DNA

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DNA

• Molecular Biology of the Gene

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Genes

• biological blueprints
• give us attributes traits
• every nucleus, in every cell carries genetic
  blueprint
• every cell has all information needed to make a
  complete you
• genes are located on chromosomes
• humans have 46
• each containing thousands of genes

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Genes

• share genes with all living organisms
• 98 match chimpanzees
• 99.9 match all other humans
• differences exist at particular sites
• causes each of us to be unique
• differences maybe as small as one base
  substitution in one gene

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Genes DNA

• genes are made of DNA
• deoxyribonucleic acid
• macromolecule
• made of 4 different nucleotides
• paired in a precise manner
• order of nucleotides is genetic code
• each 3 combinations of nucleotides one amino
  acid
• DNA gives instructions to make proteins
• smallest chromosome-Y has 50 million nucleotides
• largest has 250 million

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DNA

• nucleic acid
• macromolecule composed of smaller subunits
  nucleotides
• contains
• carbon sugar-deoxyribose
• nitrogenous base
• 1-3 PO4 groups
• contains 4 different nucleotides
• each with different nitrogenous base
• bases are found in 2 major groups
• Purines
• double ring structures
• adenine (A)
• guanine (G)
• Pyrimidines
• Single ring structures
• thymine (T)
• cytosine (C)

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DNA NUCLEOTIDES
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Sugar-Phosphate Backbone

• bases are linked via dehydration synthesis into
  phosphodiester bonds
• phosphate of one nucleotide covalently bonds to
  sugar of next
• forms sugar-PO4 backbone
• nitrogenous bases are arranged as appendages
  along backbone

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Sugar-Phosphate Backbone
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DNA

• structure determined by Watson and Crick-1953
• discovered DNA is double stranded helix
• composed of two strands
• wrapped around each other in helical formation
• core -bases of one DNA strand bonded to bases in
  other strand
• if think of DNA molecule as ladder
• sugar-phosphate backbone would be sides of
  ladder
• paired bases would be rungs

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DNA

• base pairing is specific
• A-T
• G-C
• amount of A amount of T
• one strand is complementary to the other

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Replication

• cells divide reproduce daily
• giving rise to 2 daughter cells
• with same genetic makeup
• Before cell can divide, DNA must duplicate
• replication
• uses template mechanism

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Replication

• to replicate
• strands of DNA must separate
• double helix unwound by helicase
• breaks H bonds between base pairs

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REPLICATION

• unwinding takes place in a replication bubble
• new strand of DNA is formed in both directions on
  both strands of DNA in bubble

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Replication

• proceeds in both directions
• DNA strand has 3 end 5 end
• at one end carbon 3 of sugar is attached to OH
  group
• at other end carbon 5 is attached to a phosphate
  group
• DNA polymerase
• enzyme that binds single nucleotides into new
  strand of DNA
• works only in 3' to 5' direction
• consequently DNA synthesis only occurs in 5' to
  3' direction
• means one daughter strand can be made as
  continuous strand
• leading strand
• other is made in short pieces
• linked together with DNA ligase
• lagging strand

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REPLICATION

• each strand of DNA is used as template to make
  new, complementary strand
• semi-conservative replication

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REPLICATION

• at completion of process 2 DNA molecules have
  been formed each identical to original
• one strand of each of new DNA molecules is
  strand of original DNA
• other strand is complementary strand made during
  replication
• semi conservative replication

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PHENOTYPIC EXPRESSION

• small sections of chromosomes are genes
• genetic makeup is genotype
• expression of genes into specific traits is
  phenotype
• result of proteins
• one gene?one protein
• protein production is directed by DNA

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Expression of Genotype

• protein production is dictated by DNA
• information about specific proteins is
  transferred to another nucleic acid-RNA
• RNA is translated into a protein

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Genetic Code

• DNA?mRNA?proteins
• Proteins are long strands of amino acids held by
  peptide bonds
• each has unique amino acid sequence
• language of DNA is chemical
• must be translated into different chemical
  language-that of polypeptides
• DNA language is written in linear sequence of
  nucleotide bases that comprise it-AACCDDGGGACAC
• specific sequence of bases makes up a gene

glu lys ser ala met phe leu glu
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Expression of Genotype

• transfer of information from DNA to RNA and then
  to proteins takes place in two processes
• Transcription
• Translation

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Transcription

• DNA directs ribonucleic acid synthesis
• transfers genetic information from DNA to RNA

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RNA

• made of monomers or nucleotides
• ribonucleotides
• same basic components as DNA
• single strand
• 5 C sugar-ribose
• phosphate groups
• nitrogenous bases
• same as in DNA with one exception
• RNA has Uracil (U) instead of T
• base pairing rules are same
• Uracil is substituted for thymine
• U-A not T-A

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Types of RNA

• Messenger
• mRNA
• Ribosomal
• rRNA
• Transfer
• tRNA
• all involved in translation

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Transcription

• DNA?mRNA
• nucleic acid language of DNA is rewritten as
  sequence of RNA bases

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Transcription

• process of transferring genetic information from
  DNA to RNA
• similar to DNA replication
• DNA is used as template to make RNA

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Transcription

• stands of DNA must separate
• only one serves as template
• nucleotides take their places one at a time along
  template using same base pairing rules as
  replication except A-U
• 3 stages
• Initiation
• Elongation
• Termination

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Initiation

• RNA polymerase attaches to promoter
• specific nucleotide sequence
• RNA synthesis begins
• RNA polymerase decides which strand to use as
  template
• strand used- antisense strand
• other stand-sense strand

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Elongation

• RNA strand grows longer
• RNA strand peels away from template allowing
  separated DNA strands to come back together
• bases are added at 50/second
• RNA strand formed is directly complementary to
  its DNA template
• each time C is found in antisense strand of DNA
  template a G is paired with it

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Termination

• RNA polymerase reaches special sequence of bases
  in template-terminator
• ends transcription
• RNA polymerase detaches

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Post-transcriptional Modifications

• in prokaryotic cells RNA can function immediately
• in eukaryotes RNA is processed before moving to
  cytoplasm for translation
• post-transcriptional modifications
• capping-tailing
• splicing
• ligation

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Capping-Tailing

• nucleotides are added to either end of RNA
• a G nucleotide might be added to one end
• A nucleotides might be added to other
• additions make RNA more stable
• ends protect molecule from attack by enzymes
• helps ribosomes recognize mRNA

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Splicing Ligation

• precursor mRNA contains exons introns
• exons
• segments containing information for formation of
  proteins
• Introns
• internal non-coding regions
• before mRNA can leave nucleus-introns must be
  removed from strand
• Introns are spliced out
• exons are ligated (or attached) together
• RNA can now move to cytoplasm through nuclear
  membrane pores

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Translation

• conversion of nucleic acid language into protein
  language
• proteins are macromolecules-polymers of amino
  acids
• 20 are common to all organisms
• sequence of nucleotides in mRNA dictates
  sequence of amino acids in polypeptide
• sequence of bases in a molecule of DNA is
  genetic code

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GENETIC CODE

• DNA RNA are made of 4 different nucleotides
• there are 20 amino acids
• if each nucleotide coded for one amino acid?could
  only be 4 amino acids
• if each 2 coded for one?could be 16 amino acids
• smallest number of bases that can code for 20
  amino acids is 3
• particular triplet of nucleotides in mRNA is a
  codon
• specific for a particular amino acid
• 64 possible triplet codes
• code is redundant
• more than one codon for each amino acid

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Codons

• 61 code for amino acids
• some have regulatory purposes
• start stop translation
• AUG-start codon
• codes for MET-methionine
• UAA, UAG, UGA- stop codons
• tell ribosomes to end polypeptide synthesis

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Genetic Code

• highly conserved
• same in all organisms
• genes can be transcribed translated even if
  transferred from one species into another
• opened door for genetic recombinant technology
  genetic engineering

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Translation

• amino acids are not able to recognize codons of
  mRNA
• requires an interpreter
• intermediate that can understand language of one
  form translate that message into another
• tRNA (transfer RNA) is interpreter
• pick s appropriate amino acid recognizes
  appropriate codon in mRNA
• converts 3 letter code of nucleic acids into
  amino acids?proteins

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tRNA

• structure allows it to match correct amino acids
  to mRNA sequence
• tRNA is composed of one strand of RNA
• chain twists folds on itself making some double
  stranded areas
• one end-special triplet of bases- anticodon
• contains complementary sequence of bases to
  sequence of bases in mRNA
• recognizes bases in mRNA by applying standard
  base pairing rules
• other end is site where amino acid can attach
• enzyme recognizes both tRNA and its amino acid
  partner
• there are at least 32 different tRNA in
  eukaryotic cells
• anticodons are redundant
• there is at least one anticodon for each amino
  acid

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Translation

• ribosomes coordinate process of translation
• ribosomes are formed from 2 subunits each made of
  proteins rRNA (ribosomal RNA)
• completely assembled ribosome has binding site
  for mRNA on its small subunit two binding sites
  for tRNA on its large subunit

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Translation Stages

• Initiation
• Elongation
• Termination

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Initiation

• mRNA molecule binds to small ribosomal subunit
• special initiator tRNA binds to specific
  codon-AUG
• start codon
• anticodon is UAC
• start codon also carries amino acid methionine
• next large ribosomal subunit binds to small one
  creating functional ribosome
• initiator tRNA fits into one of two tRNA binding
  sites on ribosome called P site
• other tRNA binding site-A site is vacant
• P site holds tRNA containing growing peptide
  chain
• A site holds tRNA carrying next amino acid to be
  added to chain

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Elongation

• amino acids are added one by one to first amino
  acid
• each addition is composed of 3 steps
• First
• anticodon of incoming tRNA carrying an amino acid
  pairs with mRNA codon in A site of ribosome

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Elongation

• next peptide bond forms between carboxyl group
  of one amino acid amino group of next
• to do this polypeptide leaves tRNA in P site
  attaches to amino acid on tRNA in A site
• attached by a peptide bond
• ribosome catalyzes bond formation

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Elongation

• last stage-translocation
• P site tRNA leaves ribosome
• ribosome moves or translocates tRNA in the A site
  with its attached polypeptide to P site
• movement brings next mRNA codon to be translated
  into A site
• process begins again
• elongation continues until stop codon is reached

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Termination

• UAA, UAG UGA are stop codons
• when one of these sequences is detetected?peptide
  released from last tRNA
• Ribosome splits back into its separate subunits

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Polysomes

• single mRNA has many ribosomes traveling along it
• Polysomes
• in various stages of synthesizing polypeptide

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Mutations

• any change in nucleotide sequence of DNA
• production of mutations is mutagenesis
• some are spontaneous
• Some due to mutagens
• radiation, chemicals viruses
• two categories
• base substitutions
• insertions deletions

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Base substitutions

• Point mutation
• replacement of one nucleotide for another
• may go unnoticed
• may cause significant issues
• hemophilia
• sickle cell anemia
• Huntingtons Chorea
• Tay Sachs disease

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Insertion Deletion

• mRNA is read as a series of triplet codons during
  translation
• adding or deleting one base will change reading
  frame for tRNA
• Frame-shift mutations have dramatic effects
• all nucleotides downstream from insertion or
  deletion will be regrouped into different codons
• result is usually nonfunctional protein