is two strands in opposite directions next to each other (due to hydrogen bonds), twisted into a double helix. deoxyribonucleic acid
for the living material that will be built, it regulates living cells, programs death of other cells, turns genes on or off, carries traits through generations, results in survival of the species through evolution.
The sugar is the 3' carbon and the phosphate is the 5' carbon.
RNA and DNA polymerase
read from the 3' end and made from the 5' end.
can unzip like a zipper then be copied from the 3' side.
Transmission of genetic information
Complementary base pairing property allows for DNA replication. RNA is created via a process called transcription. RNA strands are translated into amino acids
DNA has Purines
adenine and guanine
DNA has Pyrimidines
thymine and cytosine
is a 5 carbon sugar
on the 5' covalently bonds with sugar on the 3'
Adenine & Thymine
2 hydrogen bond
Guanine & Cytosine
3 hydrogen bonds
with a net positive charge at physiologic pH most likely has a basic R group.
are crucial for all living organisms. Two types of nucleic acids are DNA and RNA, which are made up of nucleotides. Genetic information is transferred using nucleic acids.
Sugar + base (= glycosylamines), Examples include cytidine, uridine, adenosine, guanosine, thymidine and inosine, Made in the liver from consumed food (contains nucleic acids), Used as antiviral and anticancer agents, Can be phosphorylated to produce nucleotides
the monomers of nucleic acids. Includes cytosine, thymine (found in DNA), adenine, guanine and uracil (found in RNA). Made up of a five-carbon sugar, a nitrogenous base and a phosphate group.Building blocks of nucleic acids. Data storage: DNA/RNA. Energy currency: ATP. Cellular communication: cAMP. Co-enzyme catalysis
Sugar phosphate backbone
Composed of alternating sugar and phosphate groups
The sugar base of one nucleotide
is linked with an adjacent nucleotide’s phosphate group by ester bonds. The sugar is at the 3’ end and The phosphate at the 5’ end
DNA is not just
an arrangement of nucleotides spiraling around each other. DNA holds all of our genetic information.
Segments of DNA
that influence certain traits or characteristics are known as genes. These genes provide information on the type of proteins that our body should produce. The actions of these proteins shape the organism physically.
DNA contains the blueprint
for for an organism, and is therefore capable of transmitting genetic information.
starts making DNA complementary to the unwound DNA (AT-GC)
RNA Primers Replaced
DNA Repair Complex & DNA Ligase
DNA Repair Complex
with DNA Polymerase I Replaces the RNA Primer (leading)
connects Okazaki fragments (lagging)
Semiconservative Nature of Replication
New DNA is made of one old (conservation) and one new strand.
Repair of DNA
Repair is a normal process. Different errors or amounts of errors lead to different repairs.
Repair During Replication
DNA polymerase proof-reads 3'-5' and removes and replaces 5'-3' when there are errors.
Repair of Mutations
Mismatch repair, Base-excision repair, Nucleotide-excision repair, Nick translation
enzymes recognize incorrectly paired base-pairs and cuts out the stretch of DNA containing the mismatch. Then polymerase re-adds the correct nucleotides in.
Base Excision Repair
Some single damaged bases (especially uracil) are removed by a glycosylase enzyme, then the sugar and phosphate and surrounding nucleotides are removed.
Nucleotide Excision Repair (Ex. Thymine Dimers)
One strand is damaged and the other is not, methylation of the older strand determines which stand is used to rebuild the damaged strand. Mismatch Repair works the same way, but it is triggered by mismatch (not damage)
Nick Translation (Ex. RNA Primer Replacement)
The proof-reading (exonuclease activity) of polymerase.
DNA strands base pair with each other, DNA probes hybridize onto DNA fragments containing a target sequence (Southern Blotting). Sticky ends from a restriction fragment of a gene base pair with the same sticky ends on a plasmid (gene cloning).
A method that involves the replication of recombinant DNA molecules in a host organism. Single DNA ➙ large population of replicated DNA. Requires a source of DNA and a host organism in which to replicate
Gene cloning process
Isolate DNA, Treat plasmid and foreign DNA with the restriction enzyme, Mix foreign DNA with plasmid fragments, Add DNA ligase, Introduce recombinant plasmid into bacterial cells, Multiplication/transformation of gene copies, Screening
Obtain a bacterial plasmid and foreign DNA with gene of interest. That way, there is a recognition sequence for a restriction enzyme
Treat plasmid and foreign DNA with the restriction enzyme
Plasmid DNA is cut at the restriction site by the restriction enzyme. Foreign DNA is also cut
Mix foreign DNA with plasmid fragments
When cut by the restriction enzyme, there are sticky ends that allow for complementary sticky ends to pair
Introduce recombinant plasmid into bacterial cells
Some recombinant plasmid will be taken up by the bacteria by transformation
Multiplication/transformation of gene copies
Recombinant plasmids are replicated and Can be identified by growth in different environment (e.g. ampicillin)
Polymerase Chain Reaction
The purpose is to take a small piece of DNA and amplify (multiply) it. The process mass produces a sample of DNA. also used to identify small segments of DNA within a larger DNA strand. e.g If we wanted to detect whether a DNA contained a viral sequence, we can use this to detect that viral sequence
PCR generally has three steps
Initialization, Annealing, Elongation
The sample containing the DNA is heated up so the hydrogen bonds holding the double-stranded DNA breaks apart. The DNA are now single stranded.
The sample is slightly heated. Polymerase goes to the site of the primers. Since the DNA polymerase is heat-sensitive, they start up and begin to polymerize the single strands of DNA
double stranded of DNA comes apart due to heating (increase in temperature in the environment) or a change in pH
if the temperature decreases to normal (or the environment changes back to normal), two single strands form double stranded DNA again due to the complementary nucleotide sequences and random molecular motion. Much slower process. Requires salt to neutralize the repulsion of sugar phosphate backbones from each strand
A molecular biology technique that compares and analyzes the degree of genetic similarity between identical or related DNA sequences. Measures the genetic distance between two species. Denatures two different DNA sequences then uses single stranded DNA from each to anneal to double-stranded DNA
Replication only occurs
in the 5’ to 3’ direction
unwinds the double helix of DNA
DNA polymerase III, Primase, Okazaki fragments, DNA Polymerase I, DNA ligase
DNA polymerase III
binds to one strand of DNA from the RNA primer and moves from the 3’ to 5’ direction, producing a leading strand of nucleotides
produces RNA primers at the 5’ end, allowing for the synthesis of Okazaki fragments
short, discontinued fragments of replication products on the lagging strand
DNA Polymerase I
removes RNA primers by the 5’ end to 3’ end
seals the spaces in the strand (between the Okazaki fragments)
is the enzyme that catalyzes protein synthesis. has 2 subunits - the large and the small.
The large subunit
is responsible for the peptidyl transfer reaction.
The small subunit
is responsible for the recognizing mRNA and binds to the Shine-Dalgarno sequence on the mRNA
An initiation complex including mRNA, initiator tRNA (fmet) and a ribosome is formed by initiation factors and GTP around an initiation codon (AUG) following a Shine-Dalgarno or Kozak sequence
protein is made from the N terminus to C terminus. mRNA are read 5' to 3' (opposite of DNA). Binding occurs between the chain of amino acids and tRNA's amino acid at the A site of the tRNA
occurs at the P site by the whole chain moving onto the A site of the tRNA. The tRNA in the P site gets kicked of the E site. The codon that was in the A site is now in the P site (translocation) and the A site is open for binding to a new aminoacyl-tRNA to a new codon
a stop codon (UAG, UGA, UAA) causes release factors bound to GTP to block the A site. The chain gets cut off at the P site, falls off and the translation complex falls apart.
Amino acid activation
enzymes called aminoacyl-tRNA synthetases attach the correct amino acids to their corresponding tRNAs. ATP required.
Role and structure of ribosomes
Ribosomes catalyze protein synthesis by using tRNA to bring amino acids and mRNA to give the proper sequence.