DNA

Molecular Basis of Inheritance

Gene to Protein

Molecular Structure

Key Proteins

vs.

Transcription

RNA Processing

Translation

DNA

Chromatin

Chromosome

when

synthesis of RNA transcript

where

how

Getting started

Helicase : untwist the double helix at replication forks and separating the two strands to become available

nitrogenous base pairs

A-T ; 2 Hydrogen bonds

C-G ; 3 HYdrogen bonds

Single-strand binding proteins: bind to unpaired DNA strands

Double Helix

Double-stranded by Hydrogen bonds b/w bases

Helical

Sugar-phosphate backbones ; Phosphate facing out and nitrogenous bases facing in

Anti-parallel ; parallel with different orientations

Adenine and Guanine are purines with two organic rings

Cytosine with Thymine are pyridines with singe organic ring

Equal amounts of each base complementary to the match

DNA

Genes are parts of chromosomes and chromosomes are made of DNA and protein

DNA was conclude to be the genetic material by testing bacteria infecting viruses, bacteriophages

information from DNA directs biochemical anatomical, physiological, and some behavioral traits

By transformation , external DNA assimilation changed the genes

DNA: polymer of nucleotides ; Adenine, guanine, Cytosine, and Thymine

Chargaff's rules

  1. DNA bases vary from specie
  1. A T bases equal and C G bases are equal

Topoismoerase: the untwisting at the fork causes strain and this enzyme breaks, swivels, and rejoins DNA strands

Replication of chromosomal DNA begins at origins of replication (short stretches of DNA)
Protein separates the strands to replicate.

At end of replication bubble, there’s a replication fork, y shaped region parental strands are unwound.

Synthesizing new DNA strand

Primase starts a complementary RNA. Enzyme DNA Polymerases catalyze synthesis by adding nucleotides.

Each nucleotide is made of a sugar attached to a base and three phosphate groups. (d(deoxyribise)ATP) --> dATP

The initial nucleotide made in replication is a short strand of RNA. This RNA is a primer synthesized by the enzyme primase.

Anti-parallel elongation

Leading strand: the new DNA strand along the template strand following the 5’  3’ direction.

Lagging strand: goes opposite of leading in segments and make the other template strand.
Strands are called Okazaki fragments

DNA polymerase can only add nucleotides to the 3’ strand never 5’.

DNA ligase joins the sugar-phosphate backbone of all Okazaki fragments into one DNA strand

DNA pol I: remove RNA nucleotides of primer from 5' end and replaces them with DNA nucleotides adde to 3' end of adjacent fragment

DNA pol II: synthesized new DNA strand by adding nucleotides to RNA primer or pre-existing DNA strand

Proofreading and repairing DNA

DNA polymerase removes wrong nucleotide and proofreads while replication.

Nuclease cuts a segment of the damaged strand and polymerase and DNA ligase fills the spot.

Replicating the ends of DNA molecules

telomerase catalyzes lengthening of telomeres, restoring original length

Telomeres are nucleotide sequences of multiple repetitions .

Protective functions; 1. prevent staggered ends from activating the systems for monitoring DNA damage; 2. buffer zone that provides protection from gene shortening

Bolded words are key proteins

complex of DNA and protein that makes eukaryotic chromosomes, that fits into the nucleus

Deoxyribonucleic acid

nucleic acid molecule,; double-helix with strands of nucleotide monomers, A T C and G, bases. Able to be replicated to determine inheritance .

When not dividing chromatin is dispersed as very long thin fibers

cellular structure of one DNA molecule with protein molecules. a cell can have multiple chromosomes line up in the nucleus.

Tightly packed DNA

Chromosome is made of chromatin that is made of DNA

found only during cell division

DNA not being used for macromolecule synthesis

Unwound DNA

Found throughout interphase

DNA IS being used for macromolecule synthesis

in nucleus entwined with proteins

In coiled form it is chromatin

where

how

when

where

when

synthesis of RNA using info in the DNA. Information is transcribed "rewritten" from DNA to RNA; makes mRNA that carries the info to protein-synthesizing machinery

synthesis of a polypeptide using info in the mRNA;

In ribosomes ; complexes that facilitate linking of amino acids into polypeptide chains.

in the nucleus; mRNA transported to cytoplasm

First stage in the central dogma

  1. elongation: polymerase moved downstream unwinding DNA and elongating RNA transcript; DNA strands reform double helix
  1. mRNA copied from DNA by unzipping the strand using the RNA polymerase and entering the complementary RNA strand.
  1. as one side is transcribed, the nucleotides will be paired to make pre-mRNA
  1. sequences called introns are removed and eons are spliced together
  1. mRNA leaves nucleus to translate in ribosomes
  1. termination: RNA transcript released and polymerase detaches
  1. initiation: RNA polymerase binds to promoter and unwinds DNA; polymerase starts RNA synthesis at start point on template strand

in RNA processing, both ends of primary transcript are altered. enzymes in nucleus modify pre mRNA before dispatching in cytoplasm

within cell nucleus

after transcription and before translation

  1. proteins synthesized from mRNA by ribosomes that read from a codon (triplet code)
  1. transfer RNAs guided by ribosome transfer amino acids from cytoplasms to amino acids in poly[peptide chain
  1. ribosome adds amino acids from tRNA to chain

tRNA has 2 recognitions

  1. once it binds to codon, carries amino acid to ribosome
    the matching is done by the enzyme aminoacyl-tRNA synthetases
  1. pairing of tRNA anticodon with mRNA codon some can bind to more than one codon by versatile called a wobble due to the bases uracil binding to A or G

Ribosomes

large and small subunit made of protein and ribosomal RNAs
made in nucleus
rRNA transcribed and exported to cytoplasm

3 binding sites

  1. P site; holds tRNA carrying growing chain
  1. A site; holds tRNA carrying next amino acid to be added to chain
  1. E site; tRNA and mRNA close to be added to carboxyl end

ribosomal DNA is responsible for structure and function of ribosome

how

after RNA processing

3 stages

  1. elongation; a. codon recognition; codon pairs w/ anticodon; b. peptide bond formation; c. translocation
  1. termination: ribosome reaches stop codon; hydrolyze polypeptide and tRNA in P site; 2 subunits dissacociate
  1. initiation: starting codon starts translation; ribosomal units bind to mRNA and tRNA ; large subunit attaches to make translation initiation complex; initiator tRNA sits in P site and A site is vacant

completing and targeting functional protein

protein folding and modifications

targeting polypeptides to specific locations

split genes and RNA splicing

Ribozymes

alteration fo mRNA ends

5'. end modified by 5' cap

at 3' end, enzyme adds A nucleotides making a poly-A tail

help protect degradation by hydrolytic enzymes

help ribosomes attach to 5' end in cytoplasm

facilitate export of mRNA

noncoding regions are introns and coding regions are eons which are expressed

pre-mRNA splicing done spliceosome

RNA splicing: RNA removed and remaining reconnected

spliceosome catalyzes splicing reaction

ribozymes, RNA molecules that works as enzymes

intron RNA functions as enzyme and does its own excision

3 properties enable top be enzyme

  1. some bases have functional groups that work in catalysis
  1. ability to hydrogen bond adds specifitivity to catalytic activity
  1. RNA is single strand and pair