Central Dogma Flashcards
Reaction catalyzed by DNA polymerase
(DNA)n + dNTP –> (DNA)n+1 + PPi
bases used in DNA replication
doeoxyNTP = deoxyATP, deoxyGTP, deoxyCTP, deoxyTTP
hydrogen bonds in base pairs
A-T = 2 hydrogen bonds G-C = 3 hydrogen bonds
key characteristics of DNA synthesis
- 4 deoxynucleoside triphosphates and Mg2+ are required
- A template strand is used to direct DNA synthesis
- A primer from which the new strand grows must be present (DNA polymerase needs a free 3’ hydroxyl)
- Many DNA polymerases have nuclease activity that allows for the removal of mismatched bases (i.e. editing ability)
helicase
separates the 2 strands of DNA so that DNA polymerase can access them for DNA replication
topoisomerase/gyrase
a protein needed to straighten out the tangling that can occur as the two helices are being pulled apart
leading strand v. lagging strand
leading strand - new bases are added at the 3’ end and the leading strand grows continually in the 5’ to 3’ direction
lagging strand - replication occurs by Okazaki fragments, whereby a new primer is put in and the synthesis occurs in fragments. DNA ligase closes the gaps at the end.
transcription
the process of synthesizing RNA from DNA. It is catalyzed by RNA polymerase. Eukaryotic transcription is significantly more complicated and has complicated regulatory mechanisms than prokaryotic b/c prokaryotes have only one circular chromosome.
RNA polymerase needs
- A template (i.e. a strand of DNA to replicate)
- four ribonucleoside triphosphates
- divalent metal ions, usually Mg2+ or Mn2+
overall equation for transcription
(RNA)n residues + ribonucleoside triphosphate –> (RNA)n+1 residues + PPi
coding strand
also known as the sense strand. the strand of DNA that has the same sequence as the RNA being synthesized. (except RNA has U’s where DNA has T’s)
template strand
also known as the antisense strand. The strand of DNA that is serving as the template for the new strand of RNA.
bacterial RNA polymerase
RNA polymerase I. Has several subunits including a special subunit called sigma. When the sigma factor is associated, the whole thing is called the holoenzyme. Without sigma, it’s called the core enzyme. The sigma factor needs to be bound in order to transcription to begin.
types of RNA
- mRNA - encodes information to generate a protein. It has the code for the order of amino acids in a protein
- tRNA - plays a key role in translating mRNA to protein. It brings the appropriate amino acid that matches the codon on the mRNA and transfers it onto the growing polypeptide chain.
- rRNA - part of ribosomal structure that also plays a key role in translating mRNA into protein. There are 4 different rRNA’s, one of which has the enzyme activity that makes the peptide bond (this is the peptidyl transferase rRNA).
- small nuclear RNA’s (snRNA) - e.g. snurps - do the processing in eukaryotes
rRNA
4 strands of rRNA are part of the structure of the ribosome and one provides the peptide transferase activity
tRNA
61 species of tRNA are loaded with a specific amino acid and binds to codons in the mRNA using their anticodon loop
translation
Ribosome is the major structure doing the translation. It has a large and small subunit with different sizes of rRNA components (these sizes differ for prokaryotes and eukaryotes). There are 3 sites on the ribosome - A site, P site, and E site. The tRNA brings an amino acid into the A site, the polypeptide bond is formed in the P site, and the tRNA exits at the E site to go pick up another amino acid.
Prokaryotic transcription v. Eukaryotic transcription
Bacteria: RNA polymerase I is composed of 5 subunits. Sigma factor is needed to find the promotor. When it does, RNA polymerase I elongates the RNA product.
Eukaryotes: More proteins are needed to recognize the promotor. These are called transcription factors. Some transcription factors bind to repressors or activators and others are called basal transcription factors because they are always needed to initiate transcription. Eukaryotes have more than one RNA Polymerase.
Eukaryotic RNA polymerases
- RNAPII - transcribes mRNA
- RNAPI - transcribes rRNA
- RNAPIII - transcribes tRNA
constitutive RNA
rRNA and tRNA are constitutive, meaning we need them all the time. They do our housekeeping.
eukaryotic mRNA
is different in different cell types. We need to regulate this more specifically than the other two types.
regulators for eukaryotic RNAPII
transcription factors - basal transcription factors or specific transcription factors
Eukaryotic promotors
RNAPII recognizes some specific promotor sequences. The main ones:
- TATA box
- CAAT box
- GC box
strong vs. weak promotors
If the promotor is close to the gene being transcribed, it is strong.
cis acting elements
DNA sequences that regulate the expression of a gene located on the same molecule of DNA. Promotors are referred to as cis-acting elements.
trans acting elements
proteins that recognize cis-acting elements and regulate RNA synthesis. They are commonly called transcription factors.
