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Genetics Exam 3

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Extranuclear Inheritance
Genetic information is transmitted to progeny through the cytoplasm, not the nuclear genes. Exhibits nonMendelian inheritance patterns.
maternal effect, infectious heredity, organelle heredity
3 forms of extranuclear inheritance
maternal effect
Results from the egg containing the stored products of the nuclear genes of the female parent
Organelle heredity
Results from the expression of DNA contained in the mitochondria or chloroplasts
infectious heredity
Results from the symbiotic or parasitic association of microorganisms with eukaryotic cells
the ovum
Where does the majority of the cytoplasm in a zygote come from?
MZT
Stage where development comes under exclusive control of zygotic genome
maternal genotype
In traits determined before the zygotic genome becomes active, the maternal effect states that what will determine the progeny's phenotype?
embryonic polarity
In drosophila, what do maternal effect genes determine?
bicoid (bcd)
-Specifies anterior development -Mother must have one wild type allele for functional anterior development
maternal ooplasm
In infectious heredity viruses or other microorganisms existing in a symbiotic relationship can be passed through the __________ to the progeny.
yes
will (nos-/ nos-) mothers produce embryos that lack abdominal structures, even if the embryos have a functional nos allele?
chloroplasts and mitochondria
what organelles contain DNA?
mother, child
Traits defined by the organellar genome exhibit a ______ to _____ inheritance pattern
Carl Correns
-Discovered variation in four o clock plants -Found inheritance determined by which plant provided the egg, genetic info contained in chloroplast or cytoplasm influencing it
Mary B. and Hershel K. Mitchell
-Discovered slow growing strain of Neospora -Phenotype of strain contributing cytoplasm determined progeny phenotype
prokaryotes
studies of chloroplast and mitochondria revealed that they more closely resembled ________ than eukaryotes
circular dna that lacks histone proteins, ribosome type
In what way does chloroplast and mitochondrial DNA resemble prokaryotes?
Lynn Margulis
Proposed embosymbiotic theory
2 billion, engulfed
Endosymbiotic theory states that: Mitochondria and chloroplasts arose about ______ years ago as free-living protobacteria that were _______ by larger, primitive eukaryotic cells
chloroplast DNA
-Multiple copies within 1 -100 to 225 kb -Includes long noncoding sequences
Mitochondrial DNA
-Multiple copies in 1 -Smaller and more variable in size than cpDNA -Very little noncoding DNA
mitochondrial function
-particularly vulnerable to mutations in the DNA -due to very little noncoding DNA, and most genes are transcribed from a single promoter
Heteroplasmy
-The presence of mixture of normal and mutant organelles in a common cytoplasm -Can dilute impact of mutant mitochondria
amitotic
There is variability in phenotype among progeny and between parents and progeny because organelles are distributed to daughter cells in this fashion.
Maternal inheritance pattern, a specific mutation in one of the mitochondrial genes, deficiency in bioenergetic function
What must be true for a human genetic disorder to be attributed to mitochondria?
Mitochondrial replacement therapy
Treatment used to attempt to stop the passing of a mitochondrial genetic disorder to child
Walter Sutton and Theodor Boveri
Proposed the chromosome theory of heredity
Friedrich Miescher
First described DNA in 1868
Phoebus Levene
Proposed DNA was composed of a repeating chain of tetranucleotides, with nucleotides found in a 1:1:1:1 ratio
proteins
What was believed to be the genetic material before DNA
Frederick Griffith
-Studied Streptococcus pneumoniae -called conversion of R cells to S cells transformation
Oswald Avery, Colin M. MacLeod, and McLean McCarty
-Identified the “transforming principle” by eliminating one molecule at a time from the extract of heat-killed S cells and testing for transformation -showed that DNA was the “transforming principle”
Nucleases
Enzymes that break phosphodiester bonds in RNA and/or DNA
Protease
Breaks peptide bonds in polypeptides
Hershey and Chase
-Blender experiment studied bacteriophage T2 which infects ecoli -Infected ecoli w/ radioactive phage and centrifuged - Showed DNA entered ecoli DNA, not protein to conclude DNA is hereditary material
Nucleotides
-basic building block of nucleic acids -Each consists of a phosphate, a pentose (a 5 C sugar) and a different nitrogenous base
ribose and deoxyribose
What are the types of pentose sugars?
smaller, cytosine, thymine, uracil
Is a pyrimidine the smaller or bigger nitrogenous base type and what are the pyrimidines?
bigger, adenine, guanine
Is a purine the smaller or bigger nitrogenous base type and what are the purines?
Nucleoside
-A base covalently linked to a sugar -Joined by a N-glycosidic linkage
1' C of sugar links to N 1 or 9 of base
what is a N-glycosidic linkage?
nucleotide
-A nucleoside covalently linked to a phosphate -Joined by a phosphoester linkage
ester linkage
link between an acid and an alcohol
phosphates
One way to name nucleotides is by the name of nucleotide plus the number of _______.
5,3, phosphodiester
In polynucleotides, nucleotides are joined by __’-to-__’ __________ bonds
phosphate, -OH
Polynucleotides always create free _______ at 5’ end and free ________ at 3’ end
2 nm
Electron microscopy during the 1940s showed that DNA was a long thread-like molecule with a diameter of what?
10^-10 m
1 Å (Angstrom) = ?
store and encode genetic info, express genetic info, replicate faithfully, be capable of mutation, have stability
What are the requirements of the hereditary molecule?
Erwin Chargaff
Measured the base composition of DNA from various species
purines, pyrimadines, T=A, G=C
Chargaffs rules state that the total amount of ______=______, so __= ___ and __ = __
Rosalind Franklind
Used X-ray diffraction to determine the structure of DNA, showed that DNA was a helical molecule composed of more than one polynucleotide chain with the bases stacked on top of each other and with a 0.34 nm distance between the bases.
Watson and Crick
Described the structure of DNA to the scientific community, awarded nobel prize
right handed double helix
What did watson and crick propose the structure of dna was?
clockwise
In a right handed helix, two helices wind around each other in a ______ fashion
sugar-phosphates
What is on the outside of the helix
antiparallel
The two polynucleotide chains are _________
central axis
What are the bases oriented towards?
non-polar covalent bonds
how are bases held together in DNA
hydrogen bonds between the bases
How are the 2 DNA helices held together?
3, 2
How many H-bonds between G-C? Between A-T?
10
Typically, how many base pairs are there per turn of the helix?
Central Dogma (Crick)
Explains flow of genetic info fromDNA to RNA to protein
B DNA
Form of DNA described by Watson and Crick
A DNA
-Characteristic of RNA/DNA hybrids -shorter/broader
Z DNA
-Synthetic DNA consisting of GC base pairs -Left handed helix -long/thin
ribose, uracil not thymine, single stranded
Typical differences in RNA from DNA are...
Svedberg Coefficient
-A measure of how quickly particles move through a substance when subjected to centrifugation -Related to molecular weight, but not directly
Spectroscopy
Characterizes molecules by the way that they interact with various wavelengths of light
ultraviolet, 260
What type of light does DNA absorb and at what wavelenght is maximum absorption?
denaturation
-The separation of the two polynucleotide chains in a DNA molecule -Accomplished by breaking H-bonds through the addition of acids, bases, or alcohols or by the removal of stabilizing counterions or by heat
Hyperchromic shift
Increase in UV absorption w/ increasing temperature
melting temperature
-The temperature at which one-half of the DNA is no longer double-stranded
G and C beacuse they have 3 H-bonds between
The presence of more of which bases increase Tm and why?
cooled quickly
If a solution of denatured DNA is ________ it will remain denatured
Held at a temp a few degrees below Tm
If the solution is ____________ , the native ds DNA can re-form
annealing
-reassociation of single stranded DNA to double stranded DNA -Occurs by incubating just below melting temp
hybridization
Annealing of single stranded DNA from two different sources
FISH
-Single stranded fluorescently labeled DNA is hybridized to a sequence of interest
semi-conservative
What fashion did Watson and Crick propose DNA replicates in?
John Cairns
-stated that semi-conservative replication would require a replication fork -Experimented w/ ecoli in autoradiograms to show this -Bacterial DNA replicates in a circle
origin of replication (ori)
What is the point that replication is initiated called?
1
How many ori in a prokaryote?
replicon
The length of DNA that is replicated from a single ori
multiple
eukaryotic DNA consists of _________ replicons
DNA polymerases
Enzymes that catylyze formation of 5’ to 3’ phosphodiester bonds
template, Mg++, primer sequence with 3’ -OH to add nucleotides to, dNTPs
What do DNA polymerases require?
anabolic
What type of reaction is DNA synthesis?
5', 3'
All DNA polymerases have ___-to-___ polymerization activity
exonuclease
Removes one nucleotide at a time from either the 5’ or 3’ end of a polynucleotide chain
Endonuclease
Cleaves within a polynucleotide chain
removes incorrect nucleotides during proofreading
What is the function of 3’-to-5’ exonuclease activity?
DNA polymerase III
Major DNA polynmerase involved in DNA replication
DNA polymerase I
-Removal of primer during DNA synthesis -Filling in the gaps that are produced during DNA synthesis
DNA polymerases II, IV, V
involved in repair of damaged DNA
core enzyme
Subunits necessary for catalytic activity
holoenzyme
All subunits required for enzyme to carryout its full functions
replisome
holoenzyme along with several other proteins functioning at the replication fork
DNA A, denatured, helicase, ATP hydrolysis
In initiation... -________ recognizes and binds the ori site on E. coli -A short stretch is ________ -________(DNA B in E. coli) binds at the ori and uses energy from __________ to break the H-bonds holding the helix together
single stranded binding proteins
-Hold the two polynucleotide strands apart -Protect the exposed single stranded regions and prevent intra-strand binding
DNA gyrase
What operates just past the replication fork and allows the supercoiling in DNA to unwind?
a free 3’OH
What does call that DNA polymerase require to add nucleotides to?
DNA primase
-An RNA polymerase (needed to initiate) -Synthesizes short RNA primers
DNA G
What is the DNA primase in E coli
semidiscontinuous
What is replication described as?
5', 3'
DNA polymerase can only synthesize from ____ to ____
leading strand
-Copies 3’-to-5’ template -Continuous replication
lagging strand
-Copies 5’-to-3’ template -Discontinuous replication
okazaki fragmaents
Short DNA segments synthesized by copying the 5’-to-3’ template
bi
Replication is _____directional in eukaryotes and prokaryotes
DNA polymerase I
-Removes the RNA primer by using its 5’--> 3’ exonuclease activity -Replaces the primer with DNA using its 5’ --> 3’ polymerase activity
DNA ligase
-Seals the single stranded nick that remains after DNA pol I -Uses energy from ATP
prokaryotic because its circular
In what kind of DNA can all RNA primers be removed and replaced and why?
5'
Which ends of linear chromosomes cannot be replicated by DNA polymerase?
telomeres
What is on the ends of eukaryotic chromosomes to stop them from getting progressively shorter?
short tandemly repeated sequences
What do telomeres consist of?
nucleoid
Bacterial genomes are condensed into a region called the _______
nucleus
Eukaryotic genomes are condensed to fit in the __________
negative
What kind of charge does DNA have?
acidic phosphate groups
Why does DNA have a negative charge?
DNA binding proteins
-Have domains that bind to DNA -These regions have basic amino acids
linking number
DNA can be characterized by the number of turns in the helix called what?
bp, bp per turn of the helix
L = number of _____ /number of ______
20
What would be the linking number for 200 bp of DNA if we assume 10bp/turn of the helix?
less
Supercoiling will occur when L is _____ than the total # of bp/10 to reestablish total number of turns
more
Supercoiled DNA is ____ compact than linear or relaxed circular DNA
topoisomers
-DNA molecules that differ only in their linking number -Same chemical formula and bond connectivities
topoisomerases
enzymes that convert molecules from one topoisomer to another
Topoisomerase type I
-Cleaves 1 strand in double helix -Does not require ATP hydrolysis -Reduces supercoiling
Topoisomerase type II
-cleaves both strands in a DNA double helix -Requires ATP hydrolysis -Involved in DNA supercoiling
chromatin
What is the form of eukaryotic DNA?
histones
packaging proteins
Nonhistone proteins
regulation of gene expression and higher order structure
euchromatin
-less condensed DNA -> dispersed appearance -Contains transcriptionally active DNA
heterochromatin
-More condensed than euchromatin -State of condensation similar to mitotic chromosomes -Trascriptionally inactive
Constitutive heterochromatin
-Always in heterochromatic state -Includes centromeric and telomeric regions and heterochromatic region of Y chromosome
Facultative heterochromatin
-Condensed in some cell lineages, euchromatic in others -Often associated with morphogenesis or differentiation
packing ratio
-The overall compression of DNA -Length of DNA/unit that contains it
9500
-DNA is 19,000 µm long if uncondensed -Mitotic chromosome is 2 µm what is the packing ratio?
10nm and 30nm
When cells are gently lysed and chromatin is viewed in the electron microscope, what types of fibers are observed?
nucleosome
Fundamental subunit of chromatin First order of DNA compaction
histones
-Basic proteins -> at least 20% arginine and lysine -bind non-specifically
H1, H2A, H2B, H3, H4
what are the 5 classes of histones?
H2A, H2B, H3, H4
What are the core histones?
linker DNA
Short stretches (~8 - ~80 bp) of DNA connecting nucleosome core particles
histone H1
Lies outside of the core particle Associated with the linker DNA Necessary for 30 nm fiber formation
solenoid, 6, hollow
a 30 nm fiber... is believed to be a ______ structure _____ nucleosomes/turn of the helix is ______
300 nm, looped domains of the 30nm fiber that coil, scaffold protein
Chromatin fiber is.... ______ in diameter Formed from _________ Chromatin fiber is assembled onto ________ to form the mitotic chromosome
chromosome banding techniques
Allow researchers to distinguish chromosomes of similar sizes with similar centromere positions
g-banding
Mitotic chromosomes digested w/ trypsin and stained w/ Giemsa Reveals unique pattern of banding for each chromosome Uniform nomenclature is used to identify diff bands using the technique
C-value
The amount of DNA in a haploid cell
Because genome size does not necessarily correlate with number of genes as expected
why is there a C value paradox?
Roy Britten and David Kohne
Worked on reassociation kinetics by denaturing DNA, then incubate just below Tm Measure A260 to follow reassociation
concentration and time
What does rate of reassociation depend on?
shorter, longer
_______ sequences reassociate more quickly than _____ sequences
Highly repetitive DNA
-Fast component -Satellite DNA -Found in centromeres/telomeres -Short tandemly repeated DNA -Noncoding -5-15% of mammalian genome
Moderately repetitive DNA
-Intermediate component -Longer sequences present less frequently in genome -micro/mini satellites -Transposable genetic elements -25 to 40% of mammal
Single copy DNA
-Slow component -Includes most functional genes and pseudognes -50-60% of mammal
single stranded
what type of dna absorbs more light?