Biochemistry Review Guide PDF

Biochemistry Unit Test Review Guide Resources: Biochemistry I and Biochemistry II Notes Packets, textbook Chapter 2 Sections 1-4, Properties of Water Activity, POGIL Worksheets, Lactase Geography Activity 1. Atoms, they make up everything! Atoms are composed of protons and neutrons in the nucleu...

Biochemistry Unit Test Review Guide Resources: Biochemistry I and Biochemistry II Notes Packets, textbook Chapter 2 Sections 1-4, Properties of Water Activity, POGIL Worksheets, Lactase Geography Activity 1. Atoms, they make up everything! Atoms are composed of protons and neutrons in the nucleus and electrons orbiting outside a. Protons determine the atom’s identity b. Electrons, valence electrons in particular, determine an atom’s behavior 2. Compounds are substances made up of two or more atoms that are bonded together by either exchanging (ionic) or sharing (covalent) electrons. Remember that molecular formulas tell you what elements and how many atoms of each element are in a single molecule of a compound. How many total atoms are in a sugar molecule (see 8ai)? 3. Energy, or the ability to do work (not homework kind of work, but physics kind of work, like motion) a. Energy conversions: energy comes in many forms (light, thermal, chemical, mechanical, etc) and can be converted from one form to another b. In living things, all energy ultimately derives from the sun: plants convert that energy into chemical energy by forming bonds in sugar molecules (see 4a), those bonds can then be broken to release that captured energy, which is what you do when you eat and digest and metabolize food. c. The energy in the motion of particles determines a substance’s phase, or state of matter (solid, liquid, gas) d. Free energy is the energy that organisms are capable of harnessing to use for their life processes 4. Chemical reactions, or the process by which bonds are broken and reformed to change reactants into products  a. Endergonic reactions vs. exergonic reactions: subtly different from endothermic and exothermic, these terms refer to the relationship of free energy in the products compared with the reactants. Can you distinguish these two? By the way, both require activation energy, or an initial “push” to get started. b. Redox reactions: these are paired reactions wherein one product is OXidized (gives up an electron) and another is REDuced (accepts an electron), hence “redox” 5. Water (or… the special molecule whose special properties make it particularly important to life) (or... the stuff that makes up the majority of YOU) a. Solutions are mixtures of different compounds. The primary component of the mixture is called the solvent, and the stuff that is dissolved in the solvent is called the solute. In most biological reactions, water is the solvent. A solution is saturated if it cannot hold any more solute in the solvent. The concentration of a solution is a quantitative measure of the amount of solute compared to the solvent. What does highly concentrated orange juice look like versus orange juice that is diluted? b. Electronegativity of oxygen causes polarity of the water molecules. Can you explain why? Polarity causes water to dissolve any other polar molecule. c. Polarity also causes water to form hydrogen bonds with other water molecules or other polar molecules such as sugar or glass. How do hydrogen bonds cause the cohesion and adhesion? d. Water can absorb a lot of heat energy without changing temperature because the energy will break the hydrogen bonds before speeding up the molecular motion (temperature) e. Mammals use evaporative cooling from perspiration to regulate body temperature (also a great example of concepts 2 & 3, see above!) 6. Acids and bases, or substances that increase H+ or OH- a. Acids: substances that increase the hydrogen ion concentration in solution; pH lower than 7; tend to taste sour or tangy; common in biological systems such as citric acid and lactic acid b. Bases: substances that increase the hydroxide ion concentration in solution; pH higher than 7; tend to feel slimy or slippery; examples include soap or baking soda c. In living organisms, pH must be tightly regulated, as important enzymes and biochemical reactions can only take place within narrow ranges. Living things employ buffer systems and homeostatic feedback loops (such as the carbonic acid buffer system in the blood) to regulate pH 7. Carbon (or the reason SciFi refers to us as “carbon-based life-forms”) a. Carbon has 4 valence electrons, which means it can form four separate bonds (or two double bonds, or a triple bond and a double bond, or two double bonds and two single bonds…. lotta options). This gives carbon remarkable versatility to form long chains, branched chains, rings, or complex molecules composed of all three. b. Carbon is often bonded to a lot of hydrogen atoms, but can also have specific functional groups that give the whole molecule predictable properties. For example, a carboxyl  group makes any molecule an acid. Make sure you are able to identify functional groups in molecules if given a table and a molecular structure. 8. Macromolecules, or polymers, are composed of linked units called monomers. They come in four types in living organisms: a. Carbohydrates, contain carbon, hydrogen, and oxygen i. Monomer: monosaccharide. Know the three most common monomers: glucose, galactose, and fructose. These are isomers of each other because they have the same chemical formula (C6H12O6) but different arrangements of the atoms. The different arrangements also yield different properties, such as varying sweetness (fructose is the sweetest) ii. Two monosaccharides undergo dehydration synthesis to form a disaccharide. Common disaccharides are sucrose (table sugar), maltose (malt sugar), and lactose (milk sugar). iii. A hydrolysis reaction reverses the process, splitting bound molecules into individual monosaccharide units with the addition of a water molecule. iv. Polysaccharides are macromolecules composed of 3 or more monosaccharides. More monomers can be added to any chain via dehydration synthesis to form these long chains. Common polysaccharides include starch and cellulose (straight-line molecules found in plants) and glycogen (a branching molecule found mostly in animals) b. Proteins i. Monomer: amino acids. There are 20 amino acids (do NOT memorize them, but do understand the difference between essential, conditionally essential, and none-essential amino acids). All amino acids have an amino functional group, a carboxylic acid group, and an “R” group which can be just a hydrogen atom or a long hydrocarbon chain. ii. Two amino acids undergo dehydration synthesis to form a dipeptide. iii. Polypeptides (AKA proteins) can be 3 or thousands of amino acids. Polypeptides take many shapes, often folding or twisting around themselves to form very intricate shapes. iv. Proteins form the structure of many biological structures from hormones to muscle fibers. One of the most important structures formed by proteins are enzymes. Enzymes are molecules that facilitate reactions by acting as biological  catalysts and reducing activation energy (see 11a). Can you explain the role of enzyme shape in their function? c. Lipids i. Monomer: Fatty acids, long hydrocarbon (hydrogen and carbon) chains with a carboxyl group (making them an acid). 1. Saturated fatty acids(contain only single bonds in the hydrocarbon chain 2. Unsaturated fatty acids(have one or more double or triple bonds in the hydrocarbon chain 3. Essential fatty acids must be eaten in the diet, non-essential fatty acids can be manufactured by the body ii. Lipid polymers include triglycerides and phospholipids 1. Triglyceride: three fatty acid chains bound to a three-carbon alcohol called glycerol 2. Phospholipid: two fatty acid chains bound to a glycerol molecule; the third glycerol carbon holds a phosphate group. These molecules make up all your cell and nuclear membranes d. Nucleic Acids i. Monomer: nucleotide, composed of a phosphate group, a deoxyribose sugar molecule, and a nitrogenous base (A, C, T, or G)  ii. Polymer: DNA (the “double helix”), or RNA (see 5b) 9. Energy in biological systems a. ATP: adenosine triphosphate is a nucleic acid carrying several phosphate functional groups that cells use to carry energy. Energy is stored in the bonds between the phosphate groups, with the highest energy between the beta and gamma group. Free energy can be liberated by breaking that bond or stored by forming it. b. All reactions require activation energy, even exergonic ones. Activation energy can be reduced by biological catalysts called enzymes. The shape of the enzyme allows it to function in a specific chemical reaction. c. Enzymes can catalyze catabolic or anabolic reactions.