Cellular Macromolecules & Protein Functions

Macromolecules Inside Cells

• Macromolecules are abundant within cells
• A bacterial cell's composition consists of 70% water and 30% chemicals
• Chemicals are made up of 4% inorganic ions and small molecules, 2% phospholipids, 1% DNA, 6% RNA and 15% protein
• Animal cells are similarly composed

General Protein Functions and Building Blocks

• Proteins serve as main building blocks of cells
• Proteins constitute most of a cell's dry mass, providing cells with their shape and its structure
• Proteins execute many functions

Examples of Protein Functions

• Enzymes catalyze covalent bond breakage or formation
• Structural proteins provide mechanical support to cells and tissues
• Transport proteins carry small molecules or ions
• Motor proteins generate movement in cells and tissues
• Storage proteins store amino acids or ions
• Signal proteins carry extracellular signals from cell to cell
• Receptor proteins detect signals and transmit them to the cell's response machinery
• Transcription regulators bind to DNA to switch genes on or off
• Special-purpose proteins are highly variable

Protein Shape and Structure

• A protein's shape is specified by its amino acid sequence
• Proteins undergo folding into stable conformations
• Proteins have a wide variety of complicated shapes
• Alpha helices and beta sheets are common folding patterns
• Helices form readily in biological structures
• Beta sheets form rigid structures at the core of many proteins
• Misfolded proteins can form amyloid structures that cause disease

The Influence of Amino Acid Sequence on Protein Shape

• The shape of a protein is specified by its amino acid sequence
• The general formula of an amino acid contains an alpha-carbon atom, amino group, carboxyl group, and a side chain (R)
• The R is commonly one of 20 different side chains
• At pH 7, both the amino and carboxyl groups are ionized

Peptide Bonds

• In proteins, amino acids are joined together to form an amide linkage AKA a peptide bond
• Four atoms involved in each peptide bond form a rigid planar unit and there is no rotation around the C-N bond
• Proteins are long polymers of amino acids linked by peptide bonds and written with the N-terminus toward the left
• Peptides are shorter, usually fewer than 50 amino acids long
• A protein is made of amino acids linked together into a polypeptide chain with peptide bonds
• Each amino acid's side chain projects
• The sequence of chemically distinct side chains can be nonpolar, polar uncharged, positively charged, or negatively charged, giving each protein its distinct, properties

Amino Acids

• Twenty different amino acids are commonly found in proteins
• Amino acids with neutral pH in an aqueous solution differ in their charge.
• The different kinds of amino acids are polar and nonpolar
• pH influences protein function as some polar R-groups can change charge, and the new attraction or repulsion can alter the shape of the protein

Protein Folding and Three Types of Noncovalent Bonds

• Proteins fold into a conformation
• Although any one of these bonds is quite weak, many of them together can create a strong bonding arrangement that stabilizes a particular three-dimensional structure
• Noncovalent bonds helping proteins fold include electrostatic attractions, van der Waals attractions, and hydrogen bonds.
• Hydrophobic forces help proteins fold into compact conformations
• polar amino acid side chains tend to be displayed on the surface and interact with water
• nonpolar amino acid side chains are buried on the inside to form a tightly packed hydrophobic atoms that are hidden from water

Hydrogen Bonds in Protein Molecules

• Hydrogen bonds within a protein molecule help stabilize its folded shape
• Nitrogen atoms are blue, oxygen atoms are red, and carbon atoms are gray
• A protein can be denatured (unfolded) by treatment with solvents which disrupt the noncovalent interactions holding the folded chain together
• Proteins denaturation can be studied using Urea which disrupts the hydrogen-bonds of water molecules
• Renaturation is the returning of protein to its natural shape in the absence of denaturing factor and the protein often refolds

Protein Folding in Living Cells

• Protein folding in a living cell is assisted in two ways:
• Chaperone proteins are large special molecules that bind to partly folded chains and assist them to fold along the most energetically favorable pathway
• Chaperones make the folding process both more efficient and reliable
• Isolation chambers are a protein folding method in which single polypeptide chains can fold without the risk of forming aggregates in the crowded cytoplasm
• Chaperone proteins (hsp 70) guide the folding of a newly synthesized polypeptide chain, binding to the protein and helping it fold in the most energetically favorable way
• Some chaperone proteins act as isolation chambers (hsp 60) that help a polypeptide fold without the risk of aggregating with other polypeptides of the cytoplasm

3D Conformation of Proteins

• Proteins range in size from about 30 amino acids to 10,000
• Most proteins have a three-dimensional conformation
• Structurally diverse macromolecules exist in the cell
• 100,000 different proteins have been determined
• The vast majority are between 50 and 2000 amino acids long

Size and Shape of Proteins

• Proteins come in a wide variety of shapes and sizes, forming filaments, sheets, rings, or spheres
• An example is deoxyribonuclease bound to a portion of a DNA molecule
• Two common folding patterns are the alpha helix and beta sheet

Common Folding Patterns

• Alpha helix contains keratin which are abundant in skin, hair, and nails
• Beta sheets contains fibroin which is a major constituent of silk
• Folding patterns result from hydrogen bonds that form between the N-H and C=O groups in the polypeptide backbone
• Alpha helices and beta sheets can be generated by many different amino acid sequences because the amino acid side chains are not bound by hydrogen bonds

Alpha Helices In Detail

• Polypeptide chains fold a helix
• In an alpha helix, a hydrogen bond is made between every fourth amino acid, linking the C=0 to the N-H in the same chain
• Alpha helices are generated when a single polypeptide chain turns around itself to form a rigid cylinder
• Many alpha helix proteins cross the lipid bilayer of cell membranes, requiring 20 amino acids to span a membrane in this way
• Hydrophobic side chains of the amino acids make contact with the hydrophobic hydrocarbon tails of the phospholipid molecules
• the shape is not a channel: no ions or small molecules can pass through it
• the hydrophilic parts of the polypeptide backbone can form hydrogen bonds along the interior of the helix

Coiled-Coil Alpha Helices

• Coiled-coil alpha helices form when two or three alpha helices wrap around one another to form a stable structure
• alpha helices have most of their nonpolar (hydrophobic) side chains along one side, so they can twist around each other with their hydrophobic side chains facing inward, minimizing contact with the aqueous cytosol
• An example is alpha-keratin in hair and skin, or myosin which is the motor protein responsible for muscle contraction

Rigid Structures, Beta Sheets and Amyloid Formation

• Beta sheets form rigid structures at the core of many proteins (A)
• A beta sheet is made when hydrogen bonds form between segments of a polypeptide chain that lie side by side
• They are antiparallel so the neighboring segments run in opposite directions
• The sheets can also be parallel where the neighboring segments run in the same orientation from the N-terminus to the C-terminus
• Both types produce a very rigid, and pleated structure to form the core of many proteins
• In an antiparallel beta sheet, several strands of an individual polypeptide chain are held together with hydrogen-bonds between the strands
• Amino acid side chains project above and below the plane of the sheet
• Beta structures can also form amyloid structures from stacks of rows
• Examples are the structure observed in the neurons of individuals suffering neurodegenerative diseases

Protein Organization and Domains

• The complete 3D conformation of proteins include several levels of organization, building upon the next
• Primary structure: the chain of amino acid sequence
• Secondary structure includes alpha helices and beta sheets that form within certain segments of the polypeptide chain
• Tertiary structure is a full, three-dimensional conformation formed by an entire polypeptide chain including the alpha helices, beta sheets, loops and folds between the N- and C-termini
• Quaternary structure is more than one polypeptide chain in a complex configuration
• Protein domain is any segment of a polypeptide chain that can fold independently that is between 40 and 350 amino acids

Extracellular Proteins and Disulfide Bonds

• Extracellular proteins are often stabilized by covalent disulfide bonds
• Covalent disulfide bonds form between adjacent cysteine side chains by the oxidation of their –SH groups
• They can join either two parts of the same polypeptide or two different polypeptide chains
• Disulfide bonds are formed in the endoplasmic reticulum

Proteins and their Binding Potentials

• Proteins function by binding to Other Molecules
• Humans Produce Billions of Different Antibodies, with a Different Binding Site
• Enzymes Are Powerful and Highly Specific Catalysts
• Enzymes Greatly Accelerate the Speed of Chemical Reactions that need a starting energy, and may not occur without this bond breakage which is known as "catalysis"
• Lysozyme Illustrates How an Enzyme Works
• Many Drugs Inhibit Enzymes for disease treatment
• Tightly Bound Small Molecules Add Extra Functions to Proteins
• The property of each protein to bind just one or a few molecules is known as protein specificity and the specific molecule is a ligand that interacts with the binding site
• Active or binding site are where the amino acid side chains associates with a ligand
• Active sites allow proteins to interact with specific ligands including cyclic AMP
• The folding of a polypeptide creates a cavity on the folded protein's surface, where specific amino acid side chains can form noncovalent bonds only with certain kinds of ligands
• Hydrogen bonds and electrostatic interaction are formed between a protein and its ligand at the binding site
• Cyclic AMP is involved in the regulation of glycogen, sugar, and lipid metabolism

Immunoglobulin Proteins, the Immune System and Antibodies

• Antibodies are immunoglobulin proteins produced by the immune system
• Capable of recognizing and binding tightly to specific ligands (antigens) found on bacteria, viruses, and other infectious agents
• Antibodies either inactivate the target antigen or destruct it
• Antibodies are proteins that bind tightly to their targets (antigens)
• They are produced in vertebrates as a defense against infection
• Antibodies are made of two identical light chains and two identical heavy chains
• Its two antigen-binding sites are therefore identical
• An example of an anti-body is the Y shape protein, and where the antibodies can bind
• These antibodies, attached

Protein Catalysis

• Enzymes are a large and very important class of proteins, responsible for nearly all of the chemical transformations in cells
• Enzymes bind to one or more ligands or substrates with specificity, and convert them into chemically modified products in high speed without being changed themselves
• Enzymes act as catalysts that lower the energy needed for covalent bonds in chemical reactions
• Enzymes are grouped into functional classes based on the chemical reactions they catalyze
• Each type of enzyme is highly specific, catalyzing only a single type of reaction
• Enzymes convert substrates to products remaining unchanged.
• Each enzyme has an active/binding site to which substrate molecules bind
• There, a covalent bond making and/or breaking reaction occurs, generating an enzyme-product complex (transition state).
• The product gets released from the enzyme product and can continue the reaction cycle

Enzymes and Velocity

• Enzymes accelerate the speed of chemical reactions; with enzymes reactions are faster
• An enzyme's performance depends on how rapidly it can process its substrate
• The rate of an enzyme reaction increases as the substrate concentration increases, until a maximum value is reached
• At its peak, all substrate-binding sites are occupied

An Example of an Enzyme In Action

• An enzyme that acts as a natural antibiotic in egg white, saliva, tears, and other secretions
• Lysozyme breaks the bond through hydrolysis, by adding a water molecule to the bond
• It forms a enzyme-substrate complex and cleaving glycosidic bonds in polysaccharide. It then dissociates releasing the products and then it can act on another product.
• Its the space filling model of lysosyme.

Protein Factors and Reactions

• some proteins extend their capabilities through binding with small, non protein molecules to perform functions that would be difficult using amino acids alone
• Cofactors are inorganic ions or nonprotein organic molecules that help enzyme reactions
• Ex. Inorganic ions are copper, zinc, or iron
• Ex. Coenzymes are organic nonprotein molecules
• Such as NAD+, FAD, and NADP+
• Vitamins are often components of coenzymes that affect health and physical fitness

Enzyme Regulation and Syntheitc Pathways

• The Catalytic Activities of Enzymes Are Often Regulated by Other Molecules to regulate complex metabolic pathways composed of chains of chemical reactions where products and substrate are one in the same through the complex pathway
• Feedback inhibition is a control in how much production is required from products being produced
• This in turn inhibits the enzymes in a cell and slowing it down
• Synthetic pathways are controlled because the product will limit the action of the enzyme
• Negative regulation can lead to an inhibition because the product will inhibit a specific process

More Detail on Feedback

• Feedback inhibition regulates connected metabolic pathways at multiple points
• Biosynthetic pathways for four amino acids in bacteria
• Examples are lysine, homoserine, threonine, methionine
• In the red lines indicate points at which products inhibit enzymes and synthesis
• It also allows initial reactants to remain.

Allosteric Enzymes

• Allosteric Enzymes have two or more binding sites that influence one another
• Allostery- "other" solid shape - change of shape of active site and binding
• When the sites have molecules or active components it regulates it and changes depending on the molecule

How Proteins are Modified by Phosporylation

• The removal of the phosphate proteins can occur by a second protein activating or modifying it in some other way
• Reversible protein phosphorylation has a specific removal and attachment that is always catalyzed.

Overview of macromolecules in cells, including proteins. Proteins, the main building blocks, constitute most of a cell's dry mass, providing shape and structure. They execute functions like catalysis, transport, movement, storage and signaling.