UNIT 9: DNA, PROTEIN SYNTHESIS, + BIOTECHNOLOGY
The Molecular Basis of Inheritance (Ch. 13)
The structure of a DNA strand + components of nucleotides
- DNA strand → deoxyribose(sugar) backbone, phosphate group, bases
- Adenine + Thymine, Cytosine + Guanine
- 5’ end + a 3’ end
The functions of DNA polymerase, DNA ligase, + nuclease in DNA replication
- DNA polymerase: constructs a new DNA strand by adding bases
- DNA ligase: seals the fragments
- Nuclease: breaks the nucleic acids when cutting at restriction sites
The organization of chromosomes
- DNA wrapped around histones → strings of histones are grouped into
nucleosomes → nucleosomes are coiled up into supercoils → chromosome
How restriction enzymes + ligases are used to make recombinant DNA
- Restriction enzymes: cut at certain sequences of a DNA strand to make sticky
ends on BOTH the plasmid + DNA sequence
- Ligase: joins 2 DNA fragments
The mechanisms + reasoning behind the semiconservative model
- Leading strand: 3’ to 5’
- Lagging strand: 5’ to 3’
- As the leading strand is from 3’ to 5’, the strand made from it is from 5’
to 3’ which is the way DNA polymerase goes, allowing it to go in the same
direction as the unzipped strand
- The lagging strand is from 5’ to 3’, so the DNA polymerase can only make it
in segments going in the opposite direction in Okazaki fragments but in the
same general direction as the helicase unzips
- Leads to two DNA molecules w/ one original + one new strand
The process of DNA replication w/ antiparallel elongation, including the
different proteins involved
- Antiparallel elongation:
- DNA (double stranded) is unzipped into two strands by helicase → primase
makes an RNA primer that starts a 3’ end for the DNA polymerase to work on →
DNA polymerase extends it by adding nucleotides to make a new DNA strand
that’s complementary to the template strand
- 3’ to 5’ strand: new strand is made continuously in the 5’ to 3’ direction
w/ DNA polymerase
- 5’ to 3’ strand: new strand is made in Okazaki fragments in the 3’ to 5’
direction but slowly building in the 5’ to 3’ direction by making primers +
then the DNA polymerase builds off of them in segments (Okazaki fragments)
- Topoisomerase: prevents DNA helix from getting too tightly wound as DNA is
opened up
- RNA primers are removed → primers are replaced → DNA ligase seals all the
bases
How restriction enzymes recognize + cut sites, + how those sites will travel on
gel electrophoresis
- Smaller fragments will move faster + farther away from the wells
- Larger fragments will move slower + closer to the wells
- Configurations:
, - Supercoiled: most common, like a twisted rubber band, very compact →
move through gel very quickly; only found in plasmids replicated in
bacteria b/c supercoiling of a plasmid requires an enzyme found in the
bacterial cell
- Nicked: large floppy circle, break in one of the covalent bonds in its
sugar-phosphate backbone, doesn’t move through gel as easily as the
supercoiled config although its the same size; shape makes it harder
to move through the gel, it will be closer to the well
- Multimer: two or more plasmids chained together, only found in
plasmids replicated in bacteria b/c multimers from when plasmids are
replicated so fast that they end up linked together migrates slower
than nicked circle
Gene Expression: From Gene to Protein (Ch. 14)
- DNA needs to get outside of the nucleus to be expressed after being
replicated → RNA = the messenger between the sequence of DNA + what happens
outside of the nucleus
The overview of transcription + translation
- DNA → Transcription → RNA → Translation
- Transcription: involves copying a gene’s DNA sequence to make an RNA
molecule
1.RNA polymerase binds to a sequence of DNA called the promoter at the
beginning of a gene
2.RNA polymerase separates the DNA strands → single stranded template
3.The template strand acts as a template for RNA polymerase
4.RNA polymerase reads template + builds a RNA molecule out of complementary
nucleotides (5’ to 3’) (contains uracil instead of thymine)
5.Once RNA transcript is finished, the transcript is released
6.RNA transcripts can become mRNAs (in bacteria), pre-mRNA (in eukaryotes)
7.Eukaryotic pre-mRNA need to have a 5’ cap + 3’ tail + introns are taken out
+ exons are spliced together
- Translation: performed by RNA polymerase, links nucleotides to form RNA
strand using DNA strand as a template
8.Ribosome assembles around the mRNA + the first tRNA matches the start codon
9.tRNA strand connect mRNA codons to the amino acids they encode, tRNA ends
have anticodons that bind to specific mRNA codons
10. Matching tRNA binds to codon → existing polypeptide chain is linked onto
the amino acid of the tRNA → mRNA shifts one codon over to read another
codon
11. Finished polypeptide chain is released when it reaches a stop codon
- Example 1:
- DNA: 3’ AGTACATCGATGCT 5’
- Pre- mRNA: 5’ UCAUGUAGCUACGA 3’
- mRNA: 5’ AUGUUA 3’
- mRNA codons: 5’ AUG UUA 3’
- tRNA anticodons:5’ UAC AAU 3’
- Amino acid sequence: Tyr - Asn
- Example 2:
- DNA: 5’ ACGTCGCCGTTA 3’ (change to the other strand that
goes in 3’-5’)
- Pre- mRNA: 5’ ACGUCGCCGUUA 3’
The Molecular Basis of Inheritance (Ch. 13)
The structure of a DNA strand + components of nucleotides
- DNA strand → deoxyribose(sugar) backbone, phosphate group, bases
- Adenine + Thymine, Cytosine + Guanine
- 5’ end + a 3’ end
The functions of DNA polymerase, DNA ligase, + nuclease in DNA replication
- DNA polymerase: constructs a new DNA strand by adding bases
- DNA ligase: seals the fragments
- Nuclease: breaks the nucleic acids when cutting at restriction sites
The organization of chromosomes
- DNA wrapped around histones → strings of histones are grouped into
nucleosomes → nucleosomes are coiled up into supercoils → chromosome
How restriction enzymes + ligases are used to make recombinant DNA
- Restriction enzymes: cut at certain sequences of a DNA strand to make sticky
ends on BOTH the plasmid + DNA sequence
- Ligase: joins 2 DNA fragments
The mechanisms + reasoning behind the semiconservative model
- Leading strand: 3’ to 5’
- Lagging strand: 5’ to 3’
- As the leading strand is from 3’ to 5’, the strand made from it is from 5’
to 3’ which is the way DNA polymerase goes, allowing it to go in the same
direction as the unzipped strand
- The lagging strand is from 5’ to 3’, so the DNA polymerase can only make it
in segments going in the opposite direction in Okazaki fragments but in the
same general direction as the helicase unzips
- Leads to two DNA molecules w/ one original + one new strand
The process of DNA replication w/ antiparallel elongation, including the
different proteins involved
- Antiparallel elongation:
- DNA (double stranded) is unzipped into two strands by helicase → primase
makes an RNA primer that starts a 3’ end for the DNA polymerase to work on →
DNA polymerase extends it by adding nucleotides to make a new DNA strand
that’s complementary to the template strand
- 3’ to 5’ strand: new strand is made continuously in the 5’ to 3’ direction
w/ DNA polymerase
- 5’ to 3’ strand: new strand is made in Okazaki fragments in the 3’ to 5’
direction but slowly building in the 5’ to 3’ direction by making primers +
then the DNA polymerase builds off of them in segments (Okazaki fragments)
- Topoisomerase: prevents DNA helix from getting too tightly wound as DNA is
opened up
- RNA primers are removed → primers are replaced → DNA ligase seals all the
bases
How restriction enzymes recognize + cut sites, + how those sites will travel on
gel electrophoresis
- Smaller fragments will move faster + farther away from the wells
- Larger fragments will move slower + closer to the wells
- Configurations:
, - Supercoiled: most common, like a twisted rubber band, very compact →
move through gel very quickly; only found in plasmids replicated in
bacteria b/c supercoiling of a plasmid requires an enzyme found in the
bacterial cell
- Nicked: large floppy circle, break in one of the covalent bonds in its
sugar-phosphate backbone, doesn’t move through gel as easily as the
supercoiled config although its the same size; shape makes it harder
to move through the gel, it will be closer to the well
- Multimer: two or more plasmids chained together, only found in
plasmids replicated in bacteria b/c multimers from when plasmids are
replicated so fast that they end up linked together migrates slower
than nicked circle
Gene Expression: From Gene to Protein (Ch. 14)
- DNA needs to get outside of the nucleus to be expressed after being
replicated → RNA = the messenger between the sequence of DNA + what happens
outside of the nucleus
The overview of transcription + translation
- DNA → Transcription → RNA → Translation
- Transcription: involves copying a gene’s DNA sequence to make an RNA
molecule
1.RNA polymerase binds to a sequence of DNA called the promoter at the
beginning of a gene
2.RNA polymerase separates the DNA strands → single stranded template
3.The template strand acts as a template for RNA polymerase
4.RNA polymerase reads template + builds a RNA molecule out of complementary
nucleotides (5’ to 3’) (contains uracil instead of thymine)
5.Once RNA transcript is finished, the transcript is released
6.RNA transcripts can become mRNAs (in bacteria), pre-mRNA (in eukaryotes)
7.Eukaryotic pre-mRNA need to have a 5’ cap + 3’ tail + introns are taken out
+ exons are spliced together
- Translation: performed by RNA polymerase, links nucleotides to form RNA
strand using DNA strand as a template
8.Ribosome assembles around the mRNA + the first tRNA matches the start codon
9.tRNA strand connect mRNA codons to the amino acids they encode, tRNA ends
have anticodons that bind to specific mRNA codons
10. Matching tRNA binds to codon → existing polypeptide chain is linked onto
the amino acid of the tRNA → mRNA shifts one codon over to read another
codon
11. Finished polypeptide chain is released when it reaches a stop codon
- Example 1:
- DNA: 3’ AGTACATCGATGCT 5’
- Pre- mRNA: 5’ UCAUGUAGCUACGA 3’
- mRNA: 5’ AUGUUA 3’
- mRNA codons: 5’ AUG UUA 3’
- tRNA anticodons:5’ UAC AAU 3’
- Amino acid sequence: Tyr - Asn
- Example 2:
- DNA: 5’ ACGTCGCCGTTA 3’ (change to the other strand that
goes in 3’-5’)
- Pre- mRNA: 5’ ACGUCGCCGUUA 3’
