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Carbon and Macromolecules Identifying Compounds Carbs and Lipids == C, H, O Protein == C, H, O, N, S Nucleic Acid == C, H, N, O, P Carbs ratio = C1H2O Lipids ratio = high high amount of hydrogen and carbon (not as much oxygen, hydrocarbons) Radioactive tracers to identify each, Tag phosphorus to identify nucleic acids, tag sulfur to identify proteins CARBON ● Carbon is essential to life ● Organic compound == carbon ● Inorganic compound != include carbon ● Carbon leads to diversity ● Determining factors of organic molecules’ properties ○ Carbon Backbone - gives structure shape, function ○ Functional Groups - part of molecule that participates in reactions ■ Backbone is unchanged, functional groups that react
● Tetravalence ○ Has four valence (outer shell) electrons (covalent) ■ Can bond with 4 other atoms ● Create wide array of molecules ○ Atom unstable unless valence shell is full, reacts with other atoms ● Organic Chemistry ○ Branch of chem that studies carbon compounds ● Carbon Backbone ○ Central part of an organic molecule, determines structure (and function/properties) of molecule ■ Rings, linear, branching, and double bonds ■ Shape determines function -- variety of different molecules ● Hydrocarbons ○ Long chains containing carbon and hydrogen ○ Make up lipids ■ Contains lots of energy (lots of bonds, for ex. fat) ■ Nonpolar (Hydrophobic) - only polar if distribution of charge with an electronegative charge ● (No O, Su, N -- electronegative atoms) ● Isomers ○ Structure leads to function ○ Compounds with same formula but different arrangement of atoms ○ Structural ■ Carbon backbone is different ○ Geometric ■ Groups branching off backbone are different (functional groups) ■ Carbons are double bonded ■ Functional groups on opposite sides = trans ■ Functional groups on same side = cis ○ Enantiomers/Stereoisomers ■ Mirror images of structure ■ Example: L-Dopa and D-Dopa - only difference is structure ● L-Dopa treats Parkinson’s, D-Dopa inactive ● Functional Groups - branch off Carbon Backbone ○ Participates in chemical reactions*** ○ Hydroxyl ■ Alcohols (OH-) ○ Carbonyl ■ Ketones (acetone) (carbon double bonded with oxygen)
■ Water formed primordial seas, location of first macromolecules and first living organisms - 3.6 billion years ago ■ Stromatolites ● Stanley Miller made experiment simulate conditions on early earth, to create macromolecules abiotically ○ Included gasses, rain, and electricity ■ Gases reacted with one another ■ Water condensed and formed “sea” found monomers, the first macromolecules ■ Abiotic synthesis of monomers → chemical reactions ● Earth covered in volcanoes, volatile, releasing gasses in atmosphere → formed primordial seas where sea meets land is where life started. ● Start of life - took 1 billion years ○ Have right elements - CHNOPS ○ Elements come together to form the first monomers (amino acids, fatty acids, glycerol, monosaccharides, etc. building blocks) ○ Form polymers (proteins, triglycerides, nucleic acids, etc.) ○ Form cells → bacterial life ● DNA (bases) and Proteins (amino acids) compare amounts that organisms share in common, more in common the more similar the organisms are ○ Molecular homology - things shared in common due to common ancestry ● Monomers are repeating sub units in polymers ○ Fused by dehydration synthesis (remove water) and defused using hydrolysis (add water) ● Carbohydrates - main energy source for ATP and cellular respiration ○ Monosaccharides -(ready energy) monomers subunits (glucose, -ose) means “one sugar” ■ Similar formulas: (CH2O)n where n is number of carbons ○ Polysaccharides -energy storage and structural support, polymers ■ Energy storage/Long term energy: ● Starch storage carbs for plants ○ quick energy in animals ● Glycogen storage found in stomach and liver cells animals ○ After glycogen reservoirs are full then stored as fat ● Cellulose - major structural molecule in plants ○ Fiber in humans ● Chitin - structural support in exoskeletons and fungi ■ Starch vs. Cellulose ● Long chains of glucose
○ Direction of bonds is different ■ Starch Alpha Glucose (hydroxyl group is down) and Cellulose Beta Glucose (hydroxyl group is up) ● (Alpha) Starch can be digested as energy ○ Alpha bonds can be broken down ● (Beta) Cellulose cannot == fiber ○ No enzymes to break down beta bonds ○ Goes through digestive system unbroken, cleans colon dead bacteria and rotten food on inside of intestines, fiber cleans it ■ Structural support ● Cellulose ○ Structural component of plants ● Chitin ○ exoskeleton of arthropods ○ Always has ring structure (hexagon (gluc) and pentagon (fruc)) ■ Glucose and Fructose are isomers ■ Glucose + Glucose = Maltose ■ Glucose + Fructose = Sucrose ○ Disaccharides - two monosaccharides held by one bond ○ Monosaccharides provide immediate energy ■ Already broken down unlike polysaccharides ● No need for hydrolysis ■ Maltose ■ Sucrose (sugar) ● Glucose + Fructose (thru Dehydration Synthesis) ○ Glycosidic Bonds link monosaccharides in to disaccharides ○ Glycogen ■ Energy storage in liver and muscles ■ Eat more energy than needed first stored as glycogen ■ When energy storage of glycogen is full, then fat storage begins ● Lipids ○ Hydrophobic (nonpolar) ○ 4 cal/gram for proteins and carbs, 9 cal/gram for lipids ○ Triglyceride fats (three fatty acids and a glycerol) makeup hydrocarbon chains ■ Fatty acids to glycerol bonded by dehydration synthesis ● Formed by an ester bond
■ Amphipathic Molecule partially hydrophilic and hydrophobic ■ When placed in water, create double layer, where nonpolar tails face each other and polar tails face water on both sides → membrane structure ○ No energy made to create cell membrane, beginnings of life, occurs naturally ○ Steroids - hormones for protein synthesis ■ Cholesterol ● Found in cell membranes and myelin sheath ● 4 carbon ring structure ● Solid ● Used in nervous system and cell membranes ○ Insulates neurons ● Good except excess ■ Estrogen and Testosterone ● Made using Cholesterol ● Proteins ○ Most important macromolecule ○ pH remains constant ○ Made up of amino acids (20 different types) ■ Contains amino group, R variable group, and carboxyl group ■ Peptide bonds link amino acids ■ Central Carbon (one C) backbone attached to H ■ Carboxyl group (Carbon double bonded to Oxygen and OH) ● Acid in “amino acid” ● Donates H+, acidic ■ Amino group (N bonded to two H’s) ● Accepts H+, basic ● Amino in “amino acid” ■ R group ● “Random group” ● What makes the amino acid special ● Polar R groups have (N, S, or O) ● Nonpolar R groups have carbon and hydrogen ■ React through dehydration synthesis ● Peptide bonds form ● OH from carboxyl and H from amino groups react ○ Four levels of protein structure ■ Primary
● Unique sequence of amino acids (most important) ○ Held by peptide bonds ○ Determined by DNA ● Takes place inside a chaperonin protein ○ If misfolding, → parkinson's and alzheimer's mad cow disease (prions) ■ Secondary ● One of two three dimensional shapes that are the result of hydrogen bonding between amino acids ○ Alpha helix - coil (like DNA) ○ Beta pleated sheet - accordion ■ BOTH determined by amino sequence ■ Tertiary ● Structure results as of R group reactions final foldings ○ Disulfide bridges ○ Hydrophobic interactions ○ Ionic bonds ● Makes single polypeptide subunit ■ Quaternary ● The 3D shape is a polypeptide subunit ● Two or more polypeptide chains into one large protein. ● Creates full protein ● Multiple tertiary structures put together ● Hemoglobin is a globular protein with structure ○ Collagen most important and abundant protein ■ Made of 3 polypeptides ○ Hemoglobin made up of 4 subunits ■ SCA caused by one amino acid mutation glutamine → valine ○ Dimer - protein with two tertiary structures (polypeptides) ○ Shape of the protein determines function ○ Structural/Fibrous Protein - strong proteins (collagen, keratin, silk, elastin etc.) ○ Globular - ■ Like a glob ■ Microtubules ■ Enzymes ■ Antibodies ■ hemoglobin ○ Chaperonins
Glycolysis Oldest process Before mitochondria, glycolysis took place Oldest prokaryotes used this for energy Cell respiration Regulated by feedback inhibition When ATP builds up, pathway is turned off Utilizes allosteric enzymes Turns off Phosphofructokinase (first enzyme in pathway) AMP turns back on, forces pathway on
● Fats and proteins can also be used in cellular respiration (triglycerides), not
just glucose and carbohydrates
○ Fats provide more energy than carbohydrates, therefore more ATP
○ Glycerol (3 carbon molecule) and three fatty acids
● Monomers of fatty acids/glycerol can enter cellular respiration
● Glycerol has the same amount of carbons as a glucose pyruvate, enters
process at pyruvate oxidation no need for glycolysis, more energy
● Beta Oxidation
○ Fatty acids from lipids need to break down long chains of carbons in
order to enter cellular respiration
○ Breaks the fatty acid chain and breaks it down into two-carbon
molecules
○ Feeds directly into the Kreb Cycle
● If you don’t have enough carbs or lipids, or too much protein, protein can
be used in cellular respiration
○ Proteins have an atom that cannot enter cellular respiration, have to
get rid of nitrogen in order to enter, stomach and small intestines
break down proteins into amino acids
■ The amino acids can go into cellular respiration
● Deamination
○ The process by which the amino group (NH2)
leaves the amino acid to enter cell respiration
■ Amino acid can enter multiple levels of the cellular respiration
● Cellular Respiration refers to both aerobic and anerobic respiration but is
mainly the aerobic respiration
○ Respiration usually tracked with glucose because it starts at the first
step
● Fermentation partial degradation of sugars that occur without O
○ Keeps pyruvate happening?
● Aerobic respiration consumes organic molecules and O2 and yields ATP
● Anerobic Respiration similar to aerobic respiration but consumes
compounds other than O
● Glycolysis occurs whether or not O2 is present
● Ecosystem - all living communities and abiotic factors (nonliving components, pH, water) ● Trophic Levels - troph = food ○ Primary producers ■ Autotroph - plants protists, cyanobacteria ■ Chemosynthesis and photosynthesis, produce their own food ■ Convert light energy to chemical energy, all consumers depend on plants ○ Primary Consumers ■ Herbivores, eat the primary producers ○ Secondary Consumers ■ Omnivores, primary carnivores ○ Tertiary consumers ■ Secondary carnivores ○ Detritivores ■ Decomposers (fungi, bacteria, earthworms, insects, scavengers, vultures) ● Food Chain - linear chart which shows who eats who ○ Grass → zebra → lion → vulture ○ Top down model (top of the food chain controls the autotrophs) and bottom up model (grass controls the rest of the chain) ● Food Webs - nonlinear expanded chart showing multiple relationships between each organism ● Keystone species ○ Most important role within the ecosystem, disproportionate effect on ecosystem ● Productivity - amount of solar energy converted into chemical energy (photosynthesis) in a community by autotrophs (amount of photosynthesis) ○ More producers → more energy ○ Most productive ecosystem - open ocean → productivity is low but so much ocean is the most productive biome on planet because of algae
○ Enzymes catalyze chemical reactions by lowering the activation energy, reactions occur at lower temperatures ■ Do not have effect on amount of energy produced from reaction ( ∆𝐺) ● Substrate - reactant an enzyme acts on ○ Enzyme binds to substrate forming enzyme-substrate complex ■ Active site - region on the enzyme where the substrate binds ● Enzymes are like lock and key, very specific ● Orienting substrates ● Straining substrate bonds ● Providing favorable microenvironment ● Covalently bonding to the substrate ○ Induced fit - substrate brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction ● Local conditions ○ Optimal temperature and optimal pH (37 C, heat bacteria use 77 C) ■ If not optimal, would denature ■ Decreasing temperature does not denature, just slows down reaction ○ Cofactors ■ Non Protein enzyme helpers ■ May be inorganic (metals in ionic form) or organic (carbon) ■ Organic cofactors called coenzymes bound to enzyme ● Include vitamins, w/o vitamins, some enzymes cannot function ● Inhibitors - stop an enzyme from functioning ○ Competitive inhibitors - resembles substrate , competes with substrate for active site, reversible → reverse action by adding more substrate, then substrate can outcompete inhibitor. ○ Noncompetitive inhibitors - bind to different region of enzyme, change shape of active site, then substrate can no longer bind to enzyme, nonreversible ■ Penicillin - antibiotic, binds to bacteria enzymes → cannot function, kills bacteria ■ DDT, nerve gas, etc. ○ Regulates enzyme activity → control metabolism ■ Chemical chaos would result if cell metabolic pathways were not tightly regulated ■ Cell does this by switching on or off the genes that encode specific enzymes or by regulating activity of enzymes ■ Allosteric regulation - enzymes that can be turned on and off ● Inactive and active forms ○ Activators - lock enzyme to be active
○ Inhibitors - lock enzyme to be inactive ○ Change in shape ● Cooperativity form of allosteric regulation that can amplify enzyme activity ○ One substrate molecule primes an enzyme to act on additional substrate molecules more readily ○ Allosteric because binding by a substrate to one active site affects catalysis in a different active site ● Allosteric regulators are good for drugs because of enzyme specificity ○ Inhibitions of proteolytic enzymes called caspases manage inflammatory responses act as inhibitor ■ Feedback Inhibition ● Regulate and shut down metabolic pathways, end product used to inhibit first step in pathway ● Prevents cell from wasting chemical resources by synthesizing more product than is needed ● Evolution ○ Proteins formed by amino acid sequence, encoded by DNA ○ Mutations in DNA cause mutations in amino acids and in enzyme ● Localization ○ Structures within cell help bring order to metabolic pathways ○ Some enzymes act as structural components of membrane ○ In Eukaryotic cells, some enzymes reside in specific organelles for example enzymes for cellular respiration are located in the mitochondria Metabolism ● Living organisms require a constant input of energy. Biological systems constantly transform this energy from one form to another in order to carry out all life functions. ● First Law of Thermodynamics - energy cannot be created or destroyed, only transformed from one form to another. ○ Law of conservation of energy ● Second Law of Thermodynamics - during energy conversions, the universe becomes more disordered→ entropy increases ● Gibb’s free energy - the way to calculate how much free energy is available to do work within a cell (G) ○ If energy is released, the reaction is said to be exergonic or exothermic and delta G is negative ■ Exergonic reactions power the endergonic ones.
● This kind of inhibition can be overcome by increasing the concentration of substrate ■ Enzymes are allosteric- a change in shape alters their efficiency ● Noncompetitive Inhibition ○ Molecules called noncompetitive inhibitors or allosteric regulators bind to a site distinct and separate from the active site of the enzyme ○ This binding of the inhibitor to the alternate site causes the enzyme to change shape in a way that inhibits the enzyme from catalyzing substrate into product ○ Other allosteric enzymes toggle between two different conformations (shapes) ■ One active ■ The other inactive ○ The binding of either an activator or an inhibitor locks or stabilizes the allosteric enzyme in either the active or inactive form ○ Feedback inhibition - where the end product of the pathway is the allosteric inhibitor for an enzyme that catalyzes an early step in the pathway ● Cooperativity ○ Type of allosteric activation ○ The binding of one substrate molecule to one active site of one subunit of the enzyme causes a change in the entire molecule and locks all subunits in an active position. ■ Amplifies the response of an enzyme to its substrates Metabolism ● Cells have thousands of chemical reactions ● Speed metabolism ○ Balanced meals ○ King in the morning (activate metabolism) prince at noon, pauper at night ● Cell extracts energy and applies energy to perform work ● Catalysis - acceleration of a chemical reaction by a catalyst ● Metabolism transforms matter and energy subject to thermodynamics ● Metabolism - totality of an organism’s chemical reactions ○ Metabolic pathway - begins with a specific molecule (reactant, substrate) and ends with a product ○ Each step catalyzed by an specific enzyme ● Catabolic Pathway release energy by breaking down complex molecules into simpler compounds to do work ○ E.g. cell respiration, glucose breakdown, etc. ● Anabolic pathways - consume energy to build complex molecules from simpler ones ○ Protein synthesis e.g. of anabolism ● Bioenergetics - study of how organisms manage their energy resources (metabolic pathways) ● Chemical reactions
○ Exergonic Reaction ■ High energy reactants and low energy products, net release of energy, spontaneous negative ∆𝐺 ● Break bonds, hydrolysis, catabolic ● Difference between exergonic and catabolic ○ Exergonic is a specific reaction ○ Catabolic is a pathway that’s made up of multiple exergonic reactions ○ Endergonic Reaction ■ Absorbs free energy from surroundings, nonspontaneous stored in bonds ● Energy from food ● Builds bonds, dehydration synthesis, anabolic ● Forms of Energy ○ Energy is the capacity to cause change, some forms of energy can perform work ○ Kinetic energy associated by motion ○ Heat (thermal energy) kinetic energy associated with random movement of molecules ■ Heat is not usable energy, wasted ○ Potential energy - energy that matter possesses bec. location and structure ○ Chemical energy potential energy released in chemical reactions (bonds) ○ Energy is converted from one form or another, never appears/disappears ■ Matter and energy can not be created/destroyed ● Free energy - energy that can be used to perform work (needs input = endergonic, spontaneous = exergonic) usable ○ Delta G (result energy) = G (final) - G (initial) ← net energy ■ == positive → endergonic ■ == negative → exergonic (spontaneous) ● Spontaneous ○ No energy is invested to make reaction happen ● Laws of Energy Transformation ○ Thermodynamics study of energy transformations ○ In an open system (organisms) energy and matter can be transferred between the system and its surroundings ○ 1st law “Principle of conservation of energy” ■ Energy can be transferred and transformed by it cannot be created or destroyed ○ 2nd law “Law of Entropy” ■ Every energy transfer or transformation increases the entropy (disorder) of the universe
○ Three phosphate groups ■ All negative charged groups → VERY unstable ■ Lots of potential energy ● Releases energy by hydrolyzing the last (terminal) phosphate group, lots of energy (7. cal) ○ Factors: energy is released ○ Phosphate group (more important than energy) ○ Phosphorylation activates things ■ Turns on chemical reactions ■ When phosphate group attaches to reactant from ATP, turns on a chemical reaction ○ Powers endergonic reactions ● ATP cannot be made by the body, ATP is converted or recycled in the body, regeneration ○ Carbs and lipids regeneration ATP, take in phosphate groups to add back to ADP (adenosine diphosphate) ■ ATP - full battery ■ ADP (+P) - low battery (little energy) when P is added, create another ATP ● Cell respiration adds phosphate to ADP → ATP ● Extra P brought back through dehydration synthesis ● ATP is unstable (potential energy) if you had all ATP, you would explode, always some energy in ADP Enzymes ● Catalyst - a chemical agent that speeds up a reaction without being consumed by the reaction ○ Reactions end when equilibrium is reached, not when enzyme is used up ● Enzyme - catalytic protein. Recycled globular ○ All enzymes are catalysts, but not all catalysts are enzymes ○ Enzymes’ functions are determined by sequence of amino acids ● Hydrolysis of sucrose by the enzyme sucrase (end with -ase ) ● Enzymes are extremely specific, each enzyme only does one thing ● Activation Energy Barrier ( 𝐸𝐴)- initial amount of energy needed to kickstart a chemical reaction used in transition state, activation energy is needed for both exergonic and endergonic reactions ○ Often from heat/thermal energy from surroundings/environment ○ Exergonic - lost energy as products (spontaneous) ○ Endergonic - gained energy as products
○ Enzymes catalyze chemical reactions by lowering the activation energy, reactions occur at lower temperatures ■ Do not have effect on amount of energy produced from reaction ( ∆𝐺) ○ Enzymes reduce amount of heat needed from environment ■ Enzymes allow chemical reactions to occur at lower temperatures ■ Chemical reactions in body can occur without enzymes, just would be slower → lots of more energy ■ Speeds up reactions, does not cause them ■ Amount of energy released ( ∆𝐺) is unaffected by enzyme ● Substrate - reactant an enzyme acts on ○ Enzyme binds to substrate forming enzyme-substrate complex ■ Active site - region on the enzyme where the substrate binds (most important part of the enzyme), specific for one substrate ● Enzymes are like lock and key, very specific ● Orienting substrates correctly to collide (physically) ● Straining substrate bonds (breaking bonds, hydrolysis) ● Providing favorable microenvironment ● Covalently bonding to the substrate ○ Induced fit - substrate brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction ■ Active site changes shape slightly envelops substrate ● Local conditions ○ Optimal temperature and optimal pH (37 C, heat bacteria use 77 C) ■ If not optimal, would denature most importantly, active site will unravel ■ Decreasing temperature does not denature, just slows down reaction ■ Enzymes work at specific temperatures and specific pHs with specific substrates ○ Cofactors ■ Non Protein enzyme helpers, bound to enzymes ■ May be inorganic (metals in ionic form, cofactor) or organic (carbon) ■ Organic cofactors called coenzymes bound to enzyme, inorganic == cofactor ● Include vitamins, w/o vitamins, some enzymes cannot function ● Vitamins are coenzymes, used in chemical reactions that’s why vitamins are essential ● Inhibitors - stop an enzyme from functioning ○ Competitive inhibitors - resembles substrate , competes with substrate for active site, reversible → reverse action by adding more substrate, then the substrate can outcompete inhibitor.
