Reading...
Play button
Play button
Use LEFT and RIGHT arrow keys to navigate between flashcards;
Use UP and DOWN arrow keys to flip the card;
H to show hint;
A reads text to speech;
54 Cards in this Set
- Front
- Back
|
Friedrick Miesher
|
1868 - first to discover nucleic acid (which was a phosphorus-rich acid) in nucleus
|
|
|
Watson & Crick
|
First to elucidate DNA structure (1953)
|
|
|
DNA backbone
|
Sugar (5'carbon pentose) + phosphate
- nitrogenous bases attach here |
|
|
Purine
|
2 rings
Adenine Guanine |
|
|
Pyrimidine
|
Thymine
Cytosine |
|
|
Components of Nucleotide
|
c. A phosphate esterified to the hydroxyl on carbon 5 of the sugar. Nucleotides also occur in activated diphosphate and triphosphate forms.
|
|
|
Nucleoside
|
base and sugar linked by N-glycosidic bond
|
|
|
Primary structure of DNA
|
1. Polymer of deoxynucleotides connected via 3' to 5' phosphodiester linkage - - - understand pic!!!
2. Had pentose-phosphate backbone |
|
|
Primers/Oligonucleotides
|
Small segments of ssDNA
|
|
|
DNA sequences are written and
synthesized.... |
5’ → 3’
|
|
|
Hydrogen Bond
|
A given donor can be oxygen or nitrogen
is the attractive interaction of a hydrogen atom with an electronegative atom |
|
|
Rosalind Franklin
|
Generated x-rays images of dsDNA that suggested a helical structure - - this allowed Crick to notice "monoclinic C2 symmetry"; the implication that 2 chains ran in opposite directions
|
|
|
Watson & Crick double helix
|
1. strands are coiled antiparallel around axis
2. Sugar and phosphate groups are on outside of molecule 3. Purine and Pyrimidine - inside of helix A=T G=-C (complementary base pairing) 4. H-bond holds chains together |
|
|
Facts about Watson & Crick double helix (dh)
|
1. Diameter of dh = 20A
2. Adjacent bases are separated by 3.4 Å and related by a rotation of 36 degrees. 3. 10 residues/turn. 4. Information is stored in the sequence of bases! (~3 billion base pairs in humans) 5. The structure suggested how both DNA replication and repair occur. |
|
|
Major and Minor Groove
|
1. Each groove is lined by potential hydrogen bond donor and acceptor atoms.
2. The larger size of the major groove makes it more accessible for interactions with proteins that recognize specific DNA sequences. 3. They arise because the glycosidic bonds of a base pair are not diametrically opposite each other. |
|
|
Major Groove
|
Makes it more accessible for interactions w/ proteins that recognize specific DNA sequences
- has more access to H-bond than minor groove - look at picture! |
|
|
Kinase
|
Adds phosphate from ATP (opo3)
- such as adding it to the ends of DNA |
|
|
Phosphatase
|
Removes phosphate
|
|
|
Circular DNA
|
Plasmid, bacterial chromosome
|
|
|
Supercoiling
|
- ?????
- Supercoiled molecules have more energy than relaxed DNA. - excess energy can do work like separating DNA |
|
|
Relaxed DNA
|
DNA lacks supercoiling
|
|
|
Positive Supercoiling
|
results from twisting two strands of DNA in the same direction as the strands in a right handed helix.
|
|
|
Negative Supercoiling
|
results from twisting two strands of DNA in the opposite direction as the strands in a right handed helix.
|
|
|
Topo I
|
cleaves just one strand.
|
|
|
Topo II
|
cleaves both strands
|
|
|
Topoisomerases
|
Enzymes that catalyze changes in DNA Supercoiling
3 steps 1. Cleavage of one or both strands of DNA. (topo I/II) 2. Passage of strand(s) of DNA through the break.(DNA uncoils) 3. Resealing of the DNA break. |
|
|
Why is coiling important
|
1. Important for regulating DNA activities (replication, recombination, transcription)
2. helps higher order of structure = chromosome |
|
|
HUMAN TOPOISOMERASES AND CLINICAL ONCOLOGY
Anticancer drug and its target Why is this important |
AD - Camptothecin -> target - topoI
AD - M-AMSA ->T- TopoII If inhibit topo then can inhibit cell growth |
|
|
Alternative Secondary Structures
|
They are structures that arise due to nucleotide arrangement & DNA supercoiling with proteins
Z DNA B DNA |
|
|
B DNA
|
right handed
|
|
|
Z DNA
|
left handed
reduces # of supercoiling |
|
|
DNA Bending
|
1. Intrinsically bent....certain sequences are inherently bent. Adenine repeats are prone to bending
2. Protein-Induced Bending. Ex: bending of DNA around histones |
|
|
Functions of DNA bending
|
Bring distant sites of DNA closer together
|
|
|
Pseudo genes
|
- for various reasons (deletions, insertions, pt mutation) they dont code for normal gene products
a copy of gene that looks like it will be used & isnt - maybe a promoter, but is messed up for doesnt have good genes |
|
|
Processed pseudogenes
|
formed when DNA copies (reverse transcriptase) of RNA molecules are inserted back into genome
|
|
|
Junk DNA
|
1. Pseudo-genes and processed pseudo-genes.
2. Proviruses 3. Repetitive DNA sequences a. Transposable elements (Sines and Lines) b. Minisatellites and microsatellites c. Satellite sequences |
|
|
Provirus
|
- the human genome contains ~1000 provirus
Ancient virus integrated and just sitting in our genome provirus - DNA copies of retrovirus inserted into chromosome |
|
|
Repetitive DNA
|
- a huge percentage of our DNA
- repetitive sequences vary from complexity from complete genes to simple repeats of 1 or few bp |
|
|
SINE
|
-Short, interspersed repeat elements (SINEs).
For example, Alu repeats. A. ~ 280 bp long. B. One Alu repeat every ~5000 bp C. Constitute ~ 10% of the human genome. - use reverse transcriptase from LINE elements |
|
|
Products of Reverse Transcription
|
1. SINE
2. LINE 3. Provirus 4. Processed Pseudogenes |
|
|
LINES
|
Long, interspersed repeat elements (LINEs).
For example, L1 family. A. > 500 bp long. B. Constitute ~ 20% of the human genome. C. Complete LINE elements are 6-8 kb long, but the majority are truncated. D. Complete LINEs encode a reverse transcriptase. - encode reverse transcriptase |
|
|
Polymorphism
|
- presence in a population of 2 or more allelic variants
- |
|
|
SSRs
|
Simple Sequence Repeats
- comprise 3% of human genome |
|
|
What are 2 kinds of SSRs
|
Microsatellites
Minisatellites |
|
|
Microsatellites
|
A. 2-5 bp repeats
B. Mean array size is ~100 C. Present at many locations (e.g. ~100,000 copies of the d(CA) repeat. D. Highly polymorphic. E. Microsatellites are present in everybody at the same specific chromosomal locations! |
|
|
MInisatellites
|
A. Repeat lengths of 14 to 500 bp
B. Mean array size is ~10 to 100 C. Also highly polymorphic |
|
|
SNP
|
Single Nucleotide Polymorphism
A. SNPs serve has biological markers. B. SNPs may fall within coding sequences of genes (alleles), non-coding regions or in the intergenic regions between genes. C. Certain diseases have characteristic SNP profiles. |
|
|
Satellite sequences
|
- highly repititive, short DNA sequence b/n 5-100 bp
- typically organized as big clusters in non-transcribed regions of chromosomes(ie centromeres), y chromosome or telomeres |
|
|
Telomeres
|
- a satellite sequence
- Protects against DNA repair mechanisms that recognize broken ends and then joins them. - are found at ends of every human chromosome - involved with chromosome replication & protection - protects against DNA repair mechanisms that recognize broken ends and joins them |
|
|
Telomere Repeats
|
(TTAGGG)n
- in humans ~ 10kb ttaggg |
|
|
What happens when telomeres run out?
|
Chromosomes get messed up, become unstable and can be degraded
- occurs with age |
|
|
Telomerase
|
- synthesizes telomeres
- restores length in germ-line of each generation - is a reverse transcriptase - |
|
|
When is telomerase repressed//activated?
|
In general, telomerase is repressed in normal human somatic tissues.
However, telomerase is reactivated in “tumor cells”! |
|
|
How is DNA packaged?
|
1. DNA condensation is done by protein-nucleic acid interaction and supercoiling of DNA----DNA is packed around histone octomer to form nucleosome
2. Histone(DNA Coils)->nucleosome(histones together)->chromatin->chromosome |
