Download Molecular Biology Unit Notes

Molecular Biology Unit Notes
DNA structure:
1. double helix structure
2. sugar- phosphate structure linked by covalent bonds
3. nitrogenous bases held together by hydrogen bonds
a. adenine and guanine are purines with two rings vs cytosine and thymine are pyridines with one ring
b. purine+ pyrimidine results in a uniform diameter
c. adenine and thymine for two hydrogen bonds vs cytosine and guanine form three hydrogen bonds
4. antiparallel- running in opposite directions
Transcription:
1. Initiation
a. Bacteriai. RNA polymerase recognizes promoter and binds itself
ii. RNA Ploymerase pries the two strands of DNA apart and joins together RNA nucleotides
complementary to the DNA template strand (strand that goes from 3’-5’ because RNA must
be 5’-3’)
b. Eurkaryotesi. transcription factors determine where the RNA polymerase binds due to the sequence of
genes (tata box)
ii. instead of using RNA polymerase it uses RNA polymerase II
c. RNA polymerase differs from DNA polymerase in how it doesn’t need a primer
d. Promoter- where RNA polymerase attaches
2. Elongation
a. As the RNA polymerase moves along the DNA it unwinds the double helix (10-20 nucleotides at
a time) as the RNA peels away the double helix structure reforms
b. adds nucleotides to the 3’ end of the RNA
3. Termination
a. Bacteriai. Terminator- sequence that signals the the end of transcription in the DNA
b. Eurkaryotesi. Terminator is found in the pre-mRNA
c. Transcription unit- part of the DNA that has been transcribed into a RNA molecules
RNA Modification in Eukaryotic Cells:
1. ends of he pre-mRNA are given a 5’ cap (modified form of guanine) added onto the 5’ end and on
the 3’ end there are added adenines that form a poly- A tail
2. Split genes and RNA splicing
a. RNA splicing- where the introns (noncoding regions of the pre-mRNA) are cut out and the
exons (doing regions that are eventually expressed) are connected together creating a
continuous sequence of coding
b. snRNPs are where splicing takes place, they are located in the cell cycles and are made of
composed RNA and protein
c. snRNA recognizes splice sites
d. snRNPs combine with other proteins to create a spliceosome, the spliceosome releases the
intron and joins the two exons.
3. Ribozymes- RNA molecules that function as enzymes (intron RNA functions as a ribozyme as it
catalyzes its own excision
Translation:
1. Takes place in a ribosome (made of proteins and RNA) that is either in in the rough ER or the
cytoplasm
a. made of proteins and RNA
b. Large subunit and small subunit
c. different sites in the ribosome
mRNA binding site
mRNA binding site
P-site holds the tRNA carrying the growing polypeptide chain
A-site holds tRNA to be added to the chain with a amino acid
E-site is where the discharged tRNAs leave the ribosome
2. tRNA (transfer) reads Codons (made up of three consecutive nucleotides)
a. tRNA transfers amio acids from the cytoplasm to the growing amio-acid chain
b. tRNA is made up of one side with a amino acid and another with a nucleotide triplet
(anticodon) that is complimentary to the codon on mRNA
3. Initiation
a. small ribosomal submit binds to a molecule of mRNA and the initiator of tRNA
(methionine/AUG)
b. Initiator tRNA forms a hydrogen bond with AUG start codon
c. Large ribosomal subunit follows after the attachment of the tRNA to mRNA
d. small subunit+ large subunit =translation initiation complex (brought together by proteins
called initiation factors)
i. formation of initiation complex is fueled by energy from hydrolysis of a GTP molecule
4. Elongationa. codon recognition recognition- tRNA base pairs with the mRNA
b. peptide bond formation- rRNA molecule of the large ribosomal submit catalyzes the formation
of a peptide bond between the polypeptide and the amino acid.
c. Translocation- movement of the tRNA to the different ribosomal sites
5. Termination
a. ends when a stop codon (UAG, UAA, or UGA) reach the A site
b. the release factor adds a water molecule to the polypeptide instead of a amino acid
c. this reaction hydrolyzes the bond between the polypeptide and the tRNA
6. Polyribosomes- ribosomes that are simultaneously copy the mRNA
i.
ii.
iii.
iv.
Mutations:
1. point mutations- changes in a single nucleotide pair
2. Substitutions
a. nucelotide-pair substitution- replacement of one nucleotide with another pair or nucleotides
i. some have no impact on the encoded protein, where it could change one codon to another but
they still result in the same amino acid (silent mutation)
ii. missense mutations- when the amio acid is changed, there is little effect not the protein aa
might have properties similar to the acid where it replaces or the region is not essential to the
proteins function
iii. nonsense mutation- where a point mutation can change a aa codon into a stop codon
terminating the translation prematurely leading to nonfunctional proteins
3. Insertions and Deletions- additions or loses of nucleotide pairs in a gene -> have disastrous
results
a. frameshift muatation- occurs when the number of nucleotides inserted/deleted is not a
multiple of three causing missense ending in nonsense and premature termination
4. Mutagens- physical and chemical agents that interact with DNA causing mutations
DNA Replication:
1. semiconservative model- where each of the two daughter cells will contain will have one
parental strand from the original and one newly made strand
2. Getting started
a. replication begins at the origin or replication (where short stretches of DNA have specific
sequences of nucleotides)
b. enzyme helicases unzip the DNA form in a replication bubble at each end a replication
fork
c. single-strand binding proteins then bind to the separated strands of DNA and prevent
them from repairing
d. Topoisomerase breaks and swivels and rejoins the parental DNA strands ahead of the
d. Topoisomerase breaks and swivels and rejoins the parental DNA strands ahead of the
replication fork relieving the strain caused by unwinding
e. primer (RNA chain) is placed along the DNA strand and synthesized by the enzyme primes
3. Synthesizing
a. DNA polymerases enzymes catalyze the synthesis of new DNA by adding new nucleotides to
a preexisting chain
b. DNA pol III adds a nucleotide to the RNA primer and then continues adding DNA nucleotides
complementary to template strand
4. Antiparallel Elongation
a. leading strand is the DNA strand that is made by the addition of new complementary base
pairs
b. lagging strand is the strand that is built as DNA elongates away from the replication fork.
i. lagging strand is synthesized discontinuously in segments (Okazaki fragments)
ii. each okazaki fragment must be primed separately
iii. after DNA pol III forms a okazaki fragment DNA polymerase I replaces the primer with DNA
nucleotides
iv. DNA ligase then joins the sugar-phosphate back bones together connecting the Okazaki
fragments
Genetic Engineering:
1. Recombinant DNA- DNA molecules created when segments of two different sources of DNA
2. plasminds- small circular DNA molecules that replicate separately form the bacterial
chromosome
a. obtain the plasmid and insert DNA from another source creating a recombinant DNA molecule
b. plasmind is returned to a bacterial cell pro ducting recombinant bacterium
c. cell reproduces through cell divisions creating clones (gene cloning)
3. Restriction enzymes- enzymes that cut DNA at specific locations
a. each enzyme recognizes a short DNA sequence (restriction site) cutting the DNA at these
points
b. the cutting of the restriction sites yields to restriction fragments
c. the most useful cutting of DNA results in fragments that are staggered with a resulting sticky
end
d. the short extensions can create hydrogen bonded base pairs with complementary sticky ends
cut with the same enzyme
e. these connections can be made permanent by the enzyme DNA ligase