Molecular Genetics Exam 1 Flashcards
For a molecule to serve as the genetic material, it must be able to
replicate, store info, express info, and mutate
What is the genetic material?
what is transmitted from parent to offspring
Describe Griffiths experiment
used S (lethal) and R (non-lethal) bacteria; heat killed S bacteria combined with R bacteria and injected in mice; mice died and S bacteria was cultured suggesting something from the S turned R into S
Describe Avery, macleod, and mccartys experiment
used S (lethal) and R (non-lethal) bacteria; killed specific components of the S cells and combined the remaining components with R to inject in mice; mice that had DNA killed were the only ones to survive and no S bacteria was cultured from them suggesting that DNA was required to turn R into S
Describe Hershey-chase experiment
used viruses and radiolabeled either the DNA or protein coat; infected cells and looked to see where the radiolabel ended up after infection; when DNA was radiolabeled the label was found in the cell but when the protein was labeled there was nothing in the cells suggesting that viruses inject their DNA into the cell and this is what is used to make more viruses
What is the indirect evidence that supports the idea that DNA is the genetic material?
Distribution of DNA and mutagenesis
What is the direct evidence that supports the idea that DNA is the genetic material?
Recombinant DNA studies
Where are chromosomes located?
in the nucleus
Each chromosome contains one
long molecule of double stranded DNA
What are DNA markers used for?
To serve as landmarks that identify physical positions along a DNA molecule, such as DNA from a chromosome
What does DNA stand for?
Deoxyribose nucleic acid
What are the 3 major components of DNA?
Phosphate, sugar, and base
What is the difference between DNA and RNA?in regards to the sugar?
DNA does not have an OH, just an H, on the 2’ carbon
Nucleotides are___phosphates
mono
Nucleoside diphosphate has __ phosphate groups
2
Nucleoside triphosphate has __ phosphate groups
3
Bases that are purines and the number of rings
adenine and guanine, 2 rings
Bases that are pyrimidines and the number of rings
cytosine, thymine, and uracil, 1 ring
Parts of a nucleoside
Sugar and base
Nucleotides are linked by ____ bonds between the __ group on the c-3’ and the ___ group at the c-5’ position
Phosphodiaster, OH, phosphate
X-ray diffraction studies by ___ of DNA showed a 3,4 angstrom periodicity, characteristic of a helical structure
Rosalind Franklin
How many hydrogen bonds attract a and t?
2
How many hydrogen bonds attract g and c?
3
Chargaff’s rule
base pairing
A=T and C=G
Pyrimidines T+C=purines A+G
DNA becomes tightly packed when it
supercoils
Shape of Bacterial DNA
circular
What are nucleosomes?
a core of 8 histones
Simplest level of DNA
chromatin as a double stranded helical structure of DNA
DNA is complexed with histones to form ___
nucleosomes
Nucleosomes fold up to form a
30 nm fiber
30nm fibers that form loops ___ in length
300 nm
300 nm loops are compressed and folded to produce a
250 nm wide fiber
Tight coiling of the 250 nm fiber produces
the chromatid of a chromosome
Heterochromatin
condensed areas and are inactive because they either lack genes or contain genes that are compressed
euchromatin
uncoiled and active
what parts of the chromosomes are heterochromatin?
Telomeres, and centromeres
Centromeres
are the primary constrictions along eukaryotic chromosomes and mediate chromosomal migration during mitosis and meiosis
Telomeres
terminal heterochromatic caps that consist of short tandem repeats that contribute to stability and integrity of the chromosome
Does the telomere code for any genes?
no
what is the sequence of telomere in humans?
TTAGGG
What is the T loop?
The loop made by the telomere. It forms an overhang that protects from degradation. It involves many proteins
What is meant by semiconservative replication?
1 original strand and one new strand
What is Conservative replication?
when there is one complete double helix of old and one of new
What is dispersive replication?
when there are chunks of old and new in a DNA molecule
What was the meselson and stahl experiment?
They wanted to show how DNA was replicated so they labeled old nucleotides with 15n and new nucleotides with 14n then centrofuged them to find where they would be in the tube
2 bands for the semiconservative
2 top bands
2 bands for conservative model
1 on top and one at bottom
2 bands for dispersive model
both in middle
DNA replication is
semiconservative
When does DNA replication occur?
The S phase of interphase
When does growth occur?
in G1 and G2 of interphase
what are the parts of mitosis?
prophase, metaphase, anaphase, telephase
what does it mean by replication is bidirectional?
Replication occurs in both directions simultaneously with the leading and lagging strand
How many strands are there on a fork that is replicating?
2
Similarities and Differencences in origins and direction of replication in prokaryotes and eukaryoties
Pro-1 origin, bidirectional
Euk-More than 1, bidirectional
what is the replication fork?
the point at which replication is actively occuring
DNA polymerase
catalyzes the elongation of new DNA at replication fork but cannot initiate synthesis of a polynucleotide and can only add nucleotides to an existing 3’ end thus the unusual strand is a short RNA primer
Primase
adds the primer to give DNA polymerase a 3’OH to begin replication at
Difference between DNA and RNA
DNA only has an H at the 2’ c and RNA has a OH
Synthesis only occurs in the ___ direction
5’ to 3’
The ___ is replicated as a continuous strand and polymerase moves toward replication fork
Leading strand
The ___ is replicated as a discontinuous strand and the polymerase moves away from replication fork
Lagging strand
Topoisomerase aka gyrase
Alleviates the supercoiling and places single stranded nicks in the DNA which are then repaired
Helicase
Unzips Double helix
the lagging strand has ____ fragments
okazaki
what makes up an Okazaki fragment
Newly senthesized DNA and RNA primer
What happens to RNA primers in the Okazaki fragments?
RNA primers are removed and the space is filled in the DNA via a polymerase and then ligated to the strand using an enzyme known as ligase
Why is the lagging strand left short?
When the primer is removed on the end and it cannot be filled in, the next round of replication will cause it to be short
Why are telomeres indicated in aging?
Telomeres are thought to be the counting mechanism for the number of times a cell has replicated. When the telomeres reach a critically short length the cell will undergo apoptosis and the shortening would be close to deleting genes
what do southern blots do?
look at DNA sequences and often show telomere shortening
What is the enzyme that elongates telomeres?
telomerase
In stem cells and cancer cells telomerase is
turned on
How does topoisomerase work?
Introduces a double stranded break ahead of the replication fork and swivels the cleaved ends around the central axis to relieve the stress of helix unwinding
What is PCR?
polymerase chain reaction. A rapid method of DNA cloning that copies a specific DNA sequence through in vitro reactions that can amplify target DNA sequences present in very small quantities
What goes into the tube for PCR?
DNA primer, taq polymerase, heat, DNA template and dNTP
What is the temperature at which 50 percent of pairs are denatured
melting temperature
3 parts of PCR
denaturation, annealing, and extention
what is denaturation?
temperature is increased to separate DNA strands
What is annealing?
Temperature is decreased to allow primers to base pair to complementary DNA template
What is extension?
Polymerase extends primer to form nascent DNA strand
What do we use to analyze DNA?
Electrophoresis
what is electrophoresis?
Seperates DNA and RNA fragments by size using polyacrylamide or agarose gels
What are the 2 types of electrophoresis?
southern blots for DNA and northern blots for RNA
why does DNA move to the + end in electrophoresis?
Phosphate groups of DNA make the DNA -
Smaller fragments move more ___ through the gel
quickly
Describe gel electrophoresis of DNA
Liquid gel is allowed to harden with an appropriately shaped mold in place to form slots for the samples. After electrophoresis, the DNA fragments, located at various positions in the gel, are made visible by immersing the gel in a solution containing a reagent that binds to or reacts with DNA.
What do we use to see the DNA in the electrophoresis gel?
Ethidium bromide which binds to DNA and glows when exposed to UV light
what are the sizes of the holes in agarose based on?
the percentages of agarose
____ hold on to the single stranded DNA so that it does not form duplexes
Single strand binding proteins
PCR is an in vitro version of
replication
PCR buffer
create the correct environment for the reaction to occur (stimulating the cell/nucleus)
Template DNA in PCR
what is being copied
dNTPs in PCR
Nucleotides (bases) that make up the new strand
Primers in PCR
Complementary to DNA and indicates the area to be copied; provides the free 3’ OH for DNA polymerase to begin
Taq polymerase in PCR
DNA polymerase that adds nucleotides
what is dideoxycy sequencing?
A primer distinguishes where to start. dNTPs are added along with dideoxyNTPs. When the polymerase adds ddNTPs the polymerization stops and lots of different fragment sizes are formed and separated by electrophoresis to identify bases
What is next generation sequencing?
Bridge PCR Allows for the whole genome to be sequenced within a few hours by either flourecence or pH changes
