Bio-Chemistry.

Bio-Chemistry

Assessing Your Prior Knowledge…
Solids Liquids Gases Plasma State Phase Atoms Elements Protons Neutrons Electrons Positive Negative Neutral Atomic number Atomic mass number Ion Isotope Ionic bonding Covalent bonding

States of Matter Review…
All of the materials around you are made up of matter. You are made of matter as are the chair you sit on and the air you breathe. Give an example of solid matter. Give an example of gaseous matter. Give an example of liquid matter. Is all Matter visible? Does all matter take up space?

Atomic Structure Atom: basic unit of matter
Smallest unit of an element with all of the properties of an element Cannot be broken down by physical changes Nucleus: contains protons (+) & neutrons (neutral) Electron Cloud: Contains electrons (-)

Elements are arranged according to increasing atomic number!
Atomic Structure Groups/Families Periods Elements are arranged according to increasing atomic number!

C Atomic Structure 6 Carbon 12.011
Atomic Number: number of protons in the nucleus of an atom Atoms of the same element always have the same number of protons 6 C Carbon 12.011

C Atomic Structure 6 Carbon 12.011
Atomic Mass Number: number of protons & neutrons in the nucleus of an atom 6 C Carbon 12.011

Atomic Structure Valence Electrons: number of electrons in the outermost energy level of an atom Lewis Dot Structure/Diagram: diagrams that show the number of valence electrons C

Atomic Structure Neutral Atom: an atom with the same number of electrons as protons

C C 12 6 6 Protons 6 Neutrons 6 Electrons Carbon 4e- 2e-
4 Valence Electrons 6p+ 6N C

Atomic Structure Review…
Particle Location Charge Mass proton nucleus + 1 a.m.u . neutron nucleus none 1 a.m.u . Outside Very electron the - small nucleus

Atomic Structure Ion: a charged atom; an atom that does not contain the same number of electrons as protons

2 Types of Ions Anion: An atom with more electrons than protons
Negatively charged - charge = add e-

C-1 C -1 means add 1 electron 12 6 -1 6 Protons 6 Neutrons 7 Electrons
Carbon C 5e- 2e- 5 Valence Electrons 6p+ 6N C-1

2 Types of Ions Cation: An atom with fewer electrons than protons
Positively charged + charge = remove e-

C+1 C +1 means remove 1 electron 12 6 +1 6 Protons 6 Neutrons
5 Electrons Carbon C 3e- 2e- 3 Valence Electrons 6p+ 6N C+1

Atomic Structure Same number of protons Isotope: atoms of the same element with differing numbers of neutrons Atomic mass is a weighted average of all isotopes (that is why it is a decimal…) Round the average atomic mass to the nearest whole number to determine the most common isotope Radioactive isotopes are important for: treating cancer, serving as tracers that follow molecules through cells, dating rocks, minerals & fossils & killing bacteria that may spoil food

C-12 C Most Common Isotope 12 6 6 Protons 6 Neutrons 6 Electrons
Carbon C 4e- 2e- 4 Valence Electrons 6p+ 6N C-12

C-13 C Atomic mass is higher than the average atom 13 6 6 Protons
7 Neutrons 6 Electrons Carbon C 4e- 2e- 4 Valence Electrons 6p+ 7N C-13

C-14 C Atomic mass is higher than the average atom 14 6 6 Protons
8 Neutrons 6 Electrons Carbon C 4e- 2e- 4 Valence Electrons 6p+ 8N C-14

Chemical Bonds Compound: a 2 or more elements chemically bonded together in definite proportions Molecule: the smallest unit of most compounds

Chemical Bonds Chemical Bond: the force of attraction that holds two or more atoms together All atoms want to have a full outer level / shell of valence electrons. Chemical bonds involve the transfer or sharing of valence electrons All atoms need to have 8 valence electrons, except Hydrogen and Helium. Hydrogen and Helium only need 2 valence electrons to have a full outer level / shell.

Types of Chemical Bonds
Ionic Bonding: bond formed when a metal lends it’s electrons to a nonmetal Metal + Nonmetal e- Lender → e- Borrower + Charge - Charge No Overall Charge!!

Ionic Bonding Na+1 Cl-1 Metal must give away all valence electrons
Ex: Na and Cl Rules: Na Cl-1 Metal must give away all valence electrons Nonmetal must have a full outer shell Use arrows to show electron transfer Total oxidation = 0 (No overall charge)

Ionic Bonding Metal Nonmetal Na+1 Cl-1 NaCl Sodium Chloride
Ex: Na and Cl Naming Rules: Na Cl-1 NaCl Sodium Chloride Metal Nonmetal Change the ending to “ide”

Types of Chemical Bonds
Covalent Bond: bond that forms as a result of nonmetals sharing electrons Nonmetal + Sharing Electrons

Covalent Bonding Must fill valence shell of all nonmetals
Ex: C and O Rules: Must fill valence shell of all nonmetals Circle shared electron pairs Electrons may not be shared more than 1 time!

Covalent Bonding CO2 Carbon Dioxide
Naming Rules: Ex: C and O Nonmetal closest to the metals (most “cation-like” nonmetal) Nonmetal closest to the Noble Gases (most “anion-like nonmetal) Change ending to “ide” Use prefixes before both non-metals to show the number of each atom EXCEPTION: never use “mono” before the first nonmetal CO2 Carbon Dioxide 1 = Mono 2 = Di 3 = Tri 4 = Tetra 5 = Penta 6 = Hexa 7 = Hepta 8 = Octa 9 = Nona 10 = Deka

Chemical Bonds Van der Waals Forces: slight attraction between the oppositely charged regions of nearby molecules

Think, Pair, Share… What information does the formula for limestone, CaCO3, tell you about the substance? Explain your answer.

2 CaCO3 Think, Pair, Share… Co-Efficient Calcium Carbon Oxygen
Sub-Script

Chemical Formulas Chemical Formulas: a combination of symbols & numbers that identify the atoms & their proportions 6C6H12O6

Chemical Formulas Symbols: ID the elements 6C6H12O6

Chemical Formulas Subscripts: the proportions 6C6H12O6

Chemical Formulas Co-efficient: number of molecules 6C6H12O6

Structural Formulas Glucose C6H12O6
Structural Formula: shows the arrangement of elements in a compound Glucose C6H12O6 What is this the structural formula of?

Think, Pair, Share… What is the structural formula for each of the following molecules? NaCl H2O CO2

Think, Pair, Share… Identify the number and type of carbon bonds in each of the following structural formulas?

Think, Pair, Share… Identify the number and type of carbon bonds in each of the following structural formulas? 25 single bonds 9 single bonds & 3 double bonds 7 single bonds & 2 double bonds 2 single bonds & 1 triple bond 4 single bonds

Solutions Substance does the dissolving (ex: water)
Solute Solvent Substance does the dissolving (ex: water) Substance that gets dissolved (ex: salt) A mixture of 2 or more substances

Properties of Water Polarity: uneven distribution of shared electrons within a molecule

Properties of Water Hydrogen Bonds: the attraction between positively charged hydrogen & the negative charge on other polar molecules Hydrogen bonds create: Cohesion: attraction between molecules of the same substance Adhesion: attraction between molecules of different substances

Think, Pair, Share… Is this cohesion or adhesion?

Think, Pair, Share… Why can very light organisms rest on the surface of water?

Solutions, Suspensions & Mixtures
Solute: Solvent: Ex: Suspension Mixture

Solution: mixture of 2 or more substances in which the solute is evenly distributed Solute: substance that gets dissolved Ex: salt Solvent: substance that does the dissolving Ex: water

Suspension: heavier molecules settle

Mixture: 2 or more elements or compounds physically together but not chemically combined

Solutions, Suspensions or Mixture?

H2O ↔ H+ + OH- Acids & Bases
Pure water will react in the following way to create hydrogen and hydroxide ions. H2O ↔ H+ + OH-

Acids & Bases Acids: substances that produce H+ ions in solution
Proton donors Ionically bonded H+ + ___ (nonmetal) Ex: HCl → H+ + Cl- Properties: Taste sour Are electrolytes Are corrosive React with indicators to produce predictable color changes Bases: substances that produce OH- ions in solution Proton acceptors Ionically bonded ___ (metal) + OH- Ex: NaOH → Na+ + OH- Properties: Bitter taste Are electrolytes Are corrosive Feel slippery Pure bases are solids Dissolve fats and oils React with indicators to produce predictable color changes

pH Scale 0 7 14 Acids Neutral Bases Strong Acids have a low pH
Acids Neutral Bases Strong Acids have a low pH Strong bases have a high pH

pH Scale

Neutralization Reaction
Neutralization Reaction: an acid plus a base produces a salt plus water Acid + Base → Salt + Water Ex: HCl + NaOH → NaCl + HOH

Maintaining Homeostasis…
Buffer: weak acids or bases that prevent sudden changes in the pH of living organisms Homeostasis: the tendency of living organisms to maintain a stable internal environment

Acid, Base or Salt? Acid Base Salt HCl NaOH NaCl Mg(OH)2 H2SO4 MgCl2
Please identify a range where each of these substances would appear on a pH Scale: Below 7 Approximately 7 Above 7

Organisms & pH Lab… The purpose of this lab is to investigate the role of buffers in maintaining homeostasis.

Think, Pair, Share… Draw the dot diagram for an atom of carbon.
How many bonds can each carbon atom form?

Carbon Chemistry Organic Compound: substances made by living organisms that consist of carbon & other elements (H, O, S, P & N) Carbon has the unique ability to combine with itself to form long chains, branched chains and rings

Examples of Carbon Compounds

Carbon Chemistry Macromolecules: giant molecules made of 100’s or 1000’s of smaller molecules Macromolecules are made by joining small units (monomers) together to form the large unit (polymer)

Polymerization

Macromolecules There are four groups of organic compounds known as macromolecules: Carbohydrates (made of C,H,O) Sugars, Starches, Cellulose, Glycogen Lipids (made of C,H,O) Fats, oils, steroids, waxes Proteins (made of C,H,O,N, & sometimes S) Enzymes, microtubules & microfilaments Nucleic acids (made of C,H,O,N,P) DNA, RNA

Chemically bonded together to make
Organic Compounds Contain Carbon Monomers Chemically bonded together to make Macromolecules Carbohydrates Lipids Proteins Nucleic Acids Contain C,H,O Contain C,H,O,N,S Contain C,H,O,N,P Starch Sugar Cellulose Glycogen Fats Oils Steroids Phospholipids Enzymes DNA RNA

Carbohydrates Elements: Function: Basic Unit: C, H, O (1:2:1)
Main source of energy Stores energy Cell structure Basic Unit: Glucose (C6H12O6)

Carbohydrates Types: 3 Major Groups: Monosaccharides Disaccharides
Polysaccharides Simple Sugars Complex Carbohydrates

Carbohydrates Monosaccharides: Source of chemical energy Examples:
Simple Sugars < 7 Carbon Atoms Source of chemical energy Examples: Glucose Galactose Fructose Ribose Deoxyribose C6H12O6 C5H10O5 C5H10O4

Carbohydrates Disaccharides: Double sugars (2 monomers)
Source of chemical energy Examples: Sucrose = glucose + fructose

Carbohydrates Disaccharides: Source of chemical energy Examples:
Double sugars (2 monomers) Source of chemical energy Examples: Sucrose = glucose + fructose Maltose = glucose + glucose

Carbohydrates Disaccharides: Source of chemical energy Examples:
Double sugars (2 monomers) Source of chemical energy Examples: Lactose = glucose + galactose

Carbohydrates Polysaccharides:
Many sugars (polymers) Cell structure & chemical energy storage Examples: Structural forms: Cellulose (made of glucose monomers; wood, leaves, cotton) Chitin (exoskeleton of insects) Peptidoglycan (bacterial coats) Storage forms: Starch (plants) Glycogen (animals)

Carbohydrates Examples/Sources: Fruits Vegetables Grains Breads

Lipids Elements: Function: Basic Unit: C, H, O (High H:O ratio)
Stores energy Regulates cell activity Cell structure (cell membrane) Basic Unit: Fatty Acid & Glycerol

Lipids Types: Saturated Fats Solid fats (animal fats) Unsaturated Fats
Liquid fats (plant fats) Polyunsaturated Fats Ex: corn oil, sesame oil, canola oil, peanut oil

Lipids Examples/Sources: Fats & Oils Waxes Steroids Some vitamins

Proteins Elements: Function: Basic Unit: C, H, O, N (sometimes S)
Used to form bones & muscles Transports substances in & out of cells Immune system responsibilities (ex: antibodies) Enzymes control reaction rates & regulate cell processes Basic Unit: Amino Acid

Proteins Types: There are over 20 amino acids (we can only synthesize 8 amino acids; plants make all 20) aa – peptide bond – aa The specific order of amino acids determines a protein (coding for a trait) Each amino acid contain 2 functional groups: Amino group -NH2 Carboxyl group -COOH

Proteins All amino acids contain two functional groups
Amino Group = -NH2 Carboxyl Group = -COOH

Proteins Examples/Sources: Meat Fish Cheese Nuts

Think, Pair, Share… How are proteins and carbohydrates similar?
How are proteins and carbohydrates different?

Nucleic Acids Elements: Function: Basic Unit: C, H, O, N, P
Controls all cell activities Stores & transmits genetic information Basic Unit: Nucleotide: 5 Carbon Sugar Phosphate Group Nitrogen Base

Nucleic Acids Types: DNA: Deoxyribonucleic Acid RNA: Ribonucleic Acid

Nucleic Acids Examples/Sources: Chromosomes

__H2 + __O2 → __H2O 2 2 Chemical Reactions
Balance the following reaction: __H2 + __O2 → __H2O 2 2

Chemical Reactions Chemical Reaction: the process that changes one set of chemicals into another Always involves changes in the bonds that hold atoms together ______ + ______ → ______ Reactants Products Yields Substances that enter into a reaction Substances produced by the reaction produces

Chemical Reactions There are several types of chemical reactions based on what happens to the reactants and products. We are going to focus on four of the major types of reactions: Synthesis Decomposition Single Replacement Double Replacement

Think, Pair, Share… What does the word synthesis mean?
What does the word decomposition mean? What do you predict is meant by single replacement? What do you predict is meant by double replacement?

Types of Reactions Synthesis Reaction: 2 or more substances combine to form 1 new substance A + B → AB → __Na + __Cl2 → __NaCl Balance the equation! 2Na + __Cl2 → 2NaCl

Types of Reactions Decomposition Reaction: 1 substance breaks down into 2 or more simpler substances AB → A + B → __NaCl → __Na + __Cl2 Balance the equation! 2NaCl → 2Na + __Cl2

Types of Reactions Single Replacement (Displacement): 1 element replaces another in a compound A + BC → AB + C → __F2 + __NaCl → __NaF + __Cl2 Balance the equation! __F2 + 2NaCl → 2NaF + __Cl2

Types of Reactions Double Replacement (Displacement): 2 different atoms in 2 different compounds replace each other 2 compound react to produce 2 new compounds AB + CD → AD + CB → __NaCl + __HF → __NaF + __HCl Balance the equation!

Chemical Reactions & Energy
Endothermic Reactions: energy must be provided or taken in from the environment for the reaction to occur Heat is absorbed Typically the container feels cool Ex: melting ice

Exothermic Reactions: energy is released (given off) in the form of heat, light, sound or electricity Typically heat is released Ex: burning wood, batteries, explosives, hot packs, CaO + H2O → Ca(OH)2 + heat

Activation Energy: the energy needed to get a reaction started The rate at which a chemical reaction occurs can be altered by the following: Inhibitors Catalysts

Activation Energy

Inhibitor: a substance that slows down the rate of a reaction Raise the activation energy of a reaction Catalyst: substances that speed up the rate of a reaction Lower the activation energy of a reaction Proteins act as enzymes: biological catalysts

Enzymes: Biological Catalysts
Reaction pathway without enzyme Activation energy Activation energy with enzyme Reactants Products

Enzymes possess active sites: specifically shaped surfaces that attract and hold a specific molecule (substrate) on which it acts Enzyme activity is affected by many factors (ex: temperature, pH) Lock & Key Model Induced Fit Model

Simple animation How Enzymes Work McGraw - Hill Hydrolysis of sucrose McGraw - Hill

Metabolism: all of the chemical reactions that occur within an organism Chemical reactions build & break down all of the molecules that an organism needs for life.

The “Liver Lab” A Study of Biochemical Reactions …
The purpose of this lab is to investigate the role of enzymes & the factors that effect enzyme function.

Bio-Chemistry.

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