Proteins Outline

Chapter 3: Protein Structure and Function Cells produce tens of thousands of distinct proteins Vital, Tremendously versatile components of cells Amino acids are the building blocks of Proteins Central Dogma- DNA- RNA- RNA codes for protein The Structure of Amino Acids Most proteins are made from 20 amino acids Amino acids are composed of a central Carbon atom bonded to H- Hydrogen Atom NH2- amino functional group COOH- Carboxyl functional group R group- a variable or side chain IN water, the amino and the carboxyl group ionize to NH+3 and COO- The amino group acts as a base and attracts a proton The carboxyl group acts as an acid and donates a proton The resulting Charges Help the amino acids stay in the solution Make the amino acids more reactive The 20 amino acids differ only in the unique R group and Side Chain The properties of amino acids are determined by their R- Group Charged- includes both acidic and basic Uncharged and Polar Non-Polar Charged and Polar side chains are hydrophilic: they interact readily with water Non-polar side chains are hydrophobic: they do not interact with water Polymerization of Proteins in Early Earth Monomers polymerize through condensation (dehydration) reactions Hydrolysis is the reverse reaction Breaks polymers apart by adding a water molecule Peptide Bond Amino acids polymerize when a bond forms between a carboxyl group of one amino acid and an amino group of another The resulting C-N bond is called a PEPTIDE BOND Unusually stable because a pair of valance electrons on nitrogen are partially charged in the C-N bond Peptide bonds have characterized of a covalent bond Peptide Bonds form a backbone with R Group orientation such that side chains extend out and can interact with each other or water Directionality End with the free amino group… N- Terminus End with the free carboxyl group…. C- Terminus Flexibility Singly bonds on either side of the peptide bond A chain of fewer than 50 amino acids is a OLIGOPEPTIDE or a peptide A chain of more than 50 amino acids is a POLYPEPTUDE Proteins are the functional form of the molecule 4 Basic levels of Structure Primary The sequence of amino acids 20 types of amino acids available length can range from 2 100000 fundamental to the higher levels of protein structure The amino acid R group affect a polypeptides properties and function A single amino acid change can change the entire protein Secondary Formed by hydrogen bonds between the carboxyl and the amino group of another A-Helices B-Pleated sheets (kinkyness folded sheet of paper) Tertiary Is the 3-dimensional shape of a protein Polypeptide results from interactions between R-Groups or between R-Groups and the peptide backbone These contacts cause the backbone to bend and fold Bending and folding contribute to the distinctive three-dimensional share of the polypeptides Types of Bonds R-Group interactions Hydrogen Hydrophobic interactions Van der Waals interactions Covalent Disulfide bonds Ionic bonds Quaternary the result of protein subunits interacting with one another Many proteins contain several distinct polypeptide subunits that interact to form a single structure The bonding of two or more distinct polypeptide subunits Folding and Function Protein structure is hierarchical 4 is based on 3 which is based on 2 which is based on 1 Combined effects of primary, secondary, tertiary, and sometimes quaternary structure. Normal Folding is crucial to function Protein folding is often spontaneous Because of the hydrogen bonds and Van Der Waals interactions The folded molecule is more energetically stable than the unfolded molecule A DENATUED (unfolded protein) protein is unable to function normally Proteins called Molecules Chaperones help proteins Environmental factors that affect protein laugh Temperature +/_-- on pH change in Ionic Concentration Hydrophilic or hydrophobic Protein Function Catalysis- Speed up chemical reactions Defense- Antibodies attack pathogens Movement- move cells or molecules within cells Signaling- convey signals between cells Structure- Shape cells and comprise body structure Transport Why are Enzymes Good Catalysts? Catalysis is the most important protein function An enzyme is a protein that functions are a catalyst Substrates are the reactants in the enzyme-Catalyzed reactions The location on an enzyme where substrates bind and react in the active site My Notes Chapter 3: 3.1 Amino Acids and their Polymerization Amino Acids: H- a hydrogen atom NH2- an amino functional group COOH- a carboxyl Functional group A distinctive “R- Group” often referred to as the side chain Amino acids ionize in a pH solution of 7 forming NH3 Non- ionized amino acid- normal OH Ionized amino acid- O- The charges on these functional groups are important because They help amino acids stay in solution where they can interact with one another and with other solutes They affect the amino acid’s chemical reactivity Side Chains R Group Properties of amino acids vary because of the R Group Functional Groups Affect Reactivity Under the right functional groups participate in chemical reactions R groups influence protein function because it depends on the size and shape of their reactivity. Polarity and the Charge of R Groups affect solubility Both polar and Electrically charged R groups interact with water and are HYDROPHILIC They dissolve easily in water Non-Polar R groups lack charge or a high electronegativity and are HYDROPHOBIC They are COALESCE in water Amino Acid R Groups can be grouped into 3 general types Charged, Acid and Basic Uncharged Polar Non- Polar How do Amino Acids Link to Form Proteins Proteins are macromolecules Macromolecules are made up on monomers Polymer- many monomers bonded together The process of linking monomers together is called POLYMERIZATION Amino Acids are the Monomers the POLYMERIZE to form Proteins Polymerization decreases the disorder or entropy of the molecules involved Polymerization of Proteins in early Earth Monomers polymerize through CONDENSATION REACTIONS AKA DEHYDRATION SYNTHESIS HYDROLSIS is adding water to break polymers apart HYDROLYSIS dominates because it both increases entropy and is favorable energetically Peptide Bond The C-N Covalent bond that results from dehydration synthesis is a PEPTIDE BOND When water is removed the carboxyl, group is converted to a Carbonyl Functional Group (C triple bond O) and the amino group becomes N-H Peptide bonds are STABLE due the C-N bond (valence electrons) When amino acids are linked by a peptide bond into a chain they are called RESIDUES Key Points about the peptide Bond R Group Orientation The side chains of each residue extend out from the back bone, making it possible for them to interact with each other and with water Directionality There is an amino group (-NH3+) on one end of the back bone and a carboxyl group (-COO-) on the other Flexibility Although the peptide bond itself cannot rotate because of its double bond nature, the single bonds on either side of the peptide bond can rotate. This makes the structure as a whole flexible Fewer than 50 amino acids linked together is called OLIGOPEPTIDE or Peptide More than 50 amino acids linked together is called POLYPEPTIDE The term protein is often used to describe any chain of amino acid residues 3.1 What do Proteins Look Like? TATA BOX: Binding proteins Primary Structure Sequence of Amino Acids 20 types of amino acids Hemoglobin (oxygen binding protein in human red blood cells) Some people have a Val amino acid instead of a GLUT amino acid causing them to have sickle cell anima A proteins primary structure is fundamental to its function. Primary Structure is also fundamental to the higher levels of protein structure; secondary, tertiary, and quaternary Secondary Structure Created in part by interactions between functional groups in the peptide bonded backbone Stabilized by hydrogen bonding A-Helix Alpha Helix Polypeptides backbone is Coiled Spiral looking B-Pleated Sheets Beta Pleated Sheets Bend at 180 degrees and the fold like a piece of paper One piece Secondary structure is very Stable because all the hydrogen bonds in between the Alpha helix’s and the Beta Plated Sheets Tertiary Structure 3D shape results from interactions between residues that are brought together as the chain bends and folds in space Tertiary structure uses a variety of bonds and interactions between the R Group and the backbone 5 Types of interactions involving R- Groups: Hydrogen Bonding Hydrogen bonds form between polar side chains and opposite partial charges either in the peptide backbone or other R Groups Hydrophobic Interactions Water molecules interact with the hydrophilic polar side chains of a poly peptide, forcing the hydrophobic non-polar side chain to coalesce into globular masses. Van Der Waals Interactions Once hydrophobic side chains are close to one another their association is further stabilized by electrical attractions These weak attractions occur because the constant motion of electrons gibe molecules a tiny asymmetry in charge that changes with time Covalent Bonding Form between the side chains of two side chains of two cysteines though a reaction between the sulfhydryl groups Disulfide Bonds are referred to as bridges because they create strong links between distinct regions of the same polypeptide or two separate polypeptides Ionic Bonding Forms between groups that have full and opposite charges Quaternary Structure The combination of polypeptides referred to as subunits have quaternary structure Macromolecular Machines Groups of multiple proteins that assemble to carry out a particular function Shape produced by combinations of polypeptides 3.3 Folding and Function Normal Folding is Crucial to Function Ribonuclease can be unfolded or NENATURED by treating it with compounds that break hydrogen bonds and disulfide bonds DENATURED ribonuclease cannot function Cells contain special proteins called MOLECULAR CHAPERONES Facilitate protein folding Chaperones recognize unfolded proteins by binding to hydrophobic patches that are not normally exposed This allows unfolded proteins from clumping together Chaperones help fold new proteins Protein Shape is Flexible Protein shape is flexible Protein Folding is Often Regulated Proteins involved in cell signaling are often regulated Many of these proteins are disordered and do not complete their folding until after binding to ions or other molecules Folding can be Infectious Certain normal proteins can be folded into infectious disease-causing agents- PRIONS PRION- protein infected particles Mad Cow disease 3.4 Protein Functions are as Diverse as Protein Structures Proteins are crucial to most tasks required for cells to exist Catalysis Speed up reactions Enzymes Defense Antibodies attack and destroy viruses and bacteria that cause disease Movement Motor Proteins and contractile proteins are responsible for movie the cell itself or for moving large molecules inside the cell Signaling Involved in carrying and receiving signals from the cell to cell inside the body Often in the membrane Structure Make up body components. Structural proteins keep red blood cells flexible and in their normal disc like shape Transport Allows particular molecules to enter and exist cells or carry them throughout the body Why are enzymes good Catalysts? Catalyzed reactions involve one or more reactants called substrates Lock and Key idea The location where substrates bind and react became known as the enzyme Active site Digestive Enzymes are important