DNA

Molecular Biology of the Gene

Genes• biological blueprints• give attributes & traits• every nucleus, in every

cell carries genetic blueprint

• every cell has all information needed to make a complete you

• located on chromosomes• humans have 46 • each contain thousands of

genes

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

Genes & DNA• genes are made of DNA

– deoxyribonucleic acid• macromolecule • made of 4 different

nucleotides• paired in precise manner• order of nucleotides-

genetic code• DNA gives instructions to

make proteins• each 3 combinations of

nucleotides = one amino acid

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)– uracil (U)

DNA NUCLEOTIDES

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

Sugar-Phosphate Backbone

DNA• structure determined by

Watson & 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

DNA• base pairing is

specific• A-T • G-C• amount of A =

amount of T• one strand is

complementary to the other

Replication • cells divide & reproduce

daily• giving rise to 2 daughter

cells• with same genetic

makeup• before cell can divide,

DNA must duplicate• called-replication• uses template

mechanism

Replication• to begin• strands of DNA must

separate• double helix unwound

by helicase– breaks H bonds

between base pairs

REPLICATION• unwinding takes place in a replication

bubble

• new strand of DNA is formed in both directions on both strands of DNA in bubble

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 – 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

http://i27.tinypic.com/21yhc2.jpg

REPLICATION• each strand of

DNA is used as template to make new, complementary strand

• semi-conservative replication

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

PHENOTYPIC EXPRESSION • small sections of

chromosomes are genes

• genetic makeup is genotype

• expression of genes into specific traits is phenotype

– result of proteins

• one geneone protein

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

Genetic Code• DNAmRNAproteins• 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-AACCGTTGGACAC

• specific sequence of bases makes up a gene glu lys ser ala met phe leu glu

Expression of Genotype• transfer of

information from DNA to RNA and then to proteins takes place in two processes

• Transcription• Translation

Transcription• DNA directs

ribonucleic acid synthesis

• transfers genetic information from DNA to RNA

RNA• nucleotides – ribonucleotides

• same basic components as DNA

• single strand• 5 C sugar-ribose• phosphate groups• nitrogenous bases

– same as DNA– one exception

• RNA has Uracil (U) instead of T

• base pairing rules are same• Uracil is substituted for

thymine• U-A not T-A

Types of RNA• Messenger

– mRNA

• Ribosomal – rRNA

• Transfer– tRNA

• all involved in translation

Transcription• DNAmRNA

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

Transcription• process of

transferring genetic information from DNA to RNA

• similar to DNA replication

• DNA is used as template to make RNA

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

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

Elongation• RNA strand grows longer• RNA strand peels away

from template allowing separated DNA strands to come back together

• 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

Termination• RNA polymerase

reaches special sequence of bases in template-terminator

• ends transcription• RNA polymerase

detaches

Post-transcriptional Modifications

• in prokaryotic cells RNA can function immediately

• in eukaryotic cells RNA is processed before moving to cytoplasm for translation

• post-transcriptional modifications

• capping-tailing• splicing-ligating• ligation

Capping-Tailing• nucleotides are added to either end of

RNA

• “G” nucleotide(s) might be added to one end; “A” nucleotides might be added to other

• additions make RNA more stable

• protects molecule from attack by enzymes

• helps ribosomes recognize mRNAA

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

Translation• conversion of nucleic acid

language into protein language

• proteins are macromolecules-polymers of amino acids

• 20-common to all organisms

• sequence of nucleotides in mRNA dictates sequence of amino acids in polypeptide

• sequence of bases in molecule of DNA is genetic code

GENETIC CODE• DNA & RNA are made of 4 different

nucleotides• there are 20 amino acids• if each nucleotide coded for one

amino acidcould only be 4 amino acids

• if each 2 coded for onecould 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

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

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

Translation• amino acids are not able to

recognize codons of mRNA• requires an interpreter

– intermediate that can understand language of one form & translate message into another

• tRNA (transfer RNA) is interpreter

• picks appropriate amino acid & recognizes appropriate codon in mRNA

• converts 3 letter code of nucleic acids into amino acidsproteins

tRNA• composed of one strand of RNA• chain twists & folds 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-site where amino acid can

attach• enzyme recognizes both tRNA & 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

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

Translation Stages

• Initiation• Elongation• Termination

Initiation• mRNA molecule binds to small

ribosomal subunit• special initiator tRNA binds to specific

codon-AUG– start codon

• Anticodon-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-P site

• other tRNA binding site-A site is vacant

• P site holds tRNA containing growing peptide chain

• A site holds tRNA carrying amino acidsext amino acid to be added to chain

Elongation• amino acids are added

one by one to first amino acid

• ribosome moves along mRNA in the 5'-to-3'direction

• tRNA (anticodon) corresponding to second codon binds to A site, carries amino acid

Elongation• peptide bond forms

between carboxyl group of one amino acid & amino group of next

• after peptide bond forms-ribosome shifts, or translocates, causing tRNA to occupy the P site

Elongation• movement brings next mRNA codon to

be translated into A site • process begins again• elongation continues until stop codon

is reached

Termination• UAA, UAG & UGA

are stop codons• when one of these

sequences is detetectedpeptide released from last tRNA

• ribosome splits back into its separate subunits

Mutations• any change in

nucleotide sequence of DNA

• production of mutations-mutagenesis

• some-spontaneous• some due to mutagens• radiation, chemicals &

viruses• two categories

– base substitutions– insertions & deletions

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

Insertion & Deletion• mRNA is read as a series of triplet codons during translation

• adding or deleting one base changes reading frame for tRNA

• Frame-shift mutations– dramatic effects– all nucleotides downstream

from insertion or deletion will be regrouped into different codons

– result is usually nonfunctional protein