RNA and the Genetic Code Flashcards
Ch 7
central dogma
states that DNA is transcribed to RNA, which is translated to protein
degenerate code
allows for multiple codons to encode for the same amino acid
-allows for mutations in DNA that do not always result in altered protein structure or function
initiation (start) codon
AUG
termination (stop) codon
UAA: U Are Annoying
UGA: U Go Away
UAG: U Are Gone
wobble
third base in the codon
what allows for mutations to occur without effects in the protein?
redundancy and wobble
point mutations can cause
they are often called expressed mutations:
nonsense mutations (truncation)
missense mutations
silent mutations
mutations with no effect on protein synthesis
these tend to be in mutations in the wobble position
nonsense mutations (truncation)
mutations that produce a premature stop codon
missense mutations
mutations that produce a codon that codes for a different amino acid
messenger (mRNA)
messenger of genetic information
- carries message from DNA in the nucelus via transcription of the gene
- travels into the cyptoplasm to be translated
DNA codes for
codes for proteins but cannot perform any of the important enzymatic reactions that proteins are responsible for in cells
where does the creation of the primary protein structure occur?
ribosomes
transfer RNA (tRNA)
responsible for converting the language of nucleic acids to the language of amino acids and peptides
ribosomal RNA (rRNA)
synthesized in the nucleolus, makes up ribosome
used during protein assembly in the cytoplasm
helps catalyze the formation of peptide bonds
important in splicing out its own introns within the nucleus
frameshift mutations
result from nucleotide addition or deletion, and change the reading frame of subsequent codons
RNA is similar to DNA except
- substitution of a ribose sugar for deoxyribose
- substitution of uracil for thymine
- it is single stranded instead of double stranded
there are three types of RNA in transcription
transfer RNA
messenger RNA
ribosomal RNA
transcription
the creation of mRNA from a DNA template
RNA translation
changes the language from nucleotides to amino acids
it’s translating for us!
helicase
unwinds the DNA double helix
RNA polymerase II
binds to the TATA box within the promoter region of the gene
-25 base pairs upstream from first transcribed base
does nor require a primer to start generating a transcript
what is RNA synthesized by
a DNA-dependent RNA polymerase
locates genes in promotor regions
TATA box
high concentration of thymine and adenine bases
what do transcription factors help with
help the RNA polymerase locate and bind to its promoter region of the DNA
help establish where transcription will start
RNA polymerase I
located in the nucleolus and synthesizes rRNA
RNA polymerase II
located in the nucleus and synthesizes hnRNA (processed mRNA) and some small nuclear RNA (snRNA)
RNA polymerase III
located in the nucleus and synthesizes tRNA and some rRNA
hnRNA is synthesized from
heterogeneous nuclear RNA
the DNA template (antisense) strand
what is significant about hnRNA
mRNA is derived from hnRNA via posttransciptional modifications
post-transcriptional processing includes
- intron/exon splicing
- 5’ cap
- 3- poly-A tail
what is significant about posstransciptional processing?
before the hnRNA can leave the nucleus and be translated into protein, it must undergo process to allow it to interact with the ribosome and survive the conditions of the cytoplasm
DNA - parents
hnRNA - child
the child must mature if he/she is to survive
mnemonic for introns and extrons
INtrons stay IN the nucleus
EXtrons will EXit the nucleus as part of the mRNA
intron/exon splicing in posttranscriptional processing
- removes the noncoding sequences of the intron and the ligate coding sequences of the exon
- splicing is done by snRNA and snRNPs in the spliceosome
- introns are remove in a lariat structure
- exons are ligated together
5’cap in the posstranscriptional processing
a 7-methylguanylate triphosphate cap is added
- protects the mRNA from degeneration in the cytoplasm
- added during the transcription process and recognized by the ribosome as the binding site
3’ Poly-A Tail in posttranscriptional processing
a polyadenosyl (poly-A) tail is added to the 3’ end
- protects the message against rapid degradation
- the “time bomb” for the mRNA transcript: the longer the poly-A tail, the more time the mRNA will be able to survive before being digested in the cytoplasm
polycistronic genes
starting transcription in different sites within the gene leads to different gene products
-prokaryotic cells can increase the variability of gene products from one transcript
alternative splicing
combining different exons in a modular fashion to acquire different gene products
-eukaryotic cells can increase variability of gene products
tRNA does what
translates the codon into the correct amino acid
what are the factories where translation (protein synthesis) occur?
ribosomes
what are the three stages of translation?
- initiation
- elongation
- termination
initiation (in translation)
in prokaryotes, occurs when the 30s ribosome attaches to the Shine-Dalgarno sequence and scans for the AUG start codon
-lays down N-formlymethionine in the P site of the ribosome
DNA to DNA term
replication
new DNA synthesized in 5’ to 3’ direction
DNA to RNA term
transcription
new RNA synthesized in 5’ to 3’ direction
RNA to protein
translation
mRNA read in 5’ to 3’ direction
comparison of the prokaryotic ribosome to the eukaryotic ribosome
prokaryotic ribosome: 50S + 30S = 70S
eukaryotic ribosome: 60S + 40S = 80S
when does initiation (in translation) happen in eukaryotes?
occurs when the 40S ribosome attaches to the 5’ cap and scans for a start codon
it lays down methionine in the p site of the chromosome
elongation (in translation)
involves the addition of a new aminoacyl-tRNA into the A site of the ribosome and transfer of the growing polypeptide chain from the tRNA in the P site to the tRNA in the A site
-uncharge tRNA pauses in the E site before exiting the ribosome
order of sites in the ribosome during translation
APE
termination
when the codon in the A site is a stop codon
release factor
places a water molecule on the polypeptide chain and thus releases the protein
posttranslational modifications include
- folding of chaperones
- formation of quaternary structure
- cleavage of proteins or signal sequences
- covalent addition of other biomolecules (phosphorylation, carboxylation, glycosylation, prenylation)
phosphroylation
addition of a phosphate (PO4^2-) by protein kinases to active or deactivate proteins
-in eukaryotes, most commonly seen with serine, threonine, and tyrosine
carboxylation
addition of carboxylic acid groups
-usually to serve as calcium-binding sites
glycosylation
addition of oligosaccharides as proteins pass through the ER and golgi apparatus to determine cellular destination
prenylation
addition of lipid groups to certain membrane-bound enzymes
operon
a cluster of genes transcribed as s ingle mRNA
- include bother inducible and repressible systems
- offer a simple on-off switch for gene control in prokaryotes
Jacob-Monod model
explains how operons work
-repressors and activators
two systems: inducible and repressible systems
inducible systems
ex: lac operon
allow for gene transcription only when an inducer is present to bind the otherwise present repressor protein
-negative control: the binding of a protein to DNA stops transcription
the system is normally “off” but can be made to turn “on” given a particular signal
repressible systems
allow constant production or a protein product
- continually allow gene transcription unless a corepressor binds to the repressor to stop transcription
- the system is normally “on” but can be made to turn “off”, given a particular signal
ex: trp operon
positive control
the binding of a protein to DNA increases transcription
negative control
the binding of a protein to DNA stops transcription
transcription factors
search for promoter and enhancer regions in the DNA
-two recognizable domains: a DNA-binding domain and an activation domain
promoters
within 25 base pairs of the transcription start site
enhancers
more than 25 base pairs away from the transcription start site
modification of chromatin structure affects what
the ability of transcriptional enzymes to access the DNA through histone acetylation (increases accessibility) or DNA methylation(decrease accessibility)
what is the difference between DNA regulatory base sequences and transcription factors
DNA regulatory ase sequences are known as cis because they are in the same vicinity as the genes they control
transcription factors are trans because they have to be produced and translocated back to the nucleus
DNA binding domain
binds to specific nucleotide sequence in the promoter region or to a DNA response element
activation domain
allows for the binding of several transcription factors and other important regulatory proteins
what role does peptidyl transferase play in protein synthesis?
it catalyzes the formation of a peptide bond between the incoming amino acid in the A site and the growing poly peptide chain in the P site
what stage of protein synthesis does not require energy?
THEY ALL REQUIRE LARGE AMOUNTS OF ENERGY
topoisomerase are enzymes involved in what?
DNA replication and transcription
enhancers are transcriptional regulatory sequences that function by enhancing the activity of
RNA polymerase at a single promoter site
specific transcription factors bind to a specific DNA sequence, such as an enhancer, and to a RNA polymerase at a single promoter sequence. They enable the RNA polymerase to transcribe the specific gene more efficiently
frameshift mutation
when some number of nucleotides are added to or delted from the mRNA sequece
-this will shift the rading frame and usually resulting in changes in the amino acide sequence or premature truncation of the protein
signal molecules
- enhancer in transcription factors
- ex: cyclic AMP, cortisol, estrogen, bind to specific receptors
at high ph, what happens to the amino acid
protons are scarce
rip off the protons
negative charge on the AA
deprotonate
at low pH, what happens to the amino acid
abundance of protons
load them on the AA
protonate
positive charge on the AA
oxidation
less bonds to H
reduction
more bonds to H
primary level of organization
amino acid sequence
Secondary level of organization
alpha helices
beta sheets
short range interactions
H bonds between backbone
tertiary structure
long range interactions
disulfide bonds, H bonds b/w R groups, salt bridge, hydrophobic interactions
quaternary
2 or more subunits
