Lecture 12 Flashcards
The central dogma refers to:
which is ___directional
the flow of information in the cell
unidirectional
Define a gene
a gene is a region of DNA that directs the synthesis of an RNA molecule
- it’s a unit of heredity
What’s a promoter?
a DNA sequence that directs/ regulates transcription
- site of RNA polymerase assembly
the first nucleotide to be transcribed is at ____[number] on the ____
(start site of transcription- where there’s a start codon)
+1
double stranded DNA
A common promoter in prokaryotes is the _______
- the ___ sequence is A/T rich. Why?
- the ___ sequence orients ___ ____
- the minus 10 and minus 35 combo
- minus 10. Because A and T is a weaker base pair (so it’s easier to pull apart the DNA)
- minus 35. orients RNA polymerase
What are the -10 and -35 sequences?
specific 6 base pair sequences common to most bacterial promoters
(the -10 and -35 combo)
mRNA is synthesized in what direction?
5’ to 3’
Directions:
Transcription occurs __ to ___ by reading the template strand __ to ___
5’ to 3’
template is read 3’ to 5’
True/ false
There are multiple genes on each chromosome
True
What is transcription?
the process of copying a segment of DNA into RNA
Describe the template strand
the strand of DNA that’s used in transcription
- runs 3’ to 5’ away from the promoter
Describe the coding strand
complementary and antiparallel to the template strand
- runs 5’ to 3’ away from the promoter
- NOT used in transcription
Define “transcript”
a piece of RNA that’s the product of transcription
How does RNA pol “know” where a gene is?
it’s recruited to a promoter by transcription factors
compare DNA polymerase and RNA pol.
list 3 differences
DNA:
- takes part in DNA replication
- requires a primer
- useful for both strands of DNA
RNA:
- takes part in transcription
- does not require a primer
- acts only on the template strand of DNA
Transcription vs. translation?
Transcription is DNA –> RNA
Translation is RNA –> protein
*transcription comes first
define genetic code
Genetic code is the term we use for the way that the four bases of DNA–the A, C, G, and Ts–are strung together in a way that the cellular machinery, the ribosome, can read them and turn them into a protein. In the genetic code, each three nucleotides in a row count as a triplet and code for a single amino acid.
which experiment helped determine the universal genetic code?
Nirenberg experiment
what are the 3 post-transcriptional modifications? Where do they occur?
- Addition of a methyl-guanosine cap at the 5’ end
- addition of 100-200 adenosines to the 3’ end, known as the poly-A tail
- Splicing
They occur in the nucleus of eukaryotes
what’s the function of the first 2 post-transcriptional modifications?
(meG cap and poly-A tail)
they both function to increase stability of mRNA in cytoplasm
- they prevent/ delay exonuclease digestion (of our own mRNA!)
what’s an exonuclease?
evolved from an antiviral response- degrades any foreign RNA (like covid!)
- our own RNA is protected from exonuclease digestion by the post-transcriptional modifications: meG cap and poly-A tail
- eukaryotes only
Fill in the blank (RNA Polymerase)
- RNA pol is part of a transcription initiation complex that assembles at the _____
- RNA pol synthesizes RNA ___’ to __’ (by reading DNA __’ to __’)
- RNA pol “knows” where a gene is because it’s recruited to a promoter by ____ _____
- RNA pol ____(does/ does not) require a primer and has its own “____” activity.
- promoter
- RNA: 5’ to 3’ by reading DNA 3’ to 5’
- transcription factors
- does not
helicase activity (can open DNA on its own)
template strand is chosen based on the direction of the ____
promoter
if it’s on the right, the bottom strand is the template
As mRNA is elongated, the area that’s unwound is called the ____ ____
transcription bubble
RNA splicing removes ____, which are _________
introns= “intervening sequences (non-coding)”
What is a spliceosome?
a complex of snRNPs (protein/ RNA complex; recognizes sequences at intron/ exon boundaries). In the splicing of mRNA, snRNPs bind intron/ exon boundaries and loop out the intron (into the lariat).
Explain alternative splicing
mix and matching of exons; makes similar but non identical proteins from the same gene.
This is the reason splicing has survived evolutionarily.
- eg. can splice intron 1, exon 2, and intron 2= creates muscle protein
OR splice just the 2 introns= creates neural protein
why is RNA single stranded?
because of the 2’ OH: it provides more reactivity, therefore the RNA molecule likes to be alone
transcription initiation ends after ________
the first phosphodiester bond is catalyzed.
Ingredients for translation
A) tRNAs (the translator)
B) Aminoacyl tRNA synthetases
C) Ribosomes (the “machine”)
Aminoacyl tRNA synthetase is required to attach ___ to an ___ ___
the tRNA to an amino acid
4 steps of translation in prokaryotes
- pre-initiation (charging)
- initiation
- elongation
- termination
Aminoacyl tRNA synthetases pairs the correct amino acids based on the ____ sequence
(covalently links a.a. to tRNA in sequence dependent manner)
- results in a ____ tRNA which associates with the appropriate a.a.
anticodon
- charged tRNA
Ribosomes are large protein complexes with ___s associated.
- they catalyze the formation of ____ ____
- they facilitate the specific coupling of ___ ____(codons/ anticodons) with mRNA ____ (codons/ anticodons) during protein synthesis
rRNAs
- peptide bonds
- tRNA anticodons with mRNA codons
proteins are synthesized __ to __ by reading mRNA __’ to __’
N to C
5’ to 3’
3 important sites in a ribosome
A= "approach" (furthest right) P= "polymerization" E= exit (furthest left)
compare and contrast small/ large ribosomal subunits
small: contains rRNA
- recognition of mRNA
large: contains rRNA
- catalytic site
*functions are provided by the associated rRNAs
define the rbs (ribosomal binding site)
a sequence in the mRNA that’s recognized by base pairing with rRNA in the small ribosomal subunit
- binds to the ribosome to position the message correctly for the initiation of translation. The RBS controls the accuracy and efficiency with which the translation of mRNA begins.
In prokaryotes, translation occurs in the ___
cytoplasm
In the inititaion phase of ____, the rbs positions the small subunit such that the start codon sits in the __ site
translation
- P-site
In elongation, what happens?
What’s the phrase?
BIND- BOND- SHIFT
- various elongation factors escort the next tRNA into the A site of the ribosome
- peptidyl transferase catalyzes the formation of a peptide bond b/w the F-met and 2nd amino acid
Describe what happens in the “BIND” phase of elongation
tRNA carrying the correct amino acid approaches the A-site and binds to the mRNA (codon-anticodon specificity)
Describe what happens in the “BOND” phase of elongation
a peptide bond forms b/w tRNA #1 and tRNA #2 and the growing chain moves to the tRNA in the A-site (tRNA #2)
after the “bond” phase of elongation, the whole a.a chain is in the __ site
(so tRNA #__ is empty)
A-site #1 empty (the tRNA in the P-site)
Describe what happens in the “SHIFT” phase of elongation
ribosome shifts down mRNA (to 3’ end) in a one codon step
therefore the A-site becomes available again
In the termination phase of translation, what happens when a stop codon is read?
When a stop codon is read, a release factor (which recognizes the stop codon) moves into the A site
- the polypeptide is then released from the tRNA, and all the ribosome components seperate and dismantle (they’re recycled)
release factor allows the a.a. chain to dissociate from the __ in the __-site
tRNA
P-site
transcription and translation coupling occurs in ___only
prok
Define mutation
a heritable change in base sequences that modify the info content of DNA
what is “wild type (WT)” DNA?
the “normal” sequences (generally the alleles that dominate in a wild population
Which mutation is at the DNA level? What can this cause?
base-pair substitutions= the replacement of one nucleotide & its partner with another pair
-This can cause mutations at protein level
Which mutations are at a protein level? What causes them?
- Silent mutations
- missense mutations
- nonsense mutations
- frameshift mutations
they’re caused by mutations at the DNA level (base pair substitutions)
Define a silent mutation
no change in the primary sequence
- because of the redundancy in the genetic code
Define a missense mutation
encode the wrong amino acid
- change in the primary sequence
- MAY affect protein function
define a nonsense mutation
premature stop codon
- shortened protein
- MAY affect protein function
define a frameshift mutation
single base pair added or deleted that changes the reading of a protein
If you change the primary sequence of a protein, you MAY change the ____ and thus the ___ of the protein
folding
function
Sickle cell anemia is a ___ mutation which causes _____
missense
causes: aggregation of hemoglobin and misshapen red blood cells
Muations can be spontaneous (DNA replication errors) or induced. Give some examples of induced mutations
- caused by mutagens such as:
x-rays
gamma rays
base analogs (mimic bases but don’t pair correctly)
oxidizing agents (damage bases, so they don’t pair properly)
benzene
