Biochemistry Organisms are composed of matter matter which

Biochemistry

• Organisms are composed of matter, matter which is anything that takes up space and has mass. All matter is composed of elements, pure substances that can not be broken down by chemical reactions. These elements combine together in fixed ratios of atoms to form compounds. Compounds are held together by chemical bonds. The reactivity of an atom and the chemical bond that it forms are determined by the number of electrons it has.

Chemical Bonds & Compounds • Covalent – very strong chemical bond in which electrons are shared. Results in a very stable compound called a molecule. – Examples – water, glucose, ethanol

Covalent bonds

Chemical Bonds & Compounds • Ionic – weaker bond in which electrons are transferred – that is one atom strips electron(s) away from the other. Results in 2 oppositely charged particles called ions. – Cation – positively charged – Anion – negatively charged • These ions are attracted to each other due to the difference in charge. – Examples – sodium chloride (Na. Cl) ~ table salt

• Ionic bonds

Ionic bonds

Chemical Bonds & Compounds • Chemical Formula – Description of a compound. Identifies the ratio of atoms of elements that make up the compound. – H 2 SO 4 = 2 Hydrogen atoms, 1 Sulfur atom, 4 oxygen atoms • Total # of atoms = 7 – C 6 H 12 O 6 = 6 Carbon atoms, 12 Hydrogen atoms, 6 Oxygen atoms • Total # of atoms = 24

Polarity Water is a molecule formed by covalent bonds. • The atomic number of hydrogen is 1 and the atomic number for oxygen is 8. This means that oxygen’s nucleus has 8 protons and hydrogen’s nucleus has 1 proton; therefore oxygen’s nucleus has a much stronger positive charge. • **More protons = More positive Charge = Greater attraction to Electrons**

Polarity • Shared electrons orbiting around a water molecule are more attracted to oxygen’s nucleus (great electronegativity). • **Greater attraction to electrons = greater electronegativity** • This gives the 2 hydrogen ends of the water molecule a slightly positive charge, and the oxygen end, a slightly negative charge. This is not a true charged particle or ion because the electrons are not transferred; transferred they are still shared, just not equally. At any given moment the electrons tend to be closer to the more strongly positive oxygen nucleus.

Hydrogen Bonds • A hydrogen bond is not a true chemical bond because it does not result in the formation of a new compound. This bond is simply an attraction between the slightly positively-charged hydrogen end of one polar molecule and the slightly negative charged end (usually oxygen, nitrogen, &/or sulfur) of another polar molecule. • In water, Hydrogen bonds form between the positive charged hydrogen end and the negative charged oxygen end. Hydrogen bonds are extremely important in organisms and life processes.

• Hydrogen bonds

• Polar covalent bonds

Hydrogen bonds

Properties of Water • Polarity gives water some unique properties important in maintaining homeostasis in organisms. – Cohesion & adhesion. – Water is the solvent of life. – Water has a high heat of vaporization.

Properties of water Cohesion & Adhesion Water is “sticky” – water molecules tend to stick together, called cohesion and results in surface tension. Water molecules also tend to stick to other surfaces due to slightly charged ends – adhesion. • Surface tension – due to cohesion and adhesion properties of water

• Cohesion causes water to form drops, surface tension causes them to be nearly spherical, and adhesion keeps the drops in place.

Properties of water Solvent • Water is the solvent of life – slightlycharged ends of water molecules attract and separate atoms that make up other compounds. Anything dissolved in water is referred to as a solution. Many important compounds in cells are in solution.

Properties of water Phase Changes • Water has a high heat of vaporization – perspiring cools us because it requires heat to change water from a liquid to a gas. – When perspiration evaporates, the heat required is drawn from our skin.

Phases of water • Gas liquid solid

Acids & Bases • Although the covalent bonds holding a water molecule together are very strong, at any given moment a tiny fraction of these bonds split apart, resulting in the formation of a hydrogen ion (H+) and a hydroxide ion (OH-). • As a result, pure water always has a minute, but equal concentrations of H + and OH- ions. Any substance that, when added to water, changes the concentration of H + or OH – is known as an acid or a base, depending on the change to the reaction.

Acids & Bases • Acid is a substance that increases hydrogen concentration when dissolved in water. • Ex. HCl, HNO 3 • Base is a substance that increases hydroxide concentration when dissolved in water • Ex. Na. OH • Water is a neutral substance because for every hydrogen produced or hydroxide is also produced; therefore, the net concentration of hydrogen and hydroxide does not change.

p. H Scale • Scientists use the p. H scale to measure the strength of an acid or base. The p. H scale ranges from 0 to 14. • p. H < 7 = acid • The lower the p. H, the stronger the acid, the greater concentration of hydrogen ions. • p. H > 7 = base • The higher the p. H, the stronger the base, the greater concentration of hydroxide ions • p. H = 7 = neutral • concentrations of Hydrogen ions and hydroxide ions are equal

Carbon • Although a cell is composed of 70% to 95% water, most of the rest consist of carbon – based compounds. Carbon’s importance is due largely to the arrangement of its electrons One carbon atom can form stable, covalent bonds with as many as 4 other atoms. This allows carbon to form very large and complex molecules. • Carbon compounds are called organic compounds. In general, organic compounds may be defined as any carbon-containing compound. All other compounds are known as inorganic compounds.

Carbon • Organic molecules associated with living organisms are called biomolecules. Most biomolecules are polymers. The prefix “poly” means “many”. • A polymer is a large molecule composed of many identical or similar building blocks. The sub-units, or building block molecules, of a polymer are called monomers.

Biomolecules • • • There are 4 major classes of biomolecules Carbohydrates Lipids Proteins Nucleic acids

Carbohydrates • Includes sugars and starches. • Carbohydrates are used for immediate and stored energy and as a building material. Carbohydrates contain the elements C, H, O. O • The ratio hydrogen atoms to oxygen atoms is 2: 1. In other words, for every two hydrogen atoms in a carbohydrate, there is one oxygen atom. • There are 3 groups of carbohydrates: • Monosaccharides, Disaccharides, & Polysaccharides

Monosaccharides – “one” sugar • Simplest of all sugars. Most monosaccharides taste sweet and dissolve in water. They vary in number of carbon atoms that make up the molecule, but the ratio of 2 H: 1 O is always present • 5 -Carbon Monosaccharides – examples – ribose & deoxyribose • These 2 sugars are main components in DNA & RNA • 6 -Carbon Monosaccharides – Examples are glucose, fructose, & galactose.

Monosaccharides – “one” sugar • Each of these molecules have the same chemical formula, C 6 H 12 O 6. They are isomers – compounds with the same chemical formula, but the atoms are arranged differently giving each molecule different characteristics.

Monosaccharides – “one” sugar • • • Glucose – preferred energy source for most organism, including humans. Found in fruit, honey, etc. Fructose - Very sweet! – found in fruit Galactose – Monomer of milk sugar

• Monosaccharides are the monomers or building blocks for the more complex carbohydrates – disaccharides and polysaccharides

Disaccharides – “ 2” sugars • Diasaccharides - 2 monosaccharides covalently bonded together 1. Sucrose – Table sugar. Composed of glucose + Fructose 2. Lactose – Milk sugar. Composed of Glucose + Galactose 3. Maltose – Found in seeds, grain, beer. Composed of Glucose + Glucose

Polysaccharides – “many” sugars • Polysaccharides - many monosaccharides covalently bonded together. – They are divided into 2 groups based on function – storage & structural

Storage Polysaccharide • Long polymers of glucose broken down as needed for energy. » Glycogen – storage form of glucose in animals. In humans, most glycogen is stored in liver and muscle cells. » Starch – storage form of glucose in plants. Humans are able to break down starch for energy.

Structural Polysaccharides • Used as a strong building material in plants, fungi, and some animals. » Cellulose – major component of plant cell walls. Composed of glucose monomers covalently bonded together differently than starch or glycogen. Humans cannot break down cellulose for energy, but it is important to our diet as a source of fiber. » Chitin – Major component of fungi cell walls and insect (and other arthropods) exoskeletons.

carbohydrates • Monosaccharide – Ex. fructose • Disaccharide – Ex. sucrose • Polysaccharide – Ex. cellulose

Lipids • Very diverse group of molecules defined by their insolubility in water due to their non-polar structure. Made up of C, H, & O, but lipids do not have the 2 H: 1 O ratio found in carbohydrates. • Our bodies need lipids for cushioning, insulation, energy, storage, etc. • There are 3 important groups of lipids: fats, oils, phospholipids, and steroids.

• Fats & Oils – made up of glycerol molecule + 3 fatty acid tails. • Generally referred to as fat if lipid is solid at room temperature and an oil if the lipid is liquid at room temperature. • Fats and oils may be classified as saturated or unsaturated, depending on the type of covalent bonds in the fatty acids.

• Saturated Fats – Saturated fats contain all single covalent bonds. This means each carbon shares one pair of electrons with another atom. – They usually come from animal source and are solid at room temperature. May contribute to heart disease. • Unsaturated Fats – Unsaturated fats contain some double covalent bonds, meaning some carbons in the molecule share 2 pairs of electrons with another atom. – They are usually from a plant source and liquid at room temperature. Lower health risk.

lipids • Saturated fat • Unsaturated

• Triglyceride • 3 fatty acides + glycerol

• Phospholipids – Molecule with a polar end and non-polar end that is an important component of all cell membranes.

Steroids – differ from other lipids in that they lack fatty acid tails. An important example of a steroid is cholesterol. • Cholesterol is an important component of cell membranes in animals and is also used to synthesize some hormones.

Proteins • The molecular tools of the cell; proteins are instrumental in almost everything organisms do, including support, structure, movement, protection against infection, etc. • In addition to C, H, & O, proteins contain N. The monomers of proteins are amino acids. There are 20 amino acids that combine together in different numbers, orders, and arrangements to form proteins. • Proteins are divided into 4 categories: Structural, Carriers, Regulatory, & Enzymes

• Protein structure

• Structural Proteins – Major components of bones, muscles, skin

• Transport (carrier) Proteins – Help move substances across the cell membrane or through blood

• Regulatory (messenger) Proteins – include hormones which help maintain homeostasis by serving as signals for changes in cell activities.

• Enzymes – Trigger metabolic reactions in the body by serving as a catalyst. In otherwords, an enzyme speeds up a reaction without being used up in the reaction. A chemical reaction is a process in which one set of chemicals, known as reactants are changed into another set of chemicals known as the product. An enzyme works by lowering the activation energy required to the reaction started.

• enzymes

• Enzymes share 4 common features: 1. Enzymes work best within a narrow p. H and temperature range. 2. Enzymes do not make a reaction happen that could not happen on its own; they simply make the react occur much faster. 3. Enzymes are not used up or changed in the reaction. The same enzyme may be used over and over again. 4. Enzymes are substrate-specific. A substrate is the reactant. Enzymes are substrate-specific because of their shape. The substrate fits into a portion of the enzyme called the active site. This fit between the active site of the enzyme and the substrate allows the enzyme to be specific for a certain type of reaction.

Nucleic Acids • Nucleotides are the monomers of nucleic acids, therefore nucleic acids are polymers. • Nucleotides play an important role as a cell’s power supply and in storing and carrying out the genetic code. Nucleotides contain C, H, O, N, & P.

Nucleotides • Each Nucleotide consists of 3 parts: – 5 -carbon sugar – phosphate group – N-containing base

Nucleic Acids • Nucleic acids are polymers that are composed of thousands of nucleotides. There are 2 important nucleic acids: – Deoxyribonucleic acid – DNA. Contains the instructions and the genetic code for the cell. – Ribonucleic acid – RNA Carries out the instructions in DNA.

• Suggested Question • p. 57 (2, 3, 5, 6, 7, 8, 10, 15, 17, 18, 19, 20, 21, 25)

• Acids taste sour, are corrosive to metals, change litmus (a dye extracted from lichens) red, and become less acidic when mixed with bases. • Bases feel slippery, change litmus blue, and become less basic when mixed with acids.