BISC 101 Lecture Notes - Lecture 7: Hydrolysis, Intellectual Disability, Phenylalanine Hydroxylase
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19 Jun 2015
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BISC 101 – Lecture 7 – From Gene to Protein
History of DNA and Its Structure
•Watson and Crick 1953
•DNA consisted of two separate DNA polymers called strands
•These strands are twisted around each other to form a double helix
•DNA is a nucleic acid: Deoxyribonucleic acid
•Made of long chains (polymers) of nucleotides that contain:
oPhosphate group
oDeoxyribose sugar group
oNitrogen – containing base
•Nucleoside: Sugar and base
•DNA has four kinds of bases
oThymine, Cytosine, Adenine, Guanine
oPyrimidine: Thymine and cytosine
1 carbon ring
oPurines: Adenine and guanine
2 carbon rings
•DNA is a double – stranded antiparallel helix
•Strands are antiparallel to each other
oOne end of the strand is 5’ to 3’
oThe other binding strand is 3’ to 5’
•DNA helix undergoes one complete turn every 10 base pairs
•Complementary base pairings discovered by Watson and Crick
oThymine and adenine bonded by 2 hydrogen bonds
oCytosine and guanine bonded by 3 hydrogen bonds
Base Composition in DNA
•Erwin Chargaff, an Australian biochemist analyzed base composition
•Chargaff’s Rules for double stranded DNA
oNumber of A Residues = Number of T residues
oNumber of G residues = Number of C residues
oNumber of purines (A + G) = Number of pyrimidine (T + C)
DNA vs. RNA
•DNA
oDouble stranded
oSugar = Deoxyribose at carbon #2
oThymine
oPredominantly found in nucleus
oOne type
•RNA
oSingle stranded
oSugar = Ribose at carbon #2
oUracil
oNucleus and cytoplasm
oMore than one type (mRNA, tRNA, snRNA, etc.)
Coding RNAs: Synthesize Proteins
•Messenger RNA (mRNA): 3 – 5% of all RNA
oFunctions in the nucleus, migrates to ribosomes in cytoplasm
oCarries DNA sequence information to ribosomes and codes for protein
•Transfer RNA (tRNA): 15% of all RNA
oFunctions in the cytoplasm
oProvides linkage between mRNA and amino acids and transfers amino
acids to ribosomes
•Ribosomal RNA (rRNA): 80% of all RNA
oFunctions in the cytoplasm
oStructural component of ribosomes
DNA Replication
•Origin of Replication: Sequence of DNA where replication take place
•A eukaryotic chromosome may have hundreds or thousands of replication origins
1. Replication begins at specific sites (origins of replication) where the two parental
strands separate and form replication bubbles
2. The bubbles expand laterally, as DNA replication proceeds in both directions
3. Eventually, the replication bubbles fuse and synthesis of the daughter strand is
complete
Mechanisms of DNA Replication
•DNA replication is catalyzed by DNA polymerase III which needs an RNA primer
•The initial nucleotide strand is an RNA primer
•RNA primase synthesizes primer on DNA strand
•DNA polymerase I replaces RNA primer with DNA nucleotides
•DNA polymerases add nucleotides to 3’ end of growing strand
oSynthesis of new strand is 5’ to 3’
oReads template strand 3’ to 5’
Proteins and Complex Steps for DNA Replication
1. Topoisomerase binds to DNA and relieves torsional stress experienced further
upstream along the helix that occurs as a result of unwinding
•Type I: Cuts one strand of double helix to relax DNA, and then the cut
strand is reannealed
•Type II: Cuts both strands of double helix to relax DNA, and then both
strands are reannealed
2. DNA helicases unwind the double helix by breaking hydrogen bonds between
bases of strands
•Template strands are stabilized by other proteins
•Usually occur in places rich in A – T since only two bonds are found
•Origin of Replication: Initiation point
•Replication Fork: The structure that is created (bubble)
3. Single stranded DNA binding proteins prevent DNA strands from rejoining
•They bind to the sugar phosphate backbone of the DNA strand
•Stabilizes single – stranded DNA strand until it can be used as a template
4. RNA primase catalyzes the synthesis of short RNA primers, which nucleotides
are added to
•RNA primase binds to the 3’to5’ parent strand (template strand) in the
origin of replication, starting at the 5’ end
•RNA primase attracts RNA nucleotides to bind to the nucleotides of the
3’to5’ DNA strand
•RNA primase synthesizes primers or nucleotides for the binding of DNA
nucleotides
oSingle RNA primer binds at the 5’ end of the leading strand
oRNA primer binds at the 5’ end of each Okazaki fragment of the
lagging strand
5. DNA polymerase III extends or elongates the strand in the 5’ to 3’ direction
•3’ to 5’ is template strand
oReplication of the strand (3’to5’) results in a lagging strand and
results in a 5’ to 3’ strand
oRNA primase adds more RNA primers onto the 3’ to 5’ template
strand
oDNA polymerase III reads the template and lengthens the Okazaki
fragments and adds onto the primer
oOkazaki Fragments: The gap between two RNA primers
oThe lagging strand has a discontinuous synthesis due to the need of
RNA primers
•If 5’ to 3’ strand is used as a template strand, then it is called the leading
strand
oDNA Polymerase III can continuously read the template and
continuously add nucleotides onto the primer
oAs a result, a 3’ to 5’ daughter strand will be synthesized
oThe leading strand has a continuous synthesis
6. Polymerase I degrades and removes the RNA primers and replaces it with DNA
nucleotides
•Removes primer from the 5’ end of the leading strand and replaces it with
DNA, adding on to the adjacent 3’ end
•Removes primer from the 5’ end of each fragment for the lagging strand
7. DNA Ligase joins the short DNA fragments (Okazaki fragments) on the lagging
strand into a continuous daughter strand
•Joins the 3’ end of the DNA that replaces the primer to the rest of the
leading strand