BISC 101 Lecture Notes - Lecture 7: Hydrolysis, Intellectual Disability, Phenylalanine Hydroxylase

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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
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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
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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
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