Unit One – Biochemistry
Common Themes in Biology
Theme #1 – Scientific Method
•The scientific method is a way to ask and answer scientific questions by making observations and doing experiments.
•The steps of the scientific method are followed to insure accurate and objective results.
•Step 1: Ask a question. -- Ex: What affect does temperature have on reaction rate?
•Step 2: Research the problem.
•Step 3: Construct a hypothesis.
–The hypothesis should be written in the “If …… then ……” format.
–Example: “If the solution is heated, then the reaction will proceed at a faster rate.”
•Step 4: Test your hypothesis by running an experiment.
–Always include a control.
–Only one variable should be tested.
•Step 5: Analyze your results and draw a conclusion.
–The data is usually analyzed using graphs, tables or statistical tests.
•Step 6: Run the experiment again to verify your results.
Theme #2 – Structure Determines Function
•An organism is designed in a way that will help it perform a certain function.
–Example: Afusiform fish can swim faster than a round one.
–Example: The sperm has a flagellum so that it can swim to the egg; the egg is the largest cell in the body because it contains enough nutrients to sustain the zygote until it can implant in the mother’s uterus.
–Example: Proteins are macromolecules that fold into very precise three-dimensional shapes.
•Proteins are composed of monomers called amino acids.
•Each protein is a specific combination of amino acids.
•These amino acids have physical properties that cause the protein to fold in a specific way.
•If the amino acid sequence changes because of a mutation, the protein won’t fold properly.
•When the form is lost, the function is lost.
•Sickle cell anemia, a disorder affecting red blood cells, is an illustration of this theme.
•A mutation results in a substitution of the amino acid valine for glutamic acid.
•This prevents the hemoglobin molecule from folding properly.
•This change in form results in a red blood cell that collapses under stress.
•When the red blood cell loses its form, it also loses its function, and is no longer able to carry oxygen.
Theme #3 - Energy
•Energy is the ability to do work there are two forms of energy:
–Kinetic energy is associated with motion.
–Potential energy is stored energy, such as the chemical energy stored in ATP.
•Laws of Energy Transformation
–First Law of Thermodynamics
•Energy cannot be created or destroyed It can only be transformed or transferred.
•The energy of the universe is constant.
–Second Law of Thermodynamics
•In the process of carrying out chemical reactions that perform various kinds of work, cells unavoidably convert organized forms of energy to heat.
•Every loss of energy makes the universe more disordered – entropy.
•The second law states that every energy transfer or transformation increases the entropy of the universe.
–E flows in one direction through an ecosystem – Sun → Autotrophs → Heterotrophs → Heat
•Energy from the sun is high quality energy that can perform work; heat is a highly disorganized form of energy.
•Metabolism - the collection of chemical reactions that occur in an organism.
–Catabolic reactions – break down molecules and release energy.
•Example: Digestion – turning steak into amino acids.
–Anabolic reactions – build molecules and consumes energy.
•Example: Protein synthesis combines amino acids to build proteins.
–Exergonic reaction – a reaction in which energy is released.
•Example: Cellular Respiration.
–Endergonic reaction - absorbs free energy from the environment and store this energy inmolecules.
•Example: Photosynthesis
•Cells need a constant supply of energy to do work.
–ATP is the energy source used by all cells.
–Cells create ATPduring a process called cellular respiration:
–Oxygen + Glucose ATP + Carbon dioxide + water
•Oxygen comes from the process of breathing.
•Glucose comes from food eaten.
•Both of these life-sustaining reactants are made available to us through the process of photosynthesis.
•ATP Structure
- Adenosine triphosphate is composed of the nitrogenous base adenine bonded to a ribose and three highly unstable phosphate groups.
- When the terminal phosphate is hydrolyzed, energy is released in an exergonic reaction.
- The release of the phosphate results in ADP – Adenosine Diphosphate.
- When phosphate is available, the cell recycles ADP to form a new ATP.
- Phosphorylation – the attachment of an unstable phosphorus to another molecule so that it can do work.
- ATP Powers Cellular Work
- Cells manage their energy resources by energy coupling – using an exergonic process to drive an endergonic one.
- The primary source of energy coupling is ATP.
- The exergonic release of the phosphate group is used to do the endergonic work of the cell.
- Plants are our friends!
- Photosynthesis:6 CO2 + 6 H2O + (light)→ C6H12O6 + 6 O2
- All of the oxygen we breathe is formed in the process of photosynthesis.
- We exhale carbon dioxide, which is necessary for photosynthesis.
- When plants convert solar energy (from the sun) into chemical energy, that energy is stored in starches and sugars that we use in cellular respiration.
- The reaction for cellular respiration is the reverse of the reaction for photosynthesis.
- This relationship between plants and animals sustains life on planet Earth.
- Gibb’s Free Energy
- A formula used to measure the amount of energy available to do work.
- Free energy is mainly used to make ATP.
- The formula for Gibb’s Free Energy: ∆G = ∆H - T∆S
•G = free energy
•H = total usable energy in the system (enthalpy)
•T = temperature constant, measured in Kelvin (oC + 273)
•S = amount of entropy
•If ∆G is negative then there is E available to perform work.
–Exergonic reactions such as cellular respiration.
•If ∆G is positive, E is not available; it is locked up and cannot perform work.
–Endergonic reactions such as photosynthesis.
Chemistry
•Matter consists of chemical ______in pure form and in combinations called compounds.
•Element – a substance that can’t be broken down to other substances by chemical ______.
- C, H, O and ______make up 96% of living matter.
- The properties of an element depend on the structure of its ______.
- Atoms are composed of ______, electrons and neutrons.
- Protons and neutrons are located in the ______.
- Electrons move in energy levels, or rings, around the ______.
- The atomic number tells you how many ______are found in one atom of an element.
- Because atoms are always ______, it also tells you how many electrons an atom has.
Periodic Table of Elements
- Periods: horizontal rows where the atomic number increases by one from left to right.
- Families / Groups: vertical columns. Each element has the same group number and similar properties.
- The electrons are located in ______levels.
–1st level – holds ______electrons; 2nd level – holds ______electrons; 3rd level – holds 8 (18) electrons.
•The number of electrons in the outer (______) shell determines what type of bond it will form with other atoms, or if it will bond at all.
•Atoms form bonds with other atoms to ______their valence shells.
•______are atoms of two or more different elements bonded together.
•Types of Bonds – Ionic Bonds
•Compounds formed by a ______of electrons.
•When an atom gains or loses electrons, it becomes a charged particle called an ion.
–Cation – ______charge
–Anion – ______charge
•The compound is formed by the ______between the negatively and positively charged ions.
•Ionic compounds are formed by the attraction between ______and ______charged ions
•Forms between a ______and ______elements
•Forms relatively ______bonds
•Example: Sodium Chloride (NaCl):
–Na has atomic number of 11; ______electrons in 1st ring;______electrons in 2nd ring; ______electron in valence shell.
–Cl has atomic number of 17;______electrons in 1st ring; 8 in 2nd; 7 in valence shell.
–If sodium gives its electron to chlorine, its valence shell will be complete.
•Na becomes a ______(+).
–The donated electron will ______chlorine’s valence shell.
•Cl becomes an ______(-).
–The opposite charges of the ions attract, forming an ______bond.
•When dissolved in water, ionic bonds ______to form ions.
–______is a drink loaded with ions!
–Why does Gatorade also contain sugar?
•Types of Bonds – Covalent Bonds
- Compounds that form when atoms ______valence electrons.
•This sharing of electrons ______the outer shell of both atoms.
•These are very ______bonds that form the basis of organic chemistry.
•Ex: Carbon has atomic number of six; _____ in first shell and _____ in valence shell.
–If carbon shares electrons with another ______atom, four pairs of electrons are shared forming four strong covalent bonds between the two atoms.
•These strong bonds allow for the formation of large organic molecules such as DNA and ______.
•Covalent compounds are formed when atoms ______.
•This ______of electrons completes the ______of both atoms.
•These are very______that form the basis of organic chemistry.
•
•Types of Bonds – Hydrogen Bonds
•Occur when a ______hydrogen is attracted to a negative substance, usually oxygen.
•______than ionic and covalent bonds; easily broken.
•These bonds are responsible for the unique properties of ______.
•These are the most important ______bonds!
•Types of Bonds – van der WaalsInteractions
•Weak, ______bonds between positive and negative regions of atoms and molecules.
•Ionic bonds, H bonds, and van der Waals interactions, although weak, reinforce the 3-D shape of large molecules such as proteins.
•Chemical Reactions
•Chemical reactions involve the making or ______of bonds between atoms.
•The total number of atoms remains the same, but the atoms appear in new ______.
•Three categories of chemical reactions:
•Synthesis Reaction - this type of reaction occurs when two or more atoms or molecules combine to form a ______, more complex molecule.
–Energy-absorbing reaction - energy is ______to form the bonds between the atoms or molecules.
–Important for ______and repair of damaged tissues.
–Important in the formation of many inorganic and ______compounds.
–A + B AB
–Ex. ______ proteins
•Decomposition Reaction - occurs when a molecule is broken down into ______molecules, atoms, or ions.
–Energy-releasing - as bonds are ______, energy is given off.
–AB A + B
–Ex. Glycogen glucose
•Exchange Reaction–
•Single replacement and Double replacement reactions
•involves both ______and decomposition reactions - bonds are made and broken.
–A ______is made between molecule parts and new molecules are made.
–AB + C AC + B or AB + CD AD + CB
•Most chemical reactions are ______, depending on the concentration of the reactant and/or products.
•Chemical equilibrium is reached when the forward and reverse reaction rates are ______.
Isotopes
•Atoms of the ______element with a ______number of neutrons
•Have different ______
•Unstable isotopes give off radiation
•Low levels - used as a ______for biological tests
•High levels - can ______DNA & cause ______
•Can be used to treat tumors, sterilize medical & dental products
Water
•Water is the substance that makes possible ______as we know it on Earth.
•Composes 65% - 95% of an organism’s body.
•Water is found mainly ______of cells.
•The only common substance to exist in the natural environment in all three physical states: ______.
•The structure of water is the key to its special ______.
–Water is held together by a ______covalent bond.
–In polar covalent bonds, there is an ______sharing of electrons, resulting in positive and negative regions on the molecule.
–The region around the oxygen atom is slightly ______; the region around the hydrogen atoms is slightly ______.
–This ______allows for the formation of hydrogen bonds between water molecules.
–The slightly negative oxygen atom from one water molecule is attracted to the slightly ______hydrogen end of another water molecule.
•Properties of Water - Cohesion
–Water molecules cling ______because the positive hydrogens on one molecule are attracted to the negative oxygen on another molecule (hydrogen bonds).
–Example: Water droplet
•Properties of Water - Adhesion
–Water molecules bind to a ______substance, such as a plant leaf or windshield.
–Also occurs because of hydrogen bonds.
–Transpiration – the movement of water ______through the xylem of the plant and the evaporation through pores in leaves.
–The water molecules cling to each other by ______and to the walls of xylem by adhesion.
•Properties of Water - High Surface Tension
–Water molecules link together by ______forming a strong surface.
–Example: water strider.
•Properties of Water – High Heat Capacity
–Water can absorb large amounts of heat without ______state; it acts as a huge heat piggy bank.
–Water helps with temperature regulation in organisms and on Earth, keeping temperatures relatively s______.
–Water has a high specific heat which helps to moderate the temperature of ______areas.
–During daylight, water absorbs ______from surrounding areas, lowering the temperature.
–When the temperature drops at night, water ______heat back into the area, raising the temperature.
–This keeps the temperature of areas close to bodies of water relatively ______.
•Properties of Water - Evaporative Cooling
–Sweating uses water to release ______from the body.
–The water ______and carries the heat with it, cooling the organism.
•Properties of Water - Insulation of Water by Floating Ice
–Water is one of the few substances that is less ______as a solid than as a liquid – ice floats.
–As the temperature falls to 0 degrees Celsius, water becomes locked into a crystalline ______, with each water molecule bonded to four partners.
–The lattice contains ______that make ice lighter than liquid water.
–Floating ice ______the water below, preventing freezing and allowing life to exist.
•Properties of Water - Water is the Universal Solvent
–Solution – a completely ______mixture of two or more substances.
–Two parts to a solution (equal distribution):
•______– the substance that is being dissolved.
•______– the substance that is doing the dissolving.
–Substances can be hydrophobic or hydrophilic…
•Hydrophilic – “water-loving”; water is ______to polar substances.
•Hydrophilic substances are ______; water can attach to polar regions and pull the molecule apart, mixing with it.
•This is called a ______shell.
•Hydrophilic substances include ______compounds, polar molecules (such as sugars) and some proteins.
•Hydrophobic – “water-fearing”; Water cannot attach to a hydrophobic substance because it is ______.
•Water ______mix with hydrophobic substances.
•Examples: ______, oils and waxes.
pH Scale
•Used to measure the ______or alkalinity of a solution.
–Acids – donate ______ions (H+) in solution.
–Bases – donate ______ions (OH-) in solution.
•Neutral solutions have equal amounts of hydrogen and hydroxyl ions – water has one of each.
•pH Scale- ranges from 0 to 14
–Acids – between 0 and 7 on the pH scale.
•As the pH approaches ______, the acid becomes stronger.
–Neutral – pH of ______(water)
–Bases – between 7 and 14 on the pH scale.
•As the pH approaches ______, the base becomes stronger.
•Changes in pH follow a logarithmic scale
–Strength/weakness increases or decreases by unit of 10 for every change in pH.
–Ex: pH 5 is ______times stronger than pH 6.
–Ex: pH 4 is ______times stronger than pH 6.
–Ex: pH 3 is ______times stronger than pH 6.
•pH = negative logarithm of the hydrogen ion concentration.
–Example: if concentration of hydrogen ion in a solution is 10-6, the pH of that solution is______.
–In an aqueous solution, the concentration of hydrogen and hydroxyl ions is equal to 10-14; [H+] + [OH-] = 10-14
–If you know the concentration of the ______, you can figure out the concentration of the base.
–Example: if pH of solution is 3, [H+] = 10-3 and [OH-] = 10-11
•Buffers
–______changes in pH in biological solutions.
–An acid-base pair that combines ______with hydrogen ions.
–Example – ______must maintain a pH of 7.35-7.45.
–______acid buffer helps to maintain this.
–This same buffer minimizes pH changes in ______water
–When the blood becomes basic, carbonic acid dissociates into bicarbonate and ______to lower the pH.
–If the blood becomes acidic, the reaction ______to remove the hydrogen ions from the blood and raise the pH.
•Acid Precipitation
–Refers to rain, snow, sleet, ice or fog with a low pH (less than 5.6).
–Mainly because of SO (Sulfer Oxide) and NO (Nitrous Oxide) in the air combined with H2O
•Both due to fossil fuels being burned.
Organic Chemistry
•Organic chemistry is the study of ______compounds.
•Organic compounds share the following properties:
–Always contain carbon and ______; usually contain some combination of C, H, O, N, S, and P.
–Always contain ______bonds.
–Always ______.
•At one time it was believed that organic compounds could only be made in ______cells.
–In 1953, ______and Urey disproved this theory.
–Using a lab simulation of conditions similar to those found on Earth millions of years ago, Miller used simulated l______to trigger reactions in the primitive atmosphere that resulted in the formation of a variety of organic compounds.
•Carbon can form molecules that are large, complex and diverse because it has ______valence electrons and can form up to four covalent bonds.
–These molecules can be chains, ring-shaped or ______.
•Isomers - organic molecules that have the same molecular formula but differ in their ______of atoms.
–These differences can result in molecules that behave very ______in chemical reactions.
–Types of Isomers
•Structural isomers have different ______of atoms.
•Geometric isomers differ in their ______arrangement around a double bond.
•Enantiomers - molecules that are ______images of each other
•A few chemical groups are key to the functioning of biological molecules…
–Functional groups attached to the carbon ______of organic molecules have diverse properties.
–The behavior of the organic molecule is dependent on the ______of its functional group.
•Common Functional Groups
–Hydroxyl Group
•______
•Found in ______
–Carboxyl Group
•______
•Found in ______
–Carbonyl Group
•______
•Found in ______.
–Amino Group
•______
•Found in ______.
–Sulfhydryl Group
•______
•Found in ______
•Can form ______bridges in protein folding.
–Phosphates
•______
•Found in phospholipids nucleic acids, and ______.
–Methyl
•______
•Attached to DNA it affects ______
Categories of Organic Molecules
•______- “giant molecule”
•monomer - “one unit”; ______of a polymer.
•polymer- “many units”; formed by monomers joining together via covalent bonds to form large molecules.
•Monomers join to form Polymers.
–Monomers ______to form polymers through ______synthesis reactions.
–A water molecule (-OH & an -H) is removed during the reaction.
–Example: Glucose molecules join to form ______.
•Polymers break down to form Monomers.
–Polymers are disassembled into monomers by a ______reaction.
–A water molecule (-OH & an -H) is ______.
–Example – digestion a steak is broken down into amino acids.
There are four categories of organic molecules…
- Carbohydrates
•Sugars and ______
•Contain ______atoms in a ______ratio
•Two functions of carbohydrates:
–1) main source of ______for living organisms.
–2) structural components of cells
•Three categories of carbohydrates:
–1) Monosaccharides
–2) Disaccharides
–3) Polysaccharides
•Monosaccharides
•Simple sugars
•Building blocks of ______.
•Examples:
–Glucose
–Fructose & ______
–Deoxyribose & ______
•The importance of glucose…
•During cellular respiration:
–Glucose combines with ______
–released energy is trapped in the bonds of ATP.
–______are released.
–______
•Disaccharides
•Double sugars; formed by two simple sugars in a ______reaction.
•______– covalent bond that holds two monosaccharides together.
•Examples:
–Sucrose(glucose-fructose)
–Lactose(glucose-galactose)
–Maltose (glucose-glucose)
•Disaccharides can’t be used by cells; only ______can cross the cell membrane.
–______are used in digestion to break disaccharides into monosaccharides that can be absorbed and used by the body.
•Polysaccharides
•Many monomers joined to form a polymer.
•Two functions:
–1) ______Storage
•Starch – energy storage form found in ______.
•Glycogen – energy storage form found in ______.
–2) Structural support
•Cellulose - contained in plant cell walls.
•provides ______for cell walls.
•provides dietary fiber for animals.
•Chitin - component of the ______of arthropods.
2.Lipids
•Composed of carbon, hydrogen and oxygen (but no ______).
•Insoluble in water – ______.
•Functions:
- Stored ______
- Biological membranes
- Waterproof coverings
- Chemical ______
- Categories of Lipids:
1) Neutral fats - ______