Biochemistry of Protein Interactions

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Questions and Answers

What is the primary role of phosphorylation in protein interactions?

It increases the protein's synthesis rate.

It affects a protein’s ability to interact with other molecules. (correct)

It enhances the stability of the protein.

It permanently alters the protein structure.

Which enzyme is responsible for the reversal of phosphorylation?

GTPase

eIF2B

Protein Kinase

Phosphatase (correct)

During the translation initiation process, what does eIF2 hydrolyze?

GTP to ATP

GTP to GDP (correct)

ATP to ADP

GDP to GDP

What happens to phosphorylated eIF2a in relation to eIF2B?

It binds very tightly to eIF2B and cannot be released. Signup and view all the answers

What is the function of the initiation factor eIF2B?

To regenerate the eIF2/GTP complex. Signup and view all the answers

What process involves copying DNA into RNA?

Transcription Signup and view all the answers

Which property of RNA makes it less stable compared to DNA?

Greater susceptibility to hydrolysis Signup and view all the answers

What type of structure allows interaction within RNA?

Stem-loop structures Signup and view all the answers

How many hydrogen bonds are there in G/C canonical base pairs?

3 Signup and view all the answers

Which base pairing is referred to as non-canonical in RNA?

G/U pairing Signup and view all the answers

What is the secondary structure of RNA primarily defined by?

Intramolecular base-pairing Signup and view all the answers

What contributes to the 3D shape of an RNA molecule?

Tertiary structure interactions Signup and view all the answers

Which of the following statements about the major groove in RNA is true?

It is less accessible for other molecules to interact with. Signup and view all the answers

What is the first tRNA binding site that a charged tRNA enters during translation?

A site Signup and view all the answers

What structure is formed by introns during pre-mRNA splicing?

Lariat structure Signup and view all the answers

Which factor is responsible for bringing aminoacyl-tRNA to the ribosome during translation elongation?

EF1A Signup and view all the answers

Which component is essential for pre-mRNA splicing?

Spliceosomes Signup and view all the answers

What is the role of the PTC in peptide bond formation?

It catalyzes the peptide bond formation. Signup and view all the answers

How does termination of translation occur in eukaryotic cells?

Through protein termination factors. Signup and view all the answers

What is the directionality in which mRNA codons are read?

5’ to 3’ Signup and view all the answers

What is the role of tRNA during protein synthesis?

To bring amino acids to the ribosome Signup and view all the answers

What feature differentiates eukaryotic ribosomes from prokaryotic ribosomes?

Eukaryotic ribosomes are more complex. Signup and view all the answers

Which sequence is recognized by base-pairing with the 16S rRNA in prokaryotic mRNAs?

SD sequence Signup and view all the answers

Which codon is considered the start codon in translation?

AUG Signup and view all the answers

What is unique about the amino acids Methionine and Tryptophan in the genetic code?

They are encoded by a single codon Signup and view all the answers

What drives the steps of translation elongation?

GTPases Signup and view all the answers

What is the outcome of hydrolysis of GTP during translation elongation?

Facilitates ribosome translocation. Signup and view all the answers

Which enzyme is responsible for attaching the correct amino acid to the tRNA?

Aminoacyl-tRNA synthetase Signup and view all the answers

Which type of gene expression is essential for basic cellular processes, such as enzyme production?

Housekeeping genes Signup and view all the answers

How is the genetic code described in terms of codon meanings?

Non-punctuated and degenerate Signup and view all the answers

What does 'wobble' refer to in the context of tRNA?

Base pairing flexibility at the third position Signup and view all the answers

How are significant changes in gene expression driven in multicellular organisms?

By alterations in transcript patterns. Signup and view all the answers

What are the three stop codons involved in protein synthesis?

UAA, UAG, UGA Signup and view all the answers

What ensures the correct positioning of the start codon in the ribosome during initiation?

Interactions with initiation factors. Signup and view all the answers

What type of reaction is peptide bond formation categorized as?

An RNA-catalyzed reaction. Signup and view all the answers

In tRNA structure, what forms the cloverleaf configuration?

Secondary structure stabilization Signup and view all the answers

Which type of tRNA is charged with methionine to initiate translation?

Initiator tRNA Signup and view all the answers

Which of the following describes a ribozyme?

An RNA molecule with catalytic activity Signup and view all the answers

What type of modifications are common in tRNA after transcription?

Methylations and other changes Signup and view all the answers

What characteristic of the genetic code allows different codons to encode the same amino acid?

Synonymous codons Signup and view all the answers

What is the primary function of RNA polymerase in transcription?

To transcribe DNA into RNA. Signup and view all the answers

Which components are required for the formation of the pre-initiation complex in eukaryotic RNA transcription?

Both RNA polymerases and general transcription factors. Signup and view all the answers

During RNA processing in eukaryotic cells, what happens to introns?

They are removed from the pre-mRNA. Signup and view all the answers

What is the primary level at which most genes are regulated?

Transcription level Signup and view all the answers

What distinguishes eukaryotic mRNA from prokaryotic mRNA?

Eukaryotic mRNA undergoes significant processing. Signup and view all the answers

What is a common feature of the RNA/DNA heteroduplex in the RNA polymerase active site?

It consists of a mixed sequence of DNA and RNA. Signup and view all the answers

Which factor is known to repress transcription of the lac operon?

lacI Signup and view all the answers

Which nucleotide modification occurs at the 5' end of eukaryotic mRNA?

Addition of a guanosine nucleotide with a 5’-5’ triphosphate linkage. Signup and view all the answers

Which of the following best describes the role of inducers in gene expression regulation?

They stimulate activators or inhibit repressors of transcription factors. Signup and view all the answers

What is the role of sigma factors in prokaryotic transcription?

To provide specificity for the RNA polymerase at gene promoters. Signup and view all the answers

What happens to the lac operon when glucose is present?

cAMP production is inhibited. Signup and view all the answers

What occurs during pre-mRNA splicing in eukaryotic cells?

It can lead to the production of two distinct proteins from the same pre-mRNA. Signup and view all the answers

Which statement about intron-exon relationships is correct?

Average intron length is often 8-10 times longer than exon length. Signup and view all the answers

What type of modifications can proteins undergo after translation?

Post-translational modifications that can alter protein function. Signup and view all the answers

Which type of RNA is primarily responsible for the transcription of protein-coding genes in eukaryotes?

RNA polymerase II. Signup and view all the answers

Which statement accurately describes cis and trans mutations?

Cis mutations occur within the same gene, while trans mutations affect regulation from a different gene. Signup and view all the answers

In which direction is RNA synthesized during transcription?

5' to 3'. Signup and view all the answers

In the context of gene expression, what characterizes transcriptional activators?

They promote gene expression by binding to specific DNA sequences. Signup and view all the answers

What is the role of spliceosomes in pre-mRNA splicing?

To remove introns and join exons. Signup and view all the answers

What is the role of iron sensor proteins in translation regulation?

They block protein synthesis when iron levels are low. Signup and view all the answers

Which component is essential for the stability of eukaryotic mRNA?

5' cap structure and poly(A) tail. Signup and view all the answers

What is the consequence of having a transcription factor that downregulates gene expression?

It may prevent unneeded gene expression, conserving energy. Signup and view all the answers

What is the first nucleotide typically added to the 5' end of eukaryotic mRNA?

Guanosine. Signup and view all the answers

How does lactose function in the regulation of the lac operon?

It binds to the lac repressor, inhibiting its function. Signup and view all the answers

What mechanism distinguishes between intronic and exonic sequences in pre-mRNA splicing?

Recognition of splice site sequences. Signup and view all the answers

What is the outcome when genes are under positive control in gene regulation?

They are consistently upregulated. Signup and view all the answers

What effect does cAMP have in regulating the lac operon?

It binds with CAP to stimulate transcription. Signup and view all the answers

Study Notes

DNA and RNA Structure and Function

DNA and RNA are both nucleic acids with similar geometries.
DNA has regular major and minor grooves, while RNA's grooves are irregular and have other structures.
The major groove in RNA is narrower and deeper, reducing accessibility for other molecules.
RNA molecules are less stable than DNA and more susceptible to hydrolysis.
RNA can form intramolecular base pairs, producing secondary structures like stem-loops.
Canonical base pairing (A-U, G-C) involves 2 or 3 hydrogen bonds, with G-C being more stable.
Non-canonical base pairing also occurs, such as G-U wobble base pairing, adapting to RNA's irregular structure.
The sequence within RNA dictates its three-dimensional conformation.

RNA Transcription

RNA is synthesised by DNA-dependent RNA polymerases (RNAPs) using a DNA template.
RNAPs require a DNA template, with alpha subunits interacting with transcription factors.
Nucleotide triphosphates (NTPs) are added to the 3' end of the growing RNA strand based on complementary base pairing.
The process proceeds in a 5' to 3' direction.
RNAP active sites include short RNA/DNA heteroduplexes.
Transcription units have defined start and stop positions in the genome.
In bacteria, RNA polymerase core enzyme has five subunits with diverse functions.
Sigma (σ) factors in prokaryotes provide specificity to RNA polymerase for gene promoters.
Eukaryotic cells have three RNA polymerases for different functions.

RNA Processing

Functional RNA molecules often require processing.
Major cellular RNAs: mRNA (5%), rRNA (75%), tRNA (10%), and small stable RNAs.
Eukaryotic mRNA processing involves three steps: 5' capping, intron removal (splicing), and 3' end processing (cleavage and polyadenylation).
Capping protects mRNA from degradation and promotes translation, usually by addition of a "m7G cap" structure linked via a 5'-5' triphosphate linkage to the beginning of the RNA.
Splicing creates a lariat structure from introns which are removed.

RNA Translation

Ribosomes are large RNP particles that consist of two subunits.
Ribosomes contain three binding sites (A, P, and E) that mediate tRNA binding and peptide bond formation.
Elongation involves repetitive cycles, facilitated by GTPases such as EF/G.
Translation initiation in prokaryotes involves 16S/mRNA base pairing.
In eukaryotes, the scanning mechanism targets ribosomes to the 5' end and scans until it finds an AUG codon within a Kozak sequence.

Protein Synthesization Regulation

Gene expression regulation occurs at the transcription and translation levels.
Transcription factors can activate or repress transcription.
Activator and repressor activities can be regulated through interactions with other molecules.
Operons, like the lac operon (encompassing lacZ, lacY, lacA), control lactose metabolism and regulated by lac repressor
The lac repressor inhibits transcription to save energy unless lactose is present.
Another protein, CAP, activates transcription only in the absence of glucose, only when both lactose and glucose are absent.
In eukaryotes, pre-mRNA splicing can produce multiple proteins via alternative splicing.

Translation Inhibition

The integrated stress response (ISR) in eukaryotic cells can downregulate translation globally through eIF2 phosphorylation.
When ISR occurs, eIF2a gets phosphorylated and traps eIF2B preventing it from recycling to form a complex that stops translation.
Post-translational modifications of proteins (like phosphorylation) often affect their function and interactions.

Genetic Code

The genetic code allows inferences about protein sequences, structures, and functions.
Codons are read from 5' to 3' leading to N-terminal to C-terminal protein synthesis.
Codons are recognised by anti-codons on appropriate tRNAS.
Wobble base pairing allows a single tRNA to recognize multiple synonymous codons (especially involving third codon base).

tRNA

tRNAs are folded into an L-shape structure and charged by aminoacyl-tRNA synthetases (specific enzymes).
tRNAs carry amino acids to the ribosome for translation, attached to the 3' end.
tRNAs feature a "cloverleaf" secondary structure.
tRNAs also contain modified nucleotides, maintaining structure and function.

Ribosome Synthesis,

Ribosome synthesis is an energy-intensive process occurring in nuclear structures (especially in nucleoli).
Processing and assembly steps of ribosomes involve several proteins and RNAs.

Translation Termination

Translation termination is mediated by release factors that recognize stop codons.
Two release factors work together to hydrolyze the peptide bond and release the polypeptide chain.

Gene Expression

Gene expression regulation involves factors (in cis and trans).

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Description

Test your knowledge on the role of phosphorylation in protein interactions, particularly in translation initiation processes. This quiz covers important aspects such as the actions of eIF2 and eIF2B, RNA structure, and base pairing in RNA. Dive into the intricacies of biochemistry and evaluate your understanding of these critical concepts.