Transcript APDC Unit IV Biochem

Ch’s 2*, 3, 6*
LO 2.5
Chapter 2 Chemical
Context

 What you must know:
 The three subatomic particles & their significance
 The types of bonds, how they form, and their relative
strengths
Matter VS Energy

MATTER
 Has mass & takes up
space
 Affected by gravity
 Consists of elements
and compounds
ENERGY
 Moves matter
 Potential, kinetic
 Ability to do work
 Conversions
 Sound, light, heat
Comparison

ELEMENT
 “Pure” substance
 Can’t be broken down
by “ordinary means to
another substance
 Ex. Hydrogen (H),
Nitrogen (N)
COMPOUND
 2 or more different
elements combined in a
fixed ratio
 Ex. H2O, CO2
Elements of Life

25 elements
96%: O, C, H, N
~4%: P, S, Ca, K & trace elements (ex:
Fe, I)
Hint: Remember CHNOPS!
Subatomic Particles

Atoms are composed of smaller parts called
subatomic particles
Relevant subatomic particles include
Neutrons (no electrical charge)
Protons (positive charge)
Electrons (negative charge)
Neutrons and protons form the atomic
nucleus
Electrons form a cloud around the nucleus
Subatomic Particles

MASS (dalton or
AMU)
Location
Charge
Neutron
1
Nucleus
0
Proton
1
Nucleus
+1
Electron
Negligible
Shell
-1
2
Atomic number
He
4.00
Atomic mass
Element symbol
Electron
distribution
diagram
Helium
2He
Figure 2.6
2
Hydrogen
1H
Atomic number
He
Atomic mass
First
shell
4.00
Helium
2He
Element symbol
Electron
distribution
diagram
Lithium
3Li
Beryllium
4Be
Boron
5B
Carbon
6C
Nitrogen
7N
Oxygen
8O
Fluorine
9F
Neon
10Ne
Sodium
11Na
Magnesium
12Mg
Aluminum
13Al
Silicon
14Si
Phosphorus
15P
Sulfur
16S
Chlorine
17Cl
Argon
18Ar
Second
shell
Third
shell
Isotopes

All atoms of an element have the same number
of protons but may differ in number of neutrons
Isotopes are two atoms of an element that differ
in number of neutrons
# Neutrons varies, but same # of protons
Radioactive isotopes decay spontaneously,
giving off particles and energy; used as tracers
Uncontrolled exposure causes harm
Isotopes

Carbon-12
Carbon-13
Carbon-14
Protrons
6
6
6
Neutrons
6
7
8
Electrons
6
6
6
Chemical Bonging

 Electronegativity- used to determine whether a given
bond will be nonpolar covalent, polar covalent, or ionic.
Electronegativity is a function of: the atom's ionization
energy (how strongly the atom holds on to its own
electrons)
 Strongest bonds:
1.
2.
Covalent: sharing of e-
a.
b.
Polar: covalent bond between atoms that differ in
electronegativity
Non-Polar: e- shared equally; eg. O2 or H2
a.
b.
Na+ClEffected by environment (eg. water)
Ionic: 2 ions (+/-) bond (givers/takers)
Chemical Bonding

Chemical Bonding

 Weaker Bonds
3. Hydrogen: H or polar covalent molecule bonds to
electronegative atom of other polar covalent molecules
4. Van der Waals Interactions: slight, fleeting attractions
between atoms and molecule close together
a. weakest bond
b. Eg. Gecko toe hairs + wall surface
Chemical Bonding

Covalent
Ionic
Hydrogen
All important to life
Form cell’s
molecules
Quick
H bonds to other
reactions/responses electronegative
atoms
Strong bond
Weaker bond (esp.
in H2O
Even weaker
Made an broken by chemical reactions
Chemical Bonding

 All bond affect molecule’s
SHAPE affect molecule’s
FUNCTION
Natural endorphin
Key
Carbon
Hydrogen
Nitrogen
Sulfur
Oxygen
Morphine
 Similar shapes= mimic
 Morphine, heroin, opiates
mimic endorphin (euphoria,
relieve pain)
(a) Structures of endorphin and morphine
Natural
endorphin
Brain cell
Morphine
Endorphin
receptors
Chemical Reactions

Chemical reactions are the making and breaking of
chemical bonds
The starting molecules of a chemical reaction are
called reactants
The final molecules of a chemical reaction are called
products
Figure 2.UN02
O2
2 H2
Reactants
2 H2O
Reaction
Products
Chemical Reactions

 REACTANTSPRODUCTS
 EG. 6CO2 + 6H2O  C6H12O6 + O2
 Some reactions are reversible:
 Eg. 3H2 + N2
2NH3
 Chemical equilibrium: point at which forward and
reverse reactions offset one another exactly
 Reactions still occurring, but no net change in
concentrations of reactants/products
Carbon and the molecular diversity of life
What you must know

 The role of dehydration synthesis in the formation of
organic compounds and hydrolysis in the digestion
of organic compounds
 How to recognize the 4 biologically important
organic compounds (carbs, lipids, proteins, nucleic
acids) by their structural formulas
 The cellular functions of all 4 organic compounds
 The 4 structural levels of proteins
 Water properties
Carbon Atoms

 Of all chemical elements CARBON is unparalleled in its ability
to form molecules that are large, complex, and varied.
 H, O, N, S, P are other common ingredients of these
compounds but it is the element C that accounts for the
enormous variety of biological molecules.
 For reasons- compounds containing C is said to be an organic
compound, and compounds associated with life contain H
atoms in addition to C atoms.
Biomolecules

 Why does it have to be CARBON?
 4 available bonds!
 Can form single, double, and triple bonds
 Can form chains and rings
3 Simple Organic
Molecules

Carbon
Bonding/Skeletons

Chemical Groups

 Organic molecules depend not only on the
arrangement of its CARBON skeleton but also on the
chemical groups attached to that skeleton
 The number and arrangement of chemical groups
help give each organic molecule its unique
properties
Biomolecules

 How can we fancy up the hydrocarbons?
Functional groups!
hydroxyl
carboxyl
sulfhydryl
amine
carbonyl
phosphate
Chemical Groups


Functional Groups
Hydroxyl
 Forms alcohols
 Ex: ethanol
Carboxyl
  Double-bonded O plus an
–OH
 Is acidic
 Ex: acetic acid
Functional Groups
Sulfhydryl
 An S-H group
 Often form bonds with
each other (disulfide
bridges)
 Ex: DNA links
Amine
- acts as a base
- Ex: amino acids;
norepinephrine
Functional Groups
Carbonyl
Is double-bonded O
Aldehyde if on end
Ketone if in middle
Functional Groups
Phosphate
Negative charge
Attaches to C by
one of its O’s
Ex: DNA nucleotides
Water Properties











H-Bonds
Cohesion
Surface Tension
Adhesion
Transpiration
High specific heat
Evaporative Cooling
Insulation
Solvent
pH
Polarity of Water

 O will bond with H on a different molecule of
-
+
water=Hydrogen bond
 Water can form up to 4 bonds
Water Properties

 Adhesion: attraction between UNLIKE molecules
 Cohesion: attraction between TWO waters
 Transpiration: movement of water UP plants; water clings to
each other by cohesion, cling to xylem tubes by adhesion
 Surface Tension: measure of how difficult it is to break or
stretch surface of liquid
 Heat: total amount of KE in system
 Temperature: measure intensity of HEAT due to AVERAGE KE
of molecules
 High Specific Heat: change temp less when absorbs/loses
heat, large bodies of water absorb & sore more heat, create
stable marine/land environment
Water Properties

 Evaporative Cooling: water has high heat of vaporization,
molecules with greatest KE leave as gas, stable temp in lakes &
ponds, cool plants, humans sweat
 Insulation by ice: less dense, floats, insulates under water
 Universal solvent: Dissolves more substances than any others!
 Solution: liquid, homogenous mixture of 2+ substances
 Solvent: dissolving agent (liquid)
 Solute: dissolved substances
 pH: acids & bases- acids: increases H+ concentration (HCL)
bases: reduces H+ concentration (NaOH)
Acids & Bases

 Buffers: minimize changes in concentration of H+
and OH- in a solution (weak acids and bases
 Buffers keep blood at pH of ~ 7.4
 If blood drops to 7 or up to 7.8 then DEATH
 Carbonic Acid-Bicarbonate System: important
buffers in blood plasma
Macromolecules &
Polymers

 Macromolecules in three of the four classes of life’s
organic compounds Carbohydrates, Proteins, &
Nucleic Acids are chain like molecules called
polymers
 Polymer- is a long molecules consisting of many
similar or identical building blocks linked by
covalent bonds, much as a train consisting of cars.
 The repeating units that serve as the building blocks
of a polymer are similar molecules called monomers
Monomers
Polymers
Macromolecules
*Small organic
*Used for building
blocks of polymers
*Connects with
condensation
reaction
(dehydration
synthesis)
*Long molecules of
monomers
*With many
identical or similar
blocks linked by
covalent bonds
*Giant molecules
*2 or more polymers
bonded together
i.e. Amino Acid  peptide  polypeptide  protein
Smaller
Larger
Polymers

Cells make and break down polymers by the same
process
A dehydration reaction occurs when two monomers
bond together through the loss of a water molecule
Polymers are disassembled to monomers by
hydrolysis, a reaction that is essentially the reverse of
the dehydration reaction
These processes are facilitated by enzymes, which
speed up chemical reactions
Figure 3.6
(a) Dehydration reaction: synthesizing a polymer
Short polymer
Longer polymer
(b) Hydrolysis: breaking down a polymer
Unlinked monomer
Figure 3.6a
(a) Dehydration reaction: synthesizing a polymer
Short polymer
Dehydration removes
a water molecule,
forming a new bond.
Longer polymer
Unlinked monomer
Figure 3.6b
(b) Hydrolysis: breaking down a polymer
Hydrolysis adds
a water molecule,
breaking a bond.
Diversity of Polymers

Each cell has thousands of different macromolecules
Macromolecules vary among cells of an organism,
vary more within a species, and vary even more
between species
An immense variety of polymers can be built from a
small set of monomers
Biomolecules

 Critically important molecules of all living things fall
into four main classes




Carbohydrates
Lipids
Proteins
Nucleic Acids
 The first three of these can form huge molecules
called macromolecules
1. Carbohydrates

Carbohydrates include sugars and the polymers of
sugars
The simplest carbohydrates are monosaccharides, or
simple sugars
Carbohydrate macromolecules are polysaccharides,
polymers composed of many sugar building blocks
CHO
Monosaacharides
 formulas that
 Monosaccharides have molecular
are usually multiples of CH2O
 Glucose (C6H12O6) is the most common
monosaccharide
 Monosaccharides are classified by the number of
carbons in the carbon skeleton and the placement
of the carbonyl group (C=O)
Though often drawn as linear skeletons, in aqueous solutions
many sugars form rings
Monosaccharides serve as a major fuel for cells and as raw
material for building molecules
Examples: glucose, fructose, dextrose
Figure 3.7
Triose: 3-carbon sugar (C3H6O3)
Glyceraldehyde
An initial breakdown
product of glucose in cells
Pentose: 5-carbon sugar (C5H10O5)
Ribose
A component of RNA
Hexoses: 6-carbon sugars (C6H12O6)
Glucose
Fructose
Energy sources for organisms
Dehydration Synthesis
Remove water to join molecules together;
Is an endergonic reaction – needs energy
Hydrolysis
Add water to break apart a molecule
Is an exergonic reaction – gives off energy
Figure 3.9-2
Glucose
Fructose
1–2
glycosidic
linkage
Sucrose
Polysaccharides

A disaccharide is formed when a dehydration
reaction joins two monosaccharides
This covalent bond is called a glycosidic linkage
Polysaccharides, the polymers of sugars, have
storage and structural roles
The structure and function of a polysaccharide are
determined by its sugar monomers and the positions
of glycosidic linkages
Examples: starch, glycogen, cellulose, chitin
2. Lipids

 Fats (triglycerides): store energy; 3 fatty acids +
glycerol; saturated, unsaturated, & polyunsaturated
 Steroids: cholesterol & hormones
 Phospholipids: lipid bilayer of cell memebrane
Examples

 Food – oils, butter, fatty meats, whole milk, nuts, egg
yolk
 Cell – phospholipid, cholesterol
 Plant – waxy cuticles, plant oils
 Animal – fat, egg yolk, testosterone
 Other - hormones
3. Proteins

 Proteios=first of primary
 50% dry weights of cells
 Contains CHONS
Proteins

Proteins

 Monomers used to
build proteins:
 Amino Acids
 Properties are
determined by Rgroup
 Determines
folding pattern
Protein Functions

 ENZYMES (lactase)
 DEFENSE (antibodies)
 STORAGE (milk protein=casein)
 TRANSPORT (Hemoglobin)
 HORMONES (insulin)
 MOVEMENT (motor proteins)
 STRUCTURE (keratin)
Overview of Protein
Functions

Overview of Protein
Functions

Levels of Protein

The primary structure of a protein is its unique
sequence of amino acids
Secondary structure, found in most proteins, consists
of coils and folds in the polypeptide chain
Tertiary structure is determined by interactions
among various side chains (R groups)
Quaternary structure results from interactions
between multiple polypeptide chains
Primary Structure

 Amino Acid: (AA) sequence, 20 different AA’s
 Peptide bonds- link AA’s
 R group- side chains
 Hydrophobic
 Hydrophilic
 Ion (acids & bases)
 Amino: -NH2
 Acid: -COOH
Figure 3.21a
Primary structure
Amino
acids
1
10
5
Amino end
30
35
15
20
25
45
40
50
Primary structure of transthyretin
65
70
55
60
75
80
90
85
95
115
120
110
105
100
125
Carboxyl end
Secondary

 Gains 3-D shape (folds, coils) by H-Bonding
 Alpha (α) helix, Beta (β) pleated sheet
 Principles of protein folding:
 Hydrophobic AA buried in interior of protein
(hydrophobic interactions)
 Hydrophilic AA exposed on surface of protein
(hydrogen bonds)
 Acidic + basic AA form salt bridges (ionic bonds)
 Cysteines can form disulfide bonds.
Figure 3.21ba
Secondary structure
 helix
 pleated sheet
Hydrogen bond
 strand
Hydrogen
bond
Tertiary

 Bonding between
side chains (R
groups) of AA
 H-Bonds, ionic
bonds, disulfide
bridges, van der
Waals interactions
Figure 3.21bb
Tertiary structure
Transthyretin
polypeptide
Quaternary

 2+ polypeptides bond together
Figure 3.21bc
Quaternary structure
Transthyretin
protein
Figure 3.21b
Secondary
structure
Tertiary
structure
Quaternary
structure
Transthyretin
polypeptide
Transthyretin
protein
 helix
 pleated sheet
Chaperonins: assist in proper folding of
proteins

Protein structure & function
are sensitive to chemical and
physical conditions
Unfolds or denatures if pH
and temperature are not
optimal
Figure 3.23-2
Normal protein
Denatured protein
Figure 3.23-3
Normal protein
Denatured protein
Change in structure = change in
function

4. Nucleic Acids

 Function: Store hereditary information
Nucleic Acids

 Monomer: Nucleotides sugar, base, phosphate
 Polymers: DNA, RNA’s, NADH, NADPH, ATP
The amino acid sequence of a polypeptide is programmed by a
unit of inheritance called a gene
Genes are made of DNA, a nucleic acid made of monomers
called nucleotides
DNA provides directions for its own replication
DNA directs synthesis of messenger RNA (mRNA) and,
through mRNA, controls protein synthesis
Nucleic Acids

The sugar in DNA is deoxyribose; in RNA it is ribose
A prime () is used to identify the carbon atoms in the
ribose, such as the 2 carbon or 5 carbon
A nucleoside with at least one phosphate attached is
a nucleotide
Nucleotide Polymers
Adjacent nucleotides are joined by covalent
bonds that form between the —OH group on the
3 carbon of one nucleotide and the phosphate on
the 5 carbon of the next
These links create a backbone of sugarphosphate units with nitrogenous bases as
appendages
The sequence of bases along a DNA or mRNA
polymer is unique for each gene
© 2014 Pearson Education, Inc.
Animation: DNA and RNA Structure
Right click slide / Select play


Figure 3.25-1
DNA
1 Synthesis
of mRNA
mRNA
NUCLEUS
CYTOPLASM
Figure 3.25-2
DNA
1 Synthesis
of mRNA
mRNA
NUCLEUS
CYTOPLASM
mRNA
2 Movement of
mRNA into
cytoplasm
Figure 3.25-3
DNA
1 Synthesis
of mRNA
mRNA
NUCLEUS
CYTOPLASM
mRNA
2 Movement of
mRNA into
cytoplasm
Ribosome
3 Synthesis
of protein
Polypeptide
Amino
acids
Intro to Metabolism
What You Need To Know:

Examples of endergonic and exergonic
reactions.
The key role of ATP in energy coupling.
That enzymes work by lowering the energy of
activation.
The catalytic cycle of an enzyme that results in
the production of a final product.
The factors that influence enzyme activity.
Chapter 8 Warm-Up

1. Define metabolism.
2. List 3 forms of energy.
3. Where does the energy available for
nearly all living things on earth come
from?
Ch. 8 Warm-Up

1. What are the 1st and 2nd laws of
thermodynamics?
2. Give the definition and an example of:
A. Catabolic reaction
B. Anabolic reaction
3. Is the breakdown of glucose in cellular
respiration exergonic or endergonic?
Ch. 8 Warm-Up

1. Draw and label the following: enzyme, active
site, substrate.
2. Describe what is meant by the term
induced fit.
3. What types of factors can affect an enzyme’s
function?

Metabolism is the totality of an organism’s
chemical reactions
Manage the materials and energy resources
of a cell
Catabolic pathways release energy by
breaking down complex molecules into simpler
compounds
Eg. digestive enzymes break down food 
release energy

Anabolic pathways consume energy to build
complex molecules from simpler ones
Eg. amino acids link to form muscle protein
Energy = capacity to do work
Kinetic energy (KE): energy associated with
motion
 Heat (thermal energy) is KE associated with
random movement of atoms or molecules

Potential energy (PE): stored energy as a result of
its position or structure
 Chemical energy is PE available for release in a
chemical reaction
Energy can be converted from one form to another
 Eg. chemical  mechanical  electrical
Thermodynamics is the study of
energy transformations that occur
in nature

 A closed system, such as liquid in a thermos, is
isolated from its surroundings
 In an open system, energy and matter can be
transferred between the system and its
surroundings
 Organisms are open systems
The First Law of
Thermodynamics

 The energy of the universe is constant
 Energy can be transferred and transformed
 Energy cannot be created or destroyed
 Also called the principle of Conservation of
Energy
The Second Law of
Thermodynamics

Every energy transfer or
transformation increases
the entropy (disorder) of
the universe
During every energy
transfer or transformation,
some energy is unusable,
often lost as heat
Energy

Free energy: part of a system’s energy available to
perform work
G = change in free energy
Exergonic reaction: energy is released
Spontaneous reaction
G < 0
Endergonic reaction: energy is required
Absorb free energy
G > 0
 A cell does three main kinds of work:
 Mechanical
 Transport
 Chemical

 Cells manage energy resources to do work by
energy coupling: using an exergonic process to
drive an endergonic one
ATP (adenosine triphosphate) is the cell’s
main energy source in energy coupling
ATP = adenine + ribose + 3 phosphates

When the bonds
between the phosphate
groups are broken by
hydrolysis  energy is
released
This release of energy
comes from the
chemical change to a
state of lower free
energy, not in the
phosphate bonds
themselves

How ATP Performs Work
Exergonic release of Pi is used to do the
endergonic work of cell
When ATP is hydrolyzed, it becomes ADP
(adenosine diphosphate)

Pi
P
Motor protein
Protein moved
Mechanical work: ATP phosphorylates motor proteins
Membrane
protein
ADP
+
Pi
ATP
Pi
P
Solute transported
Solute
Transport work: ATP phosphorylates transport proteins
P
Glu +
NH2
NH3
+
Glu
Pi
Reactants: Glutamic acid Product (glutamine)
and ammonia
made
Chemical work: ATP phosphorylates key reactants
Catalyst: substance that can change the rate of a
reaction without being altered in the process

Enzyme = biological catalyst
Speeds up metabolic reactions by lowering the
activation energy (energy needed to start reaction)
Enzymes lower activation energy

 This allows those reactions to work more speedy
Substrate Specificity
of Enzymes

The reactant that an enzyme acts on is called
the enzyme’s substrate
The enzyme binds to its substrate, forming an
enzyme-substrate complex
The active site is the region on the enzyme
where the substrate binds
Substrates

 Enzymes act on only one substance… the substrate
 Substrate binds at the enzyme’s active site which is
where the reaction takes place
How is the Rxn made faster?

 Enzyme strains bonds in reactants so they take less
energy to break
 May also change internal environment
 More Substrate = Faster Rxn
INDUCED FIT: ENZYME FITS SNUGLY AROUND
SUBSTRATE -- “CLASPING HANDSHAKE”

An enzyme’s activity can be
affected by:
Temperature (faster @
higher temps)
pH (normal range is
neutral areas)
Chemicals

Being too far off will
denature ENZ
Cofactors
Cofactors are nonprotein enzyme helpers such as
minerals (eg. Zn, Fe, Cu)
Coenzymes are organic cofactors (eg. vitamins)

Enzyme Inhibitors
Competitive inhibitor: binds to the active site of an
enzyme, competes with substrate
Noncompetitive inhibitor: binds to another part of
an enzyme  enzyme changes shape  active site
is nonfunctional
Inhibition of Enzyme Activity

Regulation of Enzyme Activity

To regulate metabolic pathways, the cell switches
on/off the genes that encode specific enzymes
Allosteric regulation: protein’s function at one
site is affected by binding of a regulatory
molecule to a separate site (allosteric site)
Activator – stabilizes active site
Inhibitor – stabilizes inactive form
Cooperativity – one substrate triggers shape
change in other active sites  increase catalytic
activity
Feedback Inhibition

End product of a metabolic pathway shuts down
pathway by binding to the allosteric site of an
enzyme
Prevent wasting chemical resources, increase
efficiency of cell
Feedback Inhibition

Negative Feedback
Inhibition

Many metabolic pathways
regulated this way
An end-product switches off
a previous step in the
pathway (usually as an
allosteric inhibitor)
Localization of Enzymes
Enzymes are located
where they are needed
within cells…teams of
enzymes that work on
same pathway are
together
Ex: cell respiration
enzymes in the
mitochondria

AP Lab: Enzyme
Catalysis


http://www.bozemanscience.com/science-videos/2010/9/5/ap-biology-lab-2-enzyme-catalysis.html
FRQ Practice

 Describe THREE types of bonds/interactions found in
proteins. For each, describe its role in determining protein
structure. (2008, #1A)
FRQ Practice
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 How do each of the following illustrate the link between
structure and function?
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Enzyme – Substrate complex
Enzyme Inhibition
Phospholipids
Amino acid R-groups
N-base component of nucleic acids
Relative amounts of O in carbs vs lipids