Molecular Cell Biology: Understanding Nucleotides, DNA Structure, and Protein Synthesis, Study notes of Introduction to Sociology

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Textbook :Molecular Cell Biology,

Lodish et al 5th edition

http://www.wh freeman.com/lodish/index.htm

Lijin Feng, [email protected] Ing, [email protected] Fallah Tafti, [email protected] Huang, [email protected] Lee, [email protected] Eli Lutske, [email protected] Ta, [email protected] Tan, [email protected]

DNA

RNA

Protei

transcription

translation

replication

retrovirus

(HIV, Polio)

priones

The central dogmabut---additional significant bits of truthDNA ---replicateRNA---can be converted to DNA (retrovius)

Genome of these virus is RNA prions--- Bivone Sponge Encephalopathy (BSE)

Creutsfeldt-Jacob disease (CJD)

base pentose

Nucleotide Structure^ MCB 2.14a

MCB 2.14b

RNA

DNA

the pentoses

MCB 2.

DNA

RNA

the Bases

MCB 2.14a

nucleoside

suger + base

nucleotide

suger + base + phosphate

suger base

MCB 2.14a

nucleoside

suger + base

nucleotide

suger + base + phosphate

suger base

mono (dAMP) di (dADP) tri (dATP)

ATP

(adenosine 5’-triphosphate) Capturing andtransferring free energy

GTP

(guanosine 5’-triphosphate) protein synthesissignal transduction

MCB 4.

DNA strucutre

X-ray crystal strucute data

MCB 4. 3

DNA structure

James D. Watson and Francis H. Click

proposed DNA existedas a double helical structurebased on the analysis ofx-ray diffraction patternscoupled with careful model building“The Race for the Double Helix”

Chagraff’s Rules

1. Base composition varies between species2. DNA from different tissues of same species has the same composition 3. Base composition does not change as a function of age, nutrition, environment 4. Regardless of species, base pairs are the same A base pairs with TG base pairs with Cpurines

pyrimidines

MCB 4. 4

Protein binding affects DNA structure

MCB 4. 5

DNA can undergo reversible strand separation The Van der Waals interactions and hydrogen bonds arePhysically destroyed when the native state is heated and convertedto the single stranded “denatured” stateDNA can also be denatured by low ionic concentration and addingUrea or formamide, alkaline solutionsImportant concept for recombinant DNA ( PCR)

Melting of double stranded DNACan be monitored by the ultravioletLight at 260 nm.

Tm is a function of the G-C content of the DNA:(More the G-C content, Higher the Tm)

Adenosince 5’-monophosphate (AMP)

present in RNA

phosphate moiety-----up to three

linked to the 5’ -OH

of a pentose suger

pentose suger----the 1’ carbon is linked to

an organic baseThe carbon atoms are numberedwith primes by convention.

base----furanose ring

Bases are stacked in a planar arrangement.The bases project inward, but are accessiblethrough the major and minor grooves.The hydrogen bonds between the bases arein the center of the structureThe complimentarity of the G-C and A-T pairsis one of the fundamental elementsof the DNA structureright handed

(^ two possible helical forms)

Double helix is flexible along its long axis of the DNA helix

(no hydrogen bonds parallel to the long axis of the DNA helix) This allows DNA to bind parallel to the axis of the DNA helixby bending of DNA and it is important for the dense packing ofDNA in chromatin, the DNA-protein complexNuclear DNA in eukaryotic cells are found in “chromatin structure”

The most common form is B DNA

The B from of DNA allows 0.34nm for each base1 twist equals 10 to 10.5 bases pair A form DNA: at very low humidity , B DNA changes to A DNA

pairing is more tilted11 base pairs per helical turn (more base pairs per turn than B from)due to the less hydrationmore characteristic in RNA-RNA, RNA-DNA hybrids

Z DNA: Short DNA molecules composed of alternating purine-pyrimidine nucleotides

adopt a left-handed (instead of a normal right handed) helix Triple-Helical DNA: can form in a test tube

maybe occur in cells but its function is unknownalso exist during recombination and DNA repair