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what is transcription?
making an RNA copy of a gene sequence
what happens to mRNA during transcription?
it leaves the cell’s nucleus and enters the cytoplasm, where it directs the synthesis of the protein it encodes for
what does RNA polymerase do?
uses a single-stranded DNA template to make a complementary strand of RNA
which direction does RNA polymerase build the RNA strand in?
5' to 3' direction, adding each new nucleotide to the 3' end of the strand.
what are the 3 steps of transcription?
initiation, elongation, termination
what happens during initiation (transcription)?
RNA polymerase binds to promoter and separates the DNA strands, providing the single-stranded template needed for transcription
what is a promoter region?
sequence of DNA found near the beginning of a gene that RNA polymerase binds to; each gene has a promoter
what is an operon?
each gene or group of co-transcribed genes in bacteria
what happens during elongation (transcription)?
template strand of DNA is used as a template for RNA polymerase; it reads template and builds an RNA molecules out of complementary nucleotides, making a chain that grows from 5' to 3’
what bases are in RNA?
A, U, C, G
what bases are in DNA?
A, T, C, G
what happens during termination (transcription)?
sequences called terminators signal that the RNA transcript is complete and transcript is released from RNA polymerase
what is a terminator sequence?
sequence that, once transcribed, causes the transcript of RNA to be released from the RNA polymerase during termination phase
what is an intron?
Parts of the pre-mRNA that are chopped out
what are exons?
remaining pieces of pre-mRNA after splicing that are stuck back together
what is the difference between mRNA modifications and mRNA splicing?
end modifications increase the stability of the mRNA; splicing gives the mRNA its correct sequence
what are thee mRNA modifications?
5' G-cap & poly-A tail; used to maintain stability of mRNA
transcription happens for ___ genes, not the whole genome
individual
what is translation?
translating the sequence of a mRNA molecule to a sequence of amino acids during protein synthesis
what is a ribosome?
“reader”; big, multi-subunit molecule that travels along the mRNA strand and decides which amino acids to add in what order
what is a codon?
three-letters long sequences that code for particular amino acids during translation
what is a start codon?
AUG; signals the start of translation reading; helps establish reading frame
what is a stop codon?
UGA, UAA, UAG; signals the end of translation reading; helps establish reading frame
what is the reading frame (translation)?
space of translation that the ribosome follows to correctly translate mRNA sequence; starts at start codon, ends at stop codon
what does initiation of translation require?
ribosome (large & small)
mRNA w/ instructions for the protein being built
"initiator" tRNA carrying the first amino acid in the protein (almost always methionine (met))
what are thee 3 steps of translation?
initiation, elongation, termination
what happens during initiation (translation)?
tRNA w/ MET attaches to small ribosomal subunit
tRNA binds to mRNA at 5' end (G-cap)
moves to start codon (AUG)
large subunit joins small to form initiation complex
what is a shine-dalgarno sequence?
in bacteria, marks the start of each operon, letting the ribosome find the right start codon for each gene; small ribosomal subunit attaches directly to these sequences
what is the p-site?
part of large ribosomal subunit complex where tRNA (carrying MET) binds at start of elongation
what is the a-site?
"landing site" for the 2nd tRNA during elongation; part of large ribosomal subunit
what is the e-site?
part of large ribosomal subunit; where empty tRNA can exit the ribosome after adding their amino acid to the growing polypeptide chain
what happens during elongation (translation)?
tRNA w/ complementary anti-codon binds to A site
peptide bond forms between amino acids on tRNAs in P & A sites
mRNA shifts, moving tRNA from A to P site and from P to E site
empty tRNA in E site exits ribosome
another tRNA w/ complementary anti-codon binds to A site… etc.
what happens during termination (translation)?
stop codon (UAA, UAG, or UGA) enters the A site
release factors recognize the stop codon.
ribosome adds a water molecule to the last amino acid of the chain
this reaction separates the chain from the tRNA
newly made protein is released
what are post-translational modifications?
amino acids may be chemically altered during/after translation; new polypeptide fold into a distinct 3D structure; may join w/ other polypeptides to make a multi-part protein
what is a release factor?
protein that allows for the termination of translation by recognizing the termination codon or stop codon in an mRNA sequence
what is a chaperone (of amino acids)?
proteins that assist the conformational folding/unfolding of large proteins
what is gene expression?
wide range of mechanisms used by cells to increase or decrease the production of specific gene products (protein or RNA)
how is gene expression controlled (2 levels)?
by controlling the amount of mRNA that is produced
through post-transcriptional events that regulate the translation of mRNA into protein
how do bacteria control gene expression?
w/ specific regulatory molecules that act by binding to DNA near the gene and helping OR blocking RNA polymerase
what are related genes?
often found in clusters (operons) on the chromosome; are transcribed from one promoter as a single unit
related genes are ___ in bacteria, but ___ in eukaryotes
common; rare
what are regulatory DNA sequences?
act as binding sites for regulatory proteins, which control how much the operon is transcribed
what is a repressor?
when bound to its operator, it reduces transcription by blocking RNA polymerase from moving forward on the DNA
what is an activator?
when bound to its DNA binding site, it increases transcription of the operon by helping RNA polymerase bind to the promoter; may only become active (able to bind DNA) when it's attached to a certain small molecule
how manny structural genes does the trp operon have?
5
when is the trp operon expressed? when is it repressed?
expressed (turned "on") when tryptophan levels are low; repressed (turned
"off") when they are high
what does the trp repressor do in the absence of tryptophan?
it dissociates from the operator and allows for RNA synthesis to begin
what does the trp repressor do in the presence of tryptophan?
it binds to the operator and blocks RNA synthesis
how many genes does the lac operon have involved in lactose metabolism?
3
when is the lac operon expressed?
when lactose is present or when glucose is absent
which 2 regulators turn the lac operon on/off in response to sugar levels?
lac repressor & catabolite activator protein (CAP)
what is an inducible operon?
one whose expression increases in response to an enhancer, an inducer, or a positive regulator; usually turned off but can be turned on
how does the catabolite activator protein affect the lac operon?
it acts as a glucose sensor; activates transcription of the operon, but only
when glucose levels are low; CAP senses glucose indirectly, through the
molecule cAMP
what are nucleotides?
macromolecule made up of repeating units w/ 5-carbon sugar (ribose or deoxyribose), phosphate group, & nitrogenous base
which bases are purines? which are pyrimidines?
purines: adenine (A) & cytosine (C)
pyrimidines: thymine (T) guanine (G), & uracil (U)
RNA is ___ stranded, while DNA is ___ stranded
single; double
RNA can ___ the nucleus and go to ribosomes, while DNA cannot
leave
how are the 2 strands of DNA arranged?
anti-parallel; 3’ end is the hydroxyl group of the sugar (with the 3rd carbon exposed); 5’ end is the phosphate (attached to the 5th carbon)
how many hydrogen bonds are between A & T vs. C & G?
A-T has 2 bonds; C-G has 3 bonds
what are the steps of DNA replication?
opening of the double helix and separation of the DNA strands
priming of the template strand
assembly of the new DNA segment
termination
what does helicase do?
helicase “unzips” the double helix structure of the DNA molecule at the origin of replication
what is the replication fork?
“y” shape created by the separation of DNA strands
what is the leading strand?
synthesized continuously during DNA replication; strand where DNA polymerase adds nucleotides in the 5' to 3' direction
what is the lagging strand?
synthesized discontinuously during DNA replication; strand where DNA polymerase adds nucleotides in okazaki fragments
what is are okazaki fragments?
short segments of DNA on the lagging strand; synthesized in the 5' to 3' direction and later joined by DNA ligase.
what is DNA ligase?
joins okazaki fragments together; enzyme that seals gaps between adjacent DNA fragments
what does DNA polymerase do?
replaces RNA primers with DNA; proofreads new strand to make sure there are no mistakes
what kind of replication is DNA?
semi-conservative
what is a mutation?
change in a DNA base-pair or a chromosome
what is the difference between somatic and germ-line mutations?
somatic mutations affect only the individual in which they arise; germ-line mutations alter gametes, affecting the next generation
what is a substitution (point mutation)?
replace one base-pair with another
what is a transition substitution?
convert a purine-pyrimidine pair to the other purine-pyrimidine pair (e.g., AT to GC or TA to CG)
what is a transversion substitution?
convert a purine-pyrimidine pair to a pyrimidine-purine pair (e.g., AT to TA, or AT to CG).
what is a frameshift mutation?
occurs when there is an addition or loss of nucleotides that shifts the grouping and changes the code for all downstream amino acids
what is an insertion? what is a deletion?
variants of frameshift mutations; insertions add nucleotides; deletions subtract nucleotides
what is a missense mutation?
DNA change that results in different amino acids being encoded at a particular position in the resulting protein
what is a silent mutation?
base changes that do not induce amino acid sequence changes in the affected gene product
what is a nonsense mutation?
sequence change gives rise to a stop codon rather than a codon specifying an amino acid
what is a neutral mutation?
changes in DNA sequence that are neither beneficial nor detrimental to the ability of an organism to survive and reproduce
what is a mismatch repair?
conserve DNA sequence by removing base mispairs created by replication or homologous recombination; corrects errors made by DNA replication, using the parental strand as a template
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