material, a segment or an entire arm, from one chromosome to another nonhomologous chromosome.
- occur through breakage and reunion events.
movement from one chromosome to another.
- A B . C D E F G
- l m n . o p q r s t
- A B . C D
- l m n . o p q E F G r s t
involves the EXCHANGE of material between the two chromosomes.
- A B . C D E F G
- l m n . o p q r s t
- A B . C D r s t
- l m n . o p q E F G
MEIOSIS IN TRANSLOCATIONS
since nonhomologous chromosomes are involved in the exchange there are 8 strands involved in the final meiotic configuration.
- refers to a change in the activity or expression of a gene when it's location within the genome is changed.
- most commonly the movement of a gene into a region of heterochromatin or into the centromeric region which results in suppression (turning off) of the gene.
- the occurrence of position effect indicates that chromosomes are highly organized with linkage groups occurring in nonrandom associations and having definite function in terms of gene expression and activity.
- regulatory controls are changed with a change in position.
- S Type: stable or cis-trans type.
- V Type: variegated (patches of normal and mutant).
phenomenon in which one class of gametes and resulting progeny occurs more often than is predicted by random processes.
EARLY STUDIES ON GENES
- in the genus Salmonella.
- using simple crosses it was determined that there are 5 genes involved in the production of the amino acid tryptophan from chrorismic acid and L-glutamine.
- complementation test: produced several strains that were pure breeding with out the ability to produce tryptophan (no growth on minimal media).
- strain X: trpA, trpB*, trpC, trpD, trpE
- strain Y: trpA, trpB*, trpC, trpD, trpE
- strain Z: trpA, trpB, trpC, trpD*, trpE
- X x Z full set of trp enzymes: growth.
- Y x Z full set of trp enzymes: growth.
- X x Y no functional trp B: NO GROWTH.
lack of growth in X x Y indicate that the mutations must be in the same gene while the ability to grow in X x Z and Y x Z indicates that the mutations must occur in different genes.
- mutations in the same gene produce a mutant phenotype.
- trans cis
- _*_________ __*_____*__
- _________*_ ___________
mutations in two different genes can produce a wild phenotype due to compensation of the two different wild type (non-mutant) alleles.
- *__________ ___________
- ____________ _________*_
- founding point of early biochemical molecular genetics. (Benzer)
- establishes the relatedness of different mutations.
- allows us to infer the minimum number of genes in a pathway.
- can not determine gene order or linkage.
- extension of complementation information to determine the metabolic order of the genes.
- possible due to specificity of enzymes.
DEFINITION OF THE GENE
the segment of DNA which is responsible for the production of some stable, long chain molecule which includes regions preceding and following the coding region as well as intervening sequences and individual coding sequences.
- 1.- hereditary unit.
- 2.- one gene = one enzyme.
- thought that the phenotype is controlled by controlling the individual enzymes which make up the sequential steps of the cellular reactions. not actually so due to: some gene products are not enzymes. some functional enzymes requires two or more different protein subunits.
- 3.- one gene = one polypeptide.
- much better due to less specificity required as a polypeptide vs. an enzyme. still not a solid definition due to some gene products NOT being polypeptides (RNAs).
- 4.- current state of the art is the cistron.
- basis of the genome in all organisms, either DNA or RNA.
- DNA in most cells, cellular organelles and viruses.
- RNA in some viruses.
- in most cases the genome is made up of DNA with RNA serving as an intermediate in the process of protein synthesis.
ASSIGNMENT OF DNA AS GENOME
Avery, MacLeod and McCarty's experiment.
- worked with Streptococcus pneumoniae.1- presence or absence of a polysaccharide capsule to protect bacteria from wbc's.
- smooth (S) vs. rough (R)
- 2- molecular composition of capsule
- type I, II, III.
- the phenomenon which converted living nonvirulent IIR cells into virulent IIIS cells due to some "transforming principle" from the dead IIIS cells.
AVERY, MaCLEOD AND McCARTY
- proved the purity of DNA.
- utilized some new enzyme technology to remove the purity question.
- only the extracts treated with DNAse lost the ability to transform the IIR cells.
- DNAse: degrades only DNA.
- RNAse: degrades only RNA.
- Protease (trypsin): degrades protein.
second experiment confirming DNA as genetic material which effectively put the subject to rest.
RNA AS GENETIC MATERIAL
- Frankel-Conrat and Singer.
- reconstitution experiments with tobacco mosaic virus.
- determined that the virus produced proteins based on what RNA molecule was present not which capsule protein set.
NUCLEIC ACID STRUCTURE
- two major types of nucleic acids:
- DNA -- deoxyribonucleic acid
- RNA -- ribonucleic acid
- both are long unbranched polymers made up of individual units called nucleotides.
- composed of three parts:
- five carbon (pentose) sugar.
- phosphate group.
- cyclic nitrogen containing compound called organic base.
- nucleoside plus a phosphate group.
- need three phosphate group to be incorporated into nucleic acid due to high energy bond to drive reaction.
- AMP 5'AMP 5'dAMP
- ADP 5'ADP 5'dADP
- ATP 5'ATP 5'dATP
- two different types that differ between the two types of nucleic acids:
- - RNA: D-ribose sugar.
- - DNA: 2-deoxy-D-ribose sugar.
almost identical except for the number 2 carbon which in DNA has an -H and in RNA has an -OH.
- always attaches to the number 5 carbon of the pentose sugar.
- purines: adenine and guanine.
- pyrimidines: cytosine, uracil and thymine.
- a sugar and one organic base bonded together.
- NO phosphate group.
- linkage in purines are 1'-9.
- linkage in pyridines are 1'-1.
- * numbers with the (') is the number of C in the sugars.
- *numbers without the prime symbol is the number of C in the bases.
- nucleotides and nucleosides are very common components in the cell and carry out many other functions beyond building nucleic acids.
- still need to connect nucleotides together through a phosphodiester bond.
- 5'-3' connection.
- an ester bond through the phosphate, so two ester bonds are involved with the two R groups.
PROPERTIES OF DNA
- self reproduction.
- the sugar phosphate backbone is not known to vary in nature.
- the source must reside in the organic bases.
- since there are only four different bases in DNA the source of variation must reside in the ORDER of the bases.
- due to it's length there are an incredible number of combinations possible.
WATSON CRICK DOUBLE HELIX
- DNA actually occurs as a double stranded molecule: two complementary strands wound around each other in a helical fashion.
- antiparallel in nature.
- chemical composition.
- [C] = [G]
- [A] = [T]
- infers some fixed relation ship between the bases however [A+T] vs [C+G] is highly variable.
WILKINS AND FRANKLIN: X-RAY DIFFRACTION
- incredibly consistent.
- highly ordered molecule.
- repeating unit every 3.4 angstroms along it's axis.
- molecule is 20 angstroms wide.
DOUBLE HELIX MODEL
- two long DNA molecules running in opposite chemical directions (antiparallel).
- molecules held together by H bonds between the bases.
- sugar-phosphate backbone on the outside.
- A pairs with T through 2H bonds.
- G pairs with C through 3H bonds.
WHY ARE THE TWO STRANDS COMPLEMENTARY?
- pyrimidine + pyrimidine = DNA too thin.
- purine + purine = DNA too thick.
- purine + pyrimidine = thickness compatible with X-ray data.
the two strands of DNA run in opposite chemical direction and due to the bonding nature of the bases are not identical, but are complementary.
since there is a fixed relation ship among the bases the chemical composition of one or more bases can be used to calculate the relative amount of the other bases.
- A = 17% therefore T = 17%.
- A+T= 34% so G+C= 66%.
- since G must equal G each would be 33%.
if the molecule was single stranded the system will not work because there is no complementation.
PHYSICAL STRUCTURE OF B-DNA
- diameter = 20 Å.
- 1 turn = 34 Å.
- between each nucleotide = 3.4 Å.
- 10 base pairs per turn.
- major groove = 240°.
- minor groove = 120°.
TYPES OF DNA
- B-DNA: most common.
- A-DNA: B-DNA---> A-DNA when water is removed.
- Z-DNA: highly energetic; zig-zag shaped backbone.
- large number of H-bonds between the bases.
- hydrophobic interactions between the stacked base pairs; "stacking forces".
- van der waals forces.
- covalent bonds of sugar phosphate backbone.
PROKARYOTIC DNA PACKAGING
- folding or looping off of an RNA or protein core.
- supercoiling of the DNA.
- - positive supercoiling (over wound DNA).
- - negative supercoiling (under wound DNA).
When the DNA helix has the normal number of base pairs per helical turn it is in the relaxed state. Supercoiling occurs when the molecule relieves the helical stress by twisting around itself.
controlled by a group of enzymes called topoisomerases.
: transient single strand nick
which allows rotation and unwinding of DNA.Type II:
transient double stranded cut
in the DNA which can introduce negative supercoils.
- both types can relax negative supercoils.
EUKARYOTIC DNA PACKAGING
- the DNA is complexed with cations and basic proteins which counteract the negative charges of the phosphate backbone.
- two types of proteins involved:
- - histones.
- - nonhistones.
- histones are small basic proteins found in all eukaryotic DNA.
- five major groups that vary in the lysine and arginine content.
- H1: very lysine rich.
- H2A: slightly lysine rich.
- H2B: slightly lysine rich.
- H3: arginine rich.
- H4: arginine rich.
- histones are present in a 1:1 ratio with DNA and counteract the negative charge of the phosphate groups.
- thus the synthesis of histones must be coupled with DNA synthesis in S-phase.
- overall these proteins are very conservative or stable. especially H3 and H4.
- when DNA is observed under an EM it appears as "beads on a string".
- the beads are nucleosomes.
- nucleosomes are clusters of histone proteins around which DNA is wrapped.
- nucleosome core is made up of two copies each of H2A, H2B, H3 and H4.
- a total of 8 histones often called histone octamer.
- around the core there will be 1 and 3/4 turns of DNA (approx 146 base pairs).
- there is a stretch of linker DNA between each nucleosome (approx 80 base pairs).
- the H1 histone will bind at the entry/exit point of the DNA which promoted the formation of a solenoid.
- the adjacent H1 histone proteins interact to wind the nucleosome fiber (100 Å) into a 300 Å fiber.
ORGANIZATION OF THE SOLENOIDS
- the 300 Å fiber or solenoid is then hung off of a nonhistone structural protein in long loops with supercoiling to produce 7000 Å fibers which approximate the diameter of metaphase chromosomes.
- the nonhistone proteins are called the protein scaffold and provide the shape to the chromosomes, mostly topoisomerase II's.
NUCLEIC ACID REPLICATION
the potential for self replication is due to the antiparallel nature of the molecule and the complementary base pairing.
PREREQUESITES FOR REPLICATION
- a pool of the 4 deoxy ribonucleotide triphosphates. pool of dNTP's.
- cellular environment. (pH, ions, ...)
- template DNA to model new strand.
- enzyme to polymerize the nucleotides or "form the phosphodiester bonds".
- separate the two DNA strands to form the template.
- must break the H-bonds between the bases.
- requires the helicase enzyme.
- semiconservative nature of replication means one strand is original and the other is synthesized from the original strand.
- other possibilities: conservative, dispersive.
- demonstrated in Meselson-Stahl experiment.
- semiconservative: one band 15N14N and two bands 15N14N and 14N14N.
- conservative: two bands and two bands.
- dispersive: one band and one band.
PATTERN OF REPLICATION
- replication of the DNA is initiated at a specific region or site in the DNA called the origin.the origin is characterized by a specific base sequence which can form specialized structures called hair pin loops.
REPLICATION ORIGINS AND "BUBBLES"
- separation of the strands starts at the origin and proceeds in both directions.
- actually results in two replication forks.
- physically requires:
- - topoisomerases to relax supercoils.
- - helicase to break H-bonds and separate strands.
- - DNA single stranded binding protein (SSB) to temporarily stabilize the ss (single stranded) DNA.
- all need a DNA template to copy.
- need pool of dNTP's.
- correct cellular environment (pH and Mg++)
- require a primer with a free 3'-OH end, thus all synthesis must proceeds 5' to 3'.
- all with some proofreading capabilities.
- all produce a chain of opposite chemical polarity from the template.
PROKARYOTIC VS. EUKARYOTIC DNA POLYMERASES
- prokaryotes have 3 known polymerases.
- eukaryotes have several (8+) known.
PROKARYOTIC DNA POLYMERASES
- first was discovered by A. Kornberg.
- DNA polymerase I, II, III.
- DNA polymerase III is the main replication enzyme, I and II function in repair.
- - I and III with 3'-5' exonuclease activity used to cut out mistakes (degrade DNA from 5' end).
DNA POLYMERASE I
- best characterized of the DNA pol enzymes.
- functions in repair:
- - covers about 20bp when active.
- - two major subunits.
- - at least six major binding sites.
- * template.
- * primer.
- * incoming base.
- * proofreading.
DNA POLYMERASE II
- poorly characterized.
- thought to function in repair of DNA.
DNA POLYMERASE III
- functions as the main replication enzyme.
- very large, multi-subunited.
- at least 20 different polypeptides involved.
- "core enzyme" of three subunits: alpha, epsilon and theta.
- functional enzyme called DNA polymerase III holoenzyme.functionally dimeric enzyme.
- error rate of 5x10-9 due to proof reading.
EUKARYOTIC DNA POLYMERASES
- alpha -- replication (I).
- beta -- repair.
- gamma -- founds in organelles, replication.
- delta -- replication (III).
- epsilon -- repair enzyme (II).
- eta -- replication of minor damaged DNA.
- iota -- replication of major damaged DNA.*
- zeta -- replication.*
DIRECTION OF SYNTHESIS
- all replication is 5' to 3'.
- requires a template strand which is 3' to 5'.
- since the molecule is split for semiconservative replication one strand will be 3' to 5' and the other will be 5' to 3'.
SYNTHESIS OF BOTH STRANDS
- due to the 5' to 3' direction of the polymerase and the two different directions of the template you get two "styles" of replication.
- 3' to 5' template normal continuous 5' to 3' replication.
- 5' to 3' template must have replication in short discontinuous segments, which can then be connected together to complete the strand.
continuous/leading strand: template oriented in the 3'-5' direction so replication can run in one long continuous strand. tends to be faster than alternative.
discontinuous/lagging strand: template oriented in the 5'-3' direction so replication must occur in short discontinuous sections that must be hooked together. slow process.
- okazaki fragments: relatively short DNA sections on the lagging strand.
- DNA polynucleotide ligase: DNA ligase enzyme that ligates adjacent sections together to form on long strand.
- primer: starts each fragment in RNA.
- primosome: complex group of proteins required to have a successful priming event.
- PriA PriB PriC dnaB dnaC dnaT ---> prepriming complex
- primase (dnaG) RNA polymerase
*dna_: are proteins that bind with DNA.
- the fully functional primosome produces a short antiparallel RNA on the DNA template to provide the free 3'-OH end for DNA polymerase to work.
- primer will eventually be cut out and repaired to finish out new DNA strand.
PROKARYOTIC REPLICATION FORK
VARIATION IN DNA REPLICATION
- - DNA: single stranded or double stranded. linear or circular.
- - RNA: single stranded or double stranded. linear ONLY.
VIRAL DNA REPLICATION
lots of tricks to improve rapid reproduction of viral genome.
ROLLING CIRCLE REPLICATION
- viral DNA replication.
- ends up producing a circular DNA template with DNA polymerase working continuously around the circle to produce mass quantities of the viral genome for packing.
VIRAL RNA REPLICATION
- RNA directed RNA polymerase: enzyme that makes and RNA molecule from an RNA template. direct production of RNA from RNA genome.
- RNA directed DNA polymerase: enzyme that makes DNA molecule from an RNA template. "reverse transcriptase"
use an RNA template to make DNA then use the host transcription machinery to make many copies of the RNA viral genome for packaging.
- single stranded linear RNA without a protein capsule.
- all use RNA directed RNA polymerase.
- double stranded circular DNA.
- single origin with normal bidirectional replication.
- only one functional replicon.
- mesosome; determines where chromosomes are going to attach.
- all double stranded linear DNA.
- many origins/replicons per chromosome.
- speed of replication dependent on number of replicons.
- often there is a characteristic pattern of replicon firing or usage for each chromosome.
- coordinated with histone synthesis.
- transcription of RNA from DNA and production of a polypeptide from the resulting RNA.
- DNA does not participate directly in the formation of a polypeptide (sends a messenger).
- the cistron DNA is transcribed into a variety of RNA intermediates which ultimately synthesize the polypeptide chain.
the formation of an RNA molecule from a DNA template through complementary base pairing; mediated by RNA polymerase; producing a primary transcript.
- pool of ribose nucleoside triphosphates.
- DNA template.
- suitable enviroment (pH, Mg++).
- DNA directed RNA polymerase.
- RNA synthesis is almost identical to DNA synthesis as previously outlined.
- still add bases to 3'-OH end.
- all synthesis is thus 5' to 3'.
- DNA must be in the relaxed state.
- double stranded DNA must be split into single stranded state.
- differences: ribose sugar, U instead of T.
- as usual differ between prokaryotes and eukaryotes.
- must have the ability to chose the proper strand to copy (strand selection):
- - one strand is the template.
- - the other one is not.
the non-template strand is equal to the molecule RNA with the exception of U instead of T.
PROKARYOTIC RNA POLYMERASE
- very large molecule, covers about 60 bases of DNA wehn attached and functioning.
- functional enzyme is large multisubunited:
- - core enzyme: 2 alpha, 1 beta and 1 beta'.
- - sigma subunit (initiation process).
- - rho subunit (termination process).
- - omega subunit (?).
EUKARYOTIC RNA POLYMERASE
- several different RNA polymerases known.
- all large, complex, multi-subunited (generally 2 large and 4-6 small subunits).
- class I: transcribe ribosomal RNAs (rRNA).
- class II: transcribe structural genes (mRNA).
- class III: transcribe transfer RNAs (tRNA+5SrRNA).
ATTACHMENT OF RNA POLYMERASE
- based on sequences of DNA in the leader regions.
- sequences called the promoter region.
- the sequence is located immediately in front of the point where transcription begins.
- relatively small, about 60 bp.
- termed "upstream" from the gene.
- bipartite sequence.
- -35 -10 +1
- - consensus sequence (most common).
- - the bipartite sequence has important spatially relationships to allow functionality.
- - the closer the sequence of the promoter is to the consensus sequence the stronger the promoter.
- sigma subunit probably functions in the recognition of the two parts of the promoter region and drives the binding of the RNA polymerase holoenzyme to the DNA.
- sigma only stays on for a brief time, after the first few bases are polymerized sigma will fall off.
- transcription in prokaryotes is fairly rapid 17 to 30 bp per second.
- initiation usually occurs at a purine (90%) Aor G.
- this fits into a specialized site on the enzyme with a second site open for the addition of next nucleotide.
TERMINATION OF TRANSCRIPTION
- two distinct types:
- - rho independent.
- - rho dependent.
- terminator sequence is relatively small (about 40 bp) located in the trailer region of the cistron.
- A DNA sequence signaling the termination of transcription; the rho protein is not required for termination.
- rho functionally is a hexamer.
- rho binds to the RUT site on RNA and ultimately pulls the RNA free from the RNA polymerase.
- a larger sequence needed to function a promoter.
- CCAAT site at -75 and TATA-like sequence in the -19 to -27 region.
- -75 -23 +1
- 9 bases involved; not long enough to be an unique signal.
- TATA: original strand, place where separation starts.
- Class I:18 nucleotide sequence that binds a termination protein.
- Class II: the process ends after the 3' end of the functional RNA followed by endonucleolytic bases down from the eventual 3' end of the functional RNA molecule. 11-30 base pair conserved sequence. AAUAAA or AUUAAA.
- Class III: very similar to Rho independent.