Genetic material 4 characteristics
1. Complex info
2. replicate faithfully
3. Encodes Phenotype
4. Capacity to vary
chargraff's rules
Erwin Chargaff's rules of base ratio in DNA (A+G)/(T +C) = 1'ish
Transforming principle
Griffith
Identity of Transforming principle
Oswald avery, colin macleod, maclyn mccarty
Corroborate Transforming principle
Hershey-Chase (isotopes) in bacteriophage T2
Watson and Crick help
X-ray diffraction (rosalind franklin) and Maurice Wilkins (rosalind died of cancer before nobel prize)
RNA as genetic material
Heinz Franekel-Conrat and Bea Singer on TMV. (separate RNA and Protein, mix RNA with protein of another and obtain a hybrid virus) Then; RNA determines the protein of the progeny, ie. doesn't receive protein makeup of parent, -- it receives protein makeup
Further corroborate of RNA as genetic in TMV
Alfred Gierer and Gerhard Schramm (RNA isolated is enough to infect tobacco)
Primary structure
NT structure and how they are joined
Secondary structure
DNA's stable 3-D structure (helical in general) (variations, A form, B form, Z form) Z is left handed
Tertiary Structure
DNAs complex packing arrangements
(
Transcript
DNA info to RNA
Translate
RNA from NTs to AAs
Central Dogma
DNA? RNA?Protein in a one-way fashion
Reverse Transcription
Retroviruses and some TEs (info from RNA?DNA -or- to RNA)
Special Structure RNA and DNA
hair, stem, complex(RNase of E.coli)
Triplex (H-DNA)-b/c sometimes a polyNT strand can simultaneously pair with 2 other bases
H- breaks more readily = mutations and occurs naturally in mammals
Primary structure of DNA modifications
Methylation, 5-methylcytosine (euks--but not Yeasts)
The Ultimate Storage Problem
the packing of tremendous amounts of info into the cell
Supercoiling
Relaxed state = 10bp per turn (100bp ?10turns)
Positive super= overrotated
Negative super=underrottated
Occurs in Loops at each protein stabilizer
Helped by topoisomerases
Most DNA in cells is
negatively supercoiled. (separation easier, faster, less E)
Overrotate and underotate causes strain which ____
can cause supercoil. Super coiling is controlled by topoisomerase enzymes
Bacterial DNA exist in
Not in oen relaxed, rather it's in loops with proteins in the nucleoid. It is separate from plasmids
Interphase is
G? (G?) -- S (DNA synth) --G?
(NOT M)
Chromatin types
Euchrom, Hetero
Permanent Heterochrom
constitutive (at centros and telos) and also Y-chrom has a lot of constittutive
Heterochrom that occurs during certain developmental stages
Facultative (entire X of inactive female X)
heterochromatin lacks
transcription, XO, and late S phase replication
histones have high % of
Arg & Lys (net positive)
Most basic chromatin level
Helix
Next:
1)nucleosome
2)
DNA around Histone:
145/7
Each Histone has
a flexible tail that is 11-37 AAs, which extends out from the nucleosome. Has + charges that interac with neighboring nucleosomes.
H1 binds
20-22bp of DNA that leave the octamer and helps lock DNA in place.
Is basically a clamp around the octamer
Nucleosome has
145-147 bp of DNA ; 2 turns ; 8 histones
Linker DNA has
30-40bp
Higher Order Chromatin
30nm (diameter)
300nm [length] (series of 30nm loops of 20-100k bp)
250nm (wide) (packed 300nm loops)
700nm (wide) (tight helical coiling of 250nm fiber; this is what appears in metaphase)
Individual chromatids are
approximately 700 nm in width
polytene chromosomes
Giant chromosomes in drosophila that display the changing nature of chromatin sturucture.
-arise from repeated rounds of DNA replication without division.... copies of DNA lying side-by-side
Chromosomal puffs
Localized swelling of a polytene chromosome; a region of chromatin in which DNA has unwound (relaxed) and is undergoing ACTIVE transcription.
Evidence of Change in Chromatin Structure with Gene activity
Puffs, DNase I sensitivity
(DNase sensitivity relative to packing state of DNA [histone] vs unbound])
Chicken globin research on DNase sensitivity
-5 days gene U (upstream) most sensitive
-14 days adult genes (downstream and transcribing) are more sensitive and U is insensitive
-Fully formed globin genes in brain (insensitive [all U, and adults])
What can affect chromatin structure?
-Chem mod of histones
-Methylation
-Use of various histone proteins in nucleosome
-binding of proteins to DNA and Chromatin
(These don't alter DNA sequence, but do have major effects on expression)
Some of these chromatin changes can be passed on...
epigenetic changes
(eg. agouti locus various levels of methylation = various coat colors in mice)
--- NOT MUTATION [DNA sequence], therefore can be reversed and are influenced by environment
epigenetic changes are___
alterations of chromatin or DNA structure that do not include changes in the base sequence but are stable and passed on to cells or organisms. Some epigenetic changes result from alterations of histone proteins.
Stability of chromosomes throughout repeated mitotic and meiotic cell divisions depends on
centromeres and telomeres
Most centromeres are made up of
heterochromatin, and there are not specific sequences found in centromeres.
So, what determines exactly where a centromere lies?
Research suggest epigenetic
CenH3
a variant histone that brings about change in nucleosome and chromatin structure which is believe to promote kinetochore formation and spindle fiber attachment
Telomeres research
Hermann Muller and Barbara McClintock (corn)
Telomere purpose
caps, and means for replicating the ends of chromosome (2009, Elizabeth Blackburn, Carol Greider, and Jack Szostak)
Telomeric sequences
usually A-T followed by several quanine NTs.
taking the form 5?-(A or T)mGn-3?, where m is from 1 to 4 and n is 2 or more
3' overhang
G-rich strand at telomere that goes past the C complement that binds to "shelterin" and protects the ends.
Shelterin protects inadvertant repair and sticking.
(Some G-riches forma a t-loop with a stretch of DNA)
C value & paradox
amount of DNA (complexity of organism relative to C value)
Denature, Tm, Reanneal,etc
A-T easier (less) heat than G_C pairs
Hybridization
two single strands from diff organisms (just enough base pairs to hold together)
Rate of hybridization
provides info about the sequence complexity of DNA
Types of Euk DNA sequences
-Unique (appear once/few times in genome)
-Repetitive (moderate 150-300bp thousands of times.
2 types of Moderate rep DNA
(tandem repeat sequences-clustered at particular locations)
(interspersed repeats- scattered [Alu])
Endosymbiotic Theory Evidence
1)modern single-cell euks (protists) are hosts to endosym bac
2)mito and chloro simliar in size to eubac and possess their own DNA (similar to eubac)
3)Antibiotics in eubac affect these organelles (but not Euks cells)
4) STRONGEST- mtDNA and cpDNA closest
Cp and MtDNA are
uniparental (cp usually male and Mt female) Mt may be size [sperm are small] or it may be males Mt are selected for autophagy
Replicative Segregation (11.4)
...
Nitrogenous Bases
Purines
DNA base pairing
Pentose sugars of DNA and RNA
position of covalent bonds purine NT-MPs
-Between N9 of purine and 1' carbon of the sugar
-Between 5' carbon of the sugar and the PO4 group
NT-Mp structures
NT Pyrimidine cov bonds
-Between N1 of pyrimidine and 1' carbon of the sugar
-Between 5' carbon of the sugar and the PO4 group
Nucleoside
No Phosp
Nucleotide
side + phosp
For RNA nomentclature
Drop the 'd' from NTs (GMP instead of dGMP)
phosphodiester bond is bw
5'-PO4 and 3'-OH groups of adjoining nucleotides
between comp bases of opposite strands
H-bonds
H-bond
weak electrostatic interaction betwee
H-bonds b/w comp bases
NT bps are spaced...
along the DNA duplex at intervals of 3.4�
-The planes of the bases are parallel because of base stacking
One helical turn every
10bp
BPs that have stronger bonds
G-C (requires more energy to denature)
-lab--> alkali
Kb Mb
Kbp=1000
Mbp = 1000 Kbp
3 DNA 2�
B stable,
A short and wide DNA prot complexes and bac spores
Z (LH) in active DNA
What functions does supercoiling serve for the cell?
Supercoiling compacts the DNA. Negative supercoiling helps to unwind the DNA duplex for replication and transcription.
Describe the composition and structure of the nucleosome.
The nucleosome core particle contains two molecules each of histones H2A, H2B, H3, and H4, which form a protein core with 145-147 bp of DNA wound around the core.
Describe in steps how the double helix of DNA, which is 2 nm in width, gives rise to a chromosome that is 700 nm in width.
DNA is first packaged into nucleosomes; the nucleosomes are packed to form a 30 nm fiber. The 30 nm fiber forms a series of loops that pack to form a 250 nm fiber, which in turn coils to form a 700 nm chromatid.
What are polytene chromosomes and chromosomal puffs?
Polytene chromosomes are giant chromosomes formed by repeated rounds of DNA replication without nuclear division, found only in the larval salivary glands of Drosophila and a few other species of flies. Certain regions of polytene chromosomes can become l
Describe the function and molecular structure of the centromere.
Centromeres are the points of attachment for mitotic and meiotic spindle fibers and are required for the movement of chromatids to the poles in anaphase. Centromeres have distinct centromeric DNA sequences where the kinetochore proteins bind. For some spe
Describe the function and molecular structure of a telomere.
Telomeres are the ends of the linear chromosomes in eukaryotes. They cap and stabilize the ends of the chromosomes to prevent degradation by exonucleases or joining of the ends. Telomeres also enable replication of the ends of the chromosome. Telomeric DN
What is the C value of an organism?
The C value is the amount of DNA per cell of an organism.
Describe the different types of DNA sequences that exist in eukaryotes
Unique-sequence DNA, present in only one or a few copies per haploid genome, represent most of the protein coding sequences, plus a great deal of sequences with unknown function.
Moderately repetitive sequences, between a few hundred to a few thousand bas
What are epigenetic changes and how are they brought about?
Epigenetic changes are stable alterations of gene expression that do not require changes in DNA sequences. Epigenetic changes can take place through alterations of chromatin structure.
Explain why many traits encoded by mtDNA and cpDNA exhibit considerable variation in their expression, even among members of the same family.
Mitochondria and chloroplasts are eukaryotic organelles that possess their own DNA.
Traits encoded by mtDNA and cpDNA are usually inherited from a single parent, most often the mother. Random segregation of organelles in cell division may produce phenotyp
What is the endosymbiotic theory? How does it help to explain some of the characteristics of mitochondria and chloroplasts?
...
What evidence supports the endosymbiotic theory?
Many modern single-celled eukaryotes (protists) are hosts to endosymbiotic bacteria. Mitochondria and chloroplasts are similar in size to present-day eubacteria and possess their own DNA, which has many characteristics in common with eubacterial DNA. Mito
What is meant by the term "promiscuous DNA"?
Many proteins found in modern mitochondria and chloroplasts are encoded by nuclear genes, which suggests that much of the original genetic material in the endosymbiont has probably been transferred to the nucleus. This assumption is supported by the obser
Briefly describe the organization of genes on the chloroplast genome.
...
More endosymbiotic support
Membranes � Mitochondria have their own cell membranes, just like a prokaryotic cell does.
DNA � Each mitochondrion has its own circular DNA genome, like a bacteria's genome, but much smaller. This DNA is passed from a mitochondrion to its offspring and i
Heteroplasmy
Presence of two or more distinct variants of DNA within the cytoplasm of a single cell.
Replicative segregation
Random segregation of organelles into progeny cells in cell division. If two or more versions of an organelle are present in the original cell, chance determines the proportion of each type that will segregate into each progeny cell.
Reasons for study of mtDNA in evolution
(1) the small size and abundance of mtDNA in the cell;
(2) the rapid evolution of mtDNA sequences in some organisms, facilitating study of closely related groups; and
(3) the maternal inheritance of mtDNA and lack of recombination, which makes it possible
Suppose you examined polytene chromosomes from the salivary glands of fruit fly larvae and counted the number of chromosomal puffs observed in different regions of DNA.
(a) Would you expect to observe more puffs from euchromatin or from heterochromatin? E
Euchromatin is less condensed and capable of being transcribed, whereas heterochromatin is highly condensed and rarely transcribed. Since chromosomal puffs are sites of active transcription, they should occur primarily in euchromatin
(b) Would you expect to observe more puffs in unique-sequence DNA, moderately repetitive DNA, or repetitive DNA? Why?
Highly repetitive DNA consists of simple tandem repeats usually found in heterochromatic regions and are rarely transcribed. Moderately repetitive DNA comprises transposons and remnants of transposons. Again, with the exception of the rDNA cluster, these
Would you expect to see more or less acetylation in regions of DNA that are sensitive to digestion by DNase I? Why?
More acetylation. Regions of DNase I sensitivity are less condensed than DNA that is not sensitive to DNase I, the sensitive DNA is less tightly associated with nucleosomes, and it is in a more open state. Such a state is associated with acetylation of ly
What to know about mt and cl genomes
much smaller than nuclear genomes
circular, no histones
100-1000s of copies per cell
both used for evo relationships