Proteins, Carbohydrates, and Lipids

Proteins, Carbohydrates, and Lipids Objectives

• Identify the macromolecules that characterize living things.
• Explore the functional groups that dictate the chemical properties of macromolecules.
• Learn the amino acids comprising proteins and how protein structure is determined.
• Briefly explore the relationship between protein structure and function.
• Understand the relationship between carbohydrate monomers and polymers by examining examples.
• Describe the components of lipids and their biological roles.

Four Kinds of Molecules

• Living things are characterized by four kinds of molecules: proteins, carbohydrates, lipids, and nucleic acids.
• Proteins assemble from different combinations of 20 amino acids.
• Carbohydrates form as monosaccharides link together.
• Lipids exist
• Nucleic acids assemble from four kinds of nucleotides.
• Polymers are constructed through covalent bonding of smaller molecules, called monomers.
• Large structures are assembled from a limited set of smaller molecules through noncovalent forces.

Functional Groups

• Functional groups are small groups of atoms that frequently occur in biological molecules.
• When functional groups attach to a larger molecule, they confer specific chemical properties.

Condensation and Hydrolysis

• Most macromolecules are formed by condensation and are broken down by hydrolysis.
• Condensation reactions produce water.
• Hydrolysis reactions consume water.

Proteins

• Proteins are polymers of 20 amino acids in different proportions and sequences.
• Protein size can range from small (51 amino acids in insulin) to huge (24,000-36,000 amino acids in titin).
• Proteins consist of one or more polypeptide chains.
• Polypeptide chains are unbranched, linear polymers of covalently bonded amino acids.
• Each chain folds into a particular 3D shape.

Amino Acids

• Amino acids may exist as optical isomers: D (dextro, right) and L (levo, left).
• Only L-amino acids are found in proteins of most organisms.
• Molecules can differ based on differently arranged functional groups, even with the same atoms.
• Isomers have the same chemical formula and kinds/number of atoms, but differ in arrangement.

pH Levels

• The carboxyl and amino groups of amino acids are ionized at pH levels found in cells.
• Amino acids exhibit acidic and basic properties.

Side Chains & R Groups

• The side chains (or R groups) contain functional groups that determine a protein's 3D structure and function.

Electrically Charged Amino Acids

• Five amino acids have electrically charged side chains at pH levels typical of living cells.
• Electrically charged side chains attract water (hydrophilic) and oppositely charged ions.
• Arginine, histidine, and lysine have +1 charge.
• Aspartic and glutamic acids have -1 charge.

Polar Amino Acids

• Five amino acids have polar (δ+ and δ-) side chains.
• Polar side chains attract water (are hydrophilic) and form hydrogen bonds with water and other polar substances.
• The polar cases include serine, threonine, asparagine, glutamine and tyrosine.

Nonpolar Amino Acids

• Seven amino acids have nonpolar hydrocarbon side chains.
• Nonpolar side chains are hydrophobic and cluster together in aqueous solution.
• Alanine, Isoleucine, Leucine, Methionine, Phenylalanine, Tryptophan, Valine, are included.

Special Case Amino Acids

• Three amino acids are special cases: cysteine, glycine, and proline.
• Cysteine has an -SH group that can react with another cysteine side chain in an oxidation reaction to form a covalent bond (disulfide bridge).
• Glycine has a side chain that consists of a single H atom.
• Glycine has a small enough structure to fit into tight protein corners, allowing the protein to be flexible at location, and it is generally hydrophobic
• Proline has a modified amino group that lacks an H atom, bonds covalently to hydrocarbon side chain, has a ringed structure, limited rotation around alpha carbon, often found where a protein bends or loops, and is generally hydrophobic.

Protein Structures

• A protein's primary structure consist of amino acids joined by peptide bonds, also known as a polypeptide.
• Short polymers with <20 amino acids are called oligopeptides or peptides.
• Linking amino acids involves a reaction between carboxyl and alpha carbon-attached amino groups.
• The amino group of an amino acid being added to the polypeptide interacts in a condensation reaction with the carboxyl group of the previous amino acid in the growing chain.

Protein Structure and Function

• Primary structure consists of Amino acid monomers joined, forming polypeptide chains, stabalized by peptide bonds.
• Secondary polypeptide chains may form a helices or B pleated sheets, stabilized by hydrogen bonds.
• Tertiary polypeptides fold, forming specific shapes, stabalized by Hydrogen bonds, disulfide bridges, hydrophobic interactions.
• Quaternary structure consists of multiple polypeptides that assemble to form larger protein molecules, stabalized by Hydrogen bonds, disulfide bridges, hydrophobic interactions, ionic bonds.
• A protein's tertiary structure is its definitive 3D shape.
• If a protein is heated slowly and moderately, the heat energy will disrupt only the weak interactions.
• Secondary and tertiary structure will break down
• A denatured protein has larger volume, can take on many shapes, and can be charactererized by exterior hydrogen bonds to water
• A native protein has a compact volume, one prefered shapre and interior hydrogen bonds stabilizing structure
• Many functional proteins contain two or more polypeptide chains called subunits
• The quaternary structure results from the ways in which subunits bind and interact

Protein Surfaces

• Shape and surface chemistry contribute to protein function.
• A given molecule shape will not bind to a protein unless there is a general fit between their three dimensional shapes.
• Surface chemistry: exposed R groups on the surface permit chemical reactions with other substances.
• Ionic, hydrophobic, or hydrogen bonds are noncovalent.
• Environmental conditions affect protein structure: Increased temperature causes rapid molecular movements, hydrogen and hydrophobic interactions break, pH changes can change ionization pattern of exposed R groups, concentrations of polar or nonpolar substances.
• Protein shapes can change as a result of their interactions with other molecules, or covalent modifications.

Protien

• The following is a list of protiens in living orgsnisms:
• Enzymes catalyze (speed up) biochemical reactions.
• Structural proteins provide physical stability and movement.
• Defensive proteins recognize and respond to nonself substances (e.g., antibodies).
• Signaling proteins control physiological processes (e.g., hormones).
• Receptor proteins receive and respond to chemical signals.
• Membrane transporters regulate substance passage across cellular membranes.
• Storage proteins store amino acids for later use.
• Transport proteins bind and carry substances within the organism.
• Gene regulatory proteins determine the rate of expression of a gene.
• Motor proteins cause movement of structures in the cell.

Carbohydrates

• Carbohydrates have a general formula of Cn(H2O)m, but the constituent water molecules are not intact.
• Linked carbon atoms are bonded with hydrogen atoms (-H) and hydroxyl groups (-OH).
• They have a wide range of functions for living orgsnisms:
• Stored energy source that can be released in a usable form by organisms.
• Transportation of stored energy Transport stored energy within complex organisms.
• Carbon skeletons that be rearranged to form new molecules.
• Extracellular assembliesthat provide structure to organisms.

Carbohydrate Categories

• Four categories of biologically important carbohydrates exist
• The categories are defined by number of monomers.
• Monosaccharides are simple sugars and monomers (ex. glucose).
• Disaccharides are consist of two monosaccharides linked by a covalent bond (ex. sucrose).
• Oligosaccharides consist of several (3–20) monosaccharides
• Polysaccharides are hundreds to thousands of monosaccharides (ex.starch, glycogen, cellulose).
• Glucose exists in straight chain and ring forms
• The two pentoses are ribose and deoxyribose, in which each have five carbons but different chemical and biological properties.
• The formula C6H12O6 is relevant for structural isomers.

Polysaccarides

• Disaccharides, oligosaccharides, and polysaccharides are all constructed from covalently-bonded, monosaccharides constructed through condensations and covalent glycocidic bonds.
• Polysaccharides aare lartge monomers that do not necessarily present in linear chains, branched molecules are possible
• Glycogen and starch are polymers of glucose with α-1,4 glycosidic bonds
• α-1,6 Glycosidic bonds produce branching at carbon 6.
• Starch serves as the main energy storage compound of plants
• Cellulose serves as the main component of plant cell walls, is the most abundant organic compound, and does not easily break down.
• Glycogen serves as the main energy storage compound of animals and stores glucose in liver and muscles.

Lipids

• Lipids, aka fats, aren't strictly polymers.
• Lipids consist of insoluble hydrocarbons due to many nonpolar covalent bonds thus hydrophobic.
• Lipids preferentially aggregate away from water.
• Lipids are not polymers, individual lipids are not covalently bonded
• Several lipid types and their roles in living organisms:
• Fats and oils store energy
• Phospholipids play important structural roles in cell membranes
• Carotenoids and chlorophylls help plants capture energy
• Steroids and modified fatty acids play regulatory roles as hormone and vitamins
• Fat in animal bodies serves as thermal insulation
• A lipid coating around nerves provides electrical insulation
• Oil or wax on the surfaces of skin, fur, feathers, and leaves repels water
• Fats and oils store energy and the two categories can be broken down into fat and oil.
• Triglycerides consists of glycerol with three hydroxyl (-OH) groups
• A fatty acid has a long nonpolar hydrocarbon chain; its bonds to a carboxyl (-COOH).
• These substances are highly hydrophobic!

Triglycerides

• Triglycerides are composed of fatty acids and glycerol, with each hydroxyl (-OH) group bonding to the carboxyl group (-COOH) of a fatty acid.
• This forms a covalent bond known as an ester linkage.
• The synthesis of three ester linkages releases water, a condensation reaction.
• Also the three fatty acids do not have to be the same chain length or structure
• Saturated fats contain no double bonds
• Unsaturated fats contain one or more double bond,
• At room temperature : saturated fats are solids, unsaturated are liquids
• Animal fats like meat are also solids
• Plant oils are the opposite and are liquids

Phospholipids

• Phospholipids play important structural roles in cell membranes
• Phosphatidylcholine hydrophilic head containing positive/negative charges while a hydrophobic tail does not react to water
• The hydrophobic "tails" repel the water in an aquous environment while the hydrophilic "heads" interact with the heads which is crucial for forming a bilayer.
• It is both characterized as part hydrophilic as well as hydrophobic, makingit amphipathic