Chemical Foundation for Cell | Carbohydrates | Properties Of Water

Topic 2: Chemical foundations for cells

Chapter 2 The chemistry of living things

Objectives 1. 2. 3. 4. 5. 6. 7. 8. Be able to identify the structure of an atom Define and relate matter with energy compare and contrast 3 types of bonds Covalent, Ionic and Hydrogen List the 4 most abundant elements in the body. Describe the importance of water to life. Differentiate between Acids ,Bases and buffers (the pH scale) Describe an organic molecule Be able to identify the major types of organic molecules, Carbohydrates, lipids, protiens and Nucleic acids. What does each of these do? What is denaturation?

9.

10. What are enzymes and why are they so important in our metabolism? 11. What is ATP? Figures 2.2, 2.5-2.10, 2.15-2.18, 2.20-21, 2.23 Table 2.1, 2.2 Lecture Notes

1. Sadly, you will have to learn some chemistry in order to understand human biology

A.

All living organisms including humans depend on chemical reactions (the sum of all the chemical reactions in the body is your metabolism.) Modern Chemistry has produced products that provide benefits and problems for our world. Chemicals or drugs can both do good and great harm to a body.

B.

The Structure of Atoms (be able to draw a typical atom) 1) An atom is the smallest unit of matter that is unique to a particular element 2) Atoms are composed of three particles: a) Protons (p+) are part of the atomic nucleus and have a positive charge. and Nitrogen in decreasing order (Know these elements) 3) Elements are fundamental forms of matter. A. Carbon. seven.13C . They cannot be broken down any further. C. Isotopes--variant forms of atoms 1) Atoms with the same number of protons (for example. They are the building blocks used to make molecules (an associaiton of two or more elements) 4) Energy is the capacity to do work combining elements to make a molecule is a type of work and so is breaking apart a molecule. They move around the nucleus 3) Electron activity is the basis for organization of materials and the flow of energy in living things. (12C. Matter is anything that occupies space and has mass 1) It includes solids. (sugar (complex) and oxygen to Carbon Dioxide and water. Hydrogen. a) They can be used to date rocks and fossils .4C) 2) Some radioactive isotopes are unstable (radioisotopes) and tend to decay (give off energy)into more stable atoms. liquids and gases 2) Matter is made of some ninety-two naturally occurring elements: the four most abundant in humans are Oxygen. Their quantity is equal to that of the protons. carbon with six) but different number of neutrons (carbon can have six. or eight) are called isotopes. Their quantity is called the atomic number (unique for each element). Protons plus neutrons = atomic mass c) electrons (e-) have a negative charge.2. b) Neutrons are also a part of the nucleus: they are neutral. Your body gets energy to move and metabolize by breaking complex molecules into simpiler ones. simple) B. Organization of Matter: The smallest substances that make up the body.

Important Bonds in biological Molecules A. when the outermost electron shell of the combining atoms are filled. Ionic Bonding: Electrons Gained or Lost (these chemicals are not stable in water. 4. 3) Orbitals can be thought of a occupying shells around the nucleus. NaCl . These bonds occur. electrons and Energy Levels 1) Electrons are attracted to protons. but are repelled by other electrons. for example. Combinations of Atoms 1) A molecule is a bonded unit of two or more (usually the same) atoms 2) A compound is a substance in which the relative percentage of two or more different elements never vary 3) A mixture is an intermingling of molecules in varying proportions 3. c) Atoms with ³unfilled´ Orbitals in their outermost shell tend to be reactive with other atoms to fulfill the octet rule (maximum of eight electrons in outer shell). a) The shell closest to the nucleus has one orbital holding a maximum of two electrons. b) The next shell can have four Orbitals with tow electrons each for a total of eight electrons. take table salt for an example. what happens to a salt crystal in water) 1) When an atom loses or gains one or more electrons. like in an X-ray machine or for radiotherapy for cancer D. Interactions that cause atoms to be gound to each other by actractive forces are called chemical bonds. it becomes positively or negatively charged-an ion 2) In an ionic bond. B. A chemical bond is an attraction between the electron structure of two (or more) atoms. 2) Orbitals permit electrons to stay as close to the nucleus and as far from each other as possible. Chemical bonds A.b) some can be used as tracers to follow the path of an atom in a series of reactions or to diagnose disease c) Used as sources of radiation for radiation therapy. (+) and (-) ions are linked by mutual attraction of opposite charges.

Covalent Bonding: Most of the molecules in your body use this type of bonding. 5. While the overall charge of water is neutral (no charge at all) if one was to look at the individual atoms that make up this molecule the oxygen (larger) is slightly negative and the hydrogens (smaller) is slightly positive because the oxygen shares the electron for a bit longer than the hydrogen. there is a slight difference in charge (electron electronegativity) between the two atoms participating in the bond. 1) A covalent bond holds together two atoms that share one or more pairs of electrons 2) In a nonpolar covalent bond atoms share electrons equally 3) In a polar covalent bond. 2) These bonds impart structure to liquid water and stabilize nucleic acids and other large molecules. it is said to be oxidized 4) Ionic bonds are not stable in water because the ions are separated by the polar water molecules. because atoms share the electron unequally. C. b) Polar substances are hydrophilic (water loving): nonpolar ones are hydrophobic (water dreading) and are repelled by water 3) Water displays properties useful to living systems: a) Water tends to stabilize temperature because it can absorb considerable heat before its temperature changes. Some Water Chemistry that is important to life A. a slightly negative atom of a polar molecule interacts weakly with a hydrogen atom already taking part in a polar covalent bond.3) Whenever a substance taking part in a chemical reaction gives up electrons. B. water is an example. a substance that is critical to the chemical reactions that occur in the body 2) Water is a polar molecule because of a slightly negative charge at the oxygen end and a slightly positive charge at the hydrogen end a) Water molecules can form hydrogen bonds with each other . Hydrogen Bonding 1) In a hydrogen bond. Properties of water 1) The human body is about two thirds water. it is very stable in water. This is an important property in evaporative and freezing processes .

The Molecules of life 1) These include simple sugars. held together by covalent bonds. The Molecules of life are organic compounds. convey distinct properties. meaning that they consist of atoms of carbon and one or more other elements. 6. fatty acids.g.b) The solvent properties of water are greatest with respect to polar molecules because ³spheres of hydration´ are formed around the sought (dissolved) molecules. atoms or groups of atoms covalently bonded to a carbon backbone. The pH Scale 1) pH is a measure of the H+ concentration in a solution: the greater the H+ the lower the value on the pH scale 2) The scale extends form 0 (acidic) to 7 (neutral) to 14 (basic) B. proteins and nucleic acids . gasoline) 2) Functional groups. amino acids and nucleotides 2) They are used as an energy source or as building blocks for the synthesis of macromolecules: polysaccharides. 2) Bicarbonate is one of the body¶s major buffers 7. Buffers and the pH of body fluids 1) Buffer molecule combine with . nitrogen and carbon(test quesiton?) 2) Much of the hydrogen and oxygen are linked as water 3) Carbon can form four covalent bonds with other atoms to form organic molecules of several configurations C. lipids. Properties of Organic compounds A. pH values and Buffers A. Hydrocarbons and functional Groups 1) A hydrocarbon has only hydrogen atoms attached to a carbon backbone (e. Effects of Carbon¶s bonding Behavior 1) Living organisms are mostly oxygen. B. to the complete molecule 3) D. hydrogen. or release H+ to prevent drastic changes in pH. such as solubility.

Lipids are composed mostly of hydrocarbon and are hydrophobic 1) They form the basic structures of membranes and have roles in energy metabolism 2) The sterols are important in the formation of hormones B. Lipids A. A carbohydrate is a simple sugar or a larger molecule composed of sugar units 1) Carbohydrates are the most abundant biological molecules 2) Carbohydrates serve as energy sources or have structural roles B.mit.is the simplest carbohydrate 2) Sugars are soluble in water and may be sweet tasting 3) Ribose and dextroribose (five carbon backbones) are building blocks for nucleic acids 4) Glucose (six carbon backbone) is a primary energy source and precursor of many organic molecules C.8. Fatty Acids .edu:8001/esgbio/lm/sugars/sugars. Carbohydrates http://esg-www. Oligosaccharides 1) A oligosaccharide is a short chain resulting form the covalent bonding of two or three monosaccharides 2) Sucrose (table sugar) is glucose plus fructose 3) Lactose (milk sugar) is glucose plus galactose 4) Maltose (grain sugar) is composed of two glucose units D. Polysaccharides 1) A polysaccharide consists of many sugar units (same or different) covalently linked 2) Glycogen is a storage form of glucose found in animal tissues 3) Starch (energy storage in plants) and cellulose (structure of plant cell walls) are made of glucose units but in different bonding arrangements 9.html A. Monosaccharides 1) A monosaccharide one sugar unit.

Proteins function as enzymes. Amino Acids and Proteins http://esg-www. and are derived form animal sources 3) Fatty acids with one or more double bonds between the carbons permit ³kinks´ in the tails :they tend to come form plants C. as storage and transport agents.mit. a phosphate group and a small hydrophilic group 2) They are important compounds of cell membranes E. unbranched hydrocarbon with a -COOH group at one end. an acid group. these molecules yield twice as much energy as carbohydrates D. 2) Cholesterol is a component of cell membranes in animals and can be modified to form sex hormones 10. Phospholipids 1) Phospholipids have a glycerol backbone. a hydrogen atom and one of twenty varying ³R´ groups C. Waxes 1) Waxes are special molecules with fatty acid chains attached to alcohol¶s 2) They confer extraordinary waterproofing qualities F. are solids at room temperatures. are the body¶s most abundant lipids 2) On a per weight basis.html A. and as structural material throughout the body B. two fatty acids. as hormones.1) A fatty acid is a long. as anti disease agents. in cell movements. sterols and their Derivatives 1) Steroids have a backbone of four carbon rings. 2) Fatty acids that have only single C-C bonds in their tails.edu:8001/esgbio/lm/proteins/aa/aminoacids. Neutral Fats (triglycerides) 1) Triglycerides. Primary structure of Proteins 1) Primary structure is defined as the chain (polypeptide) of amino acids 2) The amino acids are linked together in a definite sequence by peptide bonds between an amino group of one and an acid group of another . Proteins are polymers of amino acids: small organic molecules with an amino group. which have three fatty acids attached to one glycerol.

www.mit. The cell then can gain energy by removing one or all of the phosphates from this molecule. Its chemical structure consists of an Adenosine molecule attached to 3 phosphates. This is what happens when you cook an egg white. Nucleotides and Nucleic acids http://esg.html A. The properties of the protein change and the eggwhite goes from clear to white. ATP (Adenosine triphosphate) is the principal energy carrying molecul of the cell. . 12. Your cells can store energy by using energy to put these three phosphates on an adenosing molecule.edu:8001/esgbio/lm/nucleicacids/nucleicacids. Nucleic Acids-DNA and RNA 1) In nucleic acids four different kinds of nucleotides are bonded together to form large single or double stranded molecules 2) RNA is single stranded: it functions in the assembly of proteins 3) DNA is double strained: genetic messages are encoded in its base sequences. B. A. and ultimately its function in two ways a) By positioning groups so that hydrogen bonds can form between different amino acids in the chain b) By putting r groups in positions that force them to interact 2) During a process called denaturation the three demensional struture of a protein can be ireversibley changed. Nucleotides with roles in Metabolism 1) Each nucleotide has a five carbon sugar (ribose or deoxyribose). 11. Three-dimensional Structure of Proteins are important in its structure 1) The primary structure determines the protein¶s shape. a nitrogen containing base and a phosphate group 2) Examples of these kinds of molecules include a) Adenosine phosphates are chemical messengers (cAMP) and energy carriers (ATP) b) Nucleotide coenzymes transport hydrogen atoms and electrons (examples: NAD+ and FAD) B.D. C.

and is made up of a series of chemical reactions. break apart and eliminate substances.D. and proteins are broken down to form products of lower energy. lipids. Chemical bond energy is converted into ATP from which the energy is gained to move substances in to a cell or to move fibers past one another. This molecule acts like energy currency in your body. Released energy can be used for cellular work. Enzymes 1) Enzymes are protein that serve a catalysts: they speed up reactions . 2) Metabolic pathways form series of reactions that regulate the concentration of substances within cells by enzyme-mediated linear and circular sequences a) In biosynthetic pathways also called anabolism small molecules are assembled into large molecules for example. large molecules such as carbohydrates. 13. simple sugars are assembled into complex carbohydrates b) In degradative pathways (called catabolism). 3) Some terms used in describing metabolism: a) Substrates (reactants) are substances that enter a reaction b) Intermediates are substances that form between the start and conclusion of a metabolic pathway c) End products are the substances present at the conclusion of the pathway d) Enzymes are proteins that speed up a reaction e) Cofactors are organic molecules that assist enzymes in their action f) Energy carriers donate energy to substances by transferring functional groups to them g) Transport proteins adjust concentration gradients at cell membranes in ways that influence the direction of metabolic reactions 4) ³redox´ reactions a) Many metabolic pathways involve oxidation-reduction reactions (=redox) b) The donor molecule loses an electron and is oxidized c) The receptor molecule gains an electron and is reduced A. Metabolic Pathways 1) Metabolism is the controlled capacity to acquire energy and use it to build.

and HADP+ (partly derived form vitamins). 3. FAD. they just make it happen faster b) Enzymes can be reused c) Enzyme actions are reversible d) Enzymes are selective and act upon specific substrates. which transfer protons and electrons form one substrate to another. 2) Hormones also have significant enzyme regulating effects Possible Questions: things to think about 1. 4. 2. high temperatures decrease reaction rate by disrupting the bonds that maintain threedimensional shape (denaturation occurs). which are the molecules that enzymes (at their active sites) recognize and bind to. 3) Inorganic metal ions such as Fe++ also serve as cofactors when assisting membrane cytochyrome proteins in their electron transfers in mitochondria C. stimulation. Draw an atom of carbon and distinguish the parts hint What properties of water make it important to life hint What is the difference between hydrophobic and hydrophilic? hint Name the 4 basic elements of life hint Name the 4 basic molecules of life hint . 4) Most enzymes function best at pH near 7: higher or lower values disrupt enzyme shape and halt function B. 5. Enzyme cofactors 1) These are nonprotein groups that bind to many enzymes and make them more reactive. and inhibition.2) Enzymes have four features in common a) Enzymes do not make anything happen that could not happen on its own. 2) Coenzymes are large organic molecules such as NAD+. Control of Enzyme Function 1) Enzyme activity can be controlled by cellular regulation of enzyme synthesis. 3) Because enzymes operate best within defined temperature ranges.

Which of the following organic molecules make up the body a) lipids hydrogen b)oxygen e)carbohydrates c) nucleic acids d) 4. Human blood is considered a) Neutral covalent b) basic c) acidic d) blue e) Answers 1) a. Which of the following are considered subatomic particles present in an atom? d) Electron 2.c.b. What are the properties of the four basic molecules of life? What provides more energy a pound of carbohydrate or a pound of fat? Which bond dissolves in water? hint Describe the difference between a polymer and a monomer.6.Colorado.gov/chemistry/ Page: 11 .e 4) a 5) a A physics site that is worth visiting http://www. How many ionic bonds does carbon usually make a) 0 b)1 c)2 d)3 e)4 5.nist. hint Multiple choice Questions 1. 7.EDU/physics/2000/index. 9. b) Proton c) neutron d) mass e) space Which of the following elements are present in the body in the greatest amounts? a) plutonium b) oxygen c) nitrogen d)hydrogen e)trillium 3. http://webbook.c 2)b.c. 8.pl Online chemistry web book set up by NIH you can look for chemicals by a number of characteristics. Give examples of each.d 3)a.

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