Protein Synthesis and trafficking Flashcards by Meghan Hewlett

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

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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

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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

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Proks: What is the first processing step of precursor tRNAs

multimeric precursors are processed to monomeric precursors

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Proks: Ribozyme that cleaves the precursor tRNAs on the 5’ side

RNase P

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Proks: cleaves the precursor tRNAs on the 3’ side

RNase D

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Euks: How does splicing of tRNAs differ from splicing of mRNAs?

splicing of tRNAs is an ATP-dependent mechanism

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Euks: Removes 5’ leader sequence

RNase-P like enzyme

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Euks: Removes bases at the 3’ end and addition of the sequence CCA

tRNA nucleotidyltransferase

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Euks: what creates the anti-codon loop in most tRNAs?

removal of a short intron

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Have modified bases in their tRNAs

proks and euks

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Ribosome is composed of 2/3 RNA and 1/3 protein

Prok ribosome

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Ribosome is composed of 1/2 RNA and 1/2 protein

Euk ribosome

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Each precursor contains one copy of each rRNA

proks

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Proks ribosomal RNA synth: Initial transcription product is called a ___ rRNA and is cleaved by ____ to yield the individual rRNAs

30S; RNase III

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Precursor transcript may also contain one or more tRNA genes in addition to rRNA genes

Proks

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protein and RNA components can self-assemble in the absence of an overall structural assembly machinery

Proks

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In the _____ genome, there are several hundred tandem repeats of the gene encoding __, ___and ___ rRNAs

Eukaryotic; 28S, 5.8S, and 18S

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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

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Proks: rRNA(s) included in the large subunit

23S; 5S (50S)

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Proks: rRNA(s) included in the small subunit

16S (30S)

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Euks: rRNA(s) included in the large subunit

28S, 5.8S, 5S (60S)

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Euks: rRNA(s) included in the small subunit

18S (40S)

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______ transcribes the precursor of 5S rRNA, which is encoded by repetitive DNA in the ______

RNA pol III; nucleus

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Euks: Site where the individual small and large subunits are formed

nucleolus

caused by an insertion in exon 11 of the α-chain of the hexosaminidase A

Tay-Sachs

What are the six mechanisms of gene regulation?

1. Transcription 2. RNA Processing 3. RNA transport and localization 4. translation 5. mRNA degradation 6. Protein activity

As described for CRP, _____ is the most common Transcription factor DNA binding motif for prok regulators

Helix-turn-Helix (HTH)

critical for recognition between amino acid side chains and base pairs in the major groove

Hydrogen bonding

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).

alpha helical

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

bZIP proteins

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 5. Unmasking 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:

Chromatin

Densely cover transcriptionally inactive genes

nucleosomes

When a gene becomes transcriptionally active there is a major change in chromatin structure as determined by the appearance in the promoter region of:

Hypersensitive sites

regions of DNA particularly susceptible to digestion by nucleases

hypersensitive sites

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

RNaseH

inhibits the binding of aminoacyl tRNA to the ribosome and thereby blocks continued translation in proks

Tetracycline

blocks elongation, apparently by acting as a competitive inhibitor of peptidyl transferase in proks

chloramphenicol

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

Puromycin

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

Diphtheria toxin

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

phosphates proteins

The relationship between flux and concentration is ____ in a carrier-mediated system and _____ in simple diffusion.

hyperbolic, linear

What are three characteristics of carriers that influence flux (J)?

1. Substrate affinity (1/km) 2. Saturation 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

all adults are assumed to be legally competent to make health care decisions for themselves except if they are:

actively psychotic, suicidal, or in a coma