Chapter 2 Chemistry (PDF)

CHAPTER 2 The chemistry of life* *Optional HW with this chapter Objectives: Elements in living things 3 types of chemical bonds Important features of water pH, acids and bases Carbohydrates, lipids, proteins and nucleic acids  All matter is composed of atoms Atoms consist of: Protons: + cha...

CHAPTER 2 The chemistry of life* *Optional HW with this chapter Objectives: Elements in living things 3 types of chemical bonds Important features of water pH, acids and bases Carbohydrates, lipids, proteins and nucleic acids  All matter is composed of atoms Atoms consist of: Protons: + charge, have mass Neutrons: no charge, have mass Electrons: - charge, essentially no mass A helium atom. More than 99.9% of mass is in nucleus. Most of the volume is electron orbitals. Same number of protons = same element Typically, carbon has 6 protons + 6 neutrons Two atoms of the same element, but with different numbers of neutrons, are isotopes A rare carbon isotope has 6 protons + 8 neutrons (the atom is heavier, and radioactive in this case) 7 protons + 7 neutrons is nitrogen, a different element with different chemical properties What are some of the important chemical elements in humans?  Important elements in humans Element % weight Purposes Oxygen 65% Water, org. molec., respiration Carbon 18% All organic molec. built on carbon frame Hydrogen 10% Water, org. molec., stomach acid Nitrogen 3% Proteins, DNA, RNA, ATP Calcium 2% Bones, teeth, nerve / muscle action Phosphorus 1% Bones, teeth, cell membranes, ATP, DNA, RNA  Important trace elements in humans Element purpose Potassium Cell volume, nerve conduction Sodium Cell volume, nerve conduction Chlorine Hydrochloric acid in stomach Iron Hemoglobin in blood Sulfur In 2 amino acids: most proteins Ions do not have the same number of protons and electrons Ion’s charge = (# of protons) – (# of electrons) Sodium (neutral) has 11 protons, 12 neutrons, 11 electrons Sodium ion (Na+) has 11 protons, 12 neutrons, 10 electrons Atoms with a positive (+) or negative (-) charge are ions Atoms “want” their outermost electron orbitals to be filled with electrons: no more, no less. They are most stable in these conditions 3rd 2nd 8 e- 1st 8 e- 2 e- 1st orbital fills with 2 electrons (Helium) 1st 2 protons 2nd orbital fills with 8 electrons (Neon) 2nd 1st 10 protons 3rd orbital fills with 8 electrons as well (Argon) 3rd 2nd 1st 18 protons To have a filled outer orbital (to become more stable) chlorine (Cl) must gain 1 electron 3rd 2nd 1st 17 Protons To have a filled outer orbital (to become more stable) sodium (Na) must give away 1 electron 3rd 2nd 1st 11 Protons Sodium gives chlorine its 1 electron and both now have filled outer orbitals Sodium (+1) Chloride (-1) 3rd 2nd 2nd 1st 1st 11 P 17 P Ions with opposite charges attract each other. They form a molecule through ionic bonds. Ionic bonds are medium strength. (+1) (-1) 2nd 3rd 2nd 1st 1st A molecule is one or more atoms joined together by covalent or ionic bonds. Another way to complete an orbital is to share electrons between atoms (not give them away completely like ions do) Sharing electrons between atoms forms a covalent bond Covalent bonds are the strongest chemical bonds  Oxygen 2 x Hydrogen Water Each hydrogen atom needs to gain 1 electron. The oxygen atom needs to gain 2 electrons.  Carbon 4 x Hydrogen Each hydrogen atom must gain 1 electron, and each carbon atom must gain 4 electrons. Methane Note: carbon can form 4 strong covalent bonds Atoms can also share more than 1 electron, forming double covalent bonds. (Triple covalent bonds are possible too) A triglyceride molecule, formed by multiple single and double covalent bonds. Triglycerides are examples of lipids (fats and oils). This is a triglyceride with unsaturated fatty acids (it has double bonds) Which fats are healthier? Saturated? Unsaturated? Sometimes atoms form covalent bonds, but do not share the electrons equally. This results in polar molecules. Water is an important polar molecule! - + +  - - + + + + - + + Multiple water molecules, held together (temporarily) by weak hydrogen bonds Hydrogen bonds form between two polar molecules. Hydrogen bonds are the weakest chemical bonds Important examples of hydrogen bonds include: -Water molecules -Bonds holding the two strands of DNA together -Bonds forming the shapes of proteins Three Types of Chemical Bonds  Life Depends on Water Water is responsible for 60% of human body weight, and is 90% of the blood plasma. Water molecules are polar Water is liquid at body temperature  Important Biological Functions of Water Water is the biological solvent Water is polar, so it dissolves polar molecules and ions (sugars, amino acids, ions, most proteins) Water is liquid at body temperatures, so water in blood plasma can transport these dissolved substances throughout the body. These substances move to and within cells dissolved in water as well. Water is polar, and so it is an excellent solvent, as it can dissolve many polar or ionic substances (like salt here, and sugar, for example).  Important Biological Functions of Water Water helps us maintain homeostasis of body temperature: Evaporation of water takes heat from our bodies cooling us when we sweat.  Important Biological Functions of Water Water also serves as a lubricant: in saliva when we swallow, and as synovial fluid in between bones at synovial joints. Water is important in many chemical reactions, hydrolysis for example: 1) Polysaccharides and proteins broken down into simple sugars and amino acids. 2) ATP + water  ADP + P + energy.  Important Biological Functions of Water Drink more than 4 bottles of water (or liquids with water) / day. Being well hydrated improves athletic (and everyday) performance: Mild dehydration can lead to headaches, dizziness, feeling faint, muscle cramps and other problems. Consistent dehydration can lead to kidney stones. Coffee, other caffeinated (“energy”) drinks, beer and other alcoholic drinks do not help that much, as they are diuretics. How can you tell if you’re dehydrated?  The Importance of Hydrogen Ions Pure H20 occasionally breaks into: H+ ion and OH- ion. Acids release H+: HCl Hydrochloric acid (increase the amount of H+ in water / body) Bases combine with H+: NaOH sodium hydroxide (decrease the amount of H+ in water / body)  The Importance of Hydrogen Ions pH scale measures hydrogen ion concentration in a water solution Decreasing pH = more hydrogen ions present = greater acidity The pH of pure water is 7. (10-7 moles/liter H+ ion) Lemon juice is highly acidic, it has a pH of 2. Bleach is highly basic, it has a pH of 13. The pH scale is a log scale. For example, black coffee (pH 5) is 100 times more acidic than water (pH 7) The pH Scale H+ and OH- ions can react with many molecules, (including proteins). The body must maintain a nearly constant pH, otherwise death will occur. Thus the body maintains homeostasis of pH in the blood and tissue fluids (average pH in body = 7.4, but stomach = 2) Blood has a chemical buffering system, and excess H+ are also removed from the blood at the kidneys.  The Organic Molecules of Living Organisms Carbon, the building block element of living things: Comprises 18% of body by weight Forms four covalent (strong) bonds, so molecules of many shapes and chemical properties are possible. Can form single or double bonds Can build micro- or macromolecules (millions of smaller molecules can be joined together). 4 important types of organic molecules: Carbohydrates Lipids (fats and oils) Nucleic acids Proteins  Carbohydrates are used for energy Monosaccharides: glucose, fructose, ribose Disaccharides: sucrose, lactose Polysaccharides: thousands of monosaccharides joined in chains and branches Starch: made in plants, stores energy Glycogen: made in animals, stores energy Cellulose: made by plants, indigestible, but provides “roughage” in diets, (helps against constipation, hemorrhoids, colon cancer).  Glycogen: branched polysaccharide used to store glucose for the future. Glycogen is stored in the liver and the skeletal muscles.  Carbohydrates are used for energy Glucose and other monosaccharides are used as fuel by cells. Cellular respiration: the energy stored in chemical bonds of carbohydrates, proteins and fats are converted into energy stored in chemical bonds in ATP. The energy in ATP is used to do cellular work, like flexing our muscles  Carbohydrates form glycoproteins Glycoproteins are carbohydrates joined to proteins. Important in linking some cells together. Important in cell-cell recognition, so white blood cells of your immune system recognize your own cells, and don’t attack them.  Lipids (fats and oils): Insoluble in Water “Oil and water don’t mix”. Fats are “hydrophobic” Fats do not dissolve in water because they are neither polar nor ionic. They are transported in our blood in complexes with proteins. Triglycerides: energy storage molecules Glycerol + 3 fatty acids = triglycerides  Fats are important energy storage molecules: 1 g fat = more than twice the calories of 1 g carbohydrate Adipose tissue: fat stored energy in adipose cells Adipose tissue in the hypodermis (bottom layer of skin) for insulation. Stored fats cushion certain organs (kidneys). Diets: fat cells reduce their fat content, but do not go away, so it can be hard to lose weight. As fat content decreases in fat cells, a chemical signal causes our metabolism to slow down!  Phospholipids: cell membranes Phospholipids: a part of cell membranes, similar Water to triglycerides. + Phosphate group is polar (hydrophilic): - and is attracted to water inside and outside of cell. Fatty acid tails: hydrophobic, and away from water Water Slide 2.17 Copyright © 2001 Benjamin Cummings, an imprint of Addison Wesley Longman, Inc.  Steroids (lipid): Insoluble in Water Cholesterol: makes lipid bilayer (cell membrane) stiffer Steroid hormones (from cholesterol): released into blood as intercellular messengers Vitamin D made from cholesterol too Slide 2.17  Triglycerides: saturated or unsaturated. Saturated fats (like butter, fat in cheese, fat in cream, animal fat, lard) encourage cholesterol production, leading to arterial plaque build up. Unsaturated fats (oils) do not encourage this. Saturated fats converted to cholesterol, which can accumulate in plaques (build up) in arteries. Avoid foods high in saturated fats and high in cholesterol! Arteriosclerosis  heart attacks, strokes Some studies have also shown that eating saturated fats may slightly increase your risk of developing certain cancers, such as: Colon cancer Breast cancer Uterine cancer Ovarian cancer Prostate cancer Why? Structure and Function of Adenosine Triphosphate (ATP) (a nucleic acid) ATP is the “energy currency” of the body. If something in the body requires energy, the energy is supplied by ATP. ATP + water  ADP + P + energy ATP created in cells by aerobic cellular respiration from sugar, fat and protein food molecules.  Function of Nucleic Acids Functions DNA stores genetic information for making proteins mRNA copies information in DNA for making one protein DNA in nucleus is like a library, with information to make every protein. It stays in the nucleus. A gene is a small part of DNA. It is like a book, it has the information to make one protein mRNA is like a photocopy of the one book to make one protein needed at the time. It leaves the nucleus, taking information to ribosomes in the cytoplasm, which make the protein.  Structure of Nucleic Acids Structure of DNA DNA: (Deoxyribonucleic acid) Nucleotide: phosphate group, deoxyribose sugar, nitrogenous base 4 types of nucleotides, with different nitrogenous bases: adenine, thymine, cytosine, guanine (4 letters)  Nucleotides: “letters” that make up the words for protein construction: A, T, C, G Composed of: phosphate group, sugar and a base. Only nitrogenous bases differ between the nucleotides  DNA is a double helix: two strands joined by hydrogen bonds. Base pairs attached by weak hydrogen bonds. Base pairs must be broken apart for the genetic code to be “read”. Adenine pairs with thymine only and vice versa (A-T) Guanine pairs with cytosine only and vice versa (G-C)  Structure of Nucleic Acids Structure of mRNA mRNA: messenger (Ribonucleic acid) Single-stranded molecule, much shorter than DNA Leaves nucleus with information to make 1 protein (messenger) mRNA: single-stranded Sugar: ribose Nitrogenous bases: adenine, uracil, cytosine, guanine Pairing: adenine-uracil, cytosine-guanine  Messenger Ribonucleic acid (mRNA) is single stranded. The sugar is slightly different than in DNA Uracil is substituted for thymine (U-A bonds between mRNA - DNA)  The genetic code DNA is like a library with information to make all proteins. mRNA is like photocopy of one book with instructions for one protein. Includes “words” and proper order of words for the proper order of amino acids to make the protein. “Letters” are the bases (A-G-C-T) The letters make up “words” (codon), all codons are 3 letters long (AAG, AGC, CCC, etc.) Each codon (“word”) specifies only 1 amino acid The genetic code DNA T-A-G mRNA A-U-C = only the amino acid isoleucine DNA T-A-A mRNA A-U-U = only isoleucine again! (like “big” and “large” both mean the same thing) DNA A-A-A mRNA U-U-U = only the amino acid phenylalanine Mutation occurs when the DNA sequence changes and another amino acid results TAGTAATAA TAGAAATAA for example Double stranded DNA, in nucleus …TAGTAAAAA… = DNA …ATCATTTTT… DNA separates temporarily, mRNA copies information in DNA (transcription) …TAGTAAAAA… = DNA …AUCAUUUUU… = mRNA …ATCATTTTT… mRNA leaves nucleus into cytoplasm, DNA comes back together …TAGTAAAAA… = DNA …ATCATTTTT… = mRNA …AUCAUUUUU… In cytoplasm, ribosomes “read” mRNA sequence, to create the right amino acid sequence (translation) = mRNA = amino acid …AUCAUUUUU… … iso AUC = isoleucine = iso In cytoplasm, ribosomes “read” mRNA sequence, to create the right amino acid sequence (translation) = mRNA = amino acid …AUCAUUUUU… … iso iso AUU = isoleucine = iso In cytoplasm, ribosomes “read” mRNA sequence, to create the right amino acid sequence (translation) = mRNA = amino acid …AUCAUUUUU… … iso iso phe … UUU = phenyalanine =phe The finished protein has a function in our body = amino acid … iso iso phe ….  Proteins: Complex Structures made of Amino Acids 20 amino acids total. We can make 12, 8 from diets are “essential”. All have a common backbone, and an additional group. Additional group gives them unique chemical properties: polar, not polar, negatively charged, positively charged. Chemical properties of a protein depend on which of the different amino acids it is made out of, and the order of the amino acids.  Protein Structure Primary: amino acid sequence this depends on the DNA sequence of the gene for the protein Secondary: describes chain’s orientation in space; e.g., alpha helix, beta sheet Tertiary: describes three-dimensional shape of one chain of amino acids Quarternary: two or more tertiary protein chains are associated Not all proteins have quaternary structure. gxnf Ultimately, protein structure and function depends upon the DNA sequence of its gene. Protein function depends on its tertiary (or quaternary) structure Tertiary (or quaternary) structure ultimately depends on amino acid sequence Amino acid sequence depends on sequence of bases in mRNA, which depends on DNA nucleotide sequence So: protein shape and function depends on DNA sequence A change in DNA sequence (a mutation) can alter the proper shape and function of a protein. Enzymes Serve as biological catalysts Proteins that speed up biological reactions. Biological reactions occur at lower, normal body temperatures with enzymes Lower energy of activation: hold two chemical reactants in place, and close to each other, so they react faster than they would normally. Without enzymes, our bodies would have to rely on random collisions of molecules for reactions to occur. Biological reactions would not occur fast enough to sustain life. Enzymes are like “hosts at a party”: they get chemicals to react quicker than they would normally, so biological reactions occur quickly.  Enzymes hold reactants in close proximity, making them react. If not held together chemicals interact (“bump into each other”) rarely: too slowly to maintain life. An enzyme catalyzes one specific reaction over and over again, and is not used up in that reaction  Enzyme Function The functional shape of an enzyme (or any protein) is dependent on: Amino acid sequence (mutations can alter this) Temperature pH Maintaining relatively constant temperature / pH (homeostasis) is critical to proper enzyme function. Changing pH or temperature can denature proteins: change their shape so they not function properly  Amino acids can be used for energy also Energy in chemical bonds of amino acids can be converted into energy in chemical bonds of ATP. This happens in cellular respiration. This generates toxic ammonia waste though.  Campbell, Reece, Mitchell, Biology fifth edition Benjamin/Cummings MenloPark CA, 1999 Chiras DD Human Biology Health, Homeostasi, and the Environment, Jones and Bartlett Publishers, Boston, 2002