Biological Macromolecules: Condensation vs. Hydrolysis The process of building bigger or shorted macromolecules. Condensation/Dehydration Hydrolysis Makes macromolecules longer Makes macromolecules shorter Water out Water in Monomer in Monomer out Biological Macromolecules: Monomer vs. Polymer All macromolecules are held together by covalent bonds via condensation. Monomer Polymer Proteins Amino Acids Polypeptides aka Proteins Carbohydrates Monosaccharides Polysaccharides Nucleic Acids Nucleotides Nucleic Acids Lipids Fatty Acids Glycerol Triglycerides Phospholipids Steroids i.e. cholesterol, vitamin D Carotenoids i.e. vitamin A, pigments *Not polymers Biological Macromolecules: Basic Functions Basic Function Proteins Enzymes & Catalysis, Structure, Transport, Signaling, Defense Carbohydrates Fuel and Structure Nucleic Acids Genetic information Lipids Fuel storage, Membranes, and Hormones Biological Macromolecules: Basic Structures and Forms Basic Structure and Form Proteins It is composed of 20 amino acids. Carbohydrates It’s basic formula is (CH2O)n. Monomers become polymers via polymerization. Names of most sugars end in –ose. Nucleic Acids It is composed of many nucleotides. Lipids It is mostly composed on hydrocarbons, thus is mostly hydrophobic. Comes in liquid form i.e. vegetable oil and solid form i.e. butter. Liquid form is healthier for you, storing high energy content. Amino Acids: Structure Each amino acid has a carboxyl group, amino group, and R group. They differ in charge, polarity, size, and R group. Amino acids can be ionized or non-ionized. Polar R groups tend to have lots of O, N, S. Charged side groups will be obviously charged. These are both hydrophilic. Nonpolar side groups have to lots H and C, and are hydrophobic. Proteins: Functions Protein Type Role in Cell Antibodies and complement proteins Defense – destruction of disease-causing viruses and bacteria Contractile proteins and motor proteins Movement Enzymes* it’s most fundament function Catalyze reactions Hormones Act as signals that help coordinate the activities of many cells Receptor proteins Receive chemical signals from outside cell and initiate response Structural proteins Provide support for cells and tissues; form structures Transport proteins Move substances across cell membrane; substances throughout body Proteins: Structure Protein structure is highly correlated with its function. A denatured protein is a useless protein. Primary Secondary Tertiary Quaternary Structure Linear amino acid sequence; polypeptide backbone Alpha-helix or B-pleated sheets Overall 3-D shape of polypeptide Shape of multiple polypeptide subunit chains Bonds Covalent peptide bonds H bonds Hydrophobic Van der Waals H bonds Ionic bonds Disulfide bridges Covalent Ionic H bonds Hydrophobic Process Polymerization: carboxyl and amino groups linked amino acids by peptide bonds. Interactions between polypeptide backbone Interactions between R groups Bonds between R groups and backbone Uniqueness Backbone has amino end N and carboxyl end C This the first level that is active! Disulfide bridges. Examples A single amino acid substitution in a protein causes sickle-cell disease Slinky Folding of the slink shape Hemoglobin: only active when all subgroups active Proteins: Determinates of Structure The shape of the protein is extremely critical to its function – think of enzyme conformation. Sequence of amino acids of the primary structure has a domino effect. A single amino acid substitution can cause a change in quaternary structure. The cell’s temperature, salts (ions) and pH affects proteins bonds on all levels Folding aids are chaperone proteins that assist new proteins by providing sheltered environments to fold correctly. It is extremely important to not allow premature or inappropriate associations of hydrophobic regions. Proteins: Denaturation Denaturaiton is the loss of protein conformation. It is promoted by heat, pH change, chemicals. It is inhibited by chaperones. When you have a fever, chaperones protein your proteins from unfolding. For some proteins, it is easy to renature, moving back and forth between active and inactive conformations. However, mis-folding is nonreversible and fatal. Carbohydrates: Structure Primary Secondary Tertiary Quaternary Monosaccharides Disaccharides Polysaccharides Function Sugars Fuel and Structure Structure Most form rings of (CH2O)n when in aqueous solution. 2 monosaccharides Many monosaccharides Many polysaccharides Bonds Covalent bonds in CH2O Glycosidic bonds via condensation Glycosidic bonds via condensation, H bonds H bonds or peptide bonds Uniqueness They vary in carbon number, carbonyl group position, and arrangement. Bonds differ in plants, animals, bacteria Notes Similar structures can form very different structures after polymerized i.e alpha and beta Sucrose is alpha-glucose linked to fructose by glycosidic bonds Alpha forms starch. Beta forms cellulose. Cell Walls Polysaccharides: Functions Fuel Structure Plants Starch Cellulose in cell walls Animals Glycogen Chitin Polysaccharides: Structure Structure Bonds holding them together Cellulose in plant cell walls H bonds Chitin in insect exoskeleton H bonds Peptidoglycan in bacterial cell walls Peptide bonds Nucleic Acids: Structure Primary Secondary Tertiary Nucleotide Sugar Phosphate Backbone Anti-parallel Strands Structure 1 phosphate group 1 nitrogenous base 1 pentose sugar Polar nucleic acid chain: 5’ phosphate end and 3’ hydroxyl end Different between RNA and DNA. Bonds Phosphodiester bonds: phosphate joins sugar linked to OH of another sugar Hydrogen bonds form between purines and pyrimidines Notes Template determines sequences of bases, which provides genetic info Nucleic Acids: DNA vs. RNA Guanine and Cytosine forms 3 H bonds. Adenine and Thymine only form 2 H bonds. DNA RNA Pentose sugars Deoxyribose lacks O at 2’C Ribose Pyrimidines Cytosin, Thymine Thymine, Uracil Purines Guanine, Adenine Tertiary structure Double Helix Lipids: Structure Lipids store lots of energy (lots of energy is release when broken down). Amphipathic means to have both hydrophilic and hydrophobic regions. Primary Secondary Fatty Acids Triglycerides Phospholipids Cholesterol Function Makes membranes by forming lipid bilayers. Stabilize membranes Structure Hydrocarbon chain with terminal carboxyl group. Hydrocarbon chain can be saturated or unsaturated. Glycerol linked to 3 fatty acids by ester linkages. Just like triglycerides, but phosphate compound replaces 1 fatty acid. Hydrophilic head: glycerol and phosphate compound. Hydrophobic tail: 2 fatty acids linked to glycerol by ester linkages. Polar (hydrophilic) head. Nonpolar (hydrophobic) tail. Bonds Covalent Ester linkages Ester linkages Uniqueness Not water soluble aka hydrophobic Ester linkages are bonds between C-O-C Phosphate compound, Notes Synthesis by condensation aka dehydration (H2O out, monomer in) Amphipathic Amphipathic but largely hydrophobic. Highly stable. Lipids: Saturated vs. Unsaturated vs. Trans Fat Saturation is the abundance of double-bonds in fatty acids. It determines fluidity. Saturated Fat Unsaturated Fat Trans Fat Healthiness Unhealthy Healthy Unhealthy Double Bonds Less More Artificial trans Hydrogen More Less More Hydrocarbon chain is… Straight: It is more ordered since it can easily link together, forming a tight fit. It is not fluid. Kinked: the double bonds create a kink. The rest of the chain is free to rotate about the kink. Thus, it is highly fluid. Straight: to lengthen shelf life, unsaturated cis double bonds are bombarded with H atoms to become trans double bonds Phase State Solid at room temp. Liquid at room temp. Example Butter, animal fats Vegetable Oil McDonald’s Phospholipids: Inside Bilayer* Membranes Bilayers are the most stable type of membranes. Phospholipids are the major component of membranes. They have a hydrophilic head and hydrophobic tail. The tails can either be 1) both saturated or 2) one saturated and one unsaturated. Saturated tails provide stability. They are more ordered, with a stackable rectangular structure for a tight fit. There are two rows of unsaturated lipids. Hydrophilic heads reach out to H2O in the extracellular matrix or cell interior. Hydrophobic tails interact with one another, creating a hydrophobic zone. Biological Membranes: Fluidity, Permeability, and Stability Membranes are highly fluid. Fluidity, Permeability Phospholipids can laterally shift, they rarely flip though. Unsaturated tails make a membrane more fluid and permeable. Saturated tail do the opposite. Stability Hydrophobic tails of cholesterol interact with hydrophobic tails of phospholipids. It packs the lipid bilayer. Biological Membranes: Diversity Membranes are mosaics of macromolecules. All macromolecules, except nucleic acids, of course, are found on the membrane. The 2 sides of the membrane aren’t the same. Membranes vary in composition. They are different species to species, organelle to organelle, phospholipids and proteins are different on the cytoplasmic and extracellular, even within organelles. Biological Membranes: Proteins found in the Membrane Integral proteins are proteins lodged in the membrane, partially or entirely. They can integrate into the lipid bilayer because they are amphipathic. The ends have polar (hydrophilic) amino acids, the middle has Nonpolar (hydrophobic) amino acids. They can only be dislodged by detergents. Peripheral proteins are attached to the membrane. Proteins in the Membrane: Functions Transport Hydrophilic channel Enzymatic Activity Sequential steps in metabolic pathway Signal Transduction Relay chemical messages Intercellular Joining Various cell junctions Cell-cell recognition Glycoprotein identification tags Attachment to the cytoskeleton and ECM Cell shape and stabilize proteins Transport Proteins: Uniport vs. Symport vs. Antiport Transport Proteins can move more than one type of molecule in one or opposite directions. Uniport Symport Antiport 1 molecule 2 molecules 2 molecules 1 direction 1 direction 2 opposite directions Transport Proteins: Cystic Fibrosis CF is caused by a single deletion of an amino acid (genetic disorder). People with CF don’t have enough chloride channel proteins. Cl- builds up inside the cell. H2O rushes into the cell. Mucas builds up outside of the cell. Biological Membrane: Transportation The membrane is a selectively permeable barriers. A molecule’s ability to pass through is based on its size, polarity, and charge. Easy Difficult Hydrophobic Small, Uncharged, Polar Large, Uncharged, Polar Charged (Ions) Biological Membrane: Diffusion Passive Transport Active Transport Simple Diffusion Facilitated Diffusion Membrane Component Involved Phospholipids in membrane Transport proteins Transport Proteins Substrate Small, hydrophobic molecules Polar molecules can’t diffuse by themselves Binds to Substrate No No, they form channels aka pores or shuttle systems aka carriers Yes Requires Energy No No Yes Down (high to low) or Against Concentration Gradient? Down molecule’s own concentration gradient to achieve equilibrium Down concentration gradient i.e. electro-chemical gradients Against concentration gradient Specific Yes, the membrane is Yes Yes, very Saturable No Yes, due to limited amount of proteins Yes, due to limited amount of proteins Rate of Transport Slowest Mediocre Fastest Example Osmosis: H2O moves through H2O-specific pores, aquaporins, interior is hydrophilic, exterior is hydrophobic. Na+ and K+ antiport pump: pump has 3 binding sites with high affinity for Na+. 3 Na+ bind. 1 phosphate from ATP (energy) binds. Pump changes shape. Na+ diffuse to exterior. New comformation has high affinity for K+. K+ binds. Phosphate drops. Pump changes back to original shape. K+ diffuses to interior.