Today’s Plan: 1/5/09 Find a seat any place that has paperwork and Put your preferred 1 st and last name on the card. If you need to sit up front, put FRONT on the card as well On the back of the card: Write your parent/guardian’s name(s) Write your phone number(s), esp. parent numbers Email contact info for you and your parents (if you have it with you) Go over syllabus/expectations/HW (20 mins) H2Olympics Lab (40 mins) Chemistry pre-assessment (10 mins)
Transcript
Today’s Plan: 1/5/09 Find a seat any place that has paperwork
and Put your preferred 1st and last name on the card.
If you need to sit up front, put FRONT on the card as well
On the back of the card: Write your parent/guardian’s name(s) Write your phone number(s), esp. parent numbers Email contact info for you and your parents (if you
Bellwork: Set up bags for lab Monday (15 mins)-SKIP this today, we’ll do it Monday
Biochemical Modeling Activity (40 mins)
Continue notes (20 mins)
Today’s Plan: 1/11/10
Bellwork: Set-up bags for lab #2 (20 mins)
Do AP Lab #2 (40 mins) Continue notes (20 mins)
Today’s Plan: 1/12/10
Bellwork: Finish Notes (20 mins) Discussion on Lab 2 and demo (40
mins) Finish Lab 2 (the rest of class)
Today’s Plan: 8/4/09
Bellwork: Controls on enzyme function demo (20 mins)
Finish Enzyme Notes (30 mins) Focus on Biology Themes (10 mins) Study guide/finish Lab #2 (the rest of
class)
Today’s Plan: 1/13/10
Bellwork: Test Q&A (10 mins) Biochemistry Test (as needed) If you finish early, finish the enzyme
lab and Continue with homework assignments (the rest of class)
The Chemistry of Living Things Matter-2 things: Mass and space Elements vs. Compounds-The
difference? Examples? Only about 25 elements are used in
living things, the most important 6 being CHNOPS
Atoms are the smallest units of elements, composed of p+,e-,no Atomic number=? Atomic mass=?
Atomic Composition Nucleus-only part necessary for mass
determination (e- mass is negligible) Why are neutrons necessary?
Electron cloud-Consists of shells or energy levels Only outermost shell involved in bonding Only outermost shell determines
valence=valence shell Shells composed of orbitals
Isotopes=?
Atomic Interactions Bonding, to get the octet=?
The interactions that make bonds are called chemical reactions and have reactants (left side of the arrow) and products (right side of the arrow)
Ionic bonds=? Molecule=?
Chemical formula: ex: CH4
Covalent bonds=? Involve only 1 type of atom b/c have the same
electron affinity Polar-covalent bonds=?
Involve different types of atoms b/c have different electronegativites-nuclear size matters!!
Weak Atomic Interactions Necessary for most chemical signaling
between cells, but only occur when atoms/molecules are in close proximity Ionic Bond (see previous definition) Hydrogen bond=Occurs when H is covalently
bonded to N or O (usually) and is attracted to the electronegative part of another molecule
Van der Waals interactions=as electrons move, even in non-polar molecules, attraction points occur because of temporary polarity (transient dipole or induced dipole)
Consequences of Weak Atomic interactions-Water Properties
Water’s “bent” geometry allows for hydrogen bonding-Note: this is NOT a covalent bond! It’s a special case of a dipole-dipole interaction in which the partial + H is attracted to the electrons orbiting the O on the other water molecule (just as Na+ is attracted to Cl-)
This tends to make water “sticky,” giving it unique properties
Water’s properties Cohesion and Adhesion-Water is attracted
to itself (cohesion) and to other polar substances (adhesion)
Water is the universal biologic solvent-molecules surround substances and separate them
Water expands when it freezes because of the tetrahedral arrangement of its molecules when it freezes Ice is fully hydrogen-bonded while liquid water
only contains temporary hydrogen bonds
Water and Heat Heat=kinetic energy of the molecules in a
substance (temperature is a measure of this energy)
Like all energy, the flow of heat goes from high to low (Ice absorbs the heat from water to cool your drink-it does NOT release “cold”)
“Cold” does not exist in a thermodynamic sense! It’s simply the removal (absorption) of heat (kinetic energy)
Water and Heat continued Water has a high specific heat (amount of
energy it takes to raise the temperature of 1g 1 degree C)-water is good at resisting temperature change How is this useful to organisms?
Water also has a high heat of vaporization (amount of energy a substance must absorb to convert 1g from liquid to gas) Evaporative cooling-”hottest” molecules leave as
a gas How is this useful to organisms?
Aqueous Solutions and pH Water Dissociation: H2OH+ and OH- H+=Hydronium Ion=? OH-=Hydroxide Ion=? Therefore, because water has equal
amounts of these Ions, it is ? pH 0-6.9999=acid (H+conc>OH- conc) pH 7 is neutral pH 7.1-14=base (H+ conc<OH- conc) Buffers=maintain the pH of a solution by
accepting H+ when in excess and releasing H+ when there are too few (extremely important to biologists!!)
Carbon’s versatility Valence=? Capable of single bonds (-ane), double
bonds (-ene), and triple bonds (-yne) Readily forms hydrocarbons, which are the
backbones of biochemicals Carbon molecules often form isomers
(same formula, different architecture) Isomers can be Structural (chains vs. rings),
geometric (variation around a double bond), or enantiomers (chiral compounds which vary aroun an asymmetric central carbon)
Distinguishing between hydrocarbons Since many molecules are composed of C,
H, and O, functional groups are used to distinguish them, since these groups cause the molecules to behave differently: Hydroxyl group (OH-)=alcohols Carbonyl group (C=O)=if at the end, is an
aldehyde, if in the middle, is a ketone Carboxyl group (COOH)=organic acid Amino group (NH2 )=amine (organic base) Sulfhydryl group (SH)=Thiols Phosphate group (PO4)=energy transfer group
(ATP)
Polymers and Monomers Monomer=1 subunit (link in a chain) Polymer=a chain of small subunits Polymers are put together by
condensation reactions (also called dehydration synthesis reactions)
Polymers are taken apart by hydrolysis (hydro=water, lysis=splitting)
All Biochemicals are polymers
Figure 3-6a
(Water)
Condensation reaction: monomer in, water out
Figure 3-6b
(Water)
Hydrolysis: water in, monomer out
Carbohydrates Sugars are mono- or disaccharides
Disaccharides (like starches) joined by glycosidic linkage
Used for energy Starches are polysaccharides (fiber is also a
polysaccharide) Used for energy (checking account) or storage Animals use glycogen for energy and chitin for
structure Plants use cellulose for structure and amylose or
amylopectin for energy Difference is in the types of glycosidic linkage
between the monomers and the degree of branching within the molecules
Figure 5-1
Carbonylgroup atend of carbonchain
An aldose A ketose
Carbonylgroup inmiddle of carbonchain
Figure 5-2
Differentconfiguration
of hydroxyl groups
Glucose Galactose
Figure 5-3
Linear form of glucose Ring forms of glucose
-Glucose
-Glucose
Oxygen from the5-carbon bonds to the1-carbon, resulting in a ring structure
Figure 5-4
Monosaccharides polymerize when hydroxyl groups react to form glycosidic linkages…
-Glucose -Glucose
…between various carbons and with various geometries.
-Galactose -Glucose Lactose (a disaccharide)
Maltose (a disaccharide)
In this case, the hydroxyl groups fromthe 1-carbon and 4-carbon react toproduct a -1,4-glycosidic linkageand water
The hydroxyl groups from the1-carbon and 4-carbon reactto produce an -1,4-glycosidiclinkage and water
Figure 5-5-Table 5-1
Lipids Fats, oils, waxes (sterols) Energy storage-savings acount (chemically
stable, takes a lot to break them apart) Triglyceride is typical structure consisting of
a glycerol and 3 fatty acid chains Main component of phospholipids, which
form micells in water and are responsible for?
Saturated fats contain all single bonds on the main hydrocarbon chain, while unsaturated fats contain double or triple bonds.
What’s a trans-fat?
Figure 6-2Isoprene Fatty acid
Carboxylgroup
Hydrocarbonchain
Figure 6-3
Fats form via dehydration reactions. Fats consist of glycerol linked by ester linkages to three fatty acids.
Glycerol
Fatty acid
Dehydrationreaction
Esterlinkages
Figure 5-9Carbon dioxide
A carbohydrate
A fatty acid
Proteins Held together by peptide bonds, and are
therefore sometimes called polypeptides (special case of condensation where N is bonded to C)
Workhorses of cells, doing a variety of tasks such as communication, structure, movement, storage, transport, defense and enzymes
Monomer is the amino acid (20 amino acids exist in living things, distinguished by their R groups)
Figure 3-2
Non-ionized form of amino acid
Ionized form of amino acid
Amino
group
Amino
group
Carboxyl
group
Carboxyl
group
Side chain
Side chain
Non-ionized Non-ionized
IonizedIonized
Figure 3-3Nonpolar side chains
Polar side chains
Electrically chargedside chains
Glycine (G) Gly
Alanine (A) Ala
Valine (V) Val
Leucine (L) Leu
Isoleucine (I) Ile
Methionine (M)Met
Phenylalanine (F)Phe
Tryptophan (W)Trp
Proline (P)Pro
Serine (S)Ser
Threonine (T)Thr
Cysteine (C)Cys
Tyrosine (Y)Tyr
Asparagine (N) Asn
Glutamine (Q)Gln
Acidic Basic
Aspartate (D)Asp
Glutamate (E)Glu
Lysine (K)Lys
Arginine (R)Arg
Histidine (H)His
No charged or electronegative atoms to form hydrogen bonds; not soluble in water
Charged side chains form hydrogen bonds; highly soluble in water
Partial charges can form hydrogen bonds; soluble in water
Figure 3-7
Carboxyl group
Amino group
Peptide bond
Electrons shared between carbonyl group and peptide bond offer some characteristics of double bonds
Figure 3-8
Polypeptide chain
Numbering system
N-terminus
N-terminus C-terminus
C-terminus
Amino acids joined by peptide bonds
Peptide-bonded backbone
Carboxyl group
Amino group
Side chains
Levels of protein structure Shape determines how the molecule works and is extremely
important Primary structure=sequence of amino acids (read from amino
terminus to carboxyl terminus) Secondary structure=coiling or folding of the molecule b/c of
hydrogen bonds between backbone molecules (therefore, these are regular ex: alpha helices and pleated sheets)
Tertiary structure=contortion of the molecule due to attractions (van der Waals and H bonding) between R groups. Because each protein has a unique AA sequence, these are irregular patterns that are unique to each protein (ex=disulfide bridges between sulfhdryl groups, hydrophobic clustering)
Quaternary structure=overall protein structure resulting from multiple polypeptides (ex=hemoglobin has 4 polypeptide chains held together with heme groups consisting of Fe)
High temperature, extreme salinity and pH changes can cause denaturating of proteins=protein becomes misshapen because the forces controlling the levels of structure above have been interfered with
Figure 3-12b
Secondary structures of proteins result.
-helix -pleated sheet
Figure 3-13
Tertiary structures are diverse.
Interactions that determine the tertiary structure of proteins
A tertiary structure composed mostly of -helices
A tertiary structure composed mostly of -pleated sheets
A tertiary structure rich in disulfide bonds
Ionic bond
Disulfide bond
Hydrophobic interactions (van der Waals interactions)Hydrogen bond between
two side chains
Hydrogen bond between side chain and carboxyl oxygen
Nucleic Acids Information storage molecules=DNA and
RNA Monomers are nucleotides
Phosphate group (held in phosphodiester linkage with the sugar to form the backbone)
Sugar (deoxyribose in DNA, ribose in RNA) Nitrogenous base (purines=A and G
pyrimidines=T, C, and U) that bond purine to pyrimidine based on the number of H-bonds each wants to make
Sequential changes in different species are used as an evolutionary clock (more on this in the Evolution unit)
Hybrid Biochemicals
Some important biochemicals are actually combinations of 2 different families of biochemicals Glycoproteins-Protein/carbohydrate
complexes important in cell structure Lipoproteins-LDL, HDLCholesterol
packaged in protein by the liver
Figure 5-7
Outsideof cell
Insideof cell
Glycoprotein
Metabolism Metabolism is the sum total of all
Anabolic (putting together) and Catabolic (taking apart) chemical reactions in the body
Basic Cellular energy molecule fueling metabolism is ATP (adenosine triphosphate)
Releasing the last phosphate group releases 7.6 kcal of energy
Figure 9-1
ATP consists of three phosphate groups, ribose, and adenine.
Phosphate groups
Ribose
Adenine
Energy is released when ATP is hydrolyzed.
ATP Water ADP Inorganicphosphate
Energy
Enzymes as catalysts Catalyst=changes the rate of the reaction
but is not consumed (used up) by the reaction
Enzymes lower the activation energy of the reaction (activation energy or free energy of activation is usually in the form of heat and is required to make the molecules interact or break)
Enzymes are specific to their substrate because the shape of the active site conforms to the shape of the substrate (induced fit)
Figure 3-20
Substrate(glucose)
Enzyme(hexokinase)
When the substrate binds to the enzyme’s active site, the enzyme changes shape slightly. This “induced fit” results in tighter binding of the substrate to the active site.
Enzyme controls Denaturation due to pH or temperature changes Cofactors or coenzymes=non-protein attachments to the
enzyme’s active site that help it maintain it’s shape Inhibition
Competitive=mimics the substrate and blocks the active site Non-competitive inhibition=binds to another site on the
enzyme, causing the shape of the active site to change Allosteric regulation=similar to noncompetitive inhibition
but not permanent and either causes activation by stabilizing the protein shape, or can cause inhibition by destabilizing the protein shape (usually at the junction of the polypeptide chains of the enzyme)
Cooperativity=remember that since many enzymes are made of multiple polypeptides, each can have an active site. This means that induced fit at one active site may cause stabilization of other active sites on the enzyme
Figure 3-23
Competitive inhibition directly blocks the active site.
Competitive inhibitor
Substrate
Enzyme
Allosteric regulation occurs when a regulatory molecule binds somewhere other than the active site.
Substrate
Enzyme
Regulatorymolecule
Activating the enzyme Inactivating the enzyme
When the regulatory molecule binds to the enzyme’s active site, the substrate cannot bind
When the regulatory molecule binds to a different site on the enzyme, it induces a shape change that makes the active site either available to the substrate (left) or unavailable (right)
or
Metabolic pathways and enzymes
Series of chemical reactions in which the products of each step are reactants for the next step
Feedback inhibition of enzymes occurs when the end product of a pathway acts as an enzyme inhibitor
