Download Biochemistry

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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)
Molecule= simplest part of a compound
◦ Chemical formula: ex: CH4
Ionic bonds=Ions are formed due to sharing of electrons.
ATTRACTION!
Covalent bonds= Sharing electrons
◦ Involve only 1 type of atom b/c have the same electron affinity
Polar-covalent bonds= Sharing electrons
◦ Involve different types of atoms b/c have different
electronegativities (attraction of an atom for e- of a covalent
bond)
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Necessary for most chemical signaling
between cells
◦ Ionic Bond
◦ 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
 EX: Gecko walking up walls
+
–
Water (H2O)
+
Hydrogen bond
–
Ammonia (NH3)
+
+
+
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Water is a polar molecule
◦ Overall charge is unevenly distributed
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Water’s “bent” geometry allows for hydrogen
bonding-Note: this is NOT just a covalent
bond! It’s a special case of an 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

Hydrogen
bond
+
+
Polar covalent
bonds


+
+

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Cohesion and Adhesion-Water is attracted to
itself (cohesion) and to other polar substances
(adhesion)
 Contributes to movement of water & dissolved nutrients
against gravity in plants
Water is a very versatile biologic solventmolecules surround substances and separate
them
 Water expands when it freezes because of the
tetrahedral arrangement of its molecules
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 Becomes less dense & expands b/c of hydrogen bonding
 Ice is fully hydrogen-bonded while liquid water only
contains temporary hydrogen bonds
Adhesion
Two types of
water-conducting
cells
Cohesion
Direction
of water
movement
300 m
Hydrogen bond
Ice:
Hydrogen bonds
are stable
Liquid water:
Hydrogen bonds
break and re-form
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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(warm) to low(cool)
◦ Ice absorbs the heat from water to cool your drink-it does
NOT release “cold”
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“Cold” does not exist in a thermodynamic sense!
It’s simply the removal (absorption) of heat (kinetic
energy)
Biochemistry
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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)
(a) Structural isomers
(b) Cis-trans isomers
cis isomer: The two Xs
are on the same side.
trans isomer: The two Xs
are on opposite sides.
(c) Enantiomers
CO2H
CO2H
H
NH2
CH3
L isomer
NH2
H
CH3
D isomer
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Miller & Urey
experiment
◦ Concluded complex
molecules could arise
spontaneously from
conditions on early
earth
 Amino acids,
formaldehyde,
hydrocarbons
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Functional groups are used to distinguish
molecules made up of C, H, O, since these
groups cause the molecules to behave
differently:
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Hydroxyl group (OH-)
Carbonyl group (C=O)
Carboxyl group (COOH)
Amino group (NH2 )
Sulfhydryl group (SH)
Phosphate group (PO4)
Methyl (CH3 )
◦ Use the chart in your text to make key word flash
cards!
CHEMICAL
GROUP
Hydroxyl
Carbonyl
Carboxyl
STRUCTURE
(may be written HO—)
NAME OF
COMPOUND
Alcohols (Their specific names
usually end in -ol.)
Ketones if the carbonyl group is
within a carbon skeleton
Carboxylic acids, or organic acids
Aldehydes if the carbonyl group
is at the end of the carbon skeleton
EXAMPLE
Ethanol
Acetone
Acetic acid
Propanal
FUNCTIONAL
PROPERTIES
• Is polar as a result of the
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
structural isomers with different
properties, as is the case for
acetone and propanal.
• 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).
• Acts as an acid; can donate an
H+ because the covalent bond
between oxygen and hydrogen
is so polar:
Nonionized
Ionized
• Found in cells in the ionized form
with a charge of 1 and called a
carboxylate ion.
Amino
Sulfhydryl
Phosphate
Methyl
(may be
written HS—)
Amines
Organic phosphates
Thiols
Glycine
Cysteine
Glycerol phosphate
• Acts as a base; can
pick up an H+ from the
surrounding solution
(water, in living
organisms):
• Two sulfhydryl groups can
react, forming a covalent
bond. This “cross-linking”
helps stabilize protein
structure.
• Contributes negative charge to
the molecule of which it is a part
(2– when at the end of a molecule,
as above; 1– when located
internally in a chain of
phosphates).
• Cross-linking of cysteines
in hair proteins maintains
the curliness or straightness
of hair. Straight hair can be
“permanently” curled by
shaping it around curlers
and then breaking and
re-forming the cross-linking
bonds.
• Molecules containing phosphate
groups have the potential to react
with water, releasing energy.
Nonionized
Ionized
• Found in cells in the
ionized form with a
charge of 1+.
Methylated compounds
5-Methyl cytidine
• Addition of a methyl group
to DNA, or to molecules
bound to DNA, affects the
expression of genes.
• Arrangement of methyl
groups in male and female
sex hormones affects their
shape and function.
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Model Tasks 1&2
◦ To be graded as part of your notes.
◦ 15 minutes
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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
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Polymers are taken apart by hydrolysis
(hydro=water, lysis=splitting)
◦ Broken down into monomers, water must be broken to
fulfill the valence of the open bonds.
◦ Digestion is an example of this happening in our bodies
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All Biochemicals are polymers
(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
Hydrolysis adds
a water molecule,
breaking a bond.
1
2
3
4
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Model Task 3
◦ To be graded as part of your notes.
◦ 15 minutes
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Energy Source!
Sugars are mono- or disaccharides
◦ Ex: glucose(mono), sucrose (di)
◦ Disaccharides-joined by glycosidic linkage (covalent
bond formed btwn 2 monosaccharides)
Polysaccharides
• Have hundreds to thousands of monomers.
• Animals use glycogen for energy and chitin for
structure.
• Plants use cellulose for structure and use Starch:
amylose or amylopectin for energy.
• There are difference is in the types of glycosidic
linkage between the monomers and the degree of
branching within the molecules.
Chloroplast
Starch granules
Amylopectin
Amylose
(a) Starch:
1 m
a plant polysaccharide
Mitochondria
Glycogen granules
Glycogen
(b) Glycogen:
0.5 m
an animal polysaccharide
Cellulose
microfibrils in a
plant cell wall
Cell wall
Microfibril
10 m
0.5 m
Cellulose
molecules
 Glucose
monomer
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.
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Model Task 4
◦ To be graded as part of your notes.
◦ 15 minutes
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Fats, oils, waxes
Non-polar
◦ Exception: phospholipids (part hydrophilic, part hydrophobic)
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Energy storage, insulation, protective coverings
(chemically stable, takes a lot to break them apart)
1 g fat stores more than 2x energy of polysaccharide
Composed of Fatty Acid chains
Glycerol
This is an
Ester Linkage
3 Fatty Acids
Saturated
Unsaturated
Full of hydrogen atoms
Few hydrogen atoms
Single bonds
Double and Triple bonds
Ex. Butter
Ex. Canola Oil
Unhealthy
Healthy
(a) Saturated fat
Structural
formula of a
saturated fat
molecule
Space-filling
model of stearic
acid, a saturated
fatty acid
(b) Unsaturated fat
Structural
formula of an
unsaturated fat
molecule
Space-filling model
of oleic acid, an
unsaturated fatty
acid
Cis double bond
causes bending.
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What’s a trans-fat?
◦ Unsaturated fat that has trans double bondscreated by hydrogenating process (adding
Hydrogen)
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Workhorses of cells, doing a variety of tasks such as
communication, structure, movement, storage, transport,
defense and enzymes
Monomer: amino acids (20 amino acids exist in living
things, distinguished by their R groups)
◦ have an amino end & a carboxyl end
◦ Some are hydrophobic, some hydrophilic, some positive, some
negative, uncharged
◦ Held together by peptide bonds, and are therefore sometimes
called polypeptides (special case of condensation(dehydration
synthesis) where N is bonded to C)
DRAW TWO DIFFERENT AMINO ACIDS IN YOUR NOTES.
Circle the portion of the molecule they have in common.
Nonpolar side chains; hydrophobic
Side chain
(R group)
Glycine
(Gly or G)
Alanine
(Ala or A)
Methionine
(Met or M)
Isoleucine
(Ile or I)
Leucine
(Leu or L)
Valine
(Val or V)
Phenylalanine
(Phe or F)
Tryptophan
(Trp or W)
Proline
(Pro or P)
Polar side chains; hydrophilic
Serine
(Ser or S)
Threonine
(Thr or T)
Cysteine
(Cys or C)
Electrically charged side chains; hydrophilic
Tyrosine
(Tyr or Y)
Asparagine
(Asn or N)
Glutamine
(Gln or Q)
Basic (positively charged)
Acidic (negatively charged)
Aspartic acid
(Asp or D)
Glutamic acid
(Glu or E)
Lysine
(Lys or K)
Arginine
(Arg or R)
Histidine
(His or H)
Forming a Peptide Bond: condensation
(dehydration synthesis)
O
O
H
H
H N C O H H N C O H
H
H
Amino Acid Structure
Peptide Bond
O H O
H
H N C N C O H
H
H
O H
H
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Read instructions and record information on
your “data sheet”.
Do not paste this into your notebook until we
finish notes.
Pause after Step 4 to wrap up before you
answer the ANALYSIS Questions.
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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
Primary structure
Amino
acids
Amino end
Primary structure of transthyretin
Carboxyl end
Tertiary
structure
Secondary
structure
Quaternary
structure
 helix
Hydrogen bond
 pleated sheet
 strand
Hydrogen
bond
Transthyretin
polypeptide
Transthyretin
protein
Sickle-cell hemoglobin
Normal hemoglobin
Primary
Structure
1
2
3
4
5
6
7
Secondary
and Tertiary
Structures
Quaternary
Structure
Function
Molecules do not
associate with one
another; each carries
oxygen.
Normal
hemoglobin
 subunit

Red Blood
Cell Shape

10 m
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
1
2
3
4
5
6
7
Exposed
hydrophobic
region
Sickle-cell
hemoglobin
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 subunit
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Molecules crystallize
into a fiber; capacity
to carry oxygen is
reduced.
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
10 m
High temperature, extreme salinity and pH
changes can cause denaturating of
proteins=
protein becomes misshapen because the
forces controlling the levels of structure have
been altered
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Information storage molecules
DNA and RNA
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Monomers are nucleotides.
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◦ Phosphate Group
◦ 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 has the ability to make
Sequences are the code for creating proteins.
Sequence changes are used as Biological
Clocks.
Nitrogenous bases
Pyrimidines
Cytosine
(C)
Thymine
(T, in DNA)
Uracil
(U, in RNA)
Sugars
Purines
Adenine (A)
Guanine (G)
(c) Nucleoside components
Deoxyribose
(in DNA)
Ribose
(in RNA)
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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)
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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)
Add Diagram #1 to notes.
◦ Highlight the original reaction in RED and the enzyme aided
reaction in GREEN.
◦ Circle the ONE portion of the graph (rxn) that is changed by the
addition of an enzyme.
Free energy
Course of
reaction
without
enzyme
EA
without
enzyme
EA with
enzyme
is lower
Reactants
G is unaffected
by enzyme
Course of
reaction
with enzyme
Products
Progress of the reaction
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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
Diagram #2: Use the following picture or find a
picture in the text or online that represents this
concept. Draw into your notes.
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
released.
4 Substrates are
converted to
products.
Products
1.
Bitesize Digestion:
https://www.youtube.com/watch?v=eSbmJPSnw
Bs
1.
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Denaturation occurs in enzymes due to pH,
temperature, salinity changes.
Paste Diagram #3 into your notes.
Think of test questions
for these graphics.
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2. Concentration of Enzyme/Concentration of
Substrates
3. Cofactors or coenzymes=non-substrate
attachments to the enzyme that help maintain
shape (allosteric)
◦ Ex: vitamins
4. Inhibitors
Competitive=mimics the substrate and blocks
the active site
Non-competitive=causes inhibition by destabilizing
the enzyme shape (allosteric)
 Ex: toxins & poisons
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Paste Diagrams #4 and #5 into your notes.
(a) Normal binding
(b) Competitive inhibition
(c) Noncompetitive
inhibition
Substrate
Active
site
Competitive
inhibitor
Enzyme
Noncompetitive
inhibitor
5. Cooperativity=enzymes can have multiple
active sites, so induced fit at one active site may
cause stabilization of other active sites on the
enzyme
(b) Cooperativity: another type of allosteric activation
(a) Allosteric activators and inhibitors
Allosteric enzyme
with four subunits
Active site
(one of four)
Regulatory
site (one
of four)
Substrate
Activator
Inactive form
Stabilized active form
Active form
Oscillation
Nonfunctional
active site
Inactive form
Inhibitor
Stabilized inactive
form
Stabilized active
form
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Series of chemical reactions in which the
products of each step are reactants for the
next step
Active site
available
Isoleucine
used up by
cell
Active site of
Feedback
enzyme 1 is
inhibition
no longer able
to catalyze the
conversion
of threonine to
intermediate A;
pathway is
switched off. Isoleucine
binds to
allosteric
site.
Initial
substrate
(threonine)
Threonine
in active site
Enzyme 1
(threonine
deaminase)
Intermediate A
Enzyme 2
Intermediate B
Enzyme 3
Intermediate C
Enzyme 4
Intermediate D
Enzyme 5
End product
(isoleucine)
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Read the article and discuss it at your table.
Use one of the dry erase boards to map the
enzymes, substrates and processes involved in
creating grey hair and preventing grey hair.
Put your initials on the board so it can be
checked.