Week 3: DNA, Gene Expression and Epigenetics Flashcards
Assembling subsets of the exons of a gene, which increases the number and diversity of proteins it encodes.
ALTERNATIVE SPLICING
A three-base sequence on one loop of a transfer RNA molecule that is complementary to an mRNA codon and connects the appropriate amino acid and its mRNA.
ANTICODON
The head-to-toe orientation of the two nucleotide chains of the DNA double helix.
ANTIPARALLELISM
A protein that binds a polypeptide and guides folding.
CHAPERONE PROTEIN
A part of a gene and its corresponding mRNA that encodes amino acids.
EXON
A mutation that alters a gene’s reading frame.
FRMAESHIFT MUTATION
A type of protein around which DNA coils in a regular pattern.
HISTONE
Part of a gene that is transcribed but is excised from the mRNA before translation into protein
INTRON
Pentose sugar + Nitrogenous Base
NUCLEOSIDE
Nucleoside or (Pentose sugar + Nitrogenous Base) + Phosphate Group
NUCLEOTIDE
A unit of chromatin structure consisting of DNA coiled around
an octet of histone proteins.
NUCLEOSOME
This was a quote from which scientist?
“A genetic material must carry out two jobs: duplicate
itself and control the development of the rest of the cell
in a specific way.”
Francis Crick, 1953
DNA is the Genetic Material, can be attributed to who?
Francis Crick, 1953
- Swiss physician and biochemist
- Isolated nuclei from white blood cells in pus
- Found an acid substance with nitrogen and phosphorus
o He called it nuclein (1871)
o Later, it was called nucleic acid
Friedrich Miescher, 1871
- English Physician
- Linked inheritance of inborn errors of metabolism with
the lack of particular enzymes.
Archibald Garrod, 1902
- English microbiologist
- Worked with Streptococcus pneumoniae bacteria,
which exists in two types: - Type S (Smooth) = Enclosed in a polysaccharide capsule
- Type R (Rough) = No capsule
Termed the conversion of one bacterial type into another
as transformation
Frederick Griffith, 1928
Transformation of one bacterial type to another is attributed to which Scientist?
Frederick Griffith, 1928
The virulent type of Streptococcus pneumoniae bacteria according to the experiments of Frederick Griffith in 1928
Type S (Smooth), the polysaccharide capsule defends it from the immune system of the body.
The animal used in Frederick Griffith’s experiments
A rat
- American physicians
- Treated lysed S bacteria with protease and DNase
- Only DNase prevented transformation
- Thus, DNA is the transforming principle
o Can convert type R bacteria into S
Avery, MacLeod and McCarty, 1944
Identified DNA as the transforming principle
Avery, MacLeod and McCarty, 1944
- American microbiologists
- Used E.coli bacteria infected with a virus that consisted
of a protein head surrounding DNA - Blender experiments showed that the virus transfers
DNA, not protein, into a bacterial cell
o Thus, DNA is the genetic material
Alfred Hershey and Martha Chase, 1953
They supported the findings of Francis Crick that DNA is indeed the genetic material
Alfred Hershey and Martha Chase, 1953
- Russian-American biochemist
- Identified the 5-carbon sugars ribose in 1909 and
deoxyribose in 1929 - Revealed chemical distinction between RNA and DNA
o RNA has ribose
o DNA has deoxyribose - Discovered that the three parts of a nucleotide are found
in equal proportions:
o Sugar
o Phosphate
o Base - Deduced that a nucleic acid building block must contain
one of each component
Phoebus Levine, 1909-1929
Discovered the three parts of a nucelotide
Phoebus Levine, 1909-1929
- Austrian-American biochemist
- Analyzed base composition of DNA from various species
and observed regular relationships:
o Adenine (A) + Guanine (G) = Thymine (T) + Cytosine (C)
A = T and C = G
Erwin Chargaff, 1951
- English scientists
- Used a technique called X-ray diffraction
o Deduced the overall structure of the
molecule from the patterns in which the X rays were
deflected - Distinguished two forms of DNA
o “A” form, which is dry and crystalline
o “B” form, which is wet and cellular - It took Franklin 100 hours to obtain “photo 51” of the B-form
of DNA
Rosalind Franklin and Maurice Wilkins, 1952
- Used the earlier research and inferences from model
building with cardboard cutouts to solve the structure of
DNA.
James Watson and Francis Crick
In the year 2008 this scientist had his genome sequenced
James Watson
Discovered that DNA transmits killing ability in bacteria
Oswald Avery, Colin MacLeod and Maclyn McCarty, 1940
4 scientists that discovered DNA components, proportions, and positions
Phoebus Levine, Erwin Chargaff, Maurice Wilkins and Rosalind Franklin (1909-early 1950’s)
A section of a DNA molecule.
Gene
Building block of DNA
Nucleotide
Sequence of building blocks specifies the sequence of amino acids in a particular protein.
Gene
Sugar found in DNA
Deoxyribose
Phosphorus atom bonded to four oxygen atoms
PHOSPHATE GROUP
Information containing parts of DNA because they form sequences.
NITROGENOUS BASE
Enumerate the Purines
Adenine and Guanine
Enumerate the Pyrimidines in DNA
Cytosine and Thymine
Enumerate the Pyrimidines in RNA
Cytosine and Uracil
are the informational parts of nucleotides.
DNA bases
Each composed of a 6-membered and 5-membered ring.
Purines
Have only a single six-membered ring
Pyrimidines
created when Phosphodiester bonds form between the deoxyribose sugars and the phosphates which causes nucleotides joint into Polynucleotide chains
Sugar Phosphate Backbone
Form between the deoxyribose sugars and the phosphates which causes nucleotides joint into Polynucleotide chains
Phosphodiester bonds
A chain of nucleotides
Polynucleotide chains
MODIFIED TRUE OR FALSE
DNA consists of two chains of two polynucleotide chains in an
PARALLEL configuration
FALSE, Antiparallel
- Derives from the structure of sugar-phosphate backbone.
- One-half of the double helix runs in a 5’ to 3’. The other half
runs in a 3’ to 5.
ANTIPARALLELISM
TRUE OR FALSE
Antiparallel nature of the DNA double helix becomes apparent when the carbons in the sugar are numbered
TRUE
TRUE OR FALSE
Carbons are numbered from 1 to 5 in deoxyribose.
TRUE
MODIFIED TRUE OR FALSE
DNA is IRREGULAR
FALSE, DNA IS DIRECTIONAL
TRUE OR FALSE
These are your complementary base pairs in DNA:
Adenine = Uracil
Guanine = Cytosine
FALSE, Adenine = Thymine
The key to the constant width of the double helix is the specific pairing of purines and pyrimidines via
Hydrogen Bonds
form frameworks that guide DNA strands.
Scaffold Proteins
The DNA coils around proteins called ________ , forming a bead-on-a string-like structure.
histones
The bead part in in the DNA coiled histone is called
Nucleosome
DNA wraps at several levels, until it is compacted into a
Chromatid
Chromosome substance is called
Chromatin
HYPOTHESIS ON DNA REPLICATION
- Watson and Crick: Envisioned the 2 strands of the DNA
double helix
unwinding and separating. - One old strand & one new strand
Semiconservative Hypothesis
HYPOTHESIS ON DNA REPLICATION
- Entirely new DNA molecule
Conservative Hypothesis
HYPOTHESIS ON DNA REPLICATION
- Max Delbruck
- Replication involves a break in the DNA backbone
every 10 nucleotide and attaches the old strand to the
new one.
Dispersive Hypothesis
ended their report on the structure of DNA with the
statement:
“It has not escaped our notice that the specific pairing we
have postulated immediately suggests a possible copying
mechanism for the genetic material.”
Watson and Crick
Semiconservative Replication was demonstrated by ______ and ______, using a series of ______ experiments
Matthew Meselson and Franklin Stahl, Density Shift
A series of Density Shift experimentation were conducted by these 2 scientists
Matthew Meselson and Franklin Stahl
This was observed in a series of Density Shift experiments, what type of DNA replication does this prove?
The two daughter double helices are identical
to the original parental double helix in DNA
sequence. However, the light blue helix
halves of the daughter DNA molecules
indicate that each consists of one strand of
parental DNA and one strand of newly
replicated DNA.
Semiconservative Replication
E. coli was labeled with a dense, heavy form of NITROGEN, and traced the pattern of replication
Density Shift Experiments
STEPS IN DNA REPLICATION
G1 –> S —> G2 —> Mitosis
Pre-DNA Synthesis part of Interphase
G1 (Gap 1)
Post-DNA Synthesis part of Interphase
G2 (Gap 2)
DNA Synthesis part of Interphase
S (Synthesis)
Mitosis lasts for about?
1hr
Gap 1 of Interphase lasts for about?
10hrs
Gap 2 of Interphase lasts for about?
4hrs
DNA Synthesis or S Phase of Interphase lasts about?
9hrs
The steps in DNA replication are as follows:
1.) Parent DNA molecule.
2.) Parental strands unwind and separate at several points.
3.) Each parental strand provides a template for DNA polymerase to bind complementary bases, A with T and G with C.
4.) Sugar-phosphate backbones of daughter strands close.
Site where DNA is locally opened, resembling a fork.
Replication Fork
Also known as the Continuous strand
Leading strand
Also known as the Discontinuous strand
Lagging strand
The unwinding protein
Helicase
Proteins that keep strands apart and stabilized, they actually do not bind but they maintain the separation, hence they are Misnomers
Binding Proteins
attracts complementary RNA nucleotides to build a
short piece of RNA called RNA primer to be added to the template strand.
Primase
A short piece of RNA
RNA primer
adds DNA nucleotides to the RNA primer, also binds nucleotides to form new strands.
DNA Polymerase (DNAP)
is an enzyme that build a polymer which is a chain
of chemical building blocks
Polymerase
engages in proofreading activity check and replaces incorrect bases.
* Excising mismatched bases
* Inserting correct bases.
DNA Polymerase (DNAP)
Continuous strand synthesis continues in this direction.
5 to 3
Discontinuous synthesis produces these fragments
Okazaki fragments
This is the reason why the growing fork proceed in one
direction when both parental strands replicate and run in
opposite direction.
Discontinuous synthesis
removes RNA primers.
Enzymes