AP Biology

Biochemistry
Todays Plan: 2/4/16
Bellwork: Unit 1 Test questions/issues (20
mins)
Bonding warm-up

Distinguish between ionic, covalent and polar

covalent bonds
Whats the difference between polarity and
charge?
What does valence mean? Of what importance is
it in biochemistry
Modeling Biochemicals (30 mins)
Biochem notes/discussion (the rest of class)
Todays Plan: 2/5/16
Bellwork: Alternate enantiomer article and
finish lesson 1 (30 mins)
Finish modeling (40 mins)
Lesson 1 discussion/notes (the rest of class)
Todays Plan: 2/8/16
Bellwork: Distinguish between the 4 layers
of protein structure (15 mins)
Protein Shape/Folding activity (45 mins)
Continue going over biochemistry (the rest

of class)
Todays Plan: 2/9/16
Bellwork: Read over the lab background and
be able to answer:
Define: Catalyst
Where do proteases come from?
What is a good source of peroxidase?
What is the chemical reaction for the
decomposition of hydrogen perioxide?
Whats the purpose of guaicol?
Enzyme lab Part 1(as needed)
If time, continue notes (the rest of class)
Todays Plan: 2/10/16
Bellwork: Discuss tomorrow (15 mins)
Enzyme Lab Part 2 (45 mins)
Notes/go over next part of HW (the rest of

class)
Todays Plan: 2/12/16
BW: Go over Test Points (10 mins)
FRQ (the rest of class)
Todays Plan: 2/4/14
Bellwork: Finish Toothpickase and turn in (15
mins)
Read Lab background and answer pre-lab

questions (20 mins)

AP Enzyme Lab Part 1 (30 mins)
Start Enzyme notes (the rest of class)
Todays Plan: 2/5/14
Turn in Homework!!!!
Bellwork: Reading Quiz 2 (20 mins)

If you finish early, finish proteins and shape

activity and turn it in
Q&A on the remaining notes (15 mins)
Breaking Peroxide: The AP Enzyme Lab Saga

Day 2 (the rest of class)

Todays Plan: 2/16/16
Bellwork: Test Q&A (15 mins)
Unit 2 Test (the rest of class)
Todays Plan: 2/7/14
Constructed response-group part (20 mins)
Test corrections/remediation (30 mins)
Begin cell microscopy (the rest of class)
Carbons versatility
Valence=?
Capable of single bonds (-ane), double bonds
(-ene), and triple bonds (-yne)
Readily forms hydrocarbons (organic
molecules of only C & H), which are the
backbones of biochemicals
Carbon molecules often form isomers (same
formula, different architecture)
Isomers can be Structural (chains vs. rings), cis-
trans (variation around a double bond), or
enantiomers (mirror images which vary around an
asymmetric central carbon)
Real world applications: vision affected by cis trans,
trans fats, pharmaceuticals)
Figure 4.7
(a) Structural isomers

(b) Cis-trans isomers

cis isomer: The two Xs trans isomer: The two Xs

are on the same side. are on opposite sides.

(c) Enantiomers

CO2H CO2H

H NH2 NH2 H
CH3 CH3
L isomer D isomer
Origin of Biochemicals
Miller & Urey
experiment
Concluded complex
molecules could
arise spontaneously
from conditions on
early earth
Amino acids,
formaldehyde,
hydrocarbons
Distinguishing between
hydrocarbons
Functional groups are used to distinguish
molecules made up of C, H, O, 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)
Methyl (CH3 )=methylated compounds
Figure 4.9_a
CHEMICAL
GROUP Hydroxyl Carbonyl Carboxyl

STRUCTURE

(may be written HO)

NAME OF Alcohols (Their specific names Ketones if the carbonyl group is Carboxylic acids, or organic acids
COMPOUND usually end in -ol.) within a carbon skeleton

Aldehydes if the carbonyl group

is at the end of the carbon skeleton

EXAMPLE

Ethanol Acetone Acetic acid

Propanal

FUNCTIONAL Is polar as a result of the
PROPERTIES electrons spending more time
near the electronegative oxygen
atom.
Can form hydrogen bonds with
water molecules, helping dissolve
organic compounds such as
sugars.
A ketone and an aldehyde may be Acts as an acid; can donate an
structural isomers with different H+ because the covalent bond
properties, as is the case for between oxygen and hydrogen
acetone and propanal. is so polar:
Ketone and aldehyde groups are
also found in sugars, giving rise
to two major groups of sugars:
ketoses (containing ketone
groups) and aldoses (containing
aldehyde groups). Nonionized Ionized

Found in cells in the ionized form

with a charge of 1 and called a
carboxylate ion.
Figure 4.9_b

Amino Sulfhydryl Phosphate Methyl

(may be
written HS)

Amines Thiols Organic phosphates Methylated compounds

Glycine Cysteine Glycerol phosphate 5-Methyl cytidine

Acts as a base; can Two sulfhydryl groups can Contributes negative charge to Addition of a methyl group
pick up an H+ from the react, forming a covalent the molecule of which it is a part to DNA, or to molecules
surrounding solution bond. This cross-linking (2 when at the end of a molecule, bound to DNA, affects the
(water, in living helps stabilize protein as above; 1 when located expression of genes.
organisms): structure. internally in a chain of Arrangement of methyl
phosphates). groups in male and female
Cross-linking of cysteines Molecules containing phosphate sex hormones affects their
in hair proteins maintains groups have the potential to react shape and function.
the curliness or straightness with water, releasing energy.
of hair. Straight hair can be
Nonionized Ionized permanently curled by
shaping it around curlers
and then breaking and
Found in cells in the re-forming the cross-linking
ionized form with a bonds.
charge of 1+.
Polymers and Monomers
Monomer=1 subunit (link in a chain)
Polymer=a chain of small subunits
Polymers are put together by dehydration
synthesis reactions
Monomers joined covalently losing a water molecule
Polymers are taken apart by hydrolysis
(hydro=water, lysis=splitting)
Broken down in to monomers
Digestion is an example of this happening in our
bodies

All Biochemicals are polymers

Figure 5.2
(a) Dehydration reaction: synthesizing a polymer

1 2 3

Short polymer Unlinked monomer

Dehydration removes
a water molecule,
forming a new bond.

1 2 3 4

Longer polymer

(b) Hydrolysis: breaking down a polymer

1 2 3 4

Hydrolysis adds
a water molecule,
breaking a bond.

1 2 3
Carbohydrates
Sugars are mono- or disaccharides
Ex: glucose(mono), sucrose (di)
Disaccharides-joined by glycosidic linkage
(covalent bond formed btwn 2 monos)
Used for energy
Starches are polysaccharides
Have hundreds-thousands of monos joined
Used for energy storage or structure
Animals store glycogen for energy and chitin
for structure
Plants use cellulose for structure and store
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 5.3
Aldoses (Aldehyde Sugars) Ketoses (Ketone Sugars)
Trioses: 3-carbon sugars (C3H6O3)

Glyceraldehyde Dihydroxyacetone

Pentoses: 5-carbon sugars (C5H10O5)

Ribose Ribulose

Hexoses: 6-carbon sugars (C6H12O6)

Glucose Galactose Fructose

Figure 5.6

Chloroplast Starch granules

Amylopectin

Amylose
(a) Starch: 1 m
a plant polysaccharide

Mitochondria Glycogen granules

Glycogen
(b) Glycogen: 0.5 m
an animal polysaccharide
Figure 5.8

Cell wall Cellulose

microfibrils in a
plant cell wall
Microfibril

10 m

0.5 m

Cellulose
molecules

Glucose
monomer
Figure 5.9
The structure
of the chitin
monomer

Chitin forms the exoskeleton

of arthropods.

Chitin is used to make a strong and flexible

surgical thread that decomposes after the
wound or incision heals.
Lipids
Fats, oils, waxes (sterols)
Non-polar
Exception: phospholipids (part hydrophilic, part hydrophobic)
Energy storage-savings account (chemically stable,
takes a lot to break them apart)
1 g fat stores more than 2x energy of polysaccharide
Triglyceride is typical structure consisting of a
glycerol and 3 fatty acid chains
Main component of phospholipids, which make up?
Saturated fats contain all single bonds btwn carbons
on the main hydrocarbon chain, while unsaturated
fats contain double or triple bonds btwn carbons.
Whats a trans-fat?
Unsaturated fat that has trans double bonds-created by
hydrogenating process (adding Hydrogen)
Figure 5.11

(b) Unsaturated fat

(a) Saturated fat

Structural
formula of a
saturated fat
molecule
Structural
formula of an
unsaturated fat
molecule
Space-filling
model of stearic
acid, a saturated
fatty acid Space-filling model
of oleic acid, an
unsaturated fatty
acid
Cis double bond
causes bending.
Proteins
Held together by peptide bonds, and are therefore
sometimes called polypeptides (special case of
condensation where N is bonded to C)
Have an amino end & a carboxyl end
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)
Physical & chemical properties of side chain
determine unique characteristics of the amino
acid
some are hydrophobic, some hydrophilic, some positive,
some negative
Figure 5.16
Nonpolar side chains; hydrophobic
Side chain
(R group)

Glycine Alanine Valine Leucine Isoleucine

(Gly or G) (Ala or A) (Val or V) (Leu or L) (Ile or I)

Methionine Phenylalanine Tryptophan Proline

(Met or M) (Phe or F) (Trp or W) (Pro or P)

Polar side chains; hydrophilic

Serine Threonine Cysteine Tyrosine Asparagine Glutamine

(Ser or S) (Thr or T) (Cys or C) (Tyr or Y) (Asn or N) (Gln or Q)

Electrically charged side chains; hydrophilic Basic (positively charged)

Acidic (negatively charged)

Aspartic acid Glutamic acid Lysine Arginine Histidine

(Asp or D) (Glu or E) (Lys or K) (Arg or R) (His or H)
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 5.20a
Primary structure

Amino
acids

Amino end

Primary structure of transthyretin

Carboxyl end
Figure 5.20b

Secondary Tertiary Quaternary

structure structure structure

helix

Hydrogen bond
pleated sheet
strand
Transthyretin
Hydrogen Transthyretin protein
bond polypeptide
Figure 5.21

Primary Secondary Quaternary Red Blood

and Tertiary Function
Structure Structure Cell Shape
Structures

1 Normal Molecules do not

hemoglobin associate with one
2
Normal hemoglobin

another; each carries

3 oxygen.
4
5
subunit 10 m
6
7

1 Exposed Sickle-cell Molecules crystallize

hydrophobic hemoglobin into a fiber; capacity
Sickle-cell hemoglobin

2 region to carry oxygen is

3 reduced.
4
5
6 10 m
7 subunit


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)
Figure 5.26b

Nitrogenous bases
Pyrimidines

Cytosine Thymine Uracil

(C) (T, in DNA) (U, in RNA)
Sugars
Purines

Deoxyribose Ribose
Adenine (A) Guanine (G) (in DNA) (in RNA)

(c) Nucleoside components

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
Enzymes as catalysts
Most enzymes are proteins
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 (reactant)
because the shape of the active site (only region
of enzyme that binds to substrate) conforms to
the shape of the substrate (induced fit)
Like a clasping handshake or lock & key
Figure 8.13

Course of
reaction EA
without without
enzyme EA with
enzyme
enzyme
is lower
Free energy

Reactants

Course of G is unaffected
reaction by enzyme
with enzyme

Products

Progress of the reaction

Figure 8.15-3
1 Substrates enter active site.
2 Substrates are held
in active site by weak
interactions.

Substrates
Enzyme-substrate
complex 3 Active site can
lower EA and speed
up a reaction.
6 Active
site is
available
for two new
substrate
molecules.
Enzyme

5 Products are 4 Substrates are

released. converted to
products.
Products
Enzyme controls
Denaturation due to pH or temperature
changes
Cofactors or coenzymes=non-protein

attachments to the enzymes active site

that help maintain its shape
Ex: vitamins
Enzyme Controls contd
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
Ex: toxins & poisons
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=enzymes can have multiple active

sites, so induced fit at one active site may cause

stabilization of other active sites on the enzyme
Figure 8.17

(a) Normal binding (b) Competitive inhibition (c) Noncompetitive

inhibition
Substrate

Active
site
Competitive
inhibitor

Enzyme

Noncompetitive
inhibitor
Figure 8.19

(a) Allosteric activators and inhibitors (b) Cooperativity: another type of allosteric activation

Allosteric enzyme Active site Substrate

with four subunits (one of four)

Regulatory
site (one
Activator Stabilized active
of four) Inactive form
Active form Stabilized active form form

Oscillation

Non- Inhibitor
Inactive form Stabilized inactive
functional
active site form
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
Figure 8.21
Initial
substrate
Active site (threonine)
available Threonine
in active site

Enzyme 1
(threonine
Isoleucine
deaminase)
used up by
cell
Intermediate A
Active site of Feedback
enzyme 1 is inhibition Enzyme 2
no longer able
to catalyze the
Intermediate B
conversion
of threonine to Enzyme 3
intermediate A;
pathway is Intermediate C
switched off. Isoleucine
binds to Enzyme 4
allosteric
site. Intermediate D

Enzyme 5

End product
(isoleucine)
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