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Chapter 2: The Chemistry of Life

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1 Chapter 2: The Chemistry of Life

2 The Nature of Matter Matter: is anything that has mass and takes up space The basic and smallest unit of matter is called the atom. Atoms are made up of subatomic particles Protons (+) (forms the nucleus) Neutrons (neutral) (forms the nucleus) Electrons (-) (outside of the nucleus) Atoms have the same number of protons and electrons. Their charges balance out, causing atoms to be electrically neutral

3 Elements and Isotopes Elements: a pure substance that consist entirely of one type of atom. Represented by one or two letters (example C stands for Carbon or Na stands for Sodium) Carbons atomic number is 6, meaning that the atom has 6 protons and 6 electrons Isotopes : Atoms of the same elements that differ in number of neutrons The total number or protons and neutrons in the nucleus of an atom is called its mass number Isotopes are identified by their mass number. All isotopes of an element have the same chemical properties Radioactive Isotopes Unstable nucleus Give off radiation Used to detect and kill cancer, kill bacteria, age fossils

4 Compounds Compound: a substance formed by the chemical combination of 2 or more elements in definite proportions Example: H2O (water), NaCl (salt) The physical and chemical properties of a compound are different from elements that form them.

5 Chemical Bonds The main types of chemical bonds are…. Covalent Ionic
Polar Non-Polar Ionic

6 Ionic Bonds Ionic bonds: formed when one or more electrons are transferred from one atom to another. An atoms that loses an electrons becomes positively charged An atom that gains electrons has a negative charge Positively and negatively charged atoms are known as ions Sodium chloride (NaCl) is an example of an ionic compound held together by ionic bonds. Sodium loses one electron to chlorine when the bonding process occurs.

7 Covalent bonds When atoms in a molecule are held together by covalent bonds, they share electrons with each other Each shared pair of electrons forms on covalent bond

8 Polar Covalent bonds In a water molecule, two hydrogen atoms each share a pair of electrons with an oxygen atom, forming a molecule with the formula H2O Molecule: the smallest unit of most compounds. Electrons in covalent bonds aren’t always shared equally In water, oxygen is more electronegative, so its basically an electron hog More time with electrons = negative charge

9 Polar Versus Non Polar Polar Non-polar
Polar molecules are attracted to water Hydrophilic (water loving) Water soluble Non-polar Not attracted to water Hydrophobic (water-hating) Soluble only in nonpolar solvents

10 Hydrogen bonds In water, the negatively charged oxygen of one molecule is attracted to the positively charged hydrogen of another water molecule. This attraction is called a hydrogen bond

11 Van der Waals Forces When molecules are close together, a slight attraction can develop between the oppositely charged regions or nearby molecules.

12 Tokay Gecko: Dispersion Forces!

13 2.2 properties of water

14 Properties of Water Most important biochemical (no water = no life)
75% planet Earth = water 70%-90% mass of cell Humans= ~60% water

15 Hydrogen bonding The attraction between a hydrogen atom with a partial positive charge and another atom with a partial negative charge is known as a hydrogen bond. Hydrogen bonding in water makes molecules more difficult to separate and affects the physical properties of water Ex: energy needed to break hydrogen bonds make it more difficult to convert water from a liquid to a gas than to convert similar compounds which lack hydrogen bonds

16 Water as a solvent Solute = substance being dissolved
Solvent= substance solute in being dissolved into Water is an excellent solvent for ions and polar molecules because the charges in water are attracted to the charges in ions and polar molecules

17 Water as a solvent When a chemical dissolves in water, the opposite charges collect and separate around the charges in water Once a chemical is in solution, it is free to move about and react with other chemicals Most processes in living organisms take place in solution this way

18 Suspension Water and non-dissolved materials

19 Hydrophobic interactions
Nonpolar substances do not dissolve in water When surrounded by water, nonpolar molecules tend to be pushed together by the water Ex: Cell membrane

20 Cohesion Cohesion: is an attraction between molecules of the same substance. Water molecule have high cohesion (tend to stick together) Allows water to move in long, unbroken columns in the vascular tissue in plants

21 Adhesion Adhesion is an attraction between molecules of different substances Molecules of different substances attract Meniscus results from both cohesion and adhesion

22 Surface tension High cohesion = high surface tension
Provides surfaces of water with think film-like covering, allowing water droplets to forms and organisms to use as habitat

23 Thermal properties of water
Because of hydrogen bonding, water has a high specific heat Takes a lot of energy to raise the temperature of water Large bodies of water (lakes, oceans) are slow to change temperature as atmospheric temperature changes

24 Thermal properties of water
Due to the high proportion of water in the bodies of living organisms, internal changes in temperature are minimized, making homeostasis easier to maintain

25 Thermal properties of water
Process of evaporation transfers a correspondingly large amount of thermal energy, and therefore is an effecting cooling method What happens when we are outside and it’s hot? Since it takes a lot of energy to freeze water, keeps our bodies from freezing

26 Density and freezing properties
Water is less dense in solid state than liquid state (ice floats on water and insulates water below) This decreases the likelihood that large bodies of water will completely freeze over

27 Acids and Bases -Acids Acids are compounds that release hydrogen ions (H+) when dissolved in water. Acids have a sour taste, can dissolve many metals, and turn litmus paper red. Examples of acids in the body are hydrochloric acid (produced by stomach cells that aids digestion), acetic acid (vinegar), and carbonic acid (in sodas).

28 Acids and Bases- Bases Bases are compounds that reduce the concentration of hydrogen ions in a solution. Many bases release hydroxide ions (OH-) when dissolved in water. Bases are bitter and slippery and turn litmus paper blue. Examples of common bases are baking soda, Milk of magnesia, ammonia, bleach, detergents, and most soaps.

29 The pH Scale The pH scale measures whether a solution is acid, basic or neutral. The scale runs from 0 to 14. A pH of 7 indicates that the solution is neutral. This means that the solution is neither an acid nor a base.

30 2.3: Biological Molecules
The study of biological molecules is called molecular biology Closely linked with biochemistry, the study of the chemical reactions of biological molecules The sum total of all the biochemical reactions in the body is known as metabolism

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32 Building blocks of life
4 most common elements in life: H, C, O, N (99% of all atoms found in living things)

33 Carbon Compounds Particularly important because carbon atoms can join together to form long chains or ring structures Basic skeletons of all organic molecules, to which other groups of atoms attach Organic molecule = at least 1 C and 1 H

34 Building blocks of life
Believed that before life evolved there was a period of chemical evolution in which thousands of carbon-based molecules evolved from the more simple molecules that existed on early Earth

35 Monomers, Polymers, and Macromolecules
Monomers= similar or identical individual organic subunits Polymers= many repeating monomers Macromolecule= “giant molecule” Polysaccharides, polypeptides, polynucleotides

36 Monomer Polymer Monosaccharides Polysaccharides Amino acids
Polypeptides (proteins) Nucleotides Polynucleotides (nucleic acids)

37 Carbohydrates General formula Cx(H2O)y 1:2:1 of CHO
Divided into three main groups: Monosaccharides, disaccharide, polysaccharides

38 Monosaccharides Monosaccharides are single sugars (mono=1)
Dissolve easily in water to produce sweet tasting solutions General formula (CH2O)n Classified according to number of C atoms Trioses (3C) Ex: glyceraldehydes Pentoses (5C) Ex: ribose, deoxyribose Hexoses (6C) Ex: glucose, fructose, galactose

39 Structural formula (straight chain) Structural formula (ring)
Glucose Molecular formula Structural formula (straight chain) Structural formula (ring) C6H12O6

40 Ring structures Pentoses and hexoses can form themselves into stable ring structures When glucose forms a ring, carbon atom 1 joins to carbon atom 5 The ring therefore contains oxygen, and carbon atoms number 6 is not part of the ring

41 Roles of monosaccharides
Source of energy in respiration Carbon-hydrogen bonds can be broken to release a lot of energy which is then transferred to make ATP from ADP Building blocks of larger molecules Used to build larger carbohydrates (starch, glycogen, cellulose) or complex molecules like RNA, DNA and ATP

42 Disaccharides Like monosaccharides, are sugars
Formed by two (di=2) monosaccharides joining together Maltose = glucose + glucose Sucrose = glucose + fructose Lactose = glucose+galactose

43 Disaccharides The joining of two monosaccharides takes place by a process known as dehydration

44 Condensation http://www.youtube.com/watch?v=b7TdWLNhMtM
For the reaction, two hydroxyl (-OH) groups line up alongside each other One combined with a hydrogen atom from the other to form a water molecule This allows an oxygen “bridge” to form between the two molecules, forming disaccharide This bridge is called a glycosidic bond

45 Hydrolysis Reverse of dehydration is the addition of water, hydrolysis
Takes place during the digestion of dissacharides and polysaccharides, when they are broken down to monosaccharides

46 Polysaccharides Polymers of monosaccharides Made by condensation rxns
Carbohydrates Starch, glycogen, cellulose

47 Polysaccharides Glucose cannot accumulate in the cell
Dissolve and affect osmosis Interfere with cell chemistry Store as polysaccharides Glycogen: animals Starch: plants

48 Starch Build up to relatively large starch grains
Commonly found in chloroplasts and storage organs Easily seen with light microscope if stained) NEVER found in animal cells

49 Glycogen Tend to be more branched than starch
Clump together to form granules (visible in liver and muscle cells)

50 Cellulose Most abundant organic molecule of the planet
Due to its presence in plant cell walls and is slow rate of breakdown Mechanically very strong

51 Cellulose 60-70 cellulose molecules cross-link to form microfibrils, held together as fibers by hydrogen bonding Cellulose: 20-40% cell wall Wood, paper High tensile strength (almost ~steel) Fiber arrangement determines shape Freely permeable: water + solutes can reach plasma membrane

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53 Lipids Very diverse group of chemicals Most common: triglycerides
Usually known as fats and oils

54 Triglycerides Triglycerides are made by the combination of three fatty acid molecules with one glycerol molecule Fatty acids: organic molecules with a –COOH group attached to a hydrocarbon tail Glycerol: type of alcohol

55 Triglycerides Tails differ in length depending on the specific type of fatty acid

56 Triglycerides Each fatty acid molecule joins to glycerol by a condensation reaction When a fatty acid combines with glycerol it forms a glyceride, hence 3 fatty acids + glycerol = triglyceride

57 Triglycerides Insoluble in water, but soluble in some nonpolar organic solvents (ether, chloroform, ethanol) Fatty acid tails are NONPOLAR so they will not dissolve in polar solvents like water. There are therefore said to be hydrophobic

58 Unsaturated fatty acids
Some fatty acids have double bonds between neighboring carbon atoms: -C=C Describe as unsaturated (as they do not contain the maximum possible amount of hydrogen)

59 Unsaturated fatty acids
Double bonds make lipids melt more easily, making them liquids (oil) at room temperature If there is 1 double bond, the fatty acid is described and monounsaturated If there is more than 1 double bond, the fatty acid is described as polyunsaturated

60 Saturated fatty acids Fatty acids that contain all single carbon bonds (C-C) and the maximum number of hydrogen on each tail Occur as solids at room temperature (fat)

61 Roles of triglycerides
Lipids make excellent energy reserves because they are even richer in C- H bonds than carbohydrates A given mass of lipid will therefore yield more energy on oxidation than the same mass of carbohydrate (lipids = calorie dense) Animals that hibernate store excess lipids for energy

62 Roles of triglycerides
Fat is stored throughout human body Just below dermis of skin, around kidneys Below the skin also acts as an insulator against the loss of heat (called blubber in sea mammals-also provides buoyancy)

63 Roles of triglycerides
Lipids also act as a metabolic source of water: When oxidized in respiration, they are converted to carbon dioxide and water VERY important in dry habitats! This furry lil guy legit NEVER drinks water! CRAY!

64 Phospholipids Phospholipids are a special type of lipid because one end is soluble in water B/c one of the three fatty acids is replaced with a phosphate group, which is polar (like dissolves like)

65 Phospholipids The phosphate group is hydrophilic and makes the head of a phospholipid molecule hydrophilic, although the two remaining tails are still hydrophobic This biological significance is in Ch 4 yayyyyy

66 Proteins Composed of monomers called amino acids
Extremely important macromolecule More than 50% dry mass of cell is protein

67 Functions of Proteins All enzymes are proteins
Essential in cell membranes Hormones (ex: insulin) Hemoglobin Antibodies Structural component (collagen, keratin, etc…) Muscle contraction

68 Amino Acids All amino acids have the same general structure:
Central carbon atom bonded to an amine group (-NH2) and a carboxylic acid group (- COOH) Differ in chemical composition of the R group bonded to central carbon

69 Amino acids 20 diff. amino acids all with diff. R groups
Commonly abbreviated as three letters (ex glycine=gly) or by single letter (glycine=G)

70 Peptide bond Strong covalent bonds
Water is removed (condensation rxn!!) 2 amino acids= dipeptide More than 2= polypeptide A complete protein may contain just one polypeptide chain, or many that interact with each other

71 Primary Structure Polypeptide chains may contain several hundred amino acids linked by peptide bonds The particular amino acids and their ORDER in the sequence is called the primary structure of the protein

72 Primary Structure There are enormous numbers of different primary structures possible A change in a single amino acid in a polypeptide can completely alter the structure and function of the final protein

73 Secondary Structure The particular amino acids in the chain have an effect on each other even if they are not directly next to one another

74 Secondary Structure Polypeptides often coil into a corkscrew shape called an α- helix Forms via hydrogen bonding between the oxygen of the –CO group of one amino acid and the –NH group of an amino acids four places ahead of it Easily broken by high temperatures and pH changes

75 Secondary Structure Hydrogen bonding is also responsible for the formation of β-pleated sheets Easily broken by high temperatures and pH changes

76 Tertiary Structure In many proteins, the secondary structure itself it coiled or folded Shapes may look “random” but are very organized and precise The way in which a protein coils up to form a precise 3D shape is known as its tertiary structure

77 Quaternary Structure Most protein molecules are made up of two or more polypeptide chains (Ex: hemoglobin) The association of different polypeptide chains is called the quaternary structure of the protein Chains are held together by same types of bonds as tertiary structure

78 Globular Proteins A protein whose molecules curl up into a “ball” shape is known as a globular protein Globular proteins usually play a role in metabolic reactions Their precise structure is key to their function! Ex: enzymes are globular proteins

79 Globular Proteins Globular proteins usually curl up so that their nonpolar (hydrophobic) R groups point into the center of the molecule, away from aqueous surroundings Globular proteins are usually water soluble because water molecules cluster around their outward-pointing hydrophilic R groups

80 Hemoglobin Hemoglobin is the oxygen carrying pigment found in red blood cells, and is a globular protein Made up of four polypeptide chains (has quaternary structure) Each chain known as globin.

81 Hemoglobin Two types of globin used to make hemoglobin:
2 α-globin (make α-chains) 2 β-globin (make β-chains)

82 Hemoglobin Nearly spherical due to tight compaction of polypeptide chains Hydrophobic R groups point toward inside of proteins, hydrophilic R groups point outwards Hydrophobic interactions are ESSENTIAL in holding shape of hemoglobin

83 Sickle cell anemia Genetic condition in which one amino acids on the surface of the β-chain, glutamic acid, which is polar, is replaced with valine, which is nonpolar Having a nonpolar (hydrophobic) R group on the outside of hemoglobin make is less soluble, and causes blood cells to be misshapen

84 Hemoglobin Each polypeptide chain of hemoglobin contains a heme (haem) group Important, permanent part of a protein molecule but is NOT made of amino acids Each heme group contains an Fe atom that can bind with one oxygen molecule A complete hemoglobin molecule can therefore carry FOUR oxygen molecules

85 Nucleic Acids (CHONP) Nucleic acids are very large macromolecules made up of carbon, hydrogen, oxygen, nitrogen, and phosphorus (CHONP). A nucleotide is the simplest subunit, or building block, of nucleic acids. Nucleotides are composed of a sugar molecule, a nitrogen base, and a phosphate group.

86 Nucleotides Nucleotides are composed of a sugar molecule, a nitrogen base, and a phosphate group.

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88 Types of Nucleic Acids DNA and RNA are two kinds of nucleic acids.
DNA makes up genes and is involved in heredity. RNA is involved in the making of proteins.

89 Nucleic Acids- DNA DNA, or deoxyribonucleic acid, consists of two strands of nucleotides that spiral around each other in a shape that is known as a double helix. Chromosomes contain long strands of DNA, which store hereditary information. DNA is located in the nucleus of all living cells.

90 Nucleic Acids- RNA RNA, or ribonucleic acid, usually consists of a single strand of nucleotides. RNA plays many key roles in the manufacture of proteins, and the replication of DNA. RNA can also act as an enzyme, promoting the chemical reactions that link amino acids to form proteins.

91 Comparing and Contrasting DNA and RNA
DNA bases: T-A, G-C Deoxyribose sugar Original information for making proteins One form or type Found primarily in the nucleus and forms chromosomes during cell division DNA is a large molecule that is a double helix. RNA bases: U-A, G-C Ribose sugar Working copy for making proteins Variety of forms: m-RNA, t-RNA, r-RNA Found in nucleus and throughout the cell RNA is made of smaller molecules and is single-stranded.

92 2.4: Chemical reactions and enzymes

93 Equations Equations are used to describe chemical reactions.
Reactants are the substances that start the reaction. The reactants are placed on the left side of the equation. Products are the substances formed by the reaction. The products are placed on the right side of the equation. The arrow means “yields,” “to make,” or “to form”.

94 Equations Reactions may be represented either by words or formulas.
The word equation for aerobic respiration is: SUGAR + OXYGEN  ENERGY + CARBON DIOXIDE + WATER A chemical equation is an equation that uses formulas instead of words. The chemical equation for aerobic respiration is: C6H12O O2  ATP + 6CO H2O

95 Energy and Chemical Reactions
Energy is the ability to move or change matter. In chemical reactions, energy is released or absorbed when chemical bonds are broken and new ones are formed. Activation energy is the energy needed to start a chemical reaction.

96 Enzymes Each chemical reaction that occurs in a living thing is controlled by an enzyme. Enzymes are large, complex protein molecules that control the rate of chemical reactions. Enzymes are the organic catalysts in cellular chemical reactions. A catalyst is a substance that causes or accelerates a chemical reaction without itself being affected.

97 Enzymes- Catalysts Catalysts can speed up or slow down a chemical reaction. An enzyme (acting as a catalyst) can increase the speed of a chemical reaction by reducing the activation energy needed by the reaction, thus conserving energy. Enzymes are not consumed by the reactions they catalyze—they can take part in many reactions.

98 Substrates A substrate is the molecule at the beginning of a chemical reaction on which an enzymes acts. An enzyme acts only on a specific substrate because only that substrate fits into the enzyme’s active site. Active sites are the pockets formed from the folds on an enzyme’s surface. An enzyme’s shape determines its activity. Typically, an enzyme is a large protein with one or more deep folds on its surface.

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102 Enzymes In organisms, enzymes allow the chemical reactions of metabolism to take place more efficiently than they otherwise would at body temperature. For example, amino acids are produced from protein digestion. The enzymes needed for this reaction are not changed, but must be present for the reaction to occur.

103 Enzymes Some examples of enzymes affecting reactions that you may be familiar with: Enzymes in biological washing powders break down protein or fat stains on clothes. Enzymes in meat tenderizers break down proteins, making the meat easier to chew.

104 Enzymes are used in the making of alcohol and cheese.

105 Enzyme Action Rate The rate of enzyme action is influenced by several factors: Temperature Relative concentrations of enzyme and substrate pH Each enzyme has an optimum temperature and pH at which it functions most efficiently and its rate of activity (or action) is the greatest (think of Goldilocks -- not too hot, not too cold, just right).

106 Enzymes and Temperature
At temperatures below the optimum, the rate of enzyme activity (action) is low. Enzyme activity increases with increasing temperature up to the optimum temperature. Above the optimum temperature, the rate of enzyme activity decreases.

107 Enzymes and pH At pH levels below the optimum, the rate of enzyme activity (action) is low. Enzyme activity increases with increasing pH up to the optimum pH. Above the optimum pH, the rate of enzyme activity decreases.

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