Molecular Biology: Protein Synthesis and Regulation

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Questions and Answers

What molecule promotes the step of shifting tRNA within the ribosome?

  • GTP
  • EF-G (correct)
  • Aminoacyl-tRNA
  • RF

The ribosome can assemble into its subunits immediately after the termination of translation.

False (B)

What happens when a STOP codon reaches the A site of the ribosome?

A protein release factor binds and releases the polypeptide from the ribosome.

The nucleotides following the STOP codon to the poly(A) tail are known as the ______ region.

<p>3'-untranslated</p> Signup and view all the answers

Match the following components with their functions in protein synthesis:

<p>tRNA = Brings amino acids to the ribosome Ribosome = Site of protein synthesis STOP codon = Signals termination of translation Release factor = Recognizes STOP codons</p> Signup and view all the answers

What is euchromatin?

<p>A relaxed form of chromatin that is active (B)</p> Signup and view all the answers

DNA methylation generally promotes the transcription of genes.

<p>False (B)</p> Signup and view all the answers

What role do histone acetyltransferases (HATs) play in transcription?

<p>They acetylate histones to loosen chromatin and make DNA more accessible for transcription.</p> Signup and view all the answers

The process of __________ involves interconverting active and inactive forms of chromatin.

<p>chromatin remodeling</p> Signup and view all the answers

Match the regulatory processes with their descriptions:

<p>DNA methylation = Leads to gene silencing Histone acetylation = Loosens chromatin structure Histone deacetylation = Tightens chromatin structure Epigenetic regulation = Inheritance of expression patterns</p> Signup and view all the answers

What effect does histone deacetylation typically have on transcription?

<p>It inhibits transcription (A)</p> Signup and view all the answers

Maintenance methylase recognizes completely unmethylated DNA and adds methyl groups during replication.

<p>False (B)</p> Signup and view all the answers

Describe the significance of epigenetic regulation.

<p>It allows for the inheritance of gene expression patterns through cell division without mutations.</p> Signup and view all the answers

What is the primary function of the core promoter?

<p>Serves as a docking site for transcriptional machinery and PIC (B)</p> Signup and view all the answers

Silencers function to enhance transcription levels.

<p>False (B)</p> Signup and view all the answers

What is the role of transcription factors in gene regulation?

<p>They bind to regulatory regions and regulate the transcription rate of associated genes.</p> Signup and view all the answers

The TATA box is located ____ bp upstream of the transcription start site.

<p>30</p> Signup and view all the answers

Match each type of regulatory element with its function:

<p>Enhancers = Increase transcription levels Silencers = Decrease transcription levels Insulators = Block enhancer-promoter communication Transcription factors = Regulate transcription rates</p> Signup and view all the answers

Which of the following elements can loop DNA to interact with target genes?

<p>Enhancers (B)</p> Signup and view all the answers

The concentration of transcription factors affects the transcription rate.

<p>True (A)</p> Signup and view all the answers

Post-transcriptional modification of mRNA includes ____ capping.

<p>5’</p> Signup and view all the answers

What is the primary function of tRNA in the translation process?

<p>To carry amino acids to the ribosome (B)</p> Signup and view all the answers

The coding strand of DNA has the same sequence as mRNA, except it replaces uracil with thymine.

<p>False (B)</p> Signup and view all the answers

What sequence of RNA would be transcribed from the coding strand 5′-TACGTACGTACGTA-3′?

<p>5'-UACGUACGUACGUA-3'</p> Signup and view all the answers

RNA polymerase synthesizes RNA in the ______ to ______ direction.

<p>5', 3'</p> Signup and view all the answers

Which RNA polymerase is responsible for synthesizing mRNA?

<p>RNA polymerase II (D)</p> Signup and view all the answers

Match the following RNA polymerases with their specific functions:

<p>RNA polymerase I = Synthesizes the large ribosomal RNAs RNA polymerase II = Synthesizes messenger RNAs RNA polymerase III = Produces tRNA and small rRNAs</p> Signup and view all the answers

The tRNA molecules have a 3-loop structure and contain an anticodon.

<p>True (A)</p> Signup and view all the answers

The untranslated non-coding regions of mRNA are known as ______.

<p>introns</p> Signup and view all the answers

What is the function of the cap added to mRNA?

<p>It stabilizes mRNA and permits initiation of translation. (A)</p> Signup and view all the answers

The addition of a poly(A) tail occurs before transcription.

<p>False (B)</p> Signup and view all the answers

What mechanism changes the sequence of mRNA after transcription?

<p>RNA Editing</p> Signup and view all the answers

The process of removing introns and splicing exons in pre-mRNA occurs in the ______.

<p>nucleus</p> Signup and view all the answers

Which enzyme processes primary miRNA into precursor miRNA?

<p>Drosha (D)</p> Signup and view all the answers

Match the following components with their roles in mRNA regulation:

<p>Cap = Stabilizes mRNA and initiates translation Poly(A) Tail = Facilitates exit from the nucleus miRNA = Inhibits translation siRNA = Cleaved from double stranded RNA</p> Signup and view all the answers

MiRNA is transcribed by RNA polymerase I.

<p>False (B)</p> Signup and view all the answers

What is the primary function of small interfering RNA (siRNA)?

<p>To bind to RISC and inhibit translation.</p> Signup and view all the answers

Which component is responsible for covalently attaching an amino acid to its corresponding tRNA?

<p>Aminoacyl-tRNA synthetases (C)</p> Signup and view all the answers

The ribosome has three binding sites: A, P, and O.

<p>False (B)</p> Signup and view all the answers

What is the role of initiation factors during the translation process?

<p>They help assemble the components of the translation system and recognize the initiating codon on mRNA.</p> Signup and view all the answers

During elongation, the amino acid chain is formed by the peptide bond between the amino acid on the A site and the amino acid from the t-RNA on the ______ site.

<p>P</p> Signup and view all the answers

Match the following components of translation with their roles:

<p>Amino acids = Building blocks of proteins t-RNA = Transfers amino acids to the ribosome Ribosomes = Site of protein synthesis GTP = Source of energy during elongation</p> Signup and view all the answers

Which of the following statements is true about the initiating amino acid in translation?

<p>It is formylated in prokaryotes but not in eukaryotes. (A)</p> Signup and view all the answers

A-site tRNA holds the growing polypeptide chain during protein synthesis.

<p>False (B)</p> Signup and view all the answers

What energizes the attachment of amino acids to tRNA in the initial step of translation?

<p>ATP</p> Signup and view all the answers

Flashcards

Codon

The sequence of nucleotides in mRNA that codes for a specific amino acid during protein synthesis.

Anticodon

The sequence of nucleotides in tRNA that is complementary to a codon in mRNA, ensuring the correct amino acid is added during protein synthesis.

Transfer RNA (tRNA)

A type of RNA that carries amino acids to the ribosome during protein synthesis, where they are added to a growing polypeptide chain.

RNA Transcription

The process of copying genetic information from DNA to RNA.

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Promoter

The region on DNA where RNA polymerase binds to initiate transcription.

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RNA Polymerase

An enzyme that catalyzes the synthesis of RNA using a DNA template.

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Introns

Non-coding regions of mRNA that are removed during RNA processing.

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Exons

Coding regions of mRNA that are translated into protein.

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Chromatin Remodeling

The process of converting DNA from a tightly packed, inactive form to a more relaxed, active form, making it accessible for transcription.

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Euchromatin

A type of chromatin that is loosely packed and allows for easy access to DNA by transcription factors.

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Heterochromatin

A type of chromatin that is tightly packed and restricts access to DNA by transcription factors.

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DNA Methylation

Attachment of a methyl group to a cytosine base in DNA, often leading to gene silencing.

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Histone Acetyl Transferase (HAT)

An enzyme that adds acetyl groups to histone proteins, making chromatin more relaxed and promoting transcription.

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Histone Deacetylase (HDAC)

An enzyme that removes acetyl groups from histone proteins, making chromatin more compact and inhibiting transcription.

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Epigenetic Gene Regulation

The inheritance of gene expression patterns without changes in the underlying DNA sequence, often through mechanisms like DNA methylation.

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Maintenance Methylase

An enzyme that adds a methyl group to an unmethylated cytosine base in a hemimethylated DNA strand during replication.

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Core Promoter

A specific DNA sequence located near the transcription start site (TSS) that serves as a binding site for the pre-initiation complex (PIC) and initiates RNA transcription.

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Proximal Promoter

Sequences located just upstream of the core promoters that assist in the initiation of transcription and PIC assembly.

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Transcription Factors

Proteins that bind to specific DNA motifs in regulatory regions and control the rate of gene transcription.

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Enhancers

Distal regulatory elements that enhance the expression of genes, regardless of their distance from the promoter.

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Silencers

Distal regulatory elements that decrease the level of transcription of genes by binding to repressive transcription factors.

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Insulators

Motifs on the gene that restrict the influence of regulatory elements, limiting their effect on the promoter.

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5' capping

The addition of a 7-methylguanosine cap to the 5' end of mRNA.

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Unmethylate cytosine

The removal of methyl groups from cytosine bases in DNA.

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5' Cap

A modified guanine nucleotide added to the 5' end of mRNA, providing stability and protection from degradation.

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Poly(A) Tail

A tail of 40-200 adenine nucleotides added to the 3' end of mRNA, enhancing stability and nuclear export.

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RNA Splicing

The process of removing non-coding introns from pre-mRNA and joining the remaining coding exons.

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RNA Editing

A change in the sequence of mRNA after transcription, leading to a different protein product.

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MicroRNA (miRNA)

Small non-coding RNA molecules that regulate gene expression by binding to mRNA and inhibiting translation.

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Small Interfering RNA (siRNA)

A double-stranded RNA molecule cleaved into short fragments that trigger gene silencing by binding to mRNA.

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Dicer

An enzyme that cleaves double-stranded RNA into short interfering RNA (siRNA).

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RNA-induced Silencing Complex (RISC)

A complex that binds to siRNA or miRNA and facilitates their interaction with mRNA, leading to gene silencing or translational inhibition.

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Aminoacyl-tRNA Synthetases

Enzymes that attach the correct amino acid to its corresponding tRNA molecule, ensuring accurate protein synthesis.

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P Site (Peptidyl Site)

A ribosome site that binds the tRNA carrying the growing polypeptide chain.

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A Site (Aminoacyl Site)

A ribosome site that binds the tRNA carrying the next amino acid to be added to the polypeptide chain.

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E Site (Exit Site)

A ribosome site that releases the empty tRNA after the amino acid has been added to the polypeptide chain.

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Initiation (Protein Synthesis)

The first stage of protein synthesis where all the components come together: the mRNA, ribosomes, and the first tRNA carrying methionine.

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Elongation (Protein Synthesis)

The second stage of protein synthesis where amino acids are added one by one to the growing polypeptide chain.

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Termination (Protein Synthesis)

The final stage of protein synthesis where the completed polypeptide chain is released from the ribosome.

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Initiator tRNA

A special type of tRNA that carries the first amino acid, methionine, to the ribosome during translation.

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What ends protein synthesis?

A protein release factor (RF) recognizes STOP codons (UAA, UAG, UGA) when they reach the A site of the ribosome. This binding releases the completed polypeptide chain from the ribosome.

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How does the ribosome move along the mRNA?

The ribosome moves one codon downstream, shifting the tRNA with the peptide to the P site and opening the A site for a new aminoacyl-tRNA.

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What happens to the initiator tRNA after translation?

The initiator tRNA is released from the P site and moves to the E site.

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What are the STOP codons?

The three STOP codons (UAA, UAG, UGA) in mRNA signal for the termination of translation.

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What helps the ribosome move along the mRNA?

EF-G (elongation factor G) and GTP energy promote the movement of the ribosome one codon downstream, shifting the tRNA and opening the A site.

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Study Notes

PHBC522 Biochemistry I, Winter 2024, Lecture 6: Gene Expression & Protein Synthesis

  • Learning Objectives: By the end of the lecture, students should be able to identify all RNA types and structures, understand gene transcription regulation by chromatin remodeling, describe promoter regions and roles of enhancers/inhibitors in transcription, illustrate post-transcriptional mRNA modification, recognize the role of RNA interference in gene expression regulation, describe epigenetic regulation and RNA editing, identify the genetic code, and discuss protein synthesis steps.

RNA Structure and Synthesis

  • Genetic Code: An organism's genetic key is encoded in the deoxyribonucleotide sequence in DNA.
  • Transcription to RNA: DNA information is transferred to RNA. Transcription is the copying process where one DNA strand acts as a template for mRNA synthesis.
  • mRNA Types: There are three types of RNA: ribosomal RNA (rRNA), messenger RNA (mRNA), and transfer RNA (tRNA).
  • RNA vs. DNA Differences: RNA uses ribose sugar instead of deoxyribose, uracil instead of thymine, and is usually single-stranded while DNA is double-stranded.

Ribosomal RNA (rRNA)

  • Composition: rRNA comprises about 80% of RNA in cells and is a large complex of proteins and rRNA.
  • Location and Function: Ribosomes act as protein synthesis factories, located in the cytosol or attached to the endoplasmic reticulum.
  • Svedberg Values: rRNA exists as sedimentation coefficients (S values) representing particle movement in a centrifuge, related to molecular mass and shape.
  • Ribosome Structure: Complete ribosomes have three binding sites (A, P, and E sites) extending over both subunits for amino acid attachment and polypeptide chain formation.

Messenger RNA (mRNA)

  • Function: mRNA carries genetic information from the DNA in the nucleus to the cytoplasm for protein synthesis.
  • Structure: mRNA is often monocistronic in eukaryotes andpolycistronic in prokaryotes, meaning it carries information from one or multiple genes respectively. It includes a 3′ poly A tail and a 5′ cap.
  • Exons and Introns: In eukaryotic mRNA, protein-coding regions (exons) alternate with non-coding regions (introns) which need to be removed.

Transfer RNA (tRNA)

  • Function: tRNA molecules, each with a specific amino acid attachment site, are adapter molecules that recognize specific mRNA codons and translate them into amino acids.
  • Structure: Each tRNA molecule has an anticodon loop that pairs with mRNA codons and an amino acid attachment site, and unique structural folds (e.g., D loop, T-loop). The structure is unique to each specific amino acid.

RNA Transcription

  • Transcription Process: Transcription is the copying process using one DNA strand (antisense) as a template to synthesize mRNA. The DNA strand that is not being transcribed is the Coding strand (sense).
  • Example Transcript: The sample transcript demonstrates how DNA is transcribed to mRNA using complementary base pairs (A-U, T-A, C-G).

Questions and Solutions

  • Example Question/Solution: If a coding strand has the sequence 5'-TACGTA-3', the transcribed mRNA sequence is 5'-AUGCAU-3'.

RNA Polymerase and Gene Expression

  • RNA Polymerase Classes: Eukaryotic cells have three main types of RNA polymerase (I, II, and III) in the nucleus that synthesize different kinds of RNA each.
  • RNA Polymerase I: Synthesizes rRNA.
  • RNA Polymerase II: Synthesizes mRNA and some small nuclear RNAs (snRNAs).
  • RNA Polymerase III: Synthesizes tRNA and some small ribosomal RNAs (rRNAs).
  • RNA Polymerase Function: RNA polymerase needs to recognize the promoter region of the gene and initiate RNA synthesis; it reads from 3′ to 5′ and synthesizes from 5′ to 3′ on the DNA template strand.

Pre-transcriptional Regulation

  • Chromatin Remodeling: Chromatin remodeling involves the interconversion of active chromatin (euchromatin) and inactive chromatin (hetero chromatin). influenced by DNA methylation and histone acetylation.
  • DNA Methylation: Methylation of cytosines permanently inactivates certain genes by preventing transcription factor binding.
  • Histone Acetylation: Histone acetylation relaxes chromatin structure, enhancing accessibility to transcription and gene activation. Histone deacetylase (HDAC) does the opposite, condensing chromatin and suppressing transcription.

Epigenetic Regulation

  • Inheritance of Gene Expression: The pattern of gene expression inherited through cell division without changes in the DNA sequence.
  • Maintenance Methylase: An enzyme that recognizes hemimethylated DNA during DNA replication and adds methyl groups to the complementary strand to maintain the methylation pattern.

RNA Regulation Elements

  • Core Promoter: Regions immediately adjacent to transcription start sites (TSS), having short sequences like TATA box, and serving as docking sites for the transcriptional machinery.
  • Proximal Promoters: DNA sequences located near the core promoter associated with initiation of transcription.
  • Cis-acting elements: Short sequences that work locally.

Transcription Factors

  • Function: Proteins that recognize specific DNA motifs to bind to regulatory regions and affect transcription rate.
  • Mechanism: Transcription factors bind to DNA and either inhibit or enhance the binding of RNA polymerase.
  • Location: Synthesized in cytoplasm and diffuse into nucleus.

Enhancers

  • Function: Distal regulatory DNA elements that can enhance gene expression.
  • Mechanism: Enhancers can be located far from the regulated gene but can still influence gene expression by attracting transcription factors and stimulating transcription from the start.
  • Properties: Enhancers work independently of their location.

Silencers

  • Function: Distal regulatory DNA elements that repress gene expression.
  • Mechanism: Silencers can counteract enhancers.
  • Properties: Similar to enhancers, silencers can be located far from the regulated gene.

Post-transcriptional Modifications

  • 5' Capping: A modified guanine nucleotide added to the 5' end of mRNA to facilitate mRNA processing and stability.
  • 3′ Polyadenylation: Addition of a poly(A) tail of adenine nucleotides to the 3′ end of mRNA, aiding in mRNA stability, nuclear export and translation.
  • Splicing: Removing introns and joining exons to generate mature mRNA and form a single molecule.

RNA Editing

  • mRNA Editing: Post-transcriptional alterations in mRNA sequence that can affect the protein's amino acid sequence.
  • Types of Editing: Deamination and insertions/deletions of nucleotides, sometimes involving specific tissues, cells or stages in the organism.
  • Examples: Apo B gene editing changes the protein's amino acid sequence, hence its function, in tissue-dependent ways.

Micro RNA (miRNA)

  • Mechanism: Small non-coding RNAs that regulate gene expression by either binding to specific mRNA sequences (often leading to degradation or hindering translation) to suppress gene expression.
  • Formation: Produced from larger precursor transcripts. miRNA production involves several nuclear processes and export.
  • Function: miRNA contributes to controlling gene expression at a post-transcriptional level. It plays many roles in controlling gene expression.

Small Interfering RNA (siRNA)

  • Mechanism of action: Short double stranded RNA molecules that target and cleave specific mRNA molecules. siRNA-mediated degradation of mRNA prevents translation of certain proteins
  • Function: siRNA can be used to knock down or silence gene expression.

Genetic Code

  • Sequence: The sequence of nucleotides in mRNA specify the amino acid sequence of the protein to be synthesized.
  • Characteristics: The genetic code features redundancy, or more than one codon for many amino acids. Non-overlapping and commaless; the code is read continuously and without a punctuation system. Its universality, and the correspondence of specific codons to specific amino acids.

Translation: Initiation

  • Initiation Factors: Initiator tRNA and IF required for proper translation start.
  • Formyl-methionine (fMet): Start codon in prokaryotes is methionine, formylated by transformylase.
  • Mechanism: Ribosome binding to the 5' mRNA end; recognition of start codon (AUG) by initiator tRNA and initiation factors.

Translation: Elongation

  • Transfer RNA with Amino Acid: Charged tRNA with amino acids binds the mRNA codons in the A site.
  • Peptide Bond Formation: A new peptide bond is formed between the amino acids on the tRNA in the A site and the polypeptide chain already on the tRNA in the P site by peptidyl transferase.
  • Translocation: GTP-powered ribosome and tRNA movement, shifting mRNA over one codon to expose the next codon at the A site.

Translation: Termination

  • Termination Codons: Stop codons (UAA, UAG, UGA) signal the end of protein synthesis by triggering release factors to detach the polypeptide from the ribosome.
  • Release Factors (RF): Proteins that recognize stop codons to terminate protein synthesis.

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