Chapter 9: DNA and It's Role in Heredity Flashcards
Who was Frederick Griffith?
a physician trying to find a vaccine for pneumonia
What did Frederick Griffith do?
He would heat kill bacterial and inject them into mice to see if the mice would become immune to the pneumonia-causing bacteria
What did Griffith find and how?
Found two strains of bacteria but culturing samples from mucus; characterized them as smooth and rough
What strain of pneumonia was dangerous? Why?
Smooth (S) was dangerous, rough (R) was not; S strain bacteria had a polysaccharide capsule (which hinders the ability of the immune system to detect them) around their cells and R did not
T/F Chemicals from dead R strains transformed live R cells into virulent S cells
F Chemicals from dead S strains transformed live R cells into virulent S cells
What did Avery et al. try to identify?
The transforming principle of pneumonia
How did Avery et. al perform their experiments?
Treated S bacteria samples to selectively destroy different types of macromolecules
What were Avery et. al hypothesis
If macromolecule X is the transforming material, when it is destroyed, the transforming activity will be lost
What did Avery et. al find? What was their conclusion?
R strain was still transformed when S-RNA or S-protein was destroyed, but was not transformed if the S-DNA was destroyed
What was Avery et. al conclusion?
Because only DNase destroyed the transforming substance, the transforming substance is DNA
In ______, Alfred Hershey and Martha Chase used ________, viruses which attack bacteria, to explore their ideas; What were they trying to determine?
1952
Bacteriophage
Determine whether DNA, or protein, is the genetic material
How did Hershey and Chase conduct their experiment
they grew cultures of virally infected bacteria with either radioactive phosphate or sulfur. DNA should have the radioactive P and protein would have the radioactive S, so you can see which radiation is transferred to the bacteria
what did Hershey and Chase conclude
DNA contained the information needed to make the next generation of phage; the proteins were just there as a package
What is Chargaff’s Rule?
DNA molecule has the same amounts of purines and pyrimidines present
What are purines, what are pyrimidines?
Purines (Adenine and Guanine)
Pyrimidines (Thymine and Cytosine)
X-ray crystallography showed DNA was a ________
right-handed helix of uniform diameter
What can be inferred from the diffraction pattern of X rays passing through the substance?
positions of atoms
Who prepared crystallographs of DNA in the early 1950s and what did they discover?
Rosalind Franklin
Suggested that DNA is a spiral or helical molecules and that nitrogenous bases are interior
What did Francis Crick and James Watson do?
They combined all the knowledge of DNA to determine its structure and built a model
Antiparallel strands
The polarity of strand is determined by the sugar-phosphate bonds
What do phosphate groups in DNA connect to?
The 3C of one sugar and the 5C of the next sugar
What group is on the 5 end of DNA? What group is on the 3 end?
Phosphate on 5
Hydroxyl on 3
In what order is the DNA sequence written for a single strand?
5 to 3
What defines the chemical polarity of a strand?
Deoxyribose sugar
What causes major and minor grooves?
Because of base pairing, the sugar-phosphate backbones are closer together on one side of the double helix
Which groove has atoms more available for hydrogen bonding and protein interaction?
major grooves
What is the key to protein-DNA interactions
Binding of proteins to specific base-pair sequences
Why do proteins bind to DNA
to alter its structure, regulate its transcription or replication
What are the four key structures of DNA structure
Double-stranded helix of uniform diameter
Right-handed
Strands are in antiparallel orientation based of 5’ and 3’ carbons
Outer edges of nitrogenous bases are exposed in the major and minor grooves
What are the four important functions of DNA
genetic material…
stores genetic information
is suceptible to mutation through a simple alteration in the sequence
is precisely replicated in cell division by complementary base pairing
expressed as the phenotype
Nucleotide sequence dtermines …
the sequence of amino acids in protiens
Joined sister chromatids are ___________ that are produced by semi-conservative DNA replication
two DNA molecules
Where is there circumstantial evidence for DNA
that is present in the nucleus and chromosomes, doubles during the s phase, and there is twice as much in diploid cells as in haploid
DNA amounts…
prior to S phase
following S phase
after Mitosis
1 pair of homologous chromosomes
1 pair of replicated homologous chromosomes
2 identical daughter cells
Where are new nucleotides added to a DNA strand
At the 3 end
What determines the nucleotide sequence
complementary base pairing with the template strand
What direction is the template strand read by DNA polymerase
3 -> 5 direction
What does DNA polymerase create?
A phosphodiester bond between internal phosphate at 5 carbon and hydroxyl at 3 carbon
What are semiconservative, conservative, and dispersive replication? Which is the way DNA actually replicates
semiconservative: each parental strand is a template for a new strand (this is the way it replicates)
conservative: the two parental strands remain together in one daughter molecule while serving as a template for another daughter molecule
dispersive: parent molecule is dispersed among both strands in the two daughter molecules
What did the Meselson-Stahl Experiment do?
Grow Ecoli with N15, a heavy isotope that makes DNA denser, then transferred to a medium with N14; discovered that resulting densities could only be explained by the semi-conservative model
What were the results of the Meselson-Stahl Experiment?
After one round of replication, DNA had intermediate weight
After subsequent rounds, light-weight DNA and intermediate-weight DNA were present
Why did the data from Meselson-Stahl Experiment provide that DNA replication isn’t conservative or dispersive
if conservative, the first generation would have been both high and low density with no intermediate
if dispersive, all the the density of the first gen would have been intermediate, but all future generations would shift closer to being only light
What are the 6 ingredients for PCR
DNA template, primers, dNTPs, DNA polymerase, salts and a buffer
What are the three steps to DNA replication
Initiation, Elongation, Termination
What happens during the initiation step DNA replication?
unwinding (denaturing) the DNA double helix and synthesizing RNA primers
What happens during the elongation step DNA replication?
synthesizing new strands of DNA using each of the parental strands as templates
What happens during the termination step of DNA replication?
synthesis ends
What is ori?
Origin of replication
Where does initiation of DNA replication in prokaryotes occur? How does that impact replication?
At a single ori site; one origin of replication means one replication complex per chromosome
Initiation in _____ involves many – up to tens of thousands – of ori sites on each chromosome
eukaryotes
What enzyme separates DNA strands? What does it produce?
DNA helicase; it produces a replication fork
What does topoisomerase?
protects the rest of the DNA molecule from being wound tighter while the strands separate
What are single-stranded binding proteins (SSBs)?
Keep DNA strands separate during initiation by binding to the single-stranded portions of the DNA
Are DNA strands more stable together or separate?
Together
What gets DNA polymerase to start adding nucleotides?
Primase; connects a few complimentary RNA bases to the template strand (RNA primers)
Once RNA primers are in place, DNA polymerase can add DNA bases, copying the template strand
Why does DNA copying also proceed in the opposite direction
Because it is composed of anti-parallel strands
What happens in Elongation
Each of the two strands now acts as a template to synthesize a new complimentary strand; new DNA is extended from the primer by DNA polymerase
Is the replication fork bidirectional or monodirectional?
Bidirectional from origin; leading and lagging strand in both directions
What is a replication fork, what happens within in?
the site where DNA unwinds to expose bases; the leading strand can grow continuously at its 3’ end as the fork opens, the lagging strand cannot be made this way
How is the lagging strand made?
Made in Okazaki fragments in the 5 –> 3 direction; cannot begin until the fork has advanced a little ways so it is oriented so that its 3’ end gets farther from the fork
What does DNA replication begin with? Which of these is required for the leading strand and each Okazaki fragment?
a short primer, RNA complementary to the DNA
RNA is required for the leading strand and each Okazaki fragment
What does the enzyme primase do? What happens after it acts?
synthesizes the primer RNA on nucleotide at a time; DNA polymerase adds nucleotides to the 3 end of the RNA primer
DNA polymerase is ______; what does that mean?
processive
catalyzes many polymerizations each time they bind to DNA very rapidly
On the lagging strand, synthesis is in the _________ direction to fork movement and requires constant ________
opposite
re-priming
Synthesis occurs ______ in a series of fragments called ________
discontinuously
Okazaki
After synthesis of Okazaki fragments…
A different DNA polymerase replaces RNA primers with DNA
What catalyzes the final phosphodiester linkage between fragments
DNA ligase
What is termination?
the two replication forks meet
what happens during termination?
The last primer is removed from the lagging strand, no DNA synthesis occurs because there is no 3’ end to extend – a single strand bit of DNA is left at each end (end-replication)
What is the problem with end-replication? What is the solution?
the new chromosome has a short region of single-stranded DNA overhang at one end, so the chromosome becomes shorter; telomeres
What are telomeres?
repetitive sequencees (TTAGGG) at the ends of eukaryotic chromosomes; they do not encode proteins
What are the functions of telomeres?
protect protien-coding DNA from being lost
Extend the chromosome to prevent DNA from being cut off
Prevent DNA repair mechanisms from joining chromosome ends
What does Telomerase do? How?
adds telomeres back on the end of the chromosome; some; has RNA template that base-pair with the single-strand overhang; works as a DNA polymerase to synthesize new DNA
What causes apoptosis? What is it?
Too many telomeres are lost, causes cell death
Telomers tend to shorten with _____
aging
In human cells, telomeres are so short after _________ that they die. _____ cells express telomerase
30 generations
cancer
DNA replication proeeds at a __________ requiring many proteins for distinct patterns of synthesis of ______ and ____ strands
replication fork
leading and lagging
What does PCR generate and how?
generates a large number of copies of a targeted genome region thorough cycles of DNA replication
What are mutations?
changes of the nucleotide sequence of the genome of an organism
What are mutations caused by?
any agents that damage DNA; UV light, certain chemicals, viruses, random mistakes
What do mutations alter?
phenotypes by generating a non-functional protein, changing how a protein works, altering when and where a gene is expressed
What are the repair mechanisms for replication mistakes? What enzyme makes these mistake?
Proofreading, Mismatch repair, Excision repair
DNA polymerases
Proofreading
As DNA polymerase adds a nucleotide to a growing strand, it checks if bases are paired incorrectly and fi they are DNA polymerase removes the nucleotide
Mismatch repair; what happens if it fails?
recognizes old and new strands by modifications present on the template strand; if it fails the DNA sequence may change
How are mismatched bases recognized?
abnormal hydrogen bonding
Point mutation
a single base is changed, inserted, or deleted
What do mismatches lead to?
base-pair substitutions
in some cases the old strand is removed instead of the new
Excision Repair
Enzymes constantly scan DNA for damaged bases – they are excised and DNA polymerase adds the correct ones
How does UV radiation disrupt DNA replication?
its absorbed by thymine causing it to form covalent bonds with adjacent nucleotides
What are thymine dimers
Covalent linkages between adjacent thymines formed on exposure to UV radiation
What are spontaneous mutations caused by
polymerase errors or spontaneous chemical changes in bases
Tautomeric shift
Bases have two isomers (tautomers); when a base temporarily forms it’s rare tautomer it can pair with a different base, leading to a mismatch
Deamination
loss of an NH2 group in cytosine, forming uracil; A will be inserted into the new DNA strand (A pairs with U) instead of G
Somatic mutations
occur in somatic (body) cells; are not passed to offspring
Germ Line Mutations
occur in germ line cells (gametes) and are passed to offspring
T/F Mutations always affect the phenotype
False
Silent mutations
Do not affect protein function
Loss of function mutations
prevent gene transcription or produce nonfunctional proteins; nearly always recessive
Gain of function mutations
lead to a protien with an altered function; usually dominant, common in cancer cells
Missense mutation
A point mutation in which a single nucleotide change results in a coon that codes for a different amino acied
Conditional mutations
affect the phenotype only under certain environmental conditions
Chromosomal mutations
extensive changes in genetic material involving long DNA sequences
Why are chromosomal mutations more extensive?
It doesn’t affect 1 gene, but 1 chromosome that has hundreds of genes
What do chromosomal mutations provide?
genetic diversity but can be deleterious
What do chromosomal rearrangements involve?
double strand breaks
What is a cause of chromosomal rearrangements?
an aberrant crossover between homologous or nonhomologus chromosomes
What does radiation cause?
Double strand breaks; repair mechanisms may join non-homologous ends
Why will a cell die if there are many chromosome breaks?
many pieces are lost of apoptosis is triggered
Deletions
loss of a chromosome segment; can have severe or fatal consequences
Duplications
a portion of a chromosome is replicated, resulting in multiple copies
Extra copies of genes may lead to _____ of genes
overexpression
Inversions
result from breaking and rejoining, but the segment is flipped resulting in loss-of-function mutations
Translocations
a segment of DNA breaks off and is inserted into another chromosome; it may involve reciprocal exchanges of chromosome segments
