Lecture 1: Genetic Material Flashcards
What is the DNA molecule made out of?
A polymer of nitrogenous bases linked together by a backbone consisting of an alternating series of a pentose sugar and phosphate residues.
DNA stands for what?
Deoxyribonucleic acid.
Purines
Adenine (A) and Guanine (G)
Pyrimidines
Cytosine (C) and Thymine (T)
Nitrogenous Bases
Adenine (A) and Guanine (G), Cytosine (C) and Thymine (T) in DNA.
Uracil (U) replaces thymine in RNA.
Nucleotide
Nitrogenous Base
Pentose
Phosphate Group
(A phosphate ester of a nucleoside.)
Nucleoside
Nitrogenous Base
Pentose
How are DNA’s deoxyribonucleotides connected?
3’-5’ phosphodiester linkages.
What is DNA’s backbone made out of?
Alternating pentose sugars and phosphate groups.
Oligonucleotide
A small group of nucleotides (5-50 nts) that are linked via phosphodiester bonds.
In some contexts, they are referred to as primers.
What are the two terminal ends of the polynucleotide chain?
A 5’ phosphate group and a 3’ hydroxyl group.
In general, how is DNA arranged?
Two polynucleotide chains are wound about each other in an antiparallel manner (5’ end paired with 3’ end).
The sugar-phosphate backbones are on the outside of the double helix, and the hydrophobic bases are oriented toward the interior.
How are the two antiparallel strands (primariliy) held together?
The hydrogen bonds of the bases in the interior.
Which bases pair to which bases?
Purines bond to pyrimidines.
Adenine (A) to Thymine (T)
Guanine (G) to Cytosine (C)
In RNA, Adenine (A) to Uracil (U).
Relative to each other, which are larger, purines or pyrimidines?
Purines (A and G) are larger.
How many base pairs are there per turn of the double helix?
Ten base pairs per turn.
What is the charge of DNA at physiological pH? Why?
Highly negative (-) at physiological pH due to many negatively charged phosphate groups.
Therefore, these hydrophilic phosphate groups are oriented toward the exterior.
Supercoiled DNA
When DNA becomes twisted around it’s own axis.
It is a feature of the organization of DNA into higher-order structures such as chromosomes.
Positively Supercoiled DNA
If the new twists in the DNA are introduced in the same direction as the winding of the double helix.
Negatively Supercoiled DNA
If the new twists in the DNA are introduced in the opposite direction as the winding double helix.
A molecule that lacks supercoiling is said to be?
Relaxed.
Why is supercoiled DNA favorable if it is higher-energy?
The excess energy is then available to do work, such as separating the strands of DNA.
What happens when the phosphodiester backbone of a covalently closed DNA molecule is broken?
The DNA’s ends are free to rotate, and it’s conformation is changed to that of the relaxed state.
Enzymes that catalyze changes in the supercoiling of DNA are called?
Topoisomerases (Topo).
Topo I
Topoisomerase I.
Cleaves only one strand of DNA to catalyze changes in DNA supercoiling.
Topo II
Cleaves the two strands of DNA to catalyze changes in DNA supercoiling.
Three Step Reaction of Topoisomerases:
- Cleavage of one (Topo I) or both (Topo II) strands of DNA.
- Passage of DNA around the break(s).
- Resealing of the DNA break(s).
Camptothecin
An anti-tumor drug that inactivates Topo I.
m-AMSA
An anti-tumor drug that inhibits Topo II.
Z-DNA
“Left-handed” double helix often formed in stretches of alternating purines and pyrimidines.
Adopted in response to negative supercoiling, as it reduces the number of negative supercoils.
DNA Bending
Can functions to bring distant sites on DNA together.
Some sequences are inherently bent, such as adenine repeats. Also occurs around histones.
Melting
Disrupting the duplex structure of DNA.
The melting temperature (Tm) varies with ionic conditions and sequence composition.
Which base pair has stronger bonding and resistance to melting?
G-C has stronger bonding than A-T due to having three hydrogen bonds, as opposed to two.
What is another way to denature DNA?
Aklaline environment, such as NaOH.
The reassociation of DNA
Reannealing or hybridization.
Why is reannealing an important tool for research?
It is highly specific, only bonding to pairs that are complementary. Tagging a specific sequence can identify where it’s complimentary pair is located.
How many base pairs are there in the human genome?
Approximately 3 billion.
What is the average size of a gene product (protein)?
About 400 amino acids long, which corresponds to about 1000 base pairs of DNA.
Percent of the human genome that codes for proteins?
About 2%.
Gene Cluster
A region (domain) of DNA where associated genes (gene families) are located.
Example: B-globin
Pseudogene
Closely related to functional genes, but due to various reasons (i.e. mutations, deletions, insertions) they no longer code for normal gene products.
Arose by the same duplication processes that generate gene families.
Additional genomic element.
Processed Pseudogene
Lacks introns.
Formed when DNA copies (reverse transcripts) of RNA molecules are inserted back into an organism’s genome.
Additional genomic element.
Provirus
DNA copies of retroviruses inserted into chromosomes.
Additional genomic element.
Repetitive DNA Sequence
Nucleotide sequences that occur repeatedly.
Includes:
- Transposable Elements
- Simple Sequence Repeats
- Satellite DNA
Additional Genomic Element
What has been suggested to be “junk DNA”, as only 1-2% of our genes encode proteins.
Transposable Element
DNA sequences that are capable of inserting copies of themselves into new genomic locations.
There are two classes:
1. Use reverse transcription (SINES and LINEs)
- Encode own transposase
A repetitive DNA sequence.
SINE
Short interspersed repeat elements. About 280 nucleotides.
Utilize reverse transcriptase from a source such as a LINE.
A repetitive DNA sequence.
LINE
Long interspersed repetitive sequences. About 500 nucleotides.
Utilizes a self-encoded reverse transcriptase.
A repetitive DNA sequence.
Simple Sequence Repeats (SSRs)
Approximately one SSR every 2 kb.
Two types:
- Microsatellites
- Minisatellites
Microsatellite
An SSR that is approximately 2-5 bp.
Tandem repeat sequences are highly polymorphic.
Minisatellite
An SSR that is about 14-50 bp.
Polymorphism
A common variation in the DNA sequence that can serve as a genetic marker.
Mutation
A very rare variation in the DNA sequence that can serve as a genetic marker.
Telomeres
Cap the ends of chromosomes to prevent degradation.
Hexameric element TTAGG tandemly arrayed with 1,000 - 1,700 copies.
Are polymerized by telomerase.
Mitotic Clock
Each cell division, telomeres shorten by approximately 50-200 nts.
A sufficiently short telomere may be the signal for senescence (apoptosis) in normal cells.
In what kind of cell could you find an over-expression of the gene encoding for telomerase?
A cancer cell.
It would bypass the mitotic clock.
Telomerase
A reverse transcriptase that maintains the telomeres by adding to it.
DNA coils around what group of proteins to sufficiently condense into chromatin?
Histones.
Nucleosome
A core group (octomer) of histones.
Specifically histones H2A, H2B, H3, and H4.
Chromatin Fiber
The next level of organization up from nucleosomes.
