Gene Expression and Regulation: (30-31)

Promoter

A DNA sequence that initiates transcription of a gene.

Transcriptional start site

The location on the DNA where transcription begins.

5' UTR

The untranslated region at the 5' end of an mRNA molecule.

Start codon

The codon that signals the start of translation, typically AUG.

Stop codon

A codon that signals the end of translation.

Intron

A non-coding segment of a gene that is removed during RNA splicing.

Exon

A coding segment of a gene that is retained in the final mRNA.

3' UTR

The untranslated region at the 3' end of an mRNA molecule.

Prokaryotic translation

Occurs in the cytosol where transcription and translation can occur simultaneously.

Eukaryotic translation

Occurs in the cytosol, separated from transcription.

Post-translational processing

Modifications that occur to a protein after it has been synthesized from the DNA code.

Chemical Modification

The covalent attachment of various chemical groups to specific amino acid residues in a protein.

Protein Folding

The proper folding of the polypeptide chain into its functional conformation.

Chaperone proteins

Proteins that assist in the proper folding of other proteins.

Initiation

The step where the small ribosomal subunit binds to mRNA and the initiator tRNA binds to AUG.

Elongation

The step where amino acids are added one by one to the growing protein chain.

Termination

The step where the ribosome reaches a stop codon, signaling the end of the protein chain.

Central Dogma of Molecular Biology

The framework for understanding the transfer of sequence information from DNA to RNA to protein.

Protein Synthesis

The biological process by which cells generate proteins from genetic information.

Polypeptide

A chain of amino acids linked by peptide bonds.

Ribosomes

Cellular structures where protein synthesis occurs.

tRNA

Transfer RNA, which transports amino acids to ribosomes during protein synthesis.

mRNA

Messenger RNA, which carries the genetic code from DNA to the ribosome.

rRNA

Ribosomal RNA, a component of ribosomes.

Reading frame

The way nucleotides in mRNA are divided into codons.

Release factor

A protein that recognizes the stop codon during termination of translation.

tRNA binding sites

The sites on the ribosome where tRNA molecules bind during translation (E, A, and P sites).

Transfer RNA

When tRNA is bound to an amino acid, it is called charged or an aminoacyl-tRNA.

Ribosome

The ribosome is responsible for translating the mRNA into protein.

Ribosomal Subunits

The ribosome consists of a large and small ribosomal subunit.

A-site

During translation, charged tRNAs enter the A-site, and the anticodon on the tRNA base pairs with the codon in the mRNA.

P-site

After the incoming amino acid forms a peptide bond with the growing polypeptide chain, the ribosome will move three nucleotides toward the 3' end of the mRNA, transferring the tRNA with the growing polypeptide to the P-site.

E-site

The empty tRNA exits at the E-site.

Initiation of Translation

The initiation of translation in prokaryotes involves several key steps, starting with the binding of the small ribosomal subunit to the mRNA molecule.

Initiation Complex

The next step involves the binding of an initiator tRNA molecule to the start codon, carrying the amino acid methionine.

Large Ribosomal Subunit

After the formation of the initiation complex, the large ribosomal subunit associates with the small subunit, completing the initiation complex.

Elongation Stage of Translation

The elongation phase of translation involves the sequential addition of amino acids to the growing polypeptide chain.

Binding of tRNA

The elongation phase begins when a tRNA binds to the A site of the ribosome.

Peptide Bond Formation

The ribosome catalyzes peptide bond formation between the amino acid on the tRNA in the A site and the growing polypeptide chain on the tRNA in the P site.

Termination of Translation

The ribosome reaches a stop codon, which signals the end of the protein chain.

Newly Synthesized Protein

The newly synthesized protein is then released from the ribosome and folds into its final three-dimensional structure.

Translocation

The process where the ribosome moves one codon along the mRNA in the 3' direction after peptide bond formation.

Exit of tRNA

The discharge of tRNA from the E site of the ribosome, making room for a new tRNA to enter the A site.

Recognition of the Stop Codon

When the ribosome reaches a stop codon (UAA, UAG, or UGA) on the mRNA, there are no corresponding tRNA molecules that recognize these codons.

Release Factors (RFs)

Proteins that bind to the A site of the ribosome, recognizing the stop codon.

Peptide Release

The binding of the release factor triggers hydrolysis of the bond between the completed polypeptide chain and the tRNA at the P site.

Dissociation of Ribosomal Subunits

After peptide release, the ribosomal subunits, mRNA, and any remaining tRNA molecules dissociate from each other.

Polyribosome

Groups of ribosomes bound to a single mRNA molecule simultaneously during translation.

Advantages of Polyribosomes

They increase the efficiency of protein synthesis, enable quick responses to environmental changes, and protect mRNA from degradation.

Misfolded proteins

Proteins that can be degraded by the cell's quality control machinery or can lead to protein aggregation and disease, such as Alzheimer's or Parkinson's disease.

Gene

A fundamental unit of heredity and a segment of DNA that encodes the information to make a specific product, typically a protein, but also various types of RNA.

Transcription Start Site (TSS)

The DNA sequence where RNA polymerase begins the synthesis of RNA.

Core Promoter

The minimal portion of the promoter region needed to start transcription, often containing essential elements such as the TATA box, Initiator element, and others.

Poly(A) Site

The DNA sequence where the pre-mRNA is cleaved and a polyadenylate tail is added during RNA processing, which is important for mRNA stability, nuclear export, and translation initiation.

TATA Box

A DNA sequence (TATAAA) found in the promoter region of many genes, helping to determine the transcription start site by binding the TATA-binding protein.

3' UTR

The portion of an mRNA molecule directly downstream of the coding sequence, often containing regulatory elements that influence mRNA stability and translation efficiency.

5' UTR

The portion of an mRNA molecule directly upstream of the coding sequence, often containing regulatory elements that influence translation.

Exons

Segments of a gene or mRNA molecule that contain the protein-coding sequence; they remain in the mature mRNA after splicing.

Introns

Non-coding segments of a gene that are transcribed into RNA but are removed by splicing during the processing of the pre-mRNA into mature mRNA.

Translation in Eukaryotes

Initiation occurs when ribosomal subunit binds to 5′ guanine cap; ribosomes synthesize polypeptides into the cavity of the rough endoplasmic reticulum and on free ribosomes; translation and transcription are decoupled.

Tetracycline

An antibiotic that blocks the A site on the bacterial ribosome, affecting tRNA binding to the ribosome, ribosome assembly, and growth of the protein chain.

Chloramphenicol

An antibiotic that blocks peptidyl transfer on the bacterial ribosome, affecting tRNA binding to the ribosome, ribosome assembly, and growth of the protein chain.

Gene Regulation

The ability of cells to control their level of gene expression.

Prokaryotic Gene Regulation

Primarily occurs at the transcriptional level.

Eukaryotic Gene Regulation

Involves more complex regulatory mechanisms allowing greater control over gene expression.

Transcription

The process of copying a segment of DNA into RNA.

RNA Processing

The modification of RNA before it is translated into protein.

Translation

The process of synthesizing proteins from RNA.

Post-Translational Modification

Changes made to proteins after they are synthesized.

Chromatin Structure

Influences whether genes are accessible for transcription and can be expressed.

Euchromatin

Less densely packed chromatin generally associated with gene expression.

Heterochromatin

Densely packed chromatin generally associated with gene silencing.

Methylation

The addition of methyl groups to histone proteins, which can activate or repress gene expression.

Acetylation

Neutralizes the positive charge on histones, making chromatin more open and accessible to transcription machinery.

Structural Genes

Genes that code for proteins that perform a function, such as metabolic enzymes.

Regulatory Genes

Genes that affect the transcription and translation of other genes.

Lac Repressor Protein (lacI)

A regulatory protein that prevents transcription of genes needed for lactose metabolism in the absence of lactose.

Constitutive Genes

Genes that are transcribed continually.

Non-constitutive Genes

Genes that can be switched on (induced) or off (repressed).

Gene Expression Efficiency

Regulation maintains efficiency in energy, space, and time by preventing unnecessary gene expression.

Somatic Cells

Cells that contain the full genome of an organism but do not express all genes simultaneously.

Open Chromatin

Less densely packed chromatin generally associated with gene expression.

Closed Chromatin

Densely packed chromatin generally associated with gene silencing.

Epigenetic Control

Includes histone modifications (methylation and acetylation) and DNA methylation.

Lac Repressor

Part of the lac operon, a regulatory system in E. coli and other bacteria.

Transcription Factors

Bind to DNA sequences called promoters which control the initiation of transcription in eukaryotes.

Post Transcriptional Modification

In eukaryotes, RNA transcripts must be processed into their final form before translation can begin, and this step can be regulated to control gene expression.

RNA Splicing

The process of alternatively splicing pre-mRNA to create different proteins, occurring in the nucleus.

5' Cap

A methylated guanosine triphosphate molecule (GTP) that prevents degradation of the transcript.

Poly-A Tail

Prevents degradation of the transcript and is found at the end of mRNA.

Untranslated Regions (UTRs)

The protein-coding region of mRNA is flanked by 5' and 3' UTRs.

RNA-binding Proteins (RBPs)

Influence RNA stability at UTRs, can increase or decrease the length of time mRNA is present in the cytoplasm, and regulate mRNA localization and protein translation.

Differential Gene Expression

The patterns of gene expression that arise in different cells, leading to the development of a complete organism.

Transcriptional Regulation in Prokaryotes

Occurs primarily through mechanisms like the lac operon and lac repressor.

Transcriptional Regulation in Eukaryotes

Occurs at multiple levels: transcriptional, post-transcriptional, translational, and post-translational.

Translational Control

Occurs at the ribosomes; translocation at the ribosome cannot occur when elongation factor 2 is phosphorylated.

Chemical Modifications Affect Protein Activity

Proteins can be chemically modified through the addition or removal of various markers, tags, and functional groups, regulating protein activity or length of time the protein exists in the cell.

Effects of Chemical Modifications

Can alter epigenetic accessibility, transcription, mRNA stability, translation, and protein stability.

Ubiquitin Tags

Proteins with ubiquitin tags are marked for degradation.

Protein Phosphorylation

Can regulate gene expression by altering the activity, localization, or interaction of transcription factors and other proteins involved in the gene expression machinery.