Proteins and Biological Processes

• Biochemistry is an introduction to proteins
• Video resource is What is a Protein – PDB101

What is a Protein?

• Proteins are macromolecules constructed from 21 standard amino acids
• Amino acids link via peptide bonds through dehydration synthesis
• Vital protein functions include communication, transport, defense, storage, and structural support, as well as enzymes

Amino Acids Composition

• Amino acids, the building blocks of proteins, contain C, H, O, N, and sometimes S; some contain Selenium (Se)
• Amino acids may be hydrophilic or hydrophobic, acidic or basic
• Each amino acid has a unique side chain, the "R" group

Protein Structures

• The primary structure is the amino acid sequence
• Alpha-helices and beta-sheets form the secondary structure
• The tertiary structure arises from the 3D folding of a protein
• Quaternary structure involves multiple tertiary proteins forming a larger functional protein

Protein Representation

• Space-filling models display all atoms in a protein
• Cartoon/ribbon diagrams illustrate the 3D shape
• Surface models depict the protein's surface and interaction sites with water or other molecules

Protein Shape and Function

• A protein's 3D correctly folded shape dictates its function, and improper folding prevents proper function
• Denaturation leads to a loss of natural shape and function
• Proteins denature from heat, pH, alcohols, and heavy metals

Examples of Proteins and their Roles

• Structural: collagen, keratin, spider silk
• Transport: Ca++ pump, glucose channel proteins
• Enzymes: amylase (starch), DNA polymerase
• Storage: Ferritin (Fe3+)
• Communication: Insulin
• Defense: antibodies
• Osmotic balance: albumin

Abundance and Functions of Proteins

• Proteins are abundant, making up 40-70% of a cell's dry weight
• Proteins catalyze reactions and act as chemical signals (hormones, cytokines)
• Cells communicate via direct, paracrine, or endocrine signaling using hormones

Diverse Protein Functions

• Storage: myoglobin stores oxygen, and ferritin stores iron
• Structural: elastin and collagen provide support
• Protective: antibodies defend, and skin protects Movement: actin and myosin enable muscle contraction
• Transport: hemoglobin carries oxygen, and lipoproteins transport substances in/out of cells
• Communication: glycoproteins facilitate cell interactions

Protein Structures & Functions

• Structural proteins such as collagen, keratin, and fibrin are fibers that contribute to cartilage, hair/nails, and blood clotting, respectively
• Metabolic proteins like protease function as enzymes to break down proteins
• Membrane transport proteins like sodium-potassium pumps and aquaporins facilitate the movement of molecules and ions across cell membranes
• Cell recognition proteins like MHC proteins and ABO blood groups are cell surface antigens facilitating "self" recognition

Proteins in the Body

• Osmotic concentration: albumin maintains blood's osmotic concentration
• Gene regulation: repressors and histones regulate gene transcription
• Body function regulation: insulin, vasopressin, and oxytocin control glucose levels, water retention, and milk production, affect behavior
• Transport: globins like hemoglobin and myoglobin carry O2 and CO2
• Lipoproteins and cytochromes carry lipids and electrons, respectively
• Contraction: actin and myosin proteins enable muscle contraction
• Defense: immunoglobulins/antibodies mark foreign proteins while toxins block nerve function

Motor Proteins

• Motor proteins like kinesin, dynein, and myosin drive movement within the cell
• All proteins consist of amino acid monomers linked by peptide bonds
• Cells use dehydration synthesis to form these bonds between monomers

Amino Acid Structure

• Amino acids contain an amino group, a carboxyl group, and a unique R-group attached to a central carbon
• The R-group determines an amino acid's identity and properties

Twenty Standard Amino Acids

• Twenty standard amino acids form all proteins in plants and animals
• Nine of these are essential amino acids that humans must obtain through their diet
• Plants/microorganisms can produce all 20 amino acids from inorganic compounds

Amino Acids that are Important

• Phenylalanine, Valine, Tryptophan, Threonine, Isoleucine, Methionine, Histidine, Lysine, and Leucine are essential for humans
• Lysine is often the limiting amino acid in wheat, rice, and maize
• Soy and chia seeds, lentils, tofu, seafood, poultry, meat, dairy, eggs, some legumes, bananas, avocado, buckwheat, quinoa, and mushrooms are great sources of amino acids

Recent Discoveries and Functions of Amino Acids

• Scientists are exploring new and unnatural amino acids
• Glutamate is a neurotransmitter, hydroxyproline supports collagen, and glycine aids lipid transport
• Aspartame is made from aspartic acid and phenylalanine
• 5-HTP treats neurological issues & depression, and L-DOPA treats Parkinsonism

Peptides & Assembled Amino Acids

• Peptides, shorter than 50 amino acids, are also biologically relevant
• Chains are classified by size
• Dipeptides: 2 amino acids
• Tripeptides: 3 amino acids
• Oligopeptides: 5-50 amino acids

Protein Formation

• Polypeptides contain over 50 amino acids
• Proteins are folded and complete polypeptide chains
• Insulin release signals high blood sugar, prompting cells to absorb glucose from blood
• The pancreas secretes insulin, glucagon, and somatostatin, which affect diabetes

Insulin Functions

• Transports glucose, which is secreted by the pancreas
• Insulin consists of 21 and 30 amino chains, which are linked by disulfide bonds

Polypeptides and Protein Assembly

• Proteins that are large chains of amino acids called polypeptides, are put together by ribosomes
• Ribosomes use enzymes to attach the amino acids
• Polypeptide chain folds into an alpha-helix or beta-sheet for structure
• Multiple polypeptides assemble, if needed, to form a complete protein
• Polypeptides form due to covalent bonds
• Proteins fold properly due to H-bonding
• Dehydration helps peptide bonds to be formed

Amino Acids Joining

• Ribosomes connect amino acids; -OH is removed from the carboxyl end while H is removed from the amine group
• Carbonyl carbon and nitrogen then form a bond
• This is how chains form, as the bond develops between carbon and nitrogen

Protein Shape Determination

• Proteins are amino acid chains that fold into unique 3D shapes, known as the native state, determined by amino acid sequence and interactions
• Protein properties depend on amino acid sequence and folding

Organization Level

• Protein structure has four levels: primary, secondary, tertiary, and quaternary
• The sequence is the primary
• Alpha-helices/beta-sheets give secondary
• Folding gives tertiary
• Subunits give quaternary
• Even with similar components, sequences and arrangements mean that a protein is different

Secondary Protein Structure

• This describes geometric patterns as chains fold
• Hydrogen bonding between amino acids leads to alpha-helices or beta-pleated sheets

Tertiary Protein Structure

• Alpha helices and/or beta sheets, along with unorganized sections of a peptide chain, “fold” into a more compact shape
• The final 3-D shape is due to the original sequence of amino acids
• R group dictates this
• Many different types of bonding causes the turns and bends of proteins to their shapes
• It is this shapes that determines a proteins function

Interactions in Tertiary Structure

• Hydrophobic R-groups cluster in the interior
• Hydrogen bonds appear between polar chains or groups
• Salt bridges develop from positive and negative charges
• Disulfide bridges form between cysteine residues

Quaternary Structures

• Quaternary structure: multiple polypeptide chains combine
• These chains (subunits) form a complete protein
• Forces in tertiary structures maintain shape
• Ex: Hemoglobin has polypeptide chains, two of each kind, plus heme groups

How Proteins Denature

• Denaturation: protein loses its native shape and optimal bioactivity
• Prions and tau proteins lead to diseases in humans such as Alzheimer's
• Protein shape is maintained by forces involved in secondary/tertiary/quaternary structures, including hydrogen bonds, disulfide bridges, and hydrophobic interactions

Impacts of Changing Protein Structures

• Changes disrupt the function of the protein and its natural shape via denaturation
• Heat introduces the most non-covalent intermolecular bonds
• Mechanical force, like a whisk, denatures the shape of a protein
• Soaps and detergents may denature proteins
• Polar solvents may denature proteins
• Acids and bases can also denature proteins
• Heavy metals also denature protein

Explore the crucial roles of proteins in various biological processes. From cell signaling to enzyme catalysis and stress response, understand how proteins drive life's essential functions. Learn about their structure, interactions, and significance in cellular activities.