Download Today`s Plan: 1/5/09

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
have it with you)
 Go over syllabus/expectations/HW (20
mins)
 H2Olympics Lab (40 mins)
 Chemistry pre-assessment (10 mins)
Today’s Plan: 1/6/10
 Finish Water Lab (20 mins)
 Homework Circle (20 mins)
 Compare concept maps with your group and
create a group concept map (5 mins)
 Map sharing (5 mins)
 Go over atomic structure (10 mins)
 Chemical Bonding Activity (20 mins)
 If you finish-work on the periodic properties
activity
 Biochemistry notes (20 mins)
Today’s Plan: 1/7/09
 Bellwork: Finish Discussing/modeling
bonding (20 mins)
 Water and pH Thinkables with
Chemical Model Kits (20 mins)
 Biochemical Modeling (20 mins)
 Continue notes (20 mins)
Today’s Plan: 1/8/10
 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 solventmolecules 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: H2OH+ and OHH+=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
Condensation reaction: monomer in, water out
(Water)
Figure 3-6b
Hydrolysis: water in, monomer out
(Water)
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
An aldose
A ketose
Carbonyl
group at
end of
carbon
chain
Carbonyl
group in
middle of
carbon
chain
Figure 5-2
Glucose
Galactose
Different
configuration
of hydroxyl groups
Figure 5-3
Linear form of glucose
Ring forms of glucose
Oxygen from the
5-carbon bonds to the
1-carbon, resulting in a
ring structure
-Glucose
-Glucose
Figure 5-4
Monosaccharides polymerize when hydroxyl groups react to form glycosidic linkages…
-Glucose
-Glucose
…between various carbons and with various geometries.
-Galactose
-Glucose
Maltose (a disaccharide)
The hydroxyl groups from the
1-carbon and 4-carbon react
to produce an -1,4-glycosidic
linkage and water
Lactose (a disaccharide)
In this case, the hydroxyl groups from
the 1-carbon and 4-carbon react to
product a -1,4-glycosidic linkage
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 6-2
Isoprene
Fatty acid
Carboxyl
group
Hydrocarbon
chain
Figure 6-3
Fats form via dehydration reactions.
Fats consist of glycerol linked by ester linkages to three fatty acids.
Glycerol
Ester
linkages
Dehydration
reaction
Fatty acid
Figure 5-9
Carbon 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
Amino
group
Non-ionized
Carboxyl
group
Side chain
Non-ionized
Ionized form of amino acid
Amino
group
Ionized
Carboxyl
group
Side chain
Ionized
Figure 3-3
Nonpolar
side chains
Glycine (G)
Gly
Alanine (A)
Ala
Valine (V)
Val
Leucine (L)
Leu
Isoleucine (I)
Ile
No charged or
electronegative
atoms to form
hydrogen
bonds; not
soluble in water
Methionine (M)
Met
Phenylalanine (F)
Phe
Tryptophan (W)
Trp
Proline (P)
Pro
Polar side
chains
Partial charges
can form
hydrogen
bonds; soluble
in water
Serine (S)
Ser
Electrically
charged
side chains
Threonine (T)
Thr
Cysteine (C)
Cys
Tyrosine (Y)
Tyr
Acidic
Asparagine (N)
Asn
Glutamine (Q)
Gln
Basic
Charged side
chains form
hydrogen
bonds; highly
soluble in
water
Aspartate (D)
Asp
Glutamate (E)
Glu
Lysine (K)
Lys
Arginine (R)
Arg
Histidine (H)
His
Figure 3-7
Electrons shared between
carbonyl group and peptide
bond offer some characteristics
of double bonds
Carboxyl
group
Amino
group
Peptide
bond
Figure 3-8
Polypeptide chain
Amino acids joined by peptide bonds
C-terminus
N-terminus
Peptidebonded
backbone
Amino
group
Carboxyl
group
Side chains
Numbering system
N-terminus
C-terminus
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
Interactions that determine the tertiary structure of proteins
Hydrogen bond
between side chain
and carboxyl oxygen
Hydrogen bond between
two side chains
Hydrophobic
interactions
(van der Waals
interactions)
Ionic bond
Disulfide bond
Tertiary structures are diverse.
A tertiary structure composed
mostly of -helices
A tertiary structure composed
mostly of -pleated sheets
A tertiary structure rich in
disulfide bonds
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, HDLCholesterol
packaged in protein by the liver
Figure 5-7
Glycoprotein
Outside
of cell
Inside
of cell
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.
Adenine
Phosphate groups
Ribose
Energy is released when ATP is hydrolyzed.
ATP
Water
ADP
Inorganic
phosphate
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
When the
regulatory molecule
binds to the
enzyme’s active
site, the substrate
cannot bind
Substrate
Enzyme
Allosteric regulation occurs when a regulatory molecule binds somewhere other than the active site.
Substrate
or
Enzyme
Regulatory
molecule
Activating the enzyme
Inactivating the enzyme
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)
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