Unit 2: 8 Flashcards
What is the sense strand?
The sense strand carries the coded genetic information
Discuss the central dogma of molecular biology
DNA->RNA-> Protein
genetic info is stored in the DNA - most common form is double stranded DNA composed of two antiparellel strands linked through complementary base pairing - Chargaff’s rule (A with T and C with G)
What is the anti-sense strand?
The anti sense strand consists of a complementary sequence of bases oriented in the opposite direction
From where is genetic information transcribed?
the anti-sense strand serves as the template for synthesis of the messenger RNA (mRNA) with the same base sequence 5’-3’ as the sense strand of the double helical DNA except that uracil replaces thymine (T)
in what direction if messenger RNA translated into a sequence of amino acids ?
From N-terminus to C- terminus -read from 5’-3’
define gene
a unique sequence of DNA that provides the complete instructions to make a functional product called a protein
Nucleotide
sugar, phosphate, base
Nucleoside
just sugar and base - side = simple so missing phosphate just sugar and bas
what kind of bond links nucleotides
phosphodiester
what is the directionality of the polymeric chain?
5’-3’
pyrimidine bases
C, T and U
contain a flat plannar 6 member ring with two nitrogens- the bond between the pyrimidines and the sugar-phosphate is between position 1 on the pentose sugar to position 1 (-N) in the pyrimidine
purines
A and G - a flat plannar 6 member ring fused to a 5 member ring with two nitrogens each -the bond between the purines and the sugar-phosphate is from position 1 on the pentose sugar to position 9 (-N) of the purine
Modified bases in DNA
5 methyl cytosine -influences packaging of chromosomal DNA important for X chromosome inactivation.
-5 hyroxymethylcytosine ; may regulate gene expression by inducing DNA demethylation, found at high level in the CNS
Modified bases in RNA
- hypoxanthine: found in the anticodon of tRNA, also used in purine biosynthesis
- pseudouracil: found in tRNAs
- N6-methyladenosine: found in mRNAs and may affect gene expression and splicing
adenine phosphoribosyltransferase
a salvage enzyme that recovers purine bases
catalyzes the formation of adenylate
adenine + PRPP -> adenylate + PPi (pyrophosphate)
Hypoxanthine-guanine phosphoribosyltransferase (HGPRT)
a salvage enzyme that recovers purines -catalyzes the formation of guanylate as well as inosinate (IMP) a precursor of guanylate and adenylate
guanine + PPRP -> adenylate + PPi
Hypoxanthine + PPRP -> inosinate + PPi
Gout
- impaired excretion or overproduction of uric acid
- uric acid crystals precipitate into joints (Gouty arthritis), kidneys, ureters (stones)
- lead impairs uric acid excretion -lead poisoning from pewter drinking goblets
- Xanthine oxidase inhibitors inhibit the production of uric acid, and treat gout
- Allopurinol treatment: hypoxanthine analog that binds to Xanthine Oxidase to decrease uric acid production
Lesch- Nyhan syndrome
- rare inherited disorder caused by deficiency of the enzyme HGPRT
- causes increased level of hypoxanthine and guanine (lead to increased degradation to uric acid)
- also causes accumulation of PRPP and stimulates production of purine nucleotides (and thereby increases their degradation)
- causes gout like symptoms, but also neurological symptoms: spasticity, aggressiveness and self-mutalation
- first neuropsychiatric abnormality that was attributed to a single enzyme
Cellular functions of nucleotides
- building blocks for nucleic acid polymers, DNA and RNA
- energy carriers ATP and GTP
- important components of coenzymes; FAD, NAD(P)+ and co-enzyme A
- precursors for second messengers: cAMP, cGMP
- activated intermediates in many biosynthetic pathways: eg S-adenosylmethionine (SAM) as methyl donor
Structural features of the B DNA double helix
- Right handed helx
- The plane of the base is perpendicular to the S-P backbone
- One turn of the helix equals 10.5 base pairs (34 Angstroms or 3.4 nm)
- The twisting of the helix forms major and minor grooves
What factors influence the helix conformation of DNA?
- certain sequences of bases
- salt conditions
- base modifications
- conditions of relative humidity
A- DNA
a. Right handed
b. 1 bp repeating unit
c. 11 bp/turn
d. 28 Angstroms
-most likely found in dehydrated living cells -NDA-RNA hybrid or dsRNA
z- DNA
a. left- handed strand
b. 2 bp repeating unit
c. 12 bp/turn
d. 45 Angstroms
-not favorable however alternating purine-pyrimidine sequence (esp poly(dGC)2, negative supercoiling or high salt and some cations can induce z- DNA conformation
Hoogsteen base pairs
1% of the time cells are in this transient state where the purine base flip from their normal anti conformation to a syn conformation and form a different set of hydrogen bonds with their pyrimidine partners
Tm of DNA
the temperature at which one half of the DNA molecule has melted
Name the factors that influence the Tm of a given DNA molecule
- G and C content of DNA -because there are three hydrogen bonds stronger and harder to break
- Ionic strength- Tm is proportional to the salt concentration, high salt concentration (excess NaCl in solution stabilizes double stranded DNA by binding to negatively charged phosphates in backbone and decreasing repulsion between chains
- pH: Tm is inversely proportional to the pH. High concentrations of OH denature DNA by forming hydrogen bonds with bases thereby stabilizing single stranded DNA
- Other Reagents: reagents that can form hydrogen bonds with bases (and thus stabilize the single-stranded DNA) decrease Tm
Hybridization of DNA
when single stranded DNA bound to a surface, such as nylon or a glass microchip, can still renature with a complementary DNA or RNA sequence
High stringency
at or close to the Tm- only perfect matches can form
Low stringency
below the Tm -under conditions that stabilize the double helix (high salt or low temp) imperfect bases can form
