9.3, 9.4, 11, 12 Flashcards
_____ consist of one small ribosomal subunit and one large ribosomal subunit
Ribosomes
The sequence _____ is found at the very 3′ end of all tRNAs, the amino acid attachment site.
5′-CCA-3′
Single-stranded, 75 nucleotides, cloverleaf shape with four double-helical stems and three single-stranded loops.
tRNA
A nucleotide triplet in a tRNA molecule that aligns with a particular codon in mRNA under the influence of the ribosome; the amino acid carried by the tRNA is inserted into a growing protein chain.
anticodon
anticodon is complementary to:
the mRNA codon for the amino acid carried by the tRNA
tRNAs are transcribed with:
the standard four nucleotides
;All tRNAs fold into virtually the same inverted L-shaped three-dimensional ____ conformation.
cloverleaf
The anticodon in tRNA and the codon in the mRNA interact by:
specific RNA:RNA base pairing
anticodons are oriented and written in the _____ direction
3′-to-5′
tRNAs have four important structural features:
(1) the sequence CCA at the 3′ end; (2) modified nucleotides such as dihydrouridine, pseudouridine, and inosine; (3) an overall inverted L shape; and (4) an anticodon.
Amino acids are attached to tRNAs by enzymes called:
aminoacyl-tRNA synthetases
The tRNA with an attached amino acid is said to be
charged tRNA
First step of charging tRNA
carboxyl group of the amino acid reacts with the α-phosphate of ATP to form 5′-aminoacyl-AMP and release pyrophosphate
Second step of charging tRNA
the amino acid is transferred to the adenosine (A) of the invariant CCA sequence at the 3′ end of the tRNA, and AMP is released as a by-product.
If the wrong amino acid is attached…
there is no way to prevent it from being incorporated into a growing polypeptide chain - amino acids are “illiterate”
to prevent mistakes, aminoacyl-tRNA synthetases have a ______ that discriminates between chemically similar amino acids such as valine (Val) and isoleucine (Ile), which differ by only a single CH2 group
two-step mechanism
The first discrimination step
rejects amino acids that do not fit into the activation site because they are too large
The second discrimination step
Val-tRNAIle, but not Ile-tRNAIle, fits into a separate active site of the synthetase and is hydrolyzed to valine and tRNAIle
______________ allows tRNAs to recognize more than one codon
Wobble base pairing
the third codon
the wobble position
inosine (I), a rare modified base in tRNA, can base pair to
C, U, A
Therefore, because of wobble base pairing, cells require ______ tRNAs to read all of the codons.
fewer than 61
Sedimentation coefficients in ______ measure the size of the molecule.
Svedberg (S) units
In bacteria, the small and large subunits are _________ and form a ____ particle.
30S and 50S; 70S
The eukaryotic subunits are _________, and they form an ______ particle.
40S and 60S, 80S
rRNAs fold up by _________ into stable secondary structures.
intramolecular base pairing
_____, assisted by the ribosomal proteins, catalyze protein synthesis.
rRNAs
Key sites of interaction in the ribosome:
A, P, E sites in the small subunit and the peptidyl transferase center in the large subunit.
The ___________ is a ribosomal binding site in bacterial and archaeal messenger RNA, generally located around 8 bases upstream of the start codon AUG
Shine–Dalgarno sequence
a nucleic acid motif that functions as the protein translation initiation site in most eukaryotic mRNA transcripts. (surrounding the first AUG in eukaryote mRNAs)
Kozak sequence
_______ bring the initiator tRNA to the ribosomal small subunit and prevent premature binding of the large subunit.
Initiation factors
In eukaryotes, additional initiation factors facilitate:
mRNA scanning and circularization.
What are the two protein elongation factors function repeatedly to grow the polypeptide chain?
- EF-Tu brings charged tRNAs to the ribosome A site to be joined to the polypeptide chain in the P site.
- EF-G binds in the A site and promotes the translocation of tRNAs from the P and A sites to the E and P sites.
In eukaryotes, the analogous elongation factors are:
eEF1α and eEF2.
What are the translation release factors?
Proteins
How is translation terminated?
Release factors bind stop codons and release the polypeptide chain from the tRNA in the P site.
Other factors ____ the ribosome to begin another round of translation.
recycle
A ______ counteracts the effects of a nonsense mutation
tRNA suppressor
The two criteria for gene regulation mechanisms
1) Response to environmental cues
2) Toggle on and off
Regulatory proteins and their binding sites that control transcription
Genetic switches
DNA components (cis-acting):
promoter & operator
Protein components (trans-acting):
Activator & Repressor
Activator or repressor proteins bind to ___________ to control its accessibility to RNA polymerase.
operator sequences in the vicinity of the promoter
Allosteric effectors bind to ____________
regulatory proteins
Repressor protein controls the lac operon
Negative control
The lac operon is transcribed only in the presence of _______
lactose
an operon required for the transport and metabolism of lactose in E. coli and many other enteric bacteria
lac operon
a region of DNA where RNA polymerase begins to transcribe a gene
promoter
A segment of DNA where the repressor binds to, thereby preventing the transcription of certain genes
operator
DNA-binding transcription metabolite that positively modulates an allosteric Enzyme or regulates one or more genes by increasing the rate of transcription
activator
blocks the attachment of RNA polymerase to the promoter
repressor
An agent capable of activating specific genes. A molecule that inhibits the action of the repressor of an operon, preventing it from freely binding with the operator gene and disabling its function.
Inducer
A group of genes or a segment of DNA that functions as a single transcription unit. It is comprised of an operator, a promoter, and one or more structural genes that are transcribed into one polycistronic mRNA.
operon
How are operons regulated?
They contain regulatory DNA sequences (binding sites) that control transcription of the operon
chaperons that help repair other proteins which may become partially denatured through excessive heating
Heat shock proteins (HSPs)
mechanisms that affect gene expression only on the same chromosomal allele
Cis-acting factors
The gene that encodes the soluble ______ protein can reside on any chromosome, often located far away from the gene whose expression it regulates
trans-acting
Operators are ____-acting
cis
Catabolite repression of the lac operon
positive control
_______ levels control the lac operon
Glucose
By bending the DNA template, the DNA-bound CAP and cAMP can interact physically with RNA polymerase and increases that enzyme’s affinity for:
the lac promoter.
Two regulators turn the operon “on” and “off” in response to lactose and glucose levels:
the lac repressor (negative) and catabolite activator protein (CAP) (positive)
The _____ ensures the sequential utilization of different carbon sources depending on the bacterial cells’ nutritional environment.
lac operon
Metabolic pathways and additional levels of regulation
attenuation
Gene order in the trp operon corresponds to reaction order in:
the biosynthetic pathway
Two mechanisms regulate trp operon:
1) trp repressor: trpR switch off trp operon in the presence of tryptophan
2) Attenuation
The trp mRNA leader sequence contains
an attenuator region and two tryptophan codons
The attenuation of transcription is mediated by
the abundance of tryptophan and translation of a leader peptide
Can attenuation be used as a mechanism for regulating gene expression in eukaryotes?
No - in eukaryote transcription and translation do not take place in the same region of the cell
The machinery required for regulating the distinct patterns of gene transcription in eukaryotic cells.
1) Trans-components
2) Cis-components
3) Coregulators
Trans components
Transcription factors, general transcription factors (GTFs)
Cis-components
core promoters, proximal promoters, enhancers ( proximal and distal)
bridges transcription factors and RNA polymerase II.
Coactivators
Transcriptional activator proteins - 2 functions
1) recruit the transcriptional machinery (including general transcription factors and RNA Polymerase II)
2) recruit proteins that modify chromatin structure (such as mediator)
Transcription factors have modular structure: (4 things)
1) DNA binding
2) Activation/repression
3) Dimerization of transcription factors
4) Ligand-binding domains of transcription factors
Multiple genes and their products import and convert _______ into glucose in a metabolic pathway.
galactose
GAL4 regulates the expression of galactose/glucose through:
upstream activation sequences (UAS).
GAL pathway response to environment?
controls the uptake and metabolism of the sugar
Transcription factors in the yeast GAL system:
Cis: UAS
Trans: Gal4
How is GAL4 activity regulated?
Gal4 levels are regulated by the F-box protein Grr1
How does regulation of transcription differ between prokaryotes and eukaryotes?
Transcription is responsible for most gene regulation in prokaryotes but in eukaryotes gene regulation is more complicated and genes are regulated before and after transcription
a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence.
transcription factor
What functional protein domains are found in transcription factors? - 3 things
1) a DNA binding domain, 2) one or more transcription activation and/or repressor domain, and 3) often a dimerization domain
How can an enhancer located far away from the promoter help to activate transcription?
An enhancer can activate transcription from a target gene promoter through direct interaction over a large distance by creating a chromatin loop.
________ is made up of nucleosomes that fold upon one another into a compact filament.
Chromatin
Chromatin structure of genes
(3 things)
NFR
TADs
CTCF
Mechanisms operate to enable dynamic access of the transcription machinery to DNA in ______ cells
eukaryotic
altering the chemical structure of amino acids in histones or nucleotides in DNA to affect recruitment of transcription factors, coregulators, and general transcription factors to chromatin.
Chromatin modification
remodeling nucleosomes—reposition histone octamers, remove histone octamers from DNA, or replace canonical histones in octamers with variant histones
Chromatin remodeling
Histone acetylation is a type of:
chromatin modification
______ leads to more open chromatin by loosening interactions between histones and DNA .
Acetylation
Acetylation creates ________ with a bromodomain, which increases the affinity of the transcription factors for particular genes by binding acetylated histones.
binding sited for proteins
Histone methylation
Lysine (K) and Arginine (R)
Changing ________________ in nucleosomes to render DNA either more or less accessible to transcription regulators.
histone-DNA interactions
Heritable changes to gene expression that are not due to changes in DNA sequences
Do not follow the Mendelian inheritance patterns
Epigenetic Inheritance
the stochastic transcriptional silencing of a gene positioned adjacent to heterochromatin.
Position effect variegation
the process by which only one copy of a gene in an individual (either from their mother or their father) is expressed, while the other copy is suppressed (autosomal)
Genomic imprinting
Early in embryonic development in females, one of the two X chromosomes is randomly and permanently inactivated in cells other than egg cells
X-chromosome inactivation
maternal imprinting
copy from father is turned on
paternal imprinting
copy from mother is turned on
