Biology 2nd Grading Reviewer Carbon Compounds - a substance that consists of two or more elements - has a unique composition that is always the same Molecule - smallest particle of a compound Chemical Bonds - holds molecules together - Forms when substances react with one another Chemical Reaction - a process that changes some chemical substances into others - Needed to form a compound and another chemical reaction is needed to separate substances in a compound Organic Compound - A compound found mainly in living things - make up the cells and other structures of organisms and carry out life processes Carbon - most important element to life - the central element in compounds necessary for life. - main element in organic compound Why is carbon basic to life? Carbon has the ability to form stable bonds with other elements, including itself, allowing it to form a huge variety of very large and complex molecules 4 Major Organic Compounds: ● Carbohydrates ● Lipids ● Proteins ● Nucleic Acid Macromolecules - Polymers: chain-like molecules - polys = many; meros = part (in Greek) - Linked by covalent bonds - Monomer: building blocks of polymer that are repeating units of smaller molecules - monos = single (in Greek) Polymers - Synthesized by dehydration reaction - Disassembled by hydrolysis reaction Carbohydrates Carbohydrates - most common type of organic compound - Used to store energy like sugars and starches - Also provides energy to cells and forms body structures - Brain food - CH2O Monosaccharide monomer of carbohydrates - Small repeating units of carbohydrates Types of Monosaccharides: ● Fructose (fruit sugar) ● Galactose (milk sugar) ● Glucose (blood sugar) → used for energy by the cells of most organisms and is a product of photosynthesis. Glucose (C6H12O6) and fructose (C6H12O6) are isomers. Isomers: Molecules with the same chemical formula but with atoms in a different arrangement Disaccharide - A carbohydrate made up of two monosaccharides bonded together Types of Disaccharides ● Sucrose (table sugar): fructose + glucose → product of photosynthesis ● Lactose (milk sugar): galactose + glucose → major animal energy source ● Maltose (malt/grain sugar): glucose + glucose (alpha-1,4 linkage) → important immediate in starch and glycogen digestion ● Trehalose: glucose + glucose (alpha-1, alpha-1 linkage) → an energy source for insects ● Cellobiose: glucose + glucose (beta-1,4 linkage) → essential in carbohydrate metabolism ● Gentiobiose: glucose + glucose (beta-1,6 linkage) → a constituent for plant glycosides and some polysaccharides. Monosaccharides and disaccharides are called simple sugars as they provide the major source of energy to living cells. Polysaccharides - a complex carbohydrate that forms when simple sugars bind together in a chain - two main functions: storing energy and forming structures of living things. - They’re bonded by glycosidic linkages 2 Polysaccharides that store energy: ● Starch - Used by plants to store energy. - Composed entirely of alpha glucose molecules - Can be amylose (simple, outer layer of starch) or amylopectin (complex, inner layer of starch) ● Glycogen - Used by animals to store energy. 2 Polysaccharide that forms structures: ● Cellulose - Used by plants to form rigid walls around cells. - Most abundant biopolymer - Found in a plants’ cell wall - Highly insoluble as it provides structural support to the cell ● Chitin - Used by some animals to form an external skeleton. - Major component of fungal cell wall - Found in outer coverings of crustaceans and insects for protection and support. Oligosaccharides - Combination of monosaccharides and disaccharides or two(2) monosaccharides and disaccharides → Raffinose: Galactose + Glucose + Fructose → Stachyose: Galactose + Galactose + Glucose + Fructose Fiber is a carbohydrate! Examples of Carbohydrates Simple Carbs ● ● ● ● ● White bread Fruits Candy Ice cream Honey Complex Carbs ● ● ● ● ● Legumes Whole wheat bread Sweet potatoes Quinoa Oats Lipids Lipids - Include a diverse group of compounds that are nonpolar in nature. Composed of CHON atoms highest long-term energy storage molecules consist of repeating units called fatty acids [CH3(CH2)nCOOH] also supply cells with energy Types of Lipids ● Triglycerides ● Phospholipids ● Steroids Triglycerides - main form of stored energy in animals. - Triacylglycerol - three(3) fatty acids linked to one glycerol (alcohol) molecule Steroids - Lipids characterized by a carbon skeleton consisting of four fused rings - serve as chemical messengers and have other roles Cholesterol - A type of steroid which is a common component of animal cell membranes - Precursor from which other steroids, such as the vertebrate sex hormones, are synthesized. - Vertebrates → synthesized in the liver and obtained from the diet - ↑ level of cholesterol → atherosclerosis - Mainly responsible for narrowing arteries Phospholipids - Major constituent of the plasma membrane, selectively permeable membrane - Composed of two (2) body regions: hydrophilic head and hydrophobic tails - Composed of a fatty acid tails attached to the glycerol backbone - 1st and 2nd carbon (glycerol backbone) → saturated and unsaturated fatty acid tail respectively - 3rd carbon (glycerol backbone) → phosphate group. - Made up of triglycerides Fat Functions of Fats - Energy storage → more compact reservoir of fuel Humans and other mammals stock food in long term food reserves in adipose cells ↳ cushions vital organs like kidneys and a layer of fat beneath the skin insulates the body ↳ protects marine mammals from cold ocean water Saturated Fats ● ● ● ● ● ● Lack double bonds Animal fats Solid at room temp Contribute to atherosclerosis Stearic acid and butyric acid Form straight chains Unsaturated Fats ● ● ● ● ● ● One or more double bonds Plant and fish fats Oils Liquid at room temp Oleic acid and linoleic acid Form bended chains Trans Fat - Made up of partially hydrogenated unsaturated fats - Unsaturated fats bend because of the cis transfiguration - Trans configuration results in an unsaturated fatty acid that is a straight chain like a saturated fatty acid - Rare in nature - Bad fats Why is Butter better than Margarine? It contains less trans-fat. Although margarines come from vegetables, its unsaturated fats were partially hydrogenated containing more trans-fat than butter. Fake Fat - Olestra is highly insoluble - Can cause abdominal cramps Essential fatty acids: must be consumed in food. Proteins Proteins - Greek word proteios = first or primary made up of small molecules called amino acids, the monomers of proteins - Elemental composition - contain Carbon (C), Hydrogen (H), Nitrogen (N), Oxygen (O), Sulfur (S) - more than 50% of most cells’ dry mass - Speed up chemical reactions, play a role in defense, storage, transport, cellular communication, movement, or structural support - There are 20 different amino acids commonly found in the proteins of living organisms. - The largest known proteins are titins, found in muscle and composed of over 27,000 amino acids. Essential amino acids: needed through diets because your body cannot make them Non-essential amino acids: can be synthesized by your body. Complete Protein: contains all essential amino acids in the proper amounts Incomplete Proteins: low in one or more of the essential acids (usually lysine, tryptophan, or methionine) Complementary Proteins: incomplete proteins which when served together, complement each other and provide all essential amino acids. Structure of Proteins Polypeptides: Long chains of amino acids Peptides: short chains of amino acids binded together 4 Levels of Protein Structure ● ● ● ● Primary Structure Secondary Structure Tertiary Structure Quaternary Structure Primary Structure Secondary Structure Tertiary Structure Functions of Protein Why are proteins versatile in terms of functions? Has the ability to: →bind small molecules specifically an strongly →bind other proteins and form fiber-like structures →integrated into cell membranes Quaternary Structure ⚠ Each protein has specific shape that determines its function. Changing an amino acid in a protein can either have no discernible effect or have a massive effect. Enzymatic Proteins Function: selective acceleration of chemical reactions Example: digestive enzymes Carbohydrates→sugars by amylase, sucrase-isomaltase, maltase, and lactase Proteins→amino acids by pepsin, trypsin, and peptidase Fats→fatty acids by lipase Storage Proteins Function: bind (and store) small molecules Examples: ↱ has 4 subunits & heme groups + Ferritin - iron-storage protein for use in the biosynthesis of new hemoglobin molecules + Myoglobin - oxygen-storage protein present in muscle ↳ has 1 subunit & heme group Hemoglobin - inside red blood cells & carries oxygen from the lungs to cells throughout the body. Hormonal Proteins Function: Coordination of an organism’s activities Example: Insulin Contractile and Motor Proteins Functions: Movement Examples: Myosin and Actin Defensive Proteins Function: protection against disease Example: Antibodies Transport Proteins Function: Transport of substances Examples: hemoglobin, transport proteins (channels, transporters, ATPase pumps) Receptor Proteins Function: Response of cell to chemical stimuli Example: Receptor proteins Structural Proteins Function: Support Examples: keratin, collagen and elastin Nucleic Acids Nucleic Acids - Bluprint - Contains instructions to build proteins - 2 types: DNA and RNA Monomer: Nucleotide; Polymer: Nucleic acid Phosphodiester bond: covalent bond between 5 phosphate group of one nucleotide and 3’ -OH group of another Nucleotide Structure - Coding region: nitrogenous bases - Backbone: Sugar molecule, phosphate group Nitrogenous Bases ● ● ● Pyrimidines (One ring structure) Purines (Two ring structure) CUT the PYe PUre Ad Gold Cytosine Uracil (RNA) Thymine (DNA) ● ● Adenine Guanine DNA (Deoxyribonucleic Acid) - Double helix - Hydrogen bonds connects the two nucleotides - Chargaff’s Rules: + A → T (2 H Bonds) //Apples in the Tree + C → G (3 H Bonds) //Car in the Garage - complementary base pairs - antiparallel strands → opposite direction (5’ end paired with 3’ end) - Function: codes for traits (gene) RNA (Ribonucleic Acid) - Single chain of nucleotides - Nitrogen bases: G → C, A → U - Function: deliver instructions from DNA to ribosome + Messenger RNA (mRNA) - message carrier + Ribosomal RNA (rRNA) - major components of ribosome + Transfer RNA (tRNA) - transfer aa to match the correct mRNA codon - Flow of genetic information: DNA → RNA → Protein DNA Sequencing ● Human Genome Project ● Automatic DNA sequencing machines ● Humans & Our cousins ATP (Adenosine Triphosphate) - Sugar - Nitrogenous base: adenine - 3 phosphate groups - Function: High energy molecule and supplies energy for muscle contraction and nerve impulses. Photosynthesis Photosynthesis - Discovered 415 million years ago - Process i which light energy is converted to chemical energy in the form of sugars - Energy: the glucose molecules serve as fuel for cells (cellular respiration & fermentation, ATP) - Fixed Carbon: carbon from carbon dioxide - inorganic carbon can be incorporated into organic molecules (carbon fixation) Enters through xylem Ecological Importance of Photosynthesis Photoautotrophs: use light to feed themselves and fix their own carbon; self-feeders Heterotrophs: different feeders that can’t convert carbon dioxide to organic compounds themselves. Sites of Photosynthesis Leaves ● Mesophyll - primary site of photosynthesis ● Stomata - let carbon dioxide diffuse into the mesophyll layer and oxygen diffuse out ● Chloroplasts - specialized to carry out the reactions of photosynthesis + Thylakoids - disc-like structures that contain chlorophyll, green-colored pigments that absorb light + Stroma - fluid-filled space around the grana Light-dependent reactions - Happens in the thylakoid membrane (chloroplasts) - Require continuous supply of light energy - Use light energy to make ATP (energy storage molecule) and NADPH (reduced ecarrier) - Oxygen gas - Light energy → chemical energy - Photosystems: large complexes of proteins & pigments (light-absorbing molecules) that are optimized to harvest light and plays a key role in the light reactions Two types of photosystems: photosystem I (PSI) photosystem II (PSII) - Photoexcitation - When light energy is absorbed by a chlorophyll molecule its electrons gain energy and move to higher energy levels in the molecule Light and Photosynthetic Pigments - Plants capture light energy and use it to make sugar - Pigments: special organized molecules to absorb light (only specific wavelengths of visible light, while reflecting others) - Light: form of electromagnetic radiation, a type of energy that travels in waves - Visible spectrum: only part of the electromagnetic spectrum that can be seen by the human eye. - Absorption spectrum: set of wavelengths absorbed by pigment. - A photon - Three key pigments in photosynthesis: chlorophyll ɑ, chlorophyll b, and β-carotene Calvin Cycle (Light-independent reactions) - Also called dark reactions - Happens in the stroma - Does not directly require light - Fix carbon dioxide (carbon fixation) - three -carbon sugars - glyceraldehyde-3-phosphate or G3P molecules → glucose Carbon. 3CO2 combine with 3 RuBP acceptors, making 6 molecules of glyceraldehyde-3-phosphate (G3P) ● 1 G3P molecule exits the cycle and goes towards making glucose. ● 5 G3P molecules are recycled, regenerating 3 RuBP acceptor molecules. ATP. 9 ATP are converted to 9 ADP (6 during the fixation step. 3 during the regeneration step). NADPH. 6 NADPH are converted to 6 NADP+ (during the reduction step). Cellular Respiration Cellular Respiration - Process by which cells acquire energy by breaking down glucose to form water and carbon dioxide - Requires oxygen and gives off carbon dioxide - The reason why animals breath and why plants also need oxygen - The opposite of photosynthesis - The cell uses energy to produce ATP Pathways of cellular respiration: allow energy within glucose molecule to be reduced slowly Constantly occurring Results in a maximum yield of 36 or 38 ATP molecules Only about 39% ATP molecules is used of the total energy in glucose ↱ loss of electrons - An oxidation-reduction process Gain of electrons - ↲ e-s are not easily removed from covalent compounds unless an entire atom is removed Oxidation (in living cells) involve the removal of hydrogen atom and its eReduction gains hydrogen atom and its eA hydrogen atom with its energy is usually transferred to a hydrogen acceptor compound Glucose is oxidized; oxygen is reduced Glucose: a high energy molecule and it breaks down into 2 low energy molecules, water, and carbon dioxide and energy is released. The cell uses energy to produce ATP - Pathways of cellular respiration: allow energy within glucose molecule to be reduced slowly Constantly occurring Results in a maximum yield of 36 or 38 ATP molecules Only about 39% ATP molecules is used of the total energy in glucose NAD+ and FAD - 2 important hydrogen acceptor compounds/enzymes - Can oxidize a substance by accepting e-s and reduce a substance by giving up e-s - Oxidation: NAD+ accepts 1 electrons + a hydrogen ion (H+) → NADH FAD+ accepts 2 electrons + a hydrogen ion (H+) → FADH2 4 Phases of Cellular Respiration Phase Site 02 requirement Glycolysis cytoplasm No - aerobic Preparatory reaction Matrix of mitochondria Yes - aerobic Citric acid cycle Matrix of mitochondria Yes - aerobic Electron transport chain Cristae of mitochondria Yes - aerobic Stage 1: Glycolysis - Greek words: glycos- (sugar), lysis- (splitting) - A long series of reactions with 10 enzymes each in 10 steps - 2 phases: energy-investment (first 5 steps where 2 ATP is spent), energy-harvesting (last 5 steps generates 4 ATP) - Net: 2ATP/glucose - Inputs Outputs 1 glucose 2 Pyruvate 2 NAD+ 2 NADH 2 ATP 2 ADP 4 ADP + 4P 4 ATP When 02 is available - cellular respiration continues in an aerobic faction with the end products being CO2 and H2O (pyruvate → mitochondria) - When O2 is not available - cellular respiration continues in an aerobic faction (pyruvate → cytoplasm) Anaerobic respiration (Fermentation) - Gain of 2 ATP molecules and end products like alcohol and lactate - Consists of glycolysis (pyruvate formation) then reduction of pyruvate - 2 types: lactic acid (animals) and alcoholic (yeast/bacteria) - End products of fermentation in animal cells forms either 2 lactate molecules or 2 alcohol molecules (for humans: end product is lactate) - It’s beneficial to animal cells because it regenerates NAD+ to keep ATP synthesis occurring - Animals use lactic acid fermentation for rapid bursts of energy - 02 in the cells is used up quickly and rapidly produce ATP - Lactate buildup in muscles = toxic - Products result from fermentation: wine, bread, yogurt, vinegar, beer, etc.. Stage 2: Citric Acid Cycle/Krebs Cycle - Cyclic metabolic pathway found in mitochondria’s matrix - Completely breaks down pyruvates to release energy; generates CO2 waste - Net yield: 2 ATP, 6 NADH, 2 FADH Inputs Outputs 2 acetyl groups 4 CO2 6 NAD+ 6 NADH 2 FAD 2 FADH2 2 ADP + 2 P 2 ATP Stage 3: Electron Transport Chain - Located on the cristae of the mitochondria - Charged electrons are released from NADH and FADH2 and passed along a series of enzymes, giving up energy used to fuel a proton gradient for chemiosmosis - Chemiosmosis: process by which mitochondria and chloroplasts use the energy of an e- transport chain to create a H+ gradient that drives ATP production - A series of oxidation-reduction reactions - Oxygen is the final acceptor of electrons - 6H2O → waste when e-s unite with O2 at the end of electron transport chain Summary of ATP Production ● Totals from Substrate-level ATP synthesis Glycolysis - 2; Citric Acid - 2 ● Totals from NADH oxidation at ETC 2 NADH from Glycolysis - 4 or 6; 2 NADH from Prepory Reaction - 6; 6 NADH from Citric Acid Cycle - 18 ● Totals from FADH2 oxidation at electron transport chain 2 FADH2 From citric acid cycle - 4 Grand totals are 36 or 38 ATP generated by 1 glucose molecule breakdown by cellular respiration Reason why 36 or 38 ATP is generated: 1. 2 NADH from glycolysis sometimes expand energy to get inside mitochondria 2. 1 ATP expanded to get 1 NADH from cytoplasm to mitochondria Results in net loss of 2 ATP Photosynthesis and cellular respiration Work together!! ● ● ● Matter is cycled within these two processes Sunlight provides the energy that eventually becomes ATP in you Energy flows through these two processes.
