molecular biology of gene expression Flashcards
central dogma of biology
DNA -> RNA -> PROTEIN
Basic plan of genetic information flow in living cells that relates genes
(DNA), message (RNA), and proteins
what are the two essential features of living creatures?
1) ability to reproduce own genome
2) ability to manufacture own energy
Why are proteins essential?
1) cellular architecture
2) catalysts
3) controler of cellular processes
4) act as communication channels
transcription
Process by which information from DNA is converted into its RNA equivalent - making an RNA copy of the DNA code
mRNA
messenger RNA: type of single-stranded RNA involved in protein synthesis and is made from a DNA template during the process of transcription.
translation
Making a protein using the information provided by messenger RNA
What are the basic steps of transcription?
1) uncoiling DNA
2) melting the strands
3) moving histones
4) making complementary RNA molecule from DNA template
5) stopping at the end of gene
6) RNA releases and DNA re-supercoils
template
Strand of DNA used as a guide for synthesizing a new strand by complementary base-pairing
RNA polymerase
Enzyme that synthesizes RNA
Housekeeping Genes
Genes that are switched on all the time because they are needed for
essential life functions - encode proteins that are used continuously
expressed (as pertaining to genes)
Converting a DNA region into RNA and/or protein to be used by the living cell
accessory proteins and inducers control gene expression.
what are the three main types of RNA and how are they used?
1) mRNA - translated into proteins and generated by structural genes (genes that encode protein)
2) rRNA - ribosomal RNA (regulatory - not translated)
3) tRNA - transfer RNA (regulatory - not translated)
ribozymes
RNA molecule that acts as an enzyme
cistron
Segment of DNA (or RNA) that encodes a single polypeptide chain
coding region of a gene
structural gene
Sequence of DNA (or RNA) that codes for a protein or for an untranslated RNA molecule
- related to a cistron
open reading frame (orf)
Sequence of bases (either in DNA or RNA) that can be translated (at least in theory) to give a protein - not interrupted by any stop codons for protein translation
promoter
Region of DNA in front of a gene that binds RNA polymerase and so promotes gene expression - place where transcription begins
BODER DEF: sequence that tells RNA polymerase where to bind and begin
Where are the two major recognition sites for bacterial promoters?
1) the -10 region (consensus sequence: TATAA)
2) the -35 region (consensus sequence: TTGACA)
the negative sign indicates that the location is upstream (before start site)
constitutively
Term used to describe genes that are expressed during all conditions
when a gene is transcribed constitutively, the promoter will closely match the consensus
consensus sequence
The ideal sequence - A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature.
activator protein
Protein that switches a gene on - required to bind to a promoter region when a gene is expressed only during special conditions
related to transcription factors
transcription factors
Protein that regulates gene expression by binding to DNA in the control region of the gene - related to activator protein
transcription start site
Starting point where a gene is converted into its RNA copy - where RNA polymerase will start adding nucleotides
5′ untranslated region (5′ UTR)
Region of an mRNA between the 5′ end and the translation start site - not made into protein, just has regulatory elements
3′ untranslated region (3′ UTR)
Sequence at the 3′ end of mRNA, downstream of the final stop codon that is not translated into protein - not made into protein, just has regulatory elements
What is the physical layout of transcription?
transcription start site - 5’ UTR - ORF - 3’ UTR - termination sequence
sigma subunit
Subunit of BACTERIAL RNA polymerase that recognizes and binds to the promoter sequence
core enzyme
the part of DNA or RNA polymerase that synthesizes new DNA or RNA (i.e., lacking the recognition and/or attachment subunits)
In what direction does RNA polymerase synthesize new nucleotides?
only in 5’ to 3’
what does the 3D structure of RNA polymerase look like?
has a deep groove for template DNA and a minor groove for the growing RNA
which DNA strand serves as the template for RNA synthesis?
The antisense strand, denoted by a minus sign. NOT the coding strand
secondary structure
folding of a polypeptide chain, resulting in an alpha helix, beta sheet or a random coil structure - the clover leaf structure of tRNA.
basically RNA doesn’t have to exist in only single strands
exon
Segment of a gene that codes for protein and that is still present in the messenger RNA after processing is complete
aka coding strand of eukaryotic genes that are expressed as protein
intron
Segment of a gene that does not code for protein but is transcribed and forms part of the primary transcript
aka noncoding stretch of eukaryotic genes that is removed from the mRNA transcript by splicing
splicing
the process by which introns, the noncoding regions of genes, are excised out of the primary messenger RNA transcript
alternative splicing
alterations in how the exons are stitched together
tbh this is a stupid name for this term just call it joining or something.
ribosome
molecular machine that translates the genetic code contained in mRNA into a protein amino acid sequence - comprised of proteins and two types of rRNA
tRNA function
transfers amino acids to a growing protein chain during translation - has a secondary structure.
charged (in terms of tRNA)
when a tRNA is covalently bound to its amino acid
inosine
a modified nitrogenous base in the first position of the anticodon of tRNA that has the ability to bond with all of the mRNA nucleotide bases - contributes to degeneracy of code.
lack of specificity = WOBBLE
what are the three steps of translation?
1) initiation
2) elongation
3) termination
what is the start codon and what amino acid does it specify?
AUG
methionine (formyl methionine in prokaryotes)
-all proteins begin with met
Shine-Dalgarno sequence
special short sequence in prokaryotes near the AUG start codon of mRNA where binding of small ribosomal subunit to mRNA polymer occurs to generate the translation apparatus.
how does the translation apparatus form in eukaryotes
Met-tRNA binds to small ribosomal subunit and protein factors -> whole thing binds to mRNA at 5’ end and then travels in 3’ direction until start codon is reached -> large ribosomal subunit assembles.
what are the three sites of the ribosome?
1) E (exit)
2) P (peptidyl)
3) A (aminoacyl)
how does the tRNA move through the 3 ribosomal sites?
1) initiator rRNA and initiation complex is formed in the P site
2) tRNA binds in the A site - tRNA with correct anticodon will be trapped there
3) A site amino acid displaces P site t RNA
4) whole assemble translocates in the 5’ -> 3’ along the mRNA by one codon which takes it to the E site (this leaves the second tRNA in the P site and nothing in the A site)
5) tRNA is released from ribosome
6) new charged tRNA matching the third codon will enter the A site (which displaces the P site)
7) process continues
what are the termination codons?
TAA, TAG, TGA
no tRNA contain anticodons to these
how does termination complete?
amino acid chain is cleaved from tRNA and a full length protein is released
operon
a cluster of genes that are transcribed together to give a single messenger RNA (mRNA) molecule, which therefore encodes multiple proteins
- made up of a promoter, an operator, a regulatory gene, and one or more structural genes
operator
lies adjacent to or overlaps with the promoter - serves as the binding site for a protein
repressor
a protein that inhibits the expression of one or more genes - by binding to the promoter to stop RNA polymerase from binding to the promotor.
encoded by a regulatory gene
how are repressors controlled?
by chemicals in the metabolic pathway - changing the concentration of the chemical changes the status of the operon
lac operon
the cluster of genes involved in metabolism of lactose
inducible operon
one whose expression increases quantitatively in response to an enhancer, an inducer, or a positive regulator.
trp operon
operon involved in making tryptophan
repressible operon
operon that is turned off by a metabolic substance (co-repressor)
what did Khorana, Nirenberg, and Holley do?
indentified which triplet codons coded for which amino acid
Can exons be rearranged during splicing
NO! the exons can be left out but not rearranged!!
