Protein Structure and Function

Protein Structure

• Proteins' tertiary structure is their 3D shape, formed from secondary structures.
• This shape is determined by the arrangement of hydrophilic and hydrophobic R groups along the molecule and chemical bonds/interactions between R groups.
• Quaternary structure appears when multiple polypeptides come together as subunits of a larger functional protein.

Protein Function and Environment

• Protein function can change due to environmental factors.
• Protein chaperones help newly formed proteins fold correctly and protect against denaturation.

Primary Structure to Shape Relationship

• Primary structure dictates protein shape, and shape dictates function.
• The amino acid sequence specifies the protein's shape.
• Proteins fold into specific shapes determined by the interactions between amino acids.

Translation Processes

• Translation is the process where ribosomes read mRNA to build polypeptide chains that fold into proteins.
• mRNA carries the genetic code for protein synthesis from DNA.
• Ribosomes, composed of ribosomal proteins and ribosomal RNA, read mRNA from 5' to 3'.
• Ribosomes use codons (3 nucleotides) to incorporate specific amino acids.

Ribosome Structure and Function

• Ribosomes consist of large and small subunits.
• Ribosomes have three functional sites (A, P, and E) that handle tRNA during protein synthesis.
• Three sites are binding sites for tRNAs, and the P site helps form peptide bonds.

Translation Initiation

• The ribosome binds to the mRNA and starts translation at the start codon (AUG).
• Prokaryotes use Shine-Dalgarno sequences, while eukaryotes use the 5' cap.

Translation Elongation and Termination

• During elongation, the ribosome moves along the mRNA, bringing in amino acids and building the polypeptide chain.
• Termination occurs when a stop codon is encountered, releasing the polypeptide and ribosome.

Transfer RNA (tRNA)

• tRNA carries specific amino acids to the ribosome during translation.
• Each tRNA has an anticodon that binds to a complementary codon on mRNA.

tRNA Synthetases

• Aminoacyl-tRNA synthetases attach the correct amino acid to its corresponding tRNA.
• The enzyme recognizes the correct amino acid and tRNA, connecting them.

Codon-Anticodon Interactions

• Codons on mRNA and anticodons on tRNA bind together, ensuring the correct amino acid sequence during polypeptide synthesis.
• The first base of the codon binds with the last base of the anticodon.

Genetic Code

• The genetic code dictates which codon corresponds to which amino acid.
• There are redundant codons that code for the same amino acid.
• Codons specify the amino acid sequence.

Protein Families and Folding Domains

• Similar proteins can be grouped into families based on sequence and structure.
• Folding domains, shared by members of a family, fold independently from the rest of the protein, giving them similar structure and possibly function.

Transcription

• Transcription is the process by which RNA polymerase creates an RNA sequence from a DNA sequence.
• RNA polymerase reads the DNA sequence of a gene and creates a complementary RNA sequence.

RNA Processing

• In eukaryotes, RNA processing modifies the primary RNA transcript to create mature mRNA.
• The process involves adding a 5' cap and a poly(A) tail, and splicing out introns.

mRNA Transport

• Mature mRNA travels out of the nucleus to the cytoplasm for translation by ribosomes.
• mRNAs exit the nucleus through nuclear pores, entering the cytosol for translation by ribosomes.

Translation at the RER

• Some ribosomes move to the rough endoplasmic reticulum (RER) to synthesize proteins destined for the endomembrane system.
• The SRP (signal recognition particle) binds to the signal sequence on the polypeptide, halting translation until it docks at the RER to continue translation inside the RER lumen.

Cap-dependent and Cap-independent Translation

• Cap-dependent translation relies on a 5' cap on the mRNA to initiate translation by ribosomes.
• Cap-independent translation uses internal ribosome entry sites (IRES).

Protein Sorting

• The first few amino acids of a new polypeptide chain determine the protein's final location within the cell, based on signal sequences.

Proteins for Endomembrane System

• Proteins targeted to the endomembrane system (RER, Golgi, etc.) are synthesized by ribosomes on the RER.
• The newly synthesized protein will enter the lumen of the RER after its SRP binds to a receptor.

Explore the intricate relationship between protein structure and function, from primary structure to quaternary formation. Learn how environmental factors and chaperones affect protein folding and activity. This quiz will test your understanding of translation processes and the significance of amino acid interactions.