9.4 Protein synthesis
7 min read•august 21, 2024
Protein synthesis is a fundamental process in organic chemistry, linking genetic information to functional molecules. This complex mechanism involves of DNA to RNA, followed by into polypeptides. Understanding these steps is crucial for grasping how cells create the proteins essential for life.
The process begins with , the building blocks of proteins. These molecules form peptide bonds, creating longer chains that fold into complex structures. The resulting proteins play diverse roles in cellular function, from enzymes to structural components, highlighting their importance in biochemistry.
Amino acids and peptides
- Amino acids serve as building blocks for proteins, playing a crucial role in organic chemistry and biochemistry
- Understanding amino acid structure and peptide formation provides the foundation for studying complex protein synthesis processes
Structure of amino acids
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- Amino acids consist of a central carbon atom (α-carbon) bonded to four groups
- An amino group (-NH2)
- A carboxyl group (-COOH)
- A hydrogen atom (-H)
- A unique side chain (R-group) determining the amino acid's properties
- 20 standard amino acids exist in nature, each with a distinct R-group (alanine, glycine, lysine)
- Amino acids exhibit chirality, with L-isomers predominating in biological systems
Peptide bond formation
- Peptide bonds form between the carboxyl group of one amino acid and the amino group of another
- Condensation reaction releases a water molecule during bond formation
- Peptide bonds exhibit partial double bond character, restricting rotation and influencing protein structure
- Dipeptides contain two amino acids, while oligopeptides typically contain 2-20 amino acids
Primary protein structure
- Primary structure refers to the linear sequence of amino acids in a
- Determined by the genetic code and transcription/translation processes
- Dictates the overall three-dimensional structure and function of the protein
- Represented using one-letter or three-letter amino acid codes (ALA or A for alanine)
Protein structure levels
- Protein structure hierarchy consists of four levels, each building upon the previous
- Understanding these levels helps elucidate protein function and interactions in organic systems
Secondary structure elements
- Alpha helices form spiral-like structures stabilized by hydrogen bonds
- Right-handed helices predominate in nature
- 3.6 amino acids per turn in ideal alpha helix
- Beta sheets consist of extended polypeptide strands connected by hydrogen bonds
- Parallel and antiparallel arrangements possible
- Turns and loops connect different secondary structure elements
- Often found on protein surfaces, important for folding and function
Tertiary structure formation
- Refers to the overall three-dimensional shape of a single polypeptide chain
- Driven by various interactions between amino acid side chains
- Hydrophobic interactions cause non-polar residues to cluster in the protein core
- Hydrogen bonds between polar residues stabilize the structure
- Disulfide bridges form covalent bonds between cysteine residues
- Influenced by the cellular environment (pH, temperature, ionic strength)
Quaternary structure assembly
- Involves the association of multiple polypeptide chains or subunits
- Stabilized by non-covalent interactions between subunits (hydrogen bonds, van der Waals forces)
- Examples include hemoglobin (four subunits) and antibodies (multiple chains)
- Quaternary structure often crucial for protein function and regulation
Transcription process
- Transcription represents the first step in , converting DNA information to RNA
- Critical process in organic chemistry, linking genetic code to protein synthesis
RNA polymerase function
- catalyzes the synthesis of RNA using DNA as a template
- Eukaryotes have three types of RNA polymerases (I, II, III) with distinct functions
- Requires template DNA, ribonucleotides, and cofactors (Mg2+)
- Possesses both polymerase and nuclease activities for error correction
Initiation of transcription
- Begins at specific DNA sequences called promoters
- RNA polymerase binds to the promoter with the help of transcription factors
- Formation of the transcription bubble exposes the template DNA strand
- Synthesis of the first few RNA nucleotides occurs without moving along the DNA
Elongation and termination
- RNA polymerase moves along the template DNA, adding complementary RNA nucleotides
- Nascent RNA chain grows in the 5' to 3' direction
- continues until a signal encountered
- Termination in prokaryotes often involves hairpin structures or rho factor
- Eukaryotic termination involves specific sequences and protein factors
Translation mechanism
- Translation converts the genetic information in into a polypeptide chain
- Occurs on ribosomes, utilizing various RNA molecules and protein factors
Ribosome structure and function
- Ribosomes consist of two subunits (small and large) composed of and proteins
- Contain three binding sites for molecules (A, P, and E sites)
- Catalyze peptide bond formation between amino acids
- Possess inherent proofreading mechanisms to ensure translation accuracy
tRNA and codon recognition
- tRNA molecules serve as adaptor molecules between mRNA and amino acids
- Aminoacyl-tRNA synthetases attach specific amino acids to their corresponding tRNAs
- loop of tRNA base pairs with mRNA in the ribosomal A site
- Wobble base pairing allows some tRNAs to recognize multiple codons
Peptide chain elongation
- begins with the binding of initiator tRNA (carrying methionine) to the start codon
- Elongation factors assist in bringing aminoacyl-tRNAs to the A site
- Peptidyl transferase activity of the forms peptide bonds
- Translocation moves the ribosome along the mRNA, shifting tRNAs between sites
- Process continues until a stop codon encountered, triggering release factors
Post-translational modifications
- Post-translational modifications alter proteins after their initial synthesis
- Critical for protein function, localization, and regulation in organic systems
Protein folding
- Newly synthesized polypeptides must fold into their correct three-dimensional structure
- Chaperone proteins assist in proper folding and prevent aggregation
- Folding often occurs co-translationally, beginning before the entire protein synthesized
- Misfolded proteins can lead to various diseases (Alzheimer's, Parkinson's)
Chemical modifications
- Phosphorylation adds phosphate groups to specific amino acids (serine, threonine, tyrosine)
- Glycosylation attaches sugar moieties to proteins (N-linked, O-linked glycosylation)
- Ubiquitination tags proteins for degradation or alters their function
- Other modifications include acetylation, methylation, and lipidation
Protein targeting
- Signal sequences direct proteins to specific cellular compartments
- Co-translational targeting occurs during protein synthesis (endoplasmic reticulum)
- Post-translational targeting involves specific sequences recognized by transport machinery
- Protein import into organelles (mitochondria, chloroplasts) often requires chaperones and energy
Regulation of protein synthesis
- Protein synthesis regulation occurs at multiple levels to control gene expression
- Essential for cellular responses to environmental changes and developmental cues
Transcriptional regulation
- Promoter strength influences the rate of transcription initiation
- Transcription factors bind to specific DNA sequences to activate or repress genes
- Enhancers and silencers modulate transcription from distant locations
- Chromatin remodeling and histone modifications affect DNA accessibility
Translational control
- mRNA stability affects the duration of protein synthesis
- RNA-binding proteins regulate mRNA localization and translation efficiency
- microRNAs (miRNAs) can inhibit translation or induce mRNA degradation
- Internal ribosome entry sites (IRES) allow cap-independent translation initiation
Post-translational regulation
- Protein modifications can alter activity, stability, or localization
- Allosteric regulation changes protein conformation and activity
- Protein-protein interactions modulate function or form regulatory complexes
- Subcellular localization controls access to substrates or interaction partners
Protein synthesis inhibitors
- Protein synthesis inhibitors interfere with various stages of translation
- Important in both medical applications and studying protein synthesis mechanisms
Antibiotics vs eukaryotic inhibitors
- Antibiotics target bacterial ribosomes, exploiting differences from eukaryotic ribosomes
- Eukaryotic inhibitors often used in research to study protein synthesis in higher organisms
- Some inhibitors affect both prokaryotic and eukaryotic translation (puromycin)
Mechanisms of action
- Initiation inhibitors prevent formation of the 80S ribosome (pactamycin)
- Elongation inhibitors interfere with tRNA binding or peptidyl transfer (, cycloheximide)
- Termination inhibitors prevent release of completed polypeptides (puromycin)
- Some inhibitors cause premature chain termination or induce misreading (streptomycin)
Resistance mechanisms
- Mutations in ribosomal components can confer resistance to specific inhibitors
- Enzymatic modification of antibiotics renders them inactive (chloramphenicol acetyltransferase)
- Efflux pumps actively remove inhibitors from bacterial cells
- Alternative metabolic pathways may bypass inhibited steps in protein synthesis
Protein degradation
- Protein degradation maintains cellular homeostasis and responds to changing conditions
- Critical process in organic chemistry, influencing protein turnover and cellular function
Ubiquitin-proteasome system
- Ubiquitin molecules tag proteins for degradation through a three-enzyme cascade
- Polyubiquitinated proteins recognized by the 26S proteasome
- Proteasome unfolds and degrades tagged proteins into short peptides
- Regulated process controlling levels of key regulatory proteins (cyclins, transcription factors)
Lysosomal degradation
- Lysosomes contain various hydrolytic enzymes for protein breakdown
- Autophagy delivers cytoplasmic components to lysosomes for degradation
- Endocytosed proteins can be targeted to lysosomes for breakdown
- Important for recycling cellular components and responding to nutrient deprivation
Regulation of protein turnover
- Protein half-lives vary widely, from minutes to days or longer
- N-end rule relates protein stability to its N-terminal amino acid
- PEST sequences (rich in proline, glutamate, serine, and threonine) often mark proteins for rapid degradation
- Regulated proteolysis plays crucial roles in cell cycle progression and signal transduction
Key Terms to Review (20)
Amino acids: Amino acids are organic compounds that serve as the building blocks of proteins, consisting of a central carbon atom, an amino group, a carboxyl group, a hydrogen atom, and a distinctive side chain or R group. These molecules play critical roles in biological processes, including protein synthesis, where they are linked together by peptide bonds to form polypeptides and ultimately proteins. Their structure is influenced by their amino and carboxylic acid functional groups, which also contribute to their properties and reactivity.
Anticodon: An anticodon is a sequence of three nucleotides in transfer RNA (tRNA) that pairs with a complementary codon in messenger RNA (mRNA) during protein synthesis. This pairing is crucial as it ensures that the correct amino acid is added to the growing polypeptide chain, facilitating accurate translation of genetic information into functional proteins.
Chloramphenicol: Chloramphenicol is a broad-spectrum antibiotic that inhibits bacterial protein synthesis by binding to the 50S ribosomal subunit. This compound was originally isolated from the bacterium Streptomyces venezuelae and is particularly effective against a variety of Gram-positive and Gram-negative bacteria, making it a valuable tool in treating infections. It works by preventing the formation of peptide bonds during translation, thereby blocking the growth and reproduction of bacteria.
Codon: A codon is a sequence of three nucleotides in messenger RNA (mRNA) that corresponds to a specific amino acid or a stop signal during protein synthesis. Each codon plays a crucial role in translating the genetic information encoded in DNA into proteins, which are essential for various cellular functions. The sequence of codons determines the order of amino acids in a protein, influencing its structure and function.
Elongation: Elongation is a critical phase of protein synthesis during which amino acids are sequentially added to a growing polypeptide chain. This process occurs after the initiation phase and continues until a stop codon is reached on the mRNA. The elongation phase is vital for building proteins, as it involves the ribosome moving along the mRNA and facilitating the formation of peptide bonds between amino acids.
Gene expression: Gene expression is the process by which information from a gene is used to synthesize a functional gene product, usually a protein. This involves two main steps: transcription, where the DNA sequence of a gene is copied into messenger RNA (mRNA), and translation, where the mRNA is used as a template to build a protein. Proper regulation of gene expression is crucial for cellular function, development, and response to environmental signals.
Initiation: Initiation refers to the first step in the process of protein synthesis, where the ribosome assembles around the target mRNA and the first tRNA, carrying the appropriate amino acid, binds to the start codon. This process is crucial for ensuring that protein synthesis begins correctly, as it sets the stage for subsequent elongation and termination stages. The proper assembly of initiation factors and ribosomal subunits ensures that translation occurs accurately and efficiently.
Missense mutation: A missense mutation is a type of genetic alteration where a single nucleotide change results in the coding of a different amino acid in a protein. This change can affect the protein's structure and function, leading to varying degrees of impact on the organism, depending on the importance of the altered amino acid in the protein's activity.
MRNA: mRNA, or messenger RNA, is a single-stranded molecule that carries genetic information from DNA to the ribosome, where proteins are synthesized. It serves as a template for translating the sequence of nucleotides into a specific amino acid sequence, ultimately determining the structure and function of proteins within cells.
Nonsense mutation: A nonsense mutation is a type of genetic mutation where a nucleotide change in the DNA sequence results in a premature stop codon during protein synthesis. This early termination disrupts the normal production of a protein, leading to a truncated, often nonfunctional product. Nonsense mutations can significantly impact cellular functions and are associated with various genetic disorders.
Polypeptide chain: A polypeptide chain is a linear sequence of amino acids linked together by peptide bonds, forming the primary structure of proteins. The specific sequence of amino acids in a polypeptide chain determines its unique properties and functions, playing a crucial role in the synthesis and functionality of proteins within living organisms.
Post-translational modification: Post-translational modification refers to the chemical modifications that occur to a protein after its synthesis on the ribosome. These modifications can significantly alter a protein's structure, function, and stability, thereby influencing various biological processes. Such changes can include phosphorylation, glycosylation, and ubiquitination, which play critical roles in regulating protein activity and cellular signaling.
Ribosome: A ribosome is a molecular machine found within all living cells that serves as the site for protein synthesis. It translates messenger RNA (mRNA) sequences into polypeptide chains by facilitating the formation of peptide bonds between amino acids. Ribosomes are essential for the expression of genes and play a crucial role in cellular functions.
RNA Polymerase: RNA polymerase is an enzyme responsible for synthesizing RNA from a DNA template during the process of transcription. It plays a crucial role in gene expression by catalyzing the formation of RNA strands, which are essential for translating genetic information into proteins. Without RNA polymerase, the transcription process would be halted, preventing the proper synthesis of proteins necessary for cellular functions.
RRNA: rRNA, or ribosomal RNA, is a type of RNA that plays a crucial role in protein synthesis by serving as a structural and functional component of ribosomes. Ribosomes are the cellular machinery where proteins are assembled, and rRNA helps facilitate the interaction between mRNA and tRNA during translation, ensuring that the correct amino acids are incorporated into the growing polypeptide chain.
Termination: Termination is the final stage of protein synthesis where the newly formed polypeptide chain is released from the ribosome. This process is triggered when a stop codon on the mRNA is reached, signaling that no corresponding tRNA with an amino acid is available, leading to the disassembly of the translation machinery and completion of protein synthesis.
Tetracycline: Tetracycline is a broad-spectrum antibiotic that is used to treat various bacterial infections by inhibiting protein synthesis in bacteria. It works by binding to the 30S ribosomal subunit, preventing the addition of amino acids to the growing peptide chain, ultimately blocking bacterial growth. Tetracycline is effective against a wide range of gram-positive and gram-negative bacteria, making it a versatile choice in clinical settings.
Transcription: Transcription is the biological process through which genetic information encoded in DNA is converted into messenger RNA (mRNA). This process is essential for protein synthesis as it serves as the first step in gene expression, allowing the information stored in DNA to be used to create proteins that perform various functions in the cell.
Translation: Translation is the biological process by which messenger RNA (mRNA) is decoded to produce a specific polypeptide or protein. This process takes place in the ribosomes, where the mRNA sequence is translated into an amino acid sequence, resulting in the formation of proteins that play vital roles in cellular function and structure. The accuracy of translation is crucial for maintaining the integrity of proteins and, by extension, the functionality of the organism.
TRNA: tRNA, or transfer RNA, is a type of RNA molecule that plays a crucial role in the process of protein synthesis by transporting specific amino acids to the ribosome. Each tRNA molecule has a unique structure that allows it to recognize and bind to its corresponding codon on the mRNA strand, ensuring the correct amino acid is added to the growing polypeptide chain. This accurate delivery of amino acids is essential for producing proteins that perform various functions within living organisms.