Test 3 Study Guide
DNA Structure and Analysis
1.) Definition of a gene: Fundamental units of inheritance in living organisms. Together, they old all the info necessary to reproduce a given organism and to pass on genetic traits to its offspring
2.) Scientist to Know
a. Frederik Griffiths Transformation Experiment 1928
i. First accepted demonstration of bacterial
transformation where bacteria changes its form and
function. Showed that Diplococcus pneumoniae could
transform from one strain to a different strain.
ii. Living IIIS into a mouse the mouse died; Living IIR into a mouse the mouse lived; Heat killed IIIS into a mouse
mouse lives; Living IIR and heat-killed IIIS mouse dies
because the living IIIS recovered.
b. Barbara McMlintock 1929
i. Genetic linkage corresponds to physical locations on
c. Beadle and Tatum 1941
i. Mutations in genes could cause defects in steps in
metabolic pathways. The “one gene, one enzyme” view
that lead to the “one gene, one polypeptide”.
d. Avery, McLeod and Mcarty 1944- Test tube assay instead of mice i. DNA is the “transforming factor” not proteins or other
materials and the transforming principle (that genes are
now made of DNA) was demonstrated by this
ii. DNA is the transforming factor. “a nucleic acid of the deoxyribose type is the fundamental unit of the
transforming principle…” Don't forget about the age old question of Can you grow things in dirt?
e. The Hershey Chase Experiment 1952
i. Helped to confirm that DNA was the genetic material.
Showed that when bacteriophages infect bacteria, the
DNA enters the host bacterial cell but most of their protein does not.
ii. DNA contains Phosphorus and Proteins contain sulfur.
f. Erwin Chargaff 1949-1953
i. Showed that the amount of A is proportional to the amount of T and that the amount of G is proportional to the amount of G. But the percent od A+T does not necessarily equal
the percentage of G+C.
g. Rosalind Franklin and Maurice Wilkins- Kings College, UK i. DNA has an Helical Structure
h. Francis Crick and Jim Watson- Cambridge, Uk Don't forget about the age old question of What does it mean for a market to fail?
i. DNA is a right-handed double helix in which the two strands are antiparallel and the bases are stacked on one
another. The two strands are connected by A-T and G-C We also discuss several other topics like What types of proprioceptive information are received from muscle spindles?
ii. Explained how DNA could function as the molecule of heredity
iii. Base pairing explained how genetic information could be copied
i. Linus Pauling- Caltech, US
j. Encode Project 1010
i. Identification of all functional elements in human genome ii. The gene is now replaced with open reading frames (ORF) sequence patterns.
iii. Identification of most genes is based either on their similarity to other known genes or the statistically
significant signature of a protein coding sequence.
k. Thomas Kornberg discovered DNA polymerase II and III l. Arthur Kornberg discovered DNA polymerase I
a. Nucleotides are the building blocks of DNA. They consist of a nitrogen base, a pentose sugar, and a phosphate group. We also discuss several other topics like What are the direct causes of undernutrition?
b. There are two types of nitrogenous bases: Pyrimidines (Thymine (T), Cytosine ©, and Uracil (U)) and Purines (Adenine (A), and Guanine (G))
c. AT base pairs form two hydrogen bonds, and GC base pairs form three hydrogen bonds If you want to learn more check out What is the americans with disabilities act?
d. Central Dogma of Molecular Biology
i. DNA RNA Protein → →
ii. Transcription Splicing translation post translational modification → → → → finished protein
e. DNA is reproduced by semiconservative replication i. The complementarity of DNA strands allows each strand to serve as a template for synthesis of the other
f. Three modes of DNA replication are possible
i. Conservative- original helix is conserved and two newly synthesized strands come together
ii. Semiconservative- each replicated DNA molecule
consists of one “old” strand and one new strand
iii. Dispersive- parental strands are dispersed into two new double helices.
g.) Meselson and Stahl Experiment 1958 used E. Coli to demonstrate that DNA replication is semiconservative in prokaryotes; each new DNA consists of one old strand and one newly synthesized strand.
a. Semiconservative replication became the rule in every species that was studied.
h.) DNA Polymerase enzymes that helps catalyze the polymerization of dNTPs (deoxyribonucleoside triphosphates) into DNA strands.
i.) Nucleotides arrive as nucleosides
a. DNA has its own energy from its PPP bonding If you want to learn more check out What is the regulation of glycolysis?
b. Bonded by DNA polymerase
j.) Chain elongation occurs in the 5' to 3' direction by addition of one nucleotide at a time to the 3' end
k.) • As the nucleotide is added, the two terminal phosphates are cleaved off, providing a newly exposed 3'OH group that can participate in the addition of another nucleotide as DNA synthesis proceeds
a. Bacteria have many DNA polymerase
b. DNA polymerase III is the enzyme responsible for the 5’ to 3’ polymerization essential in vivo
c. DNA polymerase II and III are the main DNA builders d. DNA polymerase I is in charge of editing, repair and primer removal
l.) DNA replication is Fast and Accurate!
m.) Seven key issues that must be resolved during DNA replication
a. Unwinding of the helix
b. Reducing increased coiling generated during
c. Synthesis of RNA primer for initiation
d. Discontinuous synthesis of the second strand
e. Removal of the RNA primers
f. Joining of the gap-filling DNA to the adjacent strand g. Proofreading
n.) DNA polymerase uses sliding clamps to move along the template without falling off. Sliding Clamps are loaded onto DNA by Clamp loaders which are ATP-fueled molecular machines that open the sliding clamp, load then onto primed DNA and unload them at the appropriate time
o.) RNA Primer- DNA polymerase III needs a primer to elongate a polynucleotide chain.
a. Primase synthesizes a RNA primer that provides the free 3’- hydroxyl required by DNA polymerase III. b. Priming is a universal phenomenon during initiation of DNA synthesis
p.) Eukaryotic DNA is like that in prokaryotes but it is more complex
a. There is more DNA in Eukaryotes
b. The chromosomes are linear
c. DNA is complexed with proteins
d. Eukaryotic chromosomes contain multiple origins of replication
q.) Telomeres provide structural support at chromosome ends but are hard to replicate. They consist of long stretches of short repeating sequences and preserve the integrity of the chromosome.
r.) Telomerase- maintains structures called telomeres, which are composed of repeated segments of DNA found at the ends of chromosomes.
a. Telomeres protect chromosomes from abnormally s2cking together or breaking down (degrading)
b. Telomeres become shorter as the cell divides which
leads to apoptosis but, Telomerase counteracts the shortening of
telomeres by adding small repeated segments of DNA to the ends of
chromosomes each 2me the cell divides.
c. Telomerase is abnormally active in cancer cells.
d. Telomerase is made of telomeres reverse transcriptase (TERT) which adds the new DNA segment to
chromosome ends and telomerase RNA (TR) which
provides a template for creating the repeated sequence
Eukaryotic Chromosomal organization
1.) The amount of DNA that eukaryotes have varies; the amount of DNA is not necessarily related to the complexity and most eukaryotes are diploid.
2.) Two types of Chromatin
a. Euchromatin uncoiled and active. Usually areas where gene expression is occurring
b. Heterochromatin condensed areas and inactive because they lack genes or they contain genes that are repressed
3.) Histone Proteins abundant, highly conserved among eukaryotes.
a. Provide first level of packaging for chromosome
b. DNA is wound around histone proteins to produce nucleosomes
4.) Nucleosomes are connected by linker DNA H1 histone to produce the “beadsona string” extended form of chromatin
5.) The 30 nm Fiber DNA is further compacted when the nucleosomes associated with one another produce 30 nm chromatin.
6.) Compaction continues by forming looped domains from the 30 nm chromatin a. Loops are arranged so that the DNA condensation can be independently controlled for gene expression
b. MARs are known to be near regions of the DNA that are actively expressed 7.) SWI/SNF Complex ATPdependent chromatin remodeling complex 8.) Histone modifications covalently attached groups usually to histone tails a. Reversible: enzyme that add or remove modification signals
b. Histone Tails
i. Acetylation (any lysine; gene activation) activates transcription; opens up chromatin
ii. Methylation (lys9 gene repression; lys4 – gene activation; lys36
1.) RNA is produced by copying part of the nucleotide sequence of DNA into complementary sequence in RNA
a. During transcription, RNA polymerase binds to DNA and separates the DNA strands. RNA polymerase then uses one strand of DNA as a template from which nucleotides are assembled into a strand of mRNA.
b. No primer is required for initiation, and the enzyme uses ribonucleotides instead of deoxy ribonucleotides
2.) Eukaryotic mRNAs have three main parts
a. 5’ untranslated region (5’UTR)
1. Varies in length
b.) The coding sequence (open reading Frame)
2. Specifies the amino acid sequence of the protein that will be
produced during translation. It varies in length according to the
size of the protein that it encodes.
c.) 3’ untranslated region (3’UTR)
3. Also varies in length and contains info influencing the stability of
3.) Transcription in prokaryotes
a. Transcription begins at the transcription start site, where DNA double helix is unwound to make the template strand accessible to the action of RNA polymerase
b. Transcriptional termination
1. Rhodependent: a protein factor helicase called “rho” binds the
RNA and destabilizes the interaction between the template and
the mRNA, thus releasing the newly synthesized mRNA from the
2. Rhoindependent: RNA transcription stops when the newly
synthesized RNA molecule forms a hairpin loop, followed by a
run of Us. this destabilizes RNAP and makes it detach from the
4.) Eukaryotic Transcription
a. Promoter: a region of DNA that “promotes” the transcription of a particular gene. Promoters are upstream from the genes that they regulate and on the same strand.
5.) Three types of RNA
a. Messenger RNA(mRNA) transfers DNA code to ribosome for translation b. Transfer RNA (tRNA) brings amino acids to ribosomes for protein synthesis c. Ribosomal RNA (rRNA) ribosomes are made of rRNA and protein.
6.) The TATA box is a core promoter element that binds the TATAbinding protein (TBP) and determines the start site of transcription
7.) 5’ cap addition
a. It is a modified guanine structure: called 7methyl G5’ ppp5’ N (m7G) which is added to the front of the 5’ end of all mRNAs
b. It consist of a terminal 7methylguanosine residue which is linked through a 5’5’ triphosphate bond to the first transcribed nucleotide.
c. The cap has three functions
i. Transport export from cytosol from nucleus
ii. Protection prevents 5’3’ RNA digestion
iii. Activity serves as a docking site for ribosomes
8.) Splicing taking out introns and connecting exons.
a. Splicing is done in a series of reactions which are catalyzed by the spliceosome.
i. The spliceosome constantly rearranges during a premRNA splicing cycle
ii. The major components of the spliceosome are specific preformed RNA protein complexes that bind together with other proteins to different
regions of the introns
9.) Alternative splicing different combinations of exons could be spliced together to produce different mRNA isoforms of a gene.