bio 207 lecture 1-3
what is a gene
basic unit of heredity, sequence of DNA that codes for a product and its regulatory regions, located on chromosomes
what is an allele
one of 2 or more versions of a gene
what is a genome
the complete set of genetic material in a cell (incl mitochondria, chloroplast, plasmid DNA). incl genes as well as non coding DNA
genes vs traits/phenotypes
genes are inherited and traits/phenotypes are not directly inherited
what are traits/ phenotypes
observable characerisitcs that manifest as a result of the genes an individual carries and the environment that influences the expression of the genes
a heritable trait is when
a particular trait can be passed genetically
what is interesting about the genetic coding of all living organisms
its the same for all of us on earth becuase we are all through to have evolved from a common ancestor around 4 billion years ago
model genetic organisms
have characteristics that are usueful for genetic analysis, the 6 are mus musculus, arabidopsis thaliana, caenorhabditis elegans, escherichia coli, drosphila melanogaster, saccharomyces cerevisiae
what are the 6 coomon charactersitcs of model organisms
short gen time, produce numerous progeny, can carry out controlled genetic crosses, can be reared in a lab environment, availability of numerous genetic variants, accumulated body of knowledge about their genetic systems
how long have humans been using genetics
10-12k years ago: domestrication of plants and animals, and ancient greeks: theories of inheritance
what is the pangenesis hypothesis
each part of the body contain genetic information for that particular part, gemmules carry infro from the parts to the reproductive organs (via blood), then is passed to embryo at conception
what are gemmules
specific particles
lamarckian inheritance
traits acquired in a persons lifetime become incorporated into that persons hereditary info and are passed onto offspring
performationism
inside the egge/sperm exists a fully formed miniature adults (a homunculus) and then that simply enlarges in the course of development
what is wrong with the preformationsim hypothesis
offspring would genetically be soley of the mother or of the father, but there are observation that individuals possess mixture of traits from both parents
blending inheritance
each traits of offsprings are a blend of parental traits, comes from observations that off spring possess traits from both paternal lines. believed that once blended can't be seperated for the next gen but becomes the new trait.
weismann: germ plasm theory helped not support what and how
tested inheritance of acquired characteristics by cutting off the tails of mice for 22 consecutive generations, this didn't alter mice tail length, no evidence to support inheritance of acquired characterisitcs
what did weismann propose
germ-plasm theory, that cells in reproductive organs carry a complete set of genetic information that is passed to the egg and sperm
what are the key ideas of charles darwin: evolution (on the origin of species in 1859)
- put for the theory of evolution through natural selection
- variation of traits within the population
- traits are inherited
- offspring with traits that inc their probability of survival will reproduce
what was darwins weaknesses
lack of understanding of heredity and unaware of medels work on inheritance
what did gregor mendel study (1866)
principles of heredity, discovered the basics by examining pea plans, conclusions were not widely known in the scientific community
what didn't mendel know
how heritable traits worked on a cellular level
what did gregor medels pea experiment refute
bledning inhertance, the traits of the plants do not blend
what did mendel reason? what was the result of the experiment
that each plant obtained two copies of a something that resulted in a particular trait? the F1 gen presented phenotype of one parent but inherited info from both parents since the f2 gen displayed both phenotypes (wrinkled info unmaked in F2)
by hybridization and observations of offspring pea plants, mendel was able to formulate 3 principles of heredity... what are they?
- the law of independent segregation
- the law of independent assortment
- the law of dominance
what is the law of independent segregation
each indiv carries 2 copies of an inherited trait (alleles) which segregate equally in the following gen
what is the law of independent assortment
different inherited traits sort independently of one another (peant plant height doesn't affect its flower colour)- all chance.
what is the law of dominance
for a trait, 1 allele is dominant and appears in a 3:1 ratio. identification of dominant and recessive alleles
what theory did schleiden and schwann (1839) come up with
the unified cell theory, all life is composed of cells, the cell is the fundamental unit of strucutre and function in living organisms, abiogenesis
what is abiogenesis?
cells arise spontaneously (not true)
what did rudolf virchow have to say about cells (1858)
cells arise only from preexisting cells
what did walther flemming propose (1879)
chromosomes, "the movement of chromosomes during cell divison"
he examined salamander embyros, published description of mitosis, "solved" the separation of chromosomes from mother to daughter cells, his observation that chromsomes double is significant
what did theodor boveri and walter sutton know (1888-1902)
sperm and eggs contribute the same # of chromosomes, behaviour of chromosomes during cell division (highly organized, appear the same in daughter cells, and doubles before cell division) can explain mendel's laws of inheritance.
the boveri sutton chromosome theory
heritable units are located on chromosomes
thomas hunt morgan (1910) studied what
what mutations meant for the emergence of new traitd and speciation, used drosophila to do so
what was thomas hunts experiment
bred male white eyed fly with wildtype red eyed female fly
f1 progeny= all had red eyes
when a male F1 was bred with a female F1= all females had red eyes and males were 50:50 red and white
when male F2 white eyes is bred with a female F2= F3 females would begin to have white eyes
why is it that females wont get white eyes till the F3 generation
the trait for white eyes is a sex linked trait on the mutant x chromosone, for the female to have white eyes she would have to receive a mutant x chrosome from both parents which isn't possible till the 3rd generation
how do we know the mutation is on the x chromosome and not the y chromosome?
if it was on the y chrosome there would be chance of females having white eyes and males would always have white eyes
mechanism of mendelian hereditary (1915) explained what
linked the heritable info for eye colour to X sex chromosome, first sex linked trait, discrete pairs of factor located on chromosmes bear hereditary info thus linking traits to chromosomes
what was confirmed from the thomas hunt experiment and the mechanism of mendelian heredity
1. mendels laws of inheritance
2. Boveri-sutton chromosomal theory that the heritable info is present on chromosomes
what are the 4 requirements of genetic material
1. contain large amounts of complex information
2. replicate faithfully
3. encode the phenotype
4. have the capacity to vary
how do johann friedrich Miescher study the substance inside the cell nucleus
isolated nuclei from white blood cells in pus from bandanges, preformed the first chemical analysis of the substance present inside nuclei
what is in the nuclei? how does miescher describe the substance in the nuclei (1869)? what was this susbtance renamed as?
the nuclei contain both nucleic acid and proteins. Miescher describes the subtance is slightly acidic and high in phosphorus - nuclein (highly unusual susbtance), this substance is called nucleic acid
what did miescher think about the role of nuclein in heredity
believed that proteins were the substance that carried hereditary info
what did albrecht kossel and phoebus levene investigate
the chemical nature of nucleic acids (DNA)
what did kossel determine about DNA (late 1800s)
that there were 4 nitrogenous bases: Adenine, Cytosine, Guanine, Thymine
what did levene discover (1905)? what did he propose
DNA is a polymer, made up repeating units of nucleotides. he proposed that DNA consisted of a series of repeating, invariant, 4-nucleotide units in a fixed sequence: the tetranucleotide hypothesis (A=C=G=T)
what is in equal amounts in the cell nucleus
proteins and nucleic acids
what do chromosomes consist of
both proteins and nucleic acid
why were proteins heavily supported as contenstor as hereditary material during the debate
- structurally more diverse
- 20+ amino acids to build from ( inc # of building blocks seemingly allowed for complexity necessary to build multicellular life)
why were nucleic acids less supported as hereditary material?
- only had 4 bases
- most believed nucleic acids were not complex enough to be able to hold the entirety of hereditary information
what did erwin chargaff find when he tested the tetranucleotide hypothesis
chargaffs rules:
Adenine is always equal to thymine (A=T)
Guanine is always equal to cytosine (G=C)
what was important that chagaff did when considering the ratio of bases?
tested more organisms than just E.coli with presented a 1:1:1:1 ratio
what did erwin chargaff disprove
the tetranucleotide hypothesis- challenged the idea that DNA was a simple, invariant molecule
what are the 3 experiments that supported the hypothesis that hereditary info is encoded in nucleic acids
- griffith experiment (1928)
- Drs. Avery, macleod, and McCartys experiment (1944)
- the hershey-chase experiment (1952)
what discovery began the identification of DNA as the carriers of genetic info
the discovery of bacterial transformation
what happened during fred griffiths experiment? what bacteria did he use?
a) type IIIS (virulent) in mouse, mouse died, IIIS (v) recovered
b) type IIR (non-vir) in mouse, mouse lives, no bac recovered
c) heat killed type IIIS in mouse, mouse lives, no bac recovered
d) heat killed type IIIS and IIR, mouse dies, type IIIS (v) recovered.
streptocococcus pneumoniae
what were the possible explanations of fred griffiths experiment?
1. did not suffciently heat kill bacteria but then how did group c mouse die...
2. type IIR mutated to be virulent but strains are different
what was the conclusions of fred griffiths experiment
the IIR bacteria had been transformed, acquiring the virulence and strain genetics of the dead type IIIS
explain Avery, Macleod & McCartys experiments
heat kills type IIIS virulent bacteria, homogenize, and filtered it. treated this type IIIS filtrate with RNase (destroys RNA), Protease (destroys proteins), DNase (destroys DNA) then added these treated samples to cultures of IIR bac
what was the results of A, M,M experiments?
the type IIIS bacterial filtrates that were treated with Rnase and Protease resulted in transformed type IIIS and type IIR bacteria while the culture treated with DNase did not have transformed type IIIS which shows the transforming substance is DNA
what is T2
bacteriophage that infects E.coli
how does the bacteriophage infect E.coli?
1. phage attaches to ecoli, puts in its chromosome
2. bacterial chromsomes breaks down and the phage chromo replicates
3. expression of phage genes produces phage structural components
4. progeny phage particles
5. bacterial wall lyses, releasing progeny phages
explain the hershey and chase experiment
there are two T2 phages, 1 phage is grew in 35S and 1 phage in 32P. T2 phage infect E coli grown in 35s, 35s is taken up in phage protein (which already contains s), alongside there is e.coli growin in 32p, 32p is taken up in Phage DNA (which already contains P). both phages infect unlabed E.coli, and their protein coats are sheared off in blender
why did they shear off the viral "coats" (phage ghosts)
hereditary info of phage in its head gets injected into bacteria and lays on top of it as a phage ghost, this needs to be sheared off to find the correct material in the bacteria
what was the result of the hershey and chase experiment
didn't contain 35s but did contain 32p which labels nucleic acids (DNA) so DNA is the genetic material in bacteriophages (although there was 35s in phage ghosts)
suppose that hershey and chase found that phage ghosts contained 32p label but not in the infected e.coli. furthermore suppose they didn't find 35s in the ghosts but in the infected e.coli?
protein was the genetic material in phage
what is the exception to DNA being the carrier of genetic info rule
some viruses use RNA to encode hereditary info
explain conrat and singers experiments with the tobacco mosaic virus (1956)
used two types of TMV and degraded them to yield RNA and coat proteins, mix RNA of one type with protein of the other to creat hybrid viruses, tobacco was then infected with hybrids. the type of RNA in the hybrid parent TMV determine the RNA and protein of the progeny viruses
what does conrat and singers experiments reveal
that RNA is sometimes the genetic material for some viruses
what becomes clear from the conrat and singers experiments
that nucleic acids are the ones that encode the hereditary info of organisms and not proteins
in all organisms DNA carries..
DNA carries genetic info
some viruses genetic info is encoded in
RNA
how did james watson and francis crick deduce the structure of DNA
watson and crick deduced a 3 dimensional model of the structure of DNA that was dependent on xray diffraction images taken by rosalind franklin
what are misconceptions about rosalind franklin which were further found in her notes
in her lab notes
- the structure of DNA as a double helix
-the implications of the complementary nucleotide base pairings for replication
- the variable sequence of DNA nucleotides allowing for coding of complex genetic info
what else did rosaline franklin discover the 3d structure of
- coal
-graphite
- TMV (first viral structure to be resolved)
how were they able to resolve the 3d structure of DNA
x-ray crystallography, the best technique to resolve the 3d strucutres of biological molecules
what is the cons of x ray crystallography? what can be used instead?
xray crystallography is an incredibly difficult technique, often takes years to work out the conditon necessary to crystalize a protein or DNA in this case. Can use bioinformatics to model protein structures (not often accurate tho)
how does xray crystallography work
crystals of substance have xrays shone at them which are diffracted off the spacing of atoms within the crystal will determine the diffraction pattern, which appear as spots on the film. this pattern gives info on the structure of the molecule.
what are important about the bases of DNA? was this apparent at first?
the bases are complementary (A-T, C-G), this was not apparent at first since tautomers can form between T-G and A-C. chargaffs rule helped show the base pairing partners.
what is the secondary structure of DNA
double helix strucutre
what is the general structure of DNA
composed of 2, nucleotide polymer antiparallel strands with a phosphate sugar backbone to the outside
how are base pairs held together
hydrogen bonds on the inside not covalent bonds, hydrogen bonds allows separation
can the sequence of bases vary in DNA
yes
a rule of genetic material to be able to contain large amounts of complex info, how does it do this?
genetic instructions can be encoded in the DNA sequence, this is the only variable component of DNA
genetic material should be able to replicate faithfully, how?
complementary nucleotide pairs, held together with hydrogen bonds allows for replication
genetic material must encode the phenotype, how?
base sequence can be read into RNA and then from RNA into protein (central dogma)
genetic material must have the capacity to vary, how?
differences in base sequences allow for genetic material to vary
how do proteins differntiate DNA from RNA
DNA uses deoxyribose, who has H at C2
RNA uses Ribose, who has an OH at C2
how do purine and pyrimidine bases pair? why is this like this?
purine (A + G) are 2 carbon nitorgen ring bases while pyrimidine (C+ T, and U) are 1 carbon nitogen ring bases, purine base only pairs with a pyrimidine base to maintain specific diameter of DNA molecule
what dictates which purine bonds with which pyrimidine? what is the criteria for A+T vs C+G.
the number of hydrogen bonds they form dictates which two pair together
- A+T= 2H bonds
- C+G= 3H bonds
where is the phosphate group on the deoxyribose sugar
the phosphate group is bound on the 5' carbon
what happens during DNA systensthis, for the phopshate group
the phosphate group of one nucleotide is covalently bound to the 3' carbon of deoxyribose sugar of another nucleotide
what is another difference between RNA and DNA considering nitrogenous bases
in RNA, uracil replace thymine
what is the name of the bond between the 5' phosphate group and the 3' oh group
a phosphodiester linkage
what is particular about the how the nucleotide strands that form a double helix run?
DNA consists of 2 complementary and antiparallel (run in opposite directions) nucleotide strands
explain central dogma simply
transcription is when RNA is synthesizes from DNA and translation is when an amino acid sequence (protein) is synthesized from RNA.
why is our genetic material made of DNA and not RNA
the deoxyribose init sugar phosphate backbone makes chains of DNA chemically more stable than chains of RNA, DNA is also less reactive chemically because of the abscence of the oxygen molecule
what is an exception to central dogma? example?
in some viruses info is transferred from RNA to DNA (reverse transcription) or to another RNA moleucle (RNA replication)
ex. retroviruses (highly error prone-high rate of mutations)
how do complex RNA structures come about
they may contain numerous hairpins