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Chemistry of Life
Properties of Water
Biological Molecules: Proteins
•Amino acids
•Synthesis & Degredation
•Structural Levels
•Factors for structure
•Domains
Reading
Ch 1-3: Chemistry
Ch 4: Proteins
Homework
Ch 5 Prequiz
Ch 5 pt 2 Prequiz
Homework 1
Mon: Bring in sow bugs
aka – rolly pollies
Biology Informational
DOWNLOAD PRACTICE TESTS!
Slides to continue from last time
Tutoring at the core
Call Replica before going there
• Email Brevity
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Checklist
Lab Seating – assigned seating
Retain your homeworks
Curve / competition / Collaboration
Covalent Bonds – Strongest – shares electrons
(50-200kcal/mole)
Shell is full
Shell NOT full
In a sense
Like we did with ion
something to
indicate difference
in electrons
Symbol + ______
Chemical
symbols
1 line = 2 e-
CH4
Chemical
formula
Subscript vs superscript
Ionic Bonds – medium - Ions of opposing charge interact
(5 kcal/mole)
cation
anion
= NaCl or Na+Cl-
overall
Chemical
symbol
Formation of an Ionic Bond
• called ionic compounds, or salts
• often found in nature as crystals
1 Na+ for every ClBut every Na+ surrounded by Clall bound by ionic bonds
Crystal
Solid
Organized
repeating
Van der Waals Interactions
• If electrons are distributed asymmetrically in
molecules or atoms, they can result in “hot
spots” of positive or negative charge
• Van der Waals interactions are attractions
between molecules that are close together as a
result of these charges
Extremely weak – but with lots of them, can add up
Hydrogen Bonding
usually H (which is d +) to
N or O (which is d -)
Unequal charge sharing
Due to electronegativity
& Bond angles
H2O overall neutral
But has partial charges
electronegative
electropositive
Nonpolar –
symmetrical
No difference
in charge
distribution
Delta
Polar – different sides
Are different charge
one side positive
One side negative
like ionic bond
pos to neg attraction
but not full charge
So not as strong
Hydrogen Bonding
weak (1-5 kcal/mole)
– attraction between electronegative
and electropositive atom
H (which is d+) to
N or O (which is d-)
Chemical
symbol
Dotted
Lines
•Hydrophilic Bond – Water loving – hydrogen bonding
•Hydrophobic Bond – water hating – ie oil and water
driven by LACK of hydrogen bonding
(van der Waal’s)
Importance of H2O
Composition of all living organisms
~20% Biological
Macromolecules
~75%
H2O
5% other:
Small metabolites
Ions, etc.
Mission to mars: looking for water
The Molecule That
Supports All of Life
• Water is the biological medium on Earth
• All living organisms require water more than any
other substance
• Most cells are surrounded by water, and cells
themselves are about 70–95% water
• The abundance of water is the main reason the
Earth is habitable
H2O in solution is structured
4 properties of water contribute
to Earth’s fitness for life
Hydrogen bonds produce a
water “lattice”
Hydrogen bonds affects
properties of:
1. cohesion (surface tension)
2. heat absorption
3. Density (expansion on
freezing)
4. Solubility (versatile solvent)
“lattice” of
water
molecules
• Cohesion – Tendency of water molecules to “stick” to
each other due to hydrogen bonding lattice
- Surface tension is a measure of how hard it is to
break the surface of a liquid
• Adhesion – Tendency of water molecules to “stick” to
other molecules that are charged or polar (walls of test
tubes)
A Lattice of Hydrogen Bonds
• Liquid water lattice – each water molecule constantly
breaks and reforms hydrogen bonds with its neighbors
(allows for absorption of heat)
• Ice lattice – rigid, crystalline structure, spaces each
water molecule farther apart
• Ice is ~10 less dense = floats
Water as a Solvent
H2O interacts with anything polar or charged
Hydration layer: Tends to coat anything polar or charged
Hydration layers reduce
attraction between molecules
or ions and promote their
entry into a solution
Water (solvent) surrounds
dissolved substance (solute) and
prevents them from reassociating
(e.g. sodium and chloride)
Therefore must have a lot more solvent
Hydrogen Bonds & the Properties of Water
• Polarity of water molecules contributes to formation of
distinct polar and nonpolar environments critical to cell
organization
Weak so easily broken and reformed
Molecules that interact with H2O
uncharged polar
sugars
Hydroxyl
groups
Functional Groups –
Responsible for a characteristic chemical reaction
-COOH
-NH2
R -OH
Carboxyl
Group
Amino
Hydroxyl
alcohol
methyl
R – is a variable, can represent anything (with C)
Like “x” in a math equation
Functional Groups –
Responsible for a characteristic
chemical reaction
-NH2
-COOH
Carboxyl
Group
aldehyde
Amino
ketone
C=O
carbonyls
methyl
R –O-H
Hydroxyl
alcohol
ester
R –S-H
Sulfhydryl
phosphate
R – is a variable, can represent anything
(with C) Like “x” in a math equation
Functional Groups –
R –O-H
Carboxyl
Group
Hydroxyl
alcohol
Functional Groups –
Carboxyl
Group
Hydroxyl
alcohol
Functional Groups –
Hydroxyl
alcohol
Carboxyl
Group
ester
Molecules that interact with H2O
Hydophillic vs Hydrophobic
Gradient rather than an absolute
polar
Non-polar
ester
Molecule
2 or more atoms held together by covalent bonds
NaCl
1p+
Not always
The same
C6H12O6
Too complicated
H
8p+
8n0
1p+
Atomic
Structure
is Not a molecule
O
H
Chemical
Symbols
H 2O
Chemical
Formula
Law of fixed proportions: always same ratio
ex: water is always 2 H’s and 1 O, H2O2 is peroxide
Atomic Structure
Chemical Symbols
H
O
H
Intermediate
Chem Formula
Chemical Formula
H2O
Abbreviated
Chemical
Symbols
Varying degrees of abbreviation
Other Notable Molecules: can you draw these?
Ammonia –
NH3
Ethanol CH3-CH2-OH
Formic acid –
HCO-OH
Acetic acid –
CH3-CO-OH
Lactic Acid
CH3-CH(OH)-CO-O(H)
Carbonic Acid –
HO-CO-OH
Hydrochloric acid – HCl (like NaCl)
Sodium Hydroxide – NaOH (like NaCl, crystal at RT)
Chemical symbols
1. chemical symbols to represent atoms
2. Lines to represent covalent bonds (1 line = 1 bond = 2 e) OH is often used for O-H
3. + or – to represent ions
4. Dotted lines represent hydrogen bonds
Chemical Formula – list of elements and their ratios: C3H6O3
Abbreviated chemical symbols:
Many C’s & H’s removed
• At the end of each line is a C if something is not
already there
• C has 4 bonds, fill in missing bonds with H’s
Chemical symbols
1.chemical symbols to represent atoms
2.Lines to represent covalent bonds (1 line = 1 bond = 2 e)
OH is often used for O-H
3.+ or – to represent ions
4.Dotted lines represent hydrogen bonds
() represent linked elements
or possibility of ions
Covalent Bonds of common elements
C has 4
Abbreviated Symbols
N 3 (or has 4 and is +)
End of every line is C unless
O 2 (or 1 & is -)
something already there.
H 1 (or 0 & is +)
C’s filled with H’s
Abbreviated chemical symbols:
Many C’s & H’s removed
• At the end of each line is a C if something is not
already there
• C has 4 bonds, fill in missing bonds with H’s
Have you had your protein today?
Organic Compounds
• Many are polymers—chains of similar units
(monomers or building blocks)
– Synthesized by dehydration synthesis / condensation
– Broken down by hydrolysis reactions
Start / Reactants
End / products
NO WATER
X
O
H +
H
Y
Dehydration
synthesis
Hydrolysis
WATER
X Y
+
Often
left out
H2O
Molecules of the body
Protein building block
monomer
Variable side chain
(R group)
What Kind of Molecule is this?
Notice different way of drawing = perspective
1000s exist
Only 20 in proteins
20 Amino Acids
Essential amino
acids
p78
Some have charged side chains
(depending on pH)
Notice different way of drawing = perspective
Some side chains are uncharged
But polar
Some R-groups are hydrophobic
Variations in side chains determine how the protein
will interact with other molecules or itself
Asparagine is:
a)Polar
b)Charged +
c)Charged d)hydrophobic
e)None of the above
Asparagine is a polar molecule and will likely
NOT interact with
a)H2O
b)Hydrophillic molecules
c)Charged molecules
d)Hydrophobic molecules
-
+
3
When amino acids are polymerized
Polymerized  Chain
Added in order
aa #1
aa #2
Backbone
aa #1
aa #2
Condensation
/
Amino terminal
N-ter
= beginning
Amino acid, dipeptide, tripeptide, polypeptide
Carboxyl
Terminal
C-ter
= end
Peptide Bond
carboxyl
amino
amide
Proteins have shape: 3D
4 Levels of protein structure
Shape is required for
function
Native = functional
Biologically active
Primarily Hydrogen bonds
But also ionic
And covalent – disulfide bonds
Cysteine
Cysteine
Dimeric
form of
cysteine
When amino acids are polymerized
Polymerized  Chain
Added in order
aa #1
aa #2
Backbone
aa #1
aa #2
Condensation
/
Amino terminal
N-ter
= beginning
Amino acid, dipeptide, tripeptide, polypeptide
Carboxyl
Terminal
C-ter
= end
Proteins have shape: 3D
4 Levels of protein structure
Shape is required for
function
Native = functional
Biologically active
Primarily Hydrogen bonds
But also ionic
And covalent – disulfide bonds
Cysteine
Cysteine
Dimeric
form of
cysteine
Proteins have shape: 3D
4 Levels of protein structure
Primary (1°) - Sequence
Secondary (2°) – Features within the
overall chain
The sequence of amino acids in a
protein is: G-Y-T-T-Q. This is an example
of what level of protein structure?
a)Primary
b)Secondary
c)Tertiary
d)Quatenary
e)None of the above
Androgen Receptor is a protein that has a
helix shape which allows it to fit into DNA.
The helix is an example of what level of
protein structure?
a)Primary
b)Secondary
c)Tertiary
d)Quatenary
How does a protein fold? Unknown
Determined by Primary sequence
Mostly through hydrogen
bonding determined by side
chains and backbone
Shape is required for
function
Native = functional
Biologically active
Proof? Protein Denaturation
Essentially: build the chain and it will fold itself
Finds most thermodynamically stable form
• If you denature a protein it can renature
Native = functional
Biologically active
Non-functional
Structure = function
Interaction with H2O
Drives globular form, hydrophobic residues
inside, hydrophillic residues on outside
Classical example of structure = function
What kind of interaction is the
most influential in protein shape?
a)Covalent
b)Ionic
c)Hydrogen
d)Hydrophobic
e)Van der waals
Sequence not the whole story
Eggs can’t renature
1.
2.
Particular proteins
Presence of other proteins
Chaperones
prions
Globular
X-ray crystallography
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-+ + +-
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- + + + -+
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-+ + ++
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- -+ + -
-+ + ++
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-+ ++
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-+
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- + + + -- - - +
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++
-+
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- -+ + +
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- - +- + -+ +- -- +
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- + + + -- - - +
+ ++
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- +- -+ ++ - - +- + +
-+ +- -- +
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-+
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+ ++
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- +- + + +
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- +- +- ++ +
-+
- -+ -
X-ray crystallography
Lysozyme
Myoglobin: 1st structure 1958 Kendrew
Ball and Stick
Ribbon (route of aa’s)
Patterns of structure & sequence
 domains
Regions that do something
Example region that interacts with Zn have similar
structure – now can identify through primary
sequence
DNA binding domain – helix loop helix
Fibrous and Globular Proteins
• Fibrous proteins
– Extended and strand-like proteins
– Water insoluble
– Examples: keratin, elastin, collagen, and certain
contractile fibers
• Globular proteins
– Compact, spherical proteins with tertiary and
quaternary structures
– Water soluble (more or less)
– Examples: antibodies, hormones, and enzymes
Phenylalanine is:
a)Polar
b)Charged +
c)Charged d)hydrophobic
e)None of the above
Many Globular proteins change shape
This structure is an example of ___
structure?
a)1°
b)2°
c)3°
d)4°
e)5°
Example of a transmembrane domain
Highly hydrophobic side chains
Binding of the red molecule gives an
alternative protein structure. What
level of protein structure is this?
a)1°
b)2°
c)3°
d)4°
e)5°
What is breaking and reforming to
allow this rearrangement?
a)Covalent
b)Ionic
c)Hydrogen
d)Hydrophobic
e)Van der waals
Shape changes
Mostly / usually alters
hydrogen bonding pattern
Different composition
means another more
thermodynamically stable
shape
When O2 binds to hemoglobin, the
protein changes shape. This is an
example of what level of protein
structure?
a)Primary
b)Secondary
c)Tertiary
d)Quatenary
How would you expect 2 proteins
to interact with each other?
Primarily through:
a)Covalent
b)Ionic
c)Hydrogen
d)Hydrophobic
e)Van der waals
How would you expect 2 proteins
to interact with each other?
Primarily through:
a)Covalent
b)Ionic
c)Hydrogen
d)Hydrophobic
e)Van der waals
Proteins
• Amino acid structure
carboxyl, amino, r-group /side chain
• Given R draw amino acid
• How peptides are held together – covalent
• How overall structure is maintained
Hydrogen bonding, ionic, covalent (disulfide)
• Levels of Protein Structure
1. Hydrogen, 2. Ionic, 3. Disulfide / covalent
Importance of hydrogen bonding
Importance of primary structure
• 2 overall classes of proteins – Diversity of structure
• X-ray chrystallography
• Terminology