2.2 Proteins and membranes

Cells and Tissues

Protein Structure and Function

Part 1

Learning Outcomes

• Summarise the four levels of protein structure

• Define the different types of proteins according to their structure and/or function

• Describe the structure and list the functions of the cell membrane

• Explain the role of the cell membrane in regulating the transport of materials into and out of the cell

• Describe the active and passive processes that transport substances across the cell membrane

Core Concepts

Genome and Proteins

• Genome is composed of chromosomes, which contain genes that provide instructions for protein synthesis

• Proteins perform various cellular functions, either independently or as part of complexes

The Human Protein Atlas

• Identifies proteins present in various human tissues including:

  • Brain, adrenal gland, thyroid gland, lung, bone marrow, heart, skeletal muscle, gastrointestinal tract, liver, kidneys, and more.

Proteins

• Essential for health and cellular function

• Involved in:

  • Cell shape and organization

  • Signal reception and responding to signals

  • Structural integrity, transportation, immunity, and communication

• polymers of amino acids

• amino acid sequence assembled according to DNA sequence

• Peptides < 50 amino acids

• Proteins > 50 amino acids

  • A peptide bond is a covalent bond that forms between the carboxyl group of one amino acid and the amino group of another amino acid, releasing a molecule of water (a process known as dehydration synthesis). This bond is fundamental in linking amino acids together to form peptides and proteins, and is characterized by its strong stability, which is essential for maintaining the protein's structure.

Polymers of Amino Acids

• Proteins are polymers formed by amino acids based on the DNA sequence

• Peptides consist of less than 50 amino acids, while proteins have more than 50.

Four Levels of Protein Structure

1. Primary Structure

   • Sequence of amino acids from amino to carboxyl terminus

   • Hydrophobic/hydrophilic composition impacts structure

   • Begins at the a Amino terminus and ends in the Carboxyl terminus

2. Secondary Structure

   • First folding level stabilized by hydrogen bonds forming alpha-helices or beta-sheets

     • Alpha-helix

       • starts with an Amino terminus and ends with a Carboxyl terminus

       • Hydrogen of a carbonyl group bonds with a hydrogen of an amine group

       • 3.6 residues per turn

       

     • Resulting in a right-handed coil structure that is stabilized by these hydrogen bonds, contributing to the overall stability and functionality of the protein.

     • This helical structure is a common motif found in many proteins, allowing them to maintain their shape and perform biological functions effectively. Additionally, the presence of specific amino acid sequences can influence the propensity of a protein to adopt an alpha-helical conformation, which is critical for the protein's interaction with other molecules and its role in cellular processes.

     • The stability of alpha helices is further enhanced by the presence of hydrophobic interactions and van der Waals forces, which help to minimise the exposure of hydrophobic residues to the aqueous environment, thus promoting a more favorable energy state for the protein.

   • Beta-sheet

     • parallel peptide chains linked by hydrogen bonds

     • side chains exposed on both side of polypeptides create a distinctive zigzag pattern, contributing to the overall stability and structural integrity of the beta-sheet. In addition, the arrangement of beta-sheets can be classified into parallel and antiparallel configurations, which differ in the orientation of the peptide chains and can influence the mechanical properties and functionality of the protein.

1. Tertiary Structure

   • Three-dimensional arrangement, involving hydrogen bonding, ionic bonds, hydrophobic interactions, and disulfide bonds

     • hydrogen bonds

       • side chains with partial positive and negative charges

     • ionic bonds

       • opposite charged side chains

     • hydrophobic interactions

       • non-polar side chains

     • disulphide bonds

       • cysteine residues

1. Quaternary Structure

   • Formation of total protein complex

     • multiple polypeptides

     • held together by

       • non-convalent bonds

       • hydrogen bonds and Van der Waals forces

     • subunits interact cooperatively

     

     • Fv (Fragment variable): This is the part of the antibody that contains the variable regions of both the heavy and light chains. It is responsible for the specific binding to the antigen. The Fv region is crucial for the diversity of antibodies, as it determines the specificity for different antigens.

     • Fab (Fragment antigen-binding): This includes the Fv region along with a portion of the constant region of the heavy chain. The Fab fragment is responsible for binding to antigens. Each antibody has two Fab fragments, allowing them to bind two identical antigens simultaneously.

     • Fc (Fragment crystallizable): This is the constant region of the antibody that is involved in mediating immune responses. The Fc region is recognized by immune cells and helps in various mechanisms of action, such as opsonization and activation of the complement system.

     In summary, the Fv and Fab regions are involved in antigen binding, while the Fc region plays a role in the immune response.

Post-Translational Modifications

• Various modifications enhance protein functionality:

  • Phosphorylation

    • adds a phosphate to serine, threonine or tyrosine, which can alter the protein's activity, localization, or interaction with other molecules.

  • glycosyation

    • attaches a sugar, usually to an '“N” or “O” in an amino acid side chain , which can affect protein folding, stability, and cell signaling pathways.

  • Ubiquitaination

    • adds ubiquitin to lysine reside of a target protein for degradation , which marks the protein for recognition by the proteasome, thus regulating protein levels and maintaining cellular homeostasis.

  • SUMOylation

    • adds a small protein SUMO (small ubiquitin-like modifier) to a target protein

  • Disulfide bond

    • Convalently links the “S” atoms of 2 different cysteine residues

  • Acetylation

    • adds an acetylene griup to an N'-terminus of a protein or at lysine residue

  • Lipidation

    • attaches a lipid, such as a fatty acid, to a protein chain

  • methylation

    • adds a methyl group, usually at lysine or arginine residues

  • hydroxylation

    • attaches a hydroxyl group (-OH) to a side chain of a protein

Structural Proteins

• Muscle Proteins: Contractile proteins (actin/myosin) and regulatory proteins (tropomyosin, troponin).

  • Function

    • form thick and thin filaments

  • types

    • actin-myosin

    • Tropomyosin-troponin

• Collagens: Fibrous proteins that constitute most of the extracellular matrix (ECM), provide strength and shape.

  • Function

    • provide strength, support and shape to tissues

  • Structure

    • 3 polypeptide chains

    • Triple superhelix stabilised by hydrogen bonding

    • 1000 different mutations associated with disease

      • osteogenesis imperfecta: A genetic disorder caused by mutations in the collagen genes, leading to brittle bones and increased fracture risk.

• Cytoskeletal Proteins:

  • cytoskeleton, cilia and flagella

  • dynamic polymer structure

  • rapidly assembles and disassembles

  • Function

    • cell protection

    • motility

    • cytokinesis

    • transport

    • cell division

    • organelle organisation

  • Types

    • actin filaments

    • microtubules

    • intermediate filaments

DNA Associated Proteins

• Histones: Basic proteins involved in DNA packaging.

• Transcription Factors: Involved in RNA polymerase recruitment and gene expression regulation, mutations can impact diseases.

Immunity Proteins

• Cytokines:

  • Manage immune responses and inflammation and haemopoisis

    • Haemopoiesis is the process of creating blood cells, mainly in the bone marrow. This includes red blood cells (which transport oxygen), white blood cells (which fight infections), and platelets (which help with blood clotting). It is important for replacing old or damaged blood cells and keeping the immune system healthy

  • Small proteins/peptides

  • produced by immune cells

• Antibodies:

  • Structure defined by polypeptide chains, involved in pathogen clearance.

  • 2 pairs of polypeptide chains

    • forms a “Y” shape

    • IgG, IgM, IgA, IgD, and IgE are the five main classes of immunoglobulins (antibodies) in the human body, each playing distinct roles in the immune response:

      1. IgG (Immunoglobulin G): The most abundant antibody in blood and extracellular fluid, it plays a crucial role in the body's defense against infections and is the only class that can cross the placenta to provide passive immunity to the fetus.

      2. IgM (Immunoglobulin M): The first antibody produced in response to an infection. It is primarily found in the blood and is effective at forming complexes for the elimination of pathogens.

      3. IgA (Immunoglobulin A): Found mainly in secretions such as saliva, tears, and breast milk, IgA plays a vital role in mucosal immunity, protecting body surfaces exposed to foreign substances.

      4. IgD (Immunoglobulin D): Although its function is not fully understood, IgD is primarily found on the surface of immature B lymphocytes and is believed to play a role in the activation and regulation of B cells.

      5. IgE (Immunoglobulin E): Involved in allergic reactions and responses to parasitic infections, IgE binds to allergens and triggers histamine release from mast cells and basophils, leading to allergic symptoms.

• Complement:

  • over 30 proteins

  • involved in the innate immune system

    • clearing invading pathogens

    • form a membrane attack complec

    • cell lysis

Antigens

• proteins, peptides or polysaccarides

  • Essential for antibody response

  • Epitope (specific part of an antigen that is recognized by the immune system, particularly by antibodies or T-cell receptors)

    • the surface of the polypeptide that binds the antibody

    • can complex with lipids and nucleic acids

• Types of antigens

  • Exogenous

    • Exogenous refers to substances that originate from outside an organism.

  • Endogenous

    • Endogenous refers to substances that are produced within an organism, such as proteins generated by the body's own cells.

  • Autoantigens

    • Autoantigens are proteins produced by the body that can trigger an immune response against its own tissues, often leading to autoimmune diseases.

  • Tumor antigen

    • Tumor antigens are proteins expressed on the surface of cancer cells that are recognized by the immune system as foreign, prompting an immune response aimed at targeting and destroying the tumor.

  • Native antigen

    • Native antigens are substances that are extracted directly from their natural source, such as a virus or bacteria.

Coagulation Proteins

• The process fo haemostasis

  • Haemostasis is the cessation of bleeding from a blood vesel

  • Blood clot formation

  • 3 steps of haemostasis

    • Vasocontrsiction

    • temporarilry blockage of a plug

    • coagulation cascade, leading to the formation of a stable fibrin clot that seals the injury and prevents further blood loss.

• Activation, adehsion and aggregation of platelets

Anticoagulation Proteins

• Maintain homeostatic balance

• natural occurring anticoagulants

  • Thrombomodulin, Protein C, Protein S, Antithrombin, Tissue factor pathway inhibitor

• Usually given to patients who are at higher risk of getting clots: amd therefore more prone to getting stroke and heart attack

Transport Proteins

• Carry substances across biological membranes

  • ions, sugars, proteins and messenger molecules

• reside within cell membranes

• form channels or a carriers

• Carrier Proteins

  • transfers substance across the lipid bilayer

    • protein binds to the substrate

    • undergoes a revrsibe conformational change

    • moving the molecule to the interior of the call

  • usis adenonie tri-phosphate (ATP)

  • opens to only 1 part of the membrane, allowing selective transport of ions or molecules across the lipid bilayer.

• Channels

  • traversing through the cell membrane

  • hydrophilic channel through their core

  • open to intracellular and extracellular space

  • facilitate travel of polar molecules and ions

  • can be gated

• Albumin

  • maintain oncotic pressure of the plasma

  • negatively changed and can bind to Cations and Hydrophobic molecules

Enzymes

• catalyse reactions

• contains a substrate binding site that perfectly fits the binding of substrate converting it into a product

• function at specific temperatures and pH ranges

• Types of Enzymes

  • Oxidoreductase (oxidation - Reduction reaction)

  • Transferases (Transfer of amino, carboxylate, acyl, carbonyl, methyl, phosphate

  • Hydrolases ( catalyze the hydrolysis of chemical bonds, breaking down molecules by the addition of water. )

  • Lyases ( Cleavage of carbon bonds)

  • Isomerases (Rearrangements of bonds)

  • Ligases (Formation of onds between Carbon, Oxygen, Sulphur and Nitrogen)

Signalling Proteins

• Essential for cellular communication via ligands, promoting receptor-ligand interactions.

• Neurotransmitters (e.g. GABA, serotonin) manage neurological functions.

• Ligands

  • Extrcellular chemicals

  • secreted by a signaling cell

  • bind to a target cell

The Cell Membrane

• Function: Protects cells, facilitates communication, and regulates chemical composition within the cell.

Membrane Structure

• Consists of a phospholipid bilayer with hydrophilic heads and hydrophobic tails, retaining structural integrity.

Membrane Proteins

• Include glycoproteins and glycolipids for recognition, integral proteins for transport, and peripheral proteins for regulation.

Transport Across the Plasma Membrane

Selective Permeability

• Permits selective passage governed by substance characteristics: size, charge, and solubility.

Passive vs Active Transport

• Passive Transport: Does not require ATP, includes simple diffusion and facilitated diffusion.

• Active Transport: Requires ATP, moves substances against the gradient, includes vesicular transport (endocytosis/exocytosis).

Mechanisms of Transport

1. Simple diffusion: Movement of non-polar molecules (e.g., O2, CO2)

2. Facilitated diffusion: Assists charged molecules through channel proteins.

3. Active transport: Upholds concentration gradients through pumps and vesicles (e.g., endocytosis).