Cell Compounds and Biological Molecules Biology 12 Unit 2 Cell Compounds and Biological Molecules Inquiry into Life pages 20-44
Basic Chemistry Matter anything that has mass and volume Element comprises all matter, living or non-living Atom the smallest unit of matter to function in chemical reactions; composed of 3 subatomic particles Isotope atoms with the same atomic number but different atomic mass
Basic Chemistry Subatomic Particle Charge Relative Mass electron 1 0 proton +1 1 neutron no charge 1
Basic Chemistry atomic number 6 12.0107 C Carbon atomic mass element symbol element name
Basic Chemistry Isotopes are different forms of the same atom The only difference is the number of neutrons present Neutrons only add mass and do not change chemical properties Some isotopes are unstable and emit radiation radioactive isotope
Molecules vs Compounds A molecule is any chemical unit that contains more than 1 atom. They can contain the same atom or different atoms A compound is any chemical unit that contains more than 1 atom, but the atoms cannot be the same.
Ionic Compounds Ionic compounds are formed when a metal and a non-metal are attracted resulting in the transfer of electrons from metal to non-metal Ionic compounds require ions or charged atoms Ions can be positive or negative, but never neutral
Ionic Compounds Positive ions are metals and have lost electrons Negative ions are non-metals and have gained electrons
Ionic Compounds Because electrons are negative particles, having more electrons means the ion is more negative Fewer electrons means more positive
Ionic Compounds This represents electron shells 1st shell = 2 e2nd shell = 8 erd 3 shell = 8 e-
Ionic Compounds C
Ionic Compounds Remember, ionic bonds transfer outer shell electrons from the metal to the non-metal
Covalent Compounds Covalent reactions occur between two non-metals Electrons are shared in covalent compounds instead of transferred The shared outer shell electrons spend equal time between the two atoms
Covalent Compounds Each pair of electrons form a single covalent bond When two pairs of electrons are shared, they form a double bond When three pairs of electrons are shared, they form a triple bond The more bonds between atoms, the more difficult it is to separate them
Covalent Compounds Electrons in the overlapping regions are shared Each H shares 1 ewith the carbon
Covalent Compounds The hydrogens share their electron with each other, forming a molecule of hydrogen gas
Water
Water H O H
Water Water is a polar molecule Since oxygen has a larger nucleus, the shared electrons spend slightly more time near the oxygen nucleus than the hydrogen nuclei This differential in time gives water a slight + and charge at its poles
H O H
Water Polar covalent molecules form weak bonds between compounds called hydrogen bonds A hydrogen bond occurs when the slight positive charge of a bound hydrogen attracts the slight negative charge of a neighbouring atom It is represented by a dashed line
Water
Water
Properties of Water 1. Liquid at room temperature 2. Facilitates chemical reactions 3. Molecules are cohesive 4. Changes temperature slowly 5. Has a high heat of vapourization 6. Solid water is less dense than liquid water
Roles of Water in Living Organisms 1. Temperature Regulator 2. Lubricant 3. Solvent
Acids and Bases Water spontaneous breaks up into two component + ions, H and OH + Acids are compounds that release H when dissociated in water Bases are compounds that release OH when dissociated in water
Acids and Bases
Acids Strong acids are characterized by the amount of H + ions that dissociate The more complete the dissociation, the stronger the acid The more H + added to the water, the more acidic the solution
Bases Strong bases are characterized by the amount of OH ions that dissociate The more complete the dissociation, the stronger the base The more OH added to the water, the more basic the solution
ph Scale This scale is used to indicate the acidity or the alkalinity of a solution Values range from 0 14 The lower the value, the more acidic the solution The higher the value, the more basic the solution
ph Scale ph is a logarithmic scale: ph 1 is 10X more acidic than ph 2 ph 1 is 100X more acidic than ph 3 ph 2 is 1000X more acidic than ph 5 ph 8 is 10X more basic than ph 7 ph 12 is 10 000X more basic than ph 8 ph 14 is 100 000 000 000 000X more basic than ph 0!
Buffers and ph A buffer is a chemical that keeps ph within certain limits Buffers resist changes in ph by absorbing excess hydrogen and hydroxide ions Buffers in human blood are carbonic acid and bicarbonate ions
Organic Molecules Characterized by the presence of carbon and hydrogen
Organic Molecules
Organic Molecules Carbon molecules can link to other carbon molecules forming a hydrocarbon molecule
Organic Molecules Functional groups can be added to hydrocarbons to impart certain characteristics Two important functional groups are: carboxyl (COOH) amine (NH3)
Carbohydrates
Carbohydrates Short-term energy storage Structural molecule in plants and bacteria Cell membrane communication
Carbohydrates Monosaccharides are simple carbohydrates that can be characterized by having 5 or 6 carbons (pentose and hexose) Common monosaccharides are: glucose fructose galactose
Carbohydrates Disaccharides are links of two monosaccharides (di meaning two and mono meaning one) Common disaccharides: sucrose lactose maltose
Carbohydrates Polysaccharides contain many monosaccharides linked together Polysaccharides are considered polymers A polymer is a long chain of monomers A monomer is a single unit
Carbohydrates monomer polymers
Carbohydrates Polysaccharides are formed through a process called condensation synthesis synthesis = making of condensation = releases water
Carbohydrates Breaking apart polysaccharides involves a process called hydrolysis hydro means water lysis means to break apart Hydrolysis reactions break down polysaccharides by adding water
Carbohydrates monomers polymer + H2O http://www.biotopics.co.uk/as/disaccharidehydrolys is.html
Carbohydrates Starch and glycogen store glucose in plants and animals Starch is a polymer of glucose with few side branches GLYCOGEN is similar to starch except it is highly branched
Carbohydrates Cellulose is found only in plants The glucose molecules are linked differently than in glycogen and starch This linkage causes the greater strength of this molecule
Lipids Lipids are the greatest energy source in biological molecules carbohydrates = 17 kj/g proteins = 17 kj/g lipids = 38 kj/g However, most lipids are not used as energy stores
Lipids Lipids have different structures and functions: long-term energy storage steroids (sex hormones) membrane components What links all lipids is that they are all insoluble in water
Lipids Fats and oils usually of animal origin and is solid at room temperature Fats have two functions: long term energy storage insulation and cushioning
Lipids Fats and oils form when one glycerol molecule react with three fatty acid molecules Sometimes called trigylcerides
Lipids Emulsification is the process of mixing fat with water Elmulsifiers are made of a polar molecules (polar head and nonpolar tail)
Lipids polar head nonpolar tail Fat globule Emulsifier (bile) (soap)
Fat Emulsification
Fatty Acids A fatty acid is a hydrocarbon chain that ends with the acidic group -COOH
Saturated Fatty Acids Saturated fatty acids have no double bonds between carbon atoms, and it is saturated, or full of, all the hydrogens that can fit Saturated fatty acids are solid at room temperature Animal fats are often saturated
Unsaturated Fatty Acids Unsaturated fatty acids have double bonds somewhere within the carbon chain, often causing kinks in the chain They occur where the carbon does not have two hydrogens attached to it Unsaturated fatty acids are liquid at room temperature Plant fats are often unsaturated
Phospholipids Phospholipids are polar molecules containing a phosphate or a phosphate/nitrogen group attached to the lipid tail They are found in cell membranes and will spontaneously form a bilayer with hydrophobic tails facing in and hydrophilic heads facing out
Phospholipids Lecithin is a common phospholipid found in soybeans and eggs It is used to emulsify fats and is basis of mayonnaise, an emulsified fat
Steroids Steroids have the common stucture of 4 fused carbon rings
Steroids Steroids differ by their atom arrangement and the functional groups attached to them Cholesterol is an important component in the cell membrane, adding to rigidity as well as the starting point for sex hormones like estrogen and testosterone
Steroids Examples of common steroids: cholesterol estrogen (estradiol) testosterone cortisol vitamin D
Proteins Proteins have many functions, from movement to antibodies to enzymes to biological messengers Proteins are polymers of amino acids monomers
Proteins
Proteins The R group is what makes the 20 amino acids different from each other R groups can be as simple as a single hydrogen (glycine) or as complex as a double benzene ring (tryptophan)
Proteins
Proteins Amino acids combine through a peptide bond, which is a condensation synthesis reaction
Proteins A chain of amino acids is called a polypeptide
Proteins Four Levels of Organization (p. 39) primary structure the linear sequence of amino acids joined by peptide bonds secondary structure polypeptides form a 3-D shape hydrogen bonds between peptide bonds keep the shape
Proteins Tertiary Structure the final 3-D shape of proteins this shape is maintained by different covalent, ionic, and hydrogen bonds between R groups, including the covalent disulphide bond between 2 cysteine amino acids Quaternary Structure two or more polypeptides arranged together (mostly enzymes)
Proteins Protein structure is extremely important because structure is related to function If protein structure is changed (denatured) then the protein cannot function
Nucleic Acids Two types: Deoxyribonucleic Acid (DNA) Ribonucleic Acid (RNA) Both are polymers of nucleotides
Nucleotide
Nucleotides All nucleotides are composed of a sugar (either ribose or deoxyribose), a phosphate and a nitrogenous base There are five bases: Adenine Thymine (DNA only) Cytosine Guanine Uracil (RNA only)
Nucleotide Chains Nucleotides join via condensation synthesis the same process as joining monosaccharides and amino acids!
Nucleic Acids Nucleic acids form strands made up of a sugar-phosphate backbone Nitrogenous bases stick out of the sides
DNA DNA is double stranded, each twisting about the other
RNA RNA is a single strand of DNA There are three types: Messenger RNA (mrna) Ribosomal RNA (rrna) Transfer RNA (trna) We will look more into DNA at a later time.
ATP
ATP ATP (adenosine triphosphate) is composed of adenine (a nitrogenous base), a ribose 5-sided sugar and three phosphate groups. This structure is actually a modified nucleotide.
ATP ATP is the "energy currency" of the cell and is spent to drive chemical reactions Glucose is converted into ATP in the mitochondria via cellular respiration. Energy is derived from breaking the bond between phosphate 2 and 3, releasing energy stored in the bond.
ATP
ATP Breaking this bond results in the production of ADP or adenosine diphosphate and a phosphate group. These molecules can be recycled and used to produce more ATP in the mitochondria.
Quiz Quiz on Lipids, Proteins, Nucleic Acids, and ATP
This used to be Unit 6 Enzymes Textbook Ch 6
Metabolism Metabolism refers to the total of all chemical and physical reactions that occur in a cell Most of these activities are driven by ATP
Metabolism Metabolism is controlled by thyroxine, a hormone produced in the thyroid gland
Metabolism Thyroxine is made from the addition of iodine to the amino acid tyrosine Thyroxine stimulates all cells to produce more ATP through cellular respiration resulting in overall increase in metabolism
Metabolism The level of thyroxine in the blood is determined by a negative feedback loop which goes like this: Thyroxine levels drop causing hypothalamus to release TRH TRH acts on the anterior pituitary to release TSH TSH acts on the thyroid causing it to produce more thyroxine High levels of thyroxine cause the hypothalamus to stop TRH production and anterior pituitary to stop TSH production
Thyroxine Control Feedback Loop
Enzyme Enzymes are protein molecules with particular shapes (active sites) to bond with particular substrates Enzymes are catalysts for cellular reactions, bringing substrates together where they can react and form new substances http://highered.mcgraw-hill.com/sites/dl/free/007242 1975/196646/lw03_enzymes_final.html
Substrate Substrates are molecules that react to produce new products with the help of an enzyme Reactions can be hydrolysis (breaking down) or synthesis (building) reactions
Coenzyme Coenzymes are smaller molecules that help enzymes function properly and are often contain vitamins
Activation Energy Activation energy refers to the amount of energy needed to make a reaction occur Enzymes reduce the activation energy needed
Lock and Key Model Enzymes are locks. Locks can only be opened by a specific key. Substrates are keys. They only work on a specific lock. Starch is the substrate, amylase is the enzyme Peptides are the substrates, peptidase is the enzyme Lipids are the substrates, lipase is the enzyme Lactose is the substrate, lactase is the enzyme
Factors Affecting Enzyme Action ph enzymes work at specific phs. Enzymes in the blood work at ph 7.4 while enzymes in the stomach work at ph 2.
Factors Affecting Enzyme Action Temperature Enzymes in our bodies work o efficiently at 37 C but their action starts to drop off dramatically after 40oC
Factors Affecting Enzyme Action Substrate Concentration The higher the concentration the more reactions that can occur up to a certain point
Factors Affecting Enzyme Action Competitive Inhibitors fight for active sites with the substrate and prevents them from binding. Enzyme Inhibition Products made by an enzymatic pathway prevent the binding of other substrates
Factors Affecting Enzyme Action
Factors Affecting Enzyme Action Heavy Metals Some metals act as enzyme cofactors (helps the enzyme function) but others (Hg and Pb) causes the enzymes to denature and no longer function
Factors Affecting Enzyme Action http://highered.mcgraw-hill.com/sites/dl/free/00724 21975/196644/feedback_inhibition.html
Enzyme Inhibition Enzyme inhibition occurs when the enzyme cannot bind substrate molecules The purpose of this enzyme inhibition is to limit the amount of product made by the enzyme so levels do not rise too high
Enzyme Inhibition As product molecules are produced, their level or concentration will rise Eventually these product molecules will interfere or inhibit the enzymes producing them, by binding the active site on the enzyme or attaching to the enzyme in a manner that alters the active site on the enzyme.
Enzyme Inhibition When the product molecules are used up or their concentration lowers, the enzyme will no longer be inhibited by the product molecules The enzyme active site will be available to bind with substrate and make new product once again
Enzyme Inhibition Enzyme inhibition is controlled by a negative feedback loop
Enzymes Lab - Catalase Catalase is an enzyme found in liver and catalyzes the reaction decomposing hydrogen peroxide into oxygen and hydrogen
Enzymes Lab - Catalase In this lab, you will combine the reactants in the test tubes and record your observations When you are finished your observations, you will explain your observations with respect to the factors affecting enzyme action. The lab sheet is provided and all reactants are included
Summary Learn your basic chemistry Water is a polar molecule and is the universal solvent meaning lots of things can dissolve in it Acids and bases dissociate into different ions and their strength can be measured using the ph scale
Summary Organic molecules contain C and H Carbohydrates are composed of monosaccharides or polymers of them Lipids are composed of gylcerol and 3 fatty acids and form fats and oils, phospholids, and steroids
Summary Proteins are composed of polymers of amino acids called polypeptides There are 4 levels of protein organization Protein function is dependent on maintaining proper structure
Unit 2 Review Reread textbook pages 20-41 Read section summaries on page 42 Answer all review questions on pages 42 43 Define all keyterms on page 44 Use the website listed on page 44 for extra practice Test is on