Biology: Protein Synthesis Fundamentals

Protein Synthesis

• Protein synthesis is the process of producing polypeptide chains (proteins).
• It occurs in two phases: transcription and translation.
• In eukaryotes, mRNA must be processed before it leaves the nucleus.

Three Types of RNA

• Messenger RNA (mRNA) carries genetic information to ribosomes, acting as a blueprint for protein construction.
• Ribosomal RNA (rRNA), along with protein, forms ribosomes, the sites where protein synthesis occurs.
• Transfer RNA (tRNA) transports amino acids to ribosomes for protein synthesis; it acts like a "truck" delivering the correct amino acid.

Genes & Proteins

• Proteins are made of amino acids linked by peptide bonds.
• There are 20 different amino acids.
• Amino acid chains are called polypeptides.
• Segments of DNA that code for amino acid sequences are called genes.
• DNA contains a triplet code.
• Every three bases on DNA represent one amino acid.
• Each three-letter unit on mRNA is called a codon.
• Most amino acids have more than one codon.
• The genetic code is nearly universal.

Overview of Transcription

• During transcription, a segment of DNA unwinds and unzips.
• DNA serves as a template for mRNA formation.
• RNA polymerase joins RNA nucleotides to create mRNA codons that are complementary to the DNA triplet code in a complementary manner.
• mRNA is created using only one DNA strand as a template.
• Transcription begins at a promoter DNA region (e.g., TATA box).
• Transcription ends at a terminator region.
• Pre-mRNA is released after transcription is complete.

RNA Polymerase

• An enzyme located in the nucleus, RNA Polymerase separates the two DNA strands and links RNA nucleotides together.

Processing Pre-mRNA

• Occurs in the nucleus.
• Pre-mRNA comprises introns and exons.
• Introns do not code for proteins, whereas exons do.
• Introns are spliced out by spliceosome enzymes.
• Exons are rejoined to create mature mRNA.
• The mature mRNA leaves the nucleus and enters the cytoplasm.

Messenger RNA (mRNA)

• Carries the information to synthesize a specific protein.
• Typically 500 to 1000 nucleotides long.
• A sequence of 3 bases forms a codon.
• AUG is the start codon, and UAA, UAG, and UGA are stop codons.

Transfer RNA (tRNA)

• 75 to 80 nucleotides long.
• Picks up the appropriate amino acid from the cytoplasm.
• Transports amino acids to mRNA on ribosomes.
• Contains anticodons that are complementary to mRNA codons.
• Bonds to mRNA through hydrogen bonds using appropriate codons.
• Four ATP's are required for each amino acid added to the polypeptide chain : Two to "charge" the tRNA, one to carry the charged tRNA to the ribosome and one to move the ribosome to the next codon.

Ribosomal RNA (rRNA)

• 100 to 3000 nucleotides long.
• Found inside the cell nucleus.
• Forms ribosomes with proteins.

Ribosomes

• Composed of large and small subunits.
• Consist of rRNA and proteins.
• Two sites, P and A, are involved in protein synthesis
• Ribonucleoproteins

Peptide Synthesis

• Incoming tRNA carries the amino acid bound to it into the ribosome A site.
• Formation of peptide bond between the two amino acids.
• Empty tRNA exits from the P site.
• Ribosome moves over one codon.

Translation

• Synthesis of proteins in the cytoplasm.
• Involves mRNA, tRNA, ribosomes, and amino acids.
• Three steps: initiation, elongation, and termination.
• Initiation starts with the start codon AUG.
• Elongation involves linking amino acids.
• Termination occurs with the stop codon (UAG, UAA, or UGA).

mRNA Codons Join the Ribosome

• mRNA codons align with ribosome sites (P and A sites).

Initiation

• First tRNA binds to the start codon in the P site.
• Second tRNA binds to the next codon in the A site.
• Peptide bond forms between the two amino acids.

Elongation

• Peptide bond forms between amino acids in the A and P site.
• Ribosome moves over one codon.
• Empty tRNA leaves the P site.

Ribosomes move over one codon

• The ribosome moves over one codon, shifting the next codon into the A site. The first empty tRNA leaves.

Termination

• Stop codon (UAG, UAA, or UGA) enters the A site.
• Release factor binds to the stop codon.
• The polypeptide chain is released.
• Ribosome subunits detach.

End Product - The Protein

• The end product of protein synthesis is a primary structure of a protein.
• A sequence of amino acids bonded by peptide bonds.

Classification of Proteins

• Simple proteins- formed of only amino acids. Hydrolyzed into amino acids.
• Further divided into fibrous proteins(Keratin, Elastin, Collagen) and globular proteins (Albumin, Globulin, Glutelin, Histones).
• Conjugated proteins- combined with non-protein moiety
• Derived proteins- derivatives or degraded products of simple and conjugated proteins. (e.g., proteans, metaproteins, proteoses, peptones, and pepides).)

Structure of a protein

• Primary structure- amino acid sequence.
• Secondary structure- alpha helix and beta sheet.
• Tertiary structure- overall 3D conformation.
• Quaternary structure- arrangement of multiple polypeptide chains.

Classes of Protein Structure

• Globular proteins- usually round and ball-shaped; involved in metabolic functions (enzymes, antibodies, hemoglobin).
• Fibrous proteins- long and narrow; involved in structural functions (collagen, keratin).

Functional Classification of Proteins

• Enzymes- biochemical catalysts.
• Transport proteins- transport molecules (e.g., hemoglobin).
• Storage proteins- store substances (e.g., ferritin).
• Mechanical support- stabilize structures (e.g., keratin, collagen).
• Movement- involved in muscle contraction (e.g., myosin).
• Nerve transmission- involved in nerve signals; receptor for acetylcholine
• Hormones- regulatory functions; insulin.
• Protection- antibodies protect against harmful agents.
• Storage of energy- proteins act as energy stores (amino acids)
• Prolonged fasting may make protein essential.

Secondary structure of a protein

• Alpha-helix: The most common type. Fingernails and toenails, etc.
• Beta sheets: Form the core of globular proteins.
• N-terminus: The end with the free amino group.
• C-terminus: The end with the free carboxyl group
• Parallel: beta-strands run in the same direction
• Antiparallel: beta-strands run in opposite directions

Alpha Helix Versus Beta Sheet

• Alpha-helix: Right-handed, rod-like structure with hydrogen bonds within the polypeptide chain. R groups are generally outside the helix.
• Beta sheet: Sheet-like structure with hydrogen bonds between amino acid residues in different sections of the chain. R groups are directed both inside and outside the sheet.. Can be parallel or antiparallel, based on chain directions

Clinical Implications of Secondary Structure of Proteins

• Secondary structure can be altered by mutations or extreme conditions.
• Spongiform encephalopathy and amyloidosis are diseases related to misfolding and beta sheet formation of proteins.
• Misfolding and beta sheet formation may lead to tissue damage.

Structural Databases

• Important in solving molecular biology problems.
• Protein Databank (PDB) is the international repository for macromolecular structure data (e.g. amino acid sequences and structures).
• Moved to Research Collaboratory for Structural Bioinformatics (RCSB)

NDB: Nucleic Acid Structure Database

• Contains information about experimentally determined nucleic acids and assemblies.
• Used for searching based on annotations relating to sequence, structure, function, and for downloads, analysis.

PDB- Protein Structure database

• Contains information about the 3D structures of proteins.
• PDB files hold experimentally determined structures of biological macromolecules.
• Structural information is determined by X-ray crystallography or NMR spectroscopy.
• PDB structure information offers a broad range of features and search parameters. Includes molecule name, primary and secondary structure, ligand, coordinates, and crystallographic information.

Protein visualizing tools Uses

• Display structural information from the PDB in 3D.
• Image manipulation for various perspectives.

RasMol/RasTop

• A molecular graphics program for visualizing proteins, nucleic acids, and small molecules.
• Reads molecule coordinate files and interactively displays the molecule with different color schemes.
• Enables different molecule representations (e.g., depth cued wireframes, sticks, space-filling, ball and stick, ribbons, etc.).

Pymol

• A molecular graphics system with an embedded Python interpreter.
• Designed for real-time visualization and high-quality image and animation generation.
• Features for creating movies, measuring bond distances, and reassembly.

Online Visualizer

• Allows for interactive viewing of PDB structures.
• Uses an online viewer, often associated with NCBI.

Secondary structure prediction algorithm

• Ab initio methods: Use single-sequence information.
• Homology-based methods: Use multiple-sequence alignment information.

Ab Initio-Based Methods

• Measure relative propensity of amino acids to occur in secondary structure elements.
• Use known crystal structures to determine propensity scores.
• Chou-Fasman and Garnier-Osguthorpe-Robson (GOR) algorithms are examples.

Homology-Based Methods

• Combine ab initio prediction and multiple-sequence alignments.
• Improve prediction accuracy by 10%.
• PHD is an example.

PHD - neural network algorithm for secondary structure prediction

• PHD predicts secondary structure based on hydrogen bonds information from multiple sequence alignments.

How good are the methods?

• Accuracy ranges from 50% for single sequence/single residue methods to 71% for multiple sequence methods.

Explore the intricate processes of protein synthesis through transcription and translation. This quiz delves into the roles of various types of RNA and the relationship between genes and proteins, guiding you through the essential concepts of molecular biology.