Genetics Exam 3

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?