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UNIT 2B BIOCHEMISTRY
PART 2
Proteins, Chemical Reactions, and pH
PROTEINS
Of all the organic compounds, proteins
are the largest, most complex, and most
diverse.
While 70% of the body is water, most of
the other 30% is protein!
PROTEINS
Made of elements C, H, O, N
Made of amino acids (the
monomer)
Peptide bonds link amino
acids together to make
polypeptides
One or more polypeptides
“fold” into a Protein
PROTEINS ARE DIVERSE
20 amino acids are used to
make proteins
Different combos of amino
acids lead to different
functioning proteins
DNA tells the proteins how to
assemble.
AMINO ACIDS
Amino acids are compounds with an amino
group (-NH 2 ) on one end and a carboxyl (-COOH)
group on the other end.
Each amino acid consists of
one of each of the
following, connected to
each other by covalent
bonds.
1) carboxyl group (-COOH)
2) amino group (-NH 2 )
3) one central carbon atom (-C-)
 Between the amino and carboxyl
groups
4) one lone hydrogen atom (-H)
 Comes off the central carbon
5) 'R' (variable) group - one of
20 different side chains
Central Carbon
Lone Hydrogen
 Circle each amino group, box each carboxyl group and label
each R group (-R).
Because of their uniform structure, any amino
acid can bond to any other amino acid using a
covalent bond called a peptide bond.
What process will link together two individual
amino acids?
On the two amino acids below, circle the
atoms that must be removed in order to
create a peptide bond.
Hint: These atoms create a __________
molecule, which is a product of the reaction.
Glycine
Valine
POLYPEPTIDES
Segments of amino acids are
called polypeptides
When they are first assembled,
polypeptides are linear (straight)
chains.
They are not yet functioning
proteins!
R groups on the amino acids interact with
each other causing the polypeptide to fold into
a specific 3-dimentional shape or structure.
Once it is completely and
correctly folded, it is
considered a protein.
(other small changes or
modifications may also
occur before the protein is
completely functional)
The structure of each
protein in unique; Structure
leads to function!
Protein Folding
 How many amino acids are shown in the
polypeptide below?
(Hint: count the R groups)
 How many peptide bonds are shown in the
polypeptide below?
(Hint: peptide bonds are
between which two atoms?)
 How many water molecules were released as this
polypeptide was formed?
(Hint: one for each
bond made!)
CHEMICAL REACTIONS
Everything that happens in an organism is based on a
chemical reaction!
 Change one set of chemicals into another
 Chemical bonds change
 Reactants- elements/compounds that enter the
reaction
 Products- are produced by the reaction
WHEN BONDS ARE MADE OR
BROKEN…
- Energy is absorbed (taken in) or released
(given off)
 Reactions releasing energy can (but not always)
occur on their own, or spontaneously.
 Reactions absorbing energy will not occur without a
source of energy
EXAMPLE
Paper is made of cellulose which burns in the
presence of oxygen, and releases energy in
the form of heat and light. But this packet is
not spontaneously bursting into flames right
now. Why not? What is missing?
WHERE DOES YOUR BODY GET ENERGY
FOR CHEMICAL REACTIONS?
Plants?
Make food by
photosynthesis
and turn it into
energy by
cellular
respiration.
Animals?
Eat food and
turn it into
energy by
cellular
respiration.
ACTIVATION ENERGY
 Is the amount of energy that a reaction needs to get
started
 Every reaction requires a certain amount of activation
energy to get started, regardless of whether it is an
energy-absorbing or energy-releasing reaction.
ENERGY ABSORBING REACTIONS
(ENDERGONIC)
Products have more
energy than the reactants
Products are larger, less
stable, and more complex
than reactants
It takes more energy to
break bonds in the
reactants than is released
by making new bonds in
the products
•Examples: dehydration
synthesis; photosynthesis
Dehydration
Synthesis
(Energy
Absorbing)
ENERGY RELEASING REACTIONS
(EXERGONIC)
•Reactants have more
energy than the products
•Reactants are larger, less
stable, and more complex
than products
•More energy is released
when new bonds are
formed in the products than
was needed to break the
old bonds in the reactants
Examples: hydrolysis;
cellular respiration
Dehydration
Synthesis
(Energy
Absorbing)
Hydrolysis
(Energy
releasing)
ENZYMES
Some chemical reactions would be too slow or
have too high of an activation energy without
a little help.
Catalyst- a substance that speeds up a
chemical reaction
 works by lowering the activation energy
Cells make special proteins called enzymes to
act as catalysts for chemical reactions.
 There is one type of enzyme for each type of
chemical reaction (its shape makes it specific for its
job)
Would the hill be
higher or lower
with an enzyme
present?
HOW DO ENZYMES WORK?
1. They provide a site for the reactants to be
brought together to react.
2. They help to break the bonds of the
reactants.
This reduces the energy needed for the
reaction.
“Enzyme Catalyzed Reaction”- a reaction sped
up by an enzyme
Substrates- what the reactants are called
in an enzyme catalyzed reaction.
Substrates bind to a place on the enzyme
called the active site which has a
specific shape.
2 MODELS HELP EXPLAIN HOW ENZYMES
WORK
1. "Lock and Key Model": The substrates fit the
active site of an enzyme like a key fits into a
lock. A very specific interaction!
 This provides the site for the reactants to
come together.
Substrate
Enzyme
2. “Induced-fit Model”:
The enzyme binds the
substrate(s) and
slightly changes its
shape to “hug” the
substrate(s) tightly
(like a handshake).
 This places “strain”
on existing bonds,
allowing bonds to
break and the
chemical reaction to
go forward.
Example of an enzyme-catalyzed
reaction: ____________ is formed
by combining
___________________ and
water in the presence of the
enzyme
“_______________________”.
WHY AREN’T ENZYMES CONSIDERED
A REACTANT OR A PRODUCT?
After the product is
released from the
enzyme, the
enzyme is recycled
and used again.
Enzymes are
reusable!
COMMON HYDROLYTIC ENZYMES
( T H E SUF F I X " – A SE " C OM M ON LY I N DI CATES T H AT A P ROT E I N
I S A N E N Z Y ME)
1. protease- any enzyme that speeds hydrolysis
or breakdown of proteins
2. sucrase (a disaccharidease) - an enzyme
which speeds the breakdown of
___________________
3. lipase - any enzyme which speeds the
breakdown of _________________________
4. nuclease - any enzyme which speeds the
breakdown of _______________________
5. amylase - an enzyme which speeds the
breakdown of amylose (=starch!)
FACTORS AFFECTING ENZYME
ACTIVITY
Temperature, pH, and regulatory molecules
affect enzyme activity
 An increase in temperature will increase the rate of a
reaction to a certain point
 After that point, the enzyme will no longer work
Denaturation - when a protein unfolds and
loses its overall shape (and thus function)
due to increased temp or changes in pH.
 Denatured enzymes lose the shape of their active
site and will no longer function.
Think!
Why are temperature and pH
important factors in
maintaining homeostasis?
PH
Water is one of the most important inorganic
substances in living organisms.
Sometime water molecules will break apart
(dissociate) to form ions.
Ion- a positively or negatively charged atom
(set of atoms) due to loss or gain of electrons
About 1 water molecule in 550 million splits
in this way.
Because the number of positive H+ ions is
equal to the number of negative OH- ions,
water is neutral.
pH scale- measures the concentration of H+
ions in solution [H+]
PH SCALE
 Measured 0-14
 Each step represents a factor of 10
 7 is neutral (like water- has equal amounts of H +
and OH - )
 Lower from 7 becomes more acidic (has more H + )
 Higher from 7 becomes more basic/alkaline (has
less H + )
Order these substances in
order of increasing acidity:
human blood, acid rain,
bleach, seawater, stomach
acid.
Acid, Base, or Neutral? Strong or
Weak?
 pH 7:_______ pH 13.5:_____
 pH 8:_______ pH 2:________
 Which one is more acidic
pH of 2
-orpH of 4
 How many times
more?___________
 Which one is more basic?
Tomato juice -orSoap
 How many times
more?________
DEFINITIONS OF ACIDS AND BASES
ACID- compound that forms H+ ions in
solution
 Acids have more H+ than OH-
BASE- compounds that forms OH- ions in
solution
 Bases have more OH- than H+
Study the reaction below. Is this substance an ACID or BASE?
(circle)
Dissociation In Water
HCl
H+
+
ClHydrogen Chloride
Hydrogen ion
Chloride ion
Study the reaction below. Is this substance an ACID or BASE?
(Circle)
Dissociation In Water
NaOH
Na+
+
OHSodium Hydroxide
Sodium ion
hydroxide ion
ACIDS
BASES
Solutions have a pH_______7
Solutions have a pH ______ 7
Taste sour
Taste bitter
Can corrode metals
Can denature proteins (feel
"slippery")
In solution: [H+] _____ [OH-]
In solution: [H+] _____ [OH-]
ACID
NEUTRAL
BASE
Draw a solution
Draw solution with Draw solution with
with more H+
equal numbers of
more OH- than
than OHH+ and OHH+
Range of pH
Range of pH
Range of pH
______________
______________
______________
[H+] ______ [OH-] [H+] ______ [OH-] [H+] ______ [OH-]
in this type of
in this type of
in this type of
solution.
solution.
solution.
SAMPLE ACIDS AND BASES
BUFFERS
Controlling pH is important
for maintaining homeostasis
in cells. The pH of most cells
in the human body must be
kept between 6.5 and 7.5.
Buffers- Weak acids or bases
that react with strong acids or
bases to prevent sharp,
sudden changes of pH.
Example: Sudden pH changes
in blood are prevented by
buffers such as bicarbonate
and phosphate ions.