Flashcards in Protein Synthesis and trafficking Deck (72):
interacts with the aminoacyl tRNA synthetase enzymes which charge the tRNA with the appropriate activated amino acid
Is it near the 5' or 3' end of the tRNA?
D loop; 5' end
interacts with the 5S rRNA and stabilizes tRNA binding within the ribosome.
Is it near the 5' or 3' end of the tRNA?
TYC loop; 3' end
What's the difference in synthesizing precursors between proks and euks?
Proks: synth as multimeric precursors
(several tRNAs on one transcript)
Euks: precursors occur as monomeric transcripts
Proks: What is the first processing step of precursor tRNAs
multimeric precursors are processed to monomeric precursors
Proks: Ribozyme that cleaves the precursor tRNAs on the 5' side
Proks: cleaves the precursor tRNAs on the 3' side
Euks: How does splicing of tRNAs differ from splicing of mRNAs?
splicing of tRNAs is an ATP-dependent mechanism
Euks: Removes 5' leader sequence
RNase-P like enzyme
Euks: Removes bases at the 3' end and addition of the sequence CCA
Euks: what creates the anti-codon loop in most tRNAs?
removal of a short intron
Have modified bases in their tRNAs
proks and euks
Ribosome is composed of 2/3 RNA and 1/3 protein
Ribosome is composed of 1/2 RNA and 1/2 protein
Each precursor contains one copy of each rRNA
Proks ribosomal RNA synth: Initial transcription product is called a ___ rRNA and is cleaved by ____ to yield the individual rRNAs
30S; RNase III
Precursor transcript may also contain one or more tRNA genes in addition to rRNA genes
protein and RNA components can self-assemble in the absence of an overall structural assembly machinery
In the _____ genome, there are several hundred tandem repeats of the gene encoding __, ___and ___ rRNAs
Eukaryotic; 28S, 5.8S, and 18S
28S, 5.8S and 18S rRNAs are located in the ______ and are transcribed by ________ which also synthesizes a ___S rRNA precursor transcript that contains one copy of each of these rRNAs
nucleolus; RNA Pol I; 45S
Proks: rRNA(s) included in the large subunit
23S; 5S (50S)
Proks: rRNA(s) included in the small subunit
Euks: rRNA(s) included in the large subunit
28S, 5.8S, 5S (60S)
Euks: rRNA(s) included in the small subunit
______ transcribes the precursor of 5S rRNA, which is encoded by repetitive DNA in the ______
RNA pol III; nucleus
Euks: Site where the individual small and large subunits are formed
caused by an insertion in exon 11 of the α-chain of the hexosaminidase A
What are the six mechanisms of gene regulation?
3. RNA transport and localization
5. mRNA degradation
6. Protein activity
As described for CRP, _____ is the most common Transcription factor DNA binding motif for prok regulators
critical for recognition between amino acid side chains and base pairs in the major groove
protein contacts with the DNA backbone involve both _____ and _______with the ____ atoms of the phosphodiester bonds.
hydrogen bonds; salt bridges; oxygen
Transcription factor DNA binding motifs whose proteins commonly form dimers
HTH motif, leucine zippers, bZIP, bHLH
a helix-turn-helix motif has a_______ α-helix that binds in the _____ groove, an _____ turn and a second α-helix known as the ______ helix
recognition; major; unstructured; stabilization
Like the HTH motif, the DNA-binding regions of zinc finger transcription factors are ______ (secondary structure).
Structure that involves a repetitive motif consisting of a pair of Cys residues and a pair of His (or Cys) residues in the sequence
Zinc Finger motif
With the Zn finger, each repeat coordinates a zinc ion via its two ____ and two ___ (or ____) residues
Cys; His (or Cys)
These transcription factors are dimers and their N-terminal, DNA-binding regions are α-helical regions known as the basic region
Leucine Zipper motif
proteins that have a similar periodicity as Leucine zipper but that have hydrophobic residues other than leucine have been found. the two polypeptides do not need to be identical
This protein dimerizes where each polypeptide has two α-helices separated from one another by a non-helical stretch of amino acids that loop out. Homo- and heterodimers can form
What does it closely resemble?
basic helix-loop-helix (bHLH) structural motif; leucine zipper
Class of transcription factors that binds the minor groove of DNA
HMG class (high mobility group)
Seven ways that transcription factors themselves are regulated:
1. Protein synthesis
2. Ligand binding
3. Protein phosphorylation
4. Addition of a subunit
6.Stimulation of nuclear entry
7.Release from membrane
What are two functions of methylating promoters
Physically blocks transcription machinery and blocks access to the promoter.
Which motifs can form heterodimers?
bZIP and bHLH motifs
Euks: the complex interplay of transcription factors and RNA polymerase occurs on:
Densely cover transcriptionally inactive genes
When a gene becomes transcriptionally active there is a major change in chromatin structure as determined by the appearance in the promoter region of:
regions of DNA particularly susceptible to digestion by nucleases
Dynamic transitions in chromatin structure and thus, switches between transcriptionally active and inactive states are mediated by:
acetylation and deacetylation of histone tails
Catalyze the transfer of an acetyl group to histones
histone acetyl transferases (HATs)
remove an acetyl group from histones
histone deacetylases (HDACs)
Histone ______ generally activates transcription
Acetylation of tail
The two families of enzymes that carry out histone methylation:
PRMT- protein arginine methyltransferases
HMT - histone lysine methyltransferase
What is the function of histone methylation?
Activate or repress transcription depending on the AA modified
Histones are phosphorylated on ____ and ____ residues by kinases,
serine and threonine
What changes occur with histone phosphorylation?
induce changes in the charge of the amino acids thought to open chromatin structure allowing transcription.
What are the roles of post-translational modifications of histone tails? (2)
1. Changes in charge of the histone tail amino acids that alter their interaction with the DNA. 2. The modifications attract specific proteins that can either cause further compaction of chromatin or facilitate access to DNA.
What are the post-translational modifications of histone tails (3)?
Acetylation, methylation, phosphorylation
non-specific endonuclease, which cleaves RNA in RNA:DNA hybrids
inhibits the binding of aminoacyl tRNA to the ribosome and thereby blocks continued translation in proks
blocks elongation, apparently by acting as a competitive inhibitor of peptidyl transferase in proks
Causes premature chain termination in proks. a portion of the molecule resembles the 3' end of the aminoacylated tRNA. it will enter the A and transfer to the growing chain, causing premature chain release. prevents translocation
Inhibitor of protein synthesis in euks. It ADP ribosylates eEF2 which is the factor that mediates translocation, leaving it non-functional, thus elongation is blocked
Facilitates rebinding at the AUG for another cycle of translation by ribosome (ribosome recycling on mRNA)
Poly A binding protein
Proteins destined to function in which locations are synthesized on free ribosomes in the cytoplasm?
Which ones don't have a signal?
cytoplasm, mitochondria, nucleus, and peroxisomes.
cytoplasmic proteins have no signal
Main anions in the ECF
Cl- and HCO3-
Main anions in the ICF
The relationship between flux and concentration is ____ in a carrier-mediated system and _____ in simple diffusion.
What are three characteristics of carriers that influence flux (J)?
1. Substrate affinity (1/km)
3. Competition (e.x. maybe non selective of either glucose or galactose and carries both)
Ratios in Ca2+ ATPase
1 Ca2+ in plasma membrane (PMCA) or 2 Ca2+ in ER (SERCA) in exchange for H+ ions in for every ATP hydrolyzed.
What are two examples of ABC transporters and their differential uses of ATP
Multidrug resistance transporters - use ATP to actively transport their substrates
CFTR - ATP regulates its function as an ion channel (can also as a modulator of other proteins). ATP needed for Cl- channel to open.
Define steady state in terms of flux and ions
Ions move at the same rate. the flux is constant with time, but it is not zero
Present in both sexes but affects males more severely. Boys show delayed cognitive function, behavior problems like hyperactivity and stereotypic movements such as hand-flapping. physical abnormalities include hyperextensible joints, large ears, an elongated face, and postpubertal enlargement of the testes.
Fragile X syndrome