Download Chemistry part 2

Chemistry and Biological
Molecules
Bio 9
Feb 18, 2010
In covalent bonding, pairs of valence electrons are
shared, and molecules are formed
Carbon (always) forms 4 bonds
Carbon can form double bonds
1-Butene
2-Butene
Skeletons may have double bonds, which can vary in location.
Carbon also forms ring structures
upon itself
Cyclohexane
Benzene
Skeletons may be arranged in rings.
The variety of carbon compounds is
limitless
All terrestrial life is based on carbon
FUNCTIONAL GROUPS
A carbon skeleton can be modified by the
addition of functional groups- familiar
groups of atoms which affect the properties
of the molecule
hydroxide group
– OH
amino group – NH2
carboxyl group – COOH
phosphate group
– PO4
methyl group – CH3
Functional groups can radically change the function
of a molecule
Estradiol
Female lion
Testosterone
Male lion
Figure 3.5
Which of the following represents an
amino group?
1.
2.
3.
4.
5.
-OH
-PO4
-CH3
- NH2
-COOH
20%
1
20%
20%
2
3
20%
4
20%
5
Most molecules in living things fall into
four categories
•
•
•
•
Carbohydrates
Lipids
Proteins
Nucleic acids
These all exhibit modular construction
Modular housing
Made of interchangeable parts
Freight trains have modular assembly
Modular assembly allows a wide
variety of products from a few pieces
Most biopolymers are formed by
dehydration synthesis
Hydrolysis is
the reverse
reaction
(Catabolic)
Metabolism
• all chemical reactions in body
• Anabolism- building up
• Catabolism- breaking down
Major Macromolecules of Life
•
•
•
•
Carbohydrates
Lipids
Proteins
Nucleic Acids
Carbohydrates
Carbohydrates
• “Carbon” + “Hydro”
• Formula (CH2O)n
• Different from
hydrocarbons
• Soluble in water
• Includes: table sugar,
honey, starch,
glycogen, cellulose,
high fructose corn
syrup
• Glucose is the primary
monomer
A Glucose monomer can cyclize to
form a ring structure
Atoms in bonds are free to rotate around the bonds
Glucose + Glucose = Maltose
(monosaccharide + monosaccharide = disaccharide)
Glucose + fructose = sucrose
A polysaccharide chain can be extended to
thousands- it is theoretically limitless
Glycogen and cellulose
Lipids
Nonpolar molecules of living things:
Fats, oils, waxes, steroids, etc.
Lipids
•
•
•
•
•
•
Non-polar
High-energy molecules
For energy storage
Forms cell membranes
Hormones
Members of family
include oils, fats, waxes,
and cholesterol
(steroids)
Lipids are non-polar
• Therefore, they are
hydrophobic
• C and H are similarly
electronegative
• Do not mix easily with
water
• C-H bond is high in
energy
• Lipids make good energy
storage molecules
Triglycerides are a primary lipid structure
Dehydration synthesis links fatty acids to
glycerol
Fatty acids can be saturated and
unsaturated (“cis” and “trans”)
Monounsaturated vs. Polyunsaturated
Cis- and Trans- fatty acids are isomers
• Melting point is very
different because of
shape
• Health effects are very
different
• Isomers- Same formula,
different shape
Triglycerides can be modified to form
phospholipids
• Phospholipids are
amphipathic- having a
polar and nonpolar
region
• Hyrophilic head,
hydrophobic tails
• Primary constituent of
cell membranes
Phospholipids are the primary
constituent of cell membranes
Proteins
Amino acid polymers which make us
what we are
Proteins have incredible versatility of
structure and function
Proteins are incredibly diverse at the
molecular level
A few examples
Insulin
Rubisco
ATP synthase
Fibrin
Nitrogenase
Protein function depends greatly on shape
Amino Acids
• Proteins consist of subunits called amino acids
Figure 2.12
Proteins are made of amino acids
• All amino acids have a
backbone and a side
group (“R” group)
• Backbone: amino
group, carboxyl group,
central carbon
• Side group: there are
20 different kinds, each
with different chemical
properties
Some amino acids are polar, others
nonpolar
Others
have sulfur,
others are
acidic, still
others are
basic
Many are sold as nutritional
supplements
Amino acids are added one by one to form a
polypeptide chain of a protein
• Dehydration synthesis forms a peptide bond
• DNA contains the instructions for the proper
sequence for a specific protein
DNA carries the information to make a
specific protein
Proteins have four levels of structure
• Primary- amino acid
sequence of polypeptide
• Secondary- coiling of amino
acid backbone
• Tertiary- Polypeptide folding
from amino acid side groups
• Quaternary- more than one
polypeptide
• Protein structure depends on
all these levels of interaction
A protein’s Primary (1o) structure is its
amino acid sequence
• Determined by the sequence
of amino acids
• Amino acids linked by peptide
bonds
• Chain is called polypeptide
• Sequence proceeds from “Nterminus” to “C-terminus”
• Amino acid sequence
determined by DNA code
Levels of Protein Structure
• The primary structure is a polypeptide chain
Figure 2.15a
Secondary (2o) structure
• Hydrogen bonding between amino acid backbones
• Amino group H’s H-bond with O’s from carboxyl end
• 2 basic 2o 2o structures: α- helix and β-pleated sheet
Alpha-helix and Beta-sheet are two
important 2o structural motifs
Tertiary structure
• The folding interactions
from amino acid side chains
of a polypeptide
• The folding of 2o domains
upon each other
• Interactions can be ionic, Hbonds, hydrophobic, or
covalent
• Proper 3o structure depends
on pH, temperature
A lightbulb filament has multiple levels
of structure
Quaternary structure
• The interactions of multiple polypeptides to form a
functional protein
• Polypeptides can be the same (collagen is a homotrimer)
or different (hemoglobin is a heterotetramer)
Changes in the 1o structure of a protein can have
far-reaching effects
The tertiary structure of proteins is
sensitive to denaturation
• Heat or chemicals (incl.
acids and bases) can
temporarily or
permanently change a
protein’s 3o structure
EnzymesCatalytic proteins
Enzymes are a special kind of protein
Enzymes are protein catalysts
• Catalysts- things which
speed up chemical reactions
• Catalysts are not consumed
in a reaction
• -ase: The enzyme suffix
Catalase
How enzymes work
 Structure aids
function
 An active site
naturally fits
substrate
 Enzyme specificity
depends on shape
 Shape changes to
fit substrateinduced fit
Enzymes increase the rates of
reactions by 108 or more
Enzyme available
with empty active
site
Enzymes
are not
consumed
by the
reactions
they
catalyze
Active site
Substrate
(sucrose)
Substrate binds
to enzyme with
induced fit
Glucose
Enzyme
(sucrase)
Fructose
H2 O
Products are
released
Substrate is
converted to
products
b-galactosidase
H 2O
galactose
lactose
b-galactosidase
(aka lactase in humans)
glucose
11
Enzymes are catalysts made of protein. Which of
these factors can slow their proper functioning?
1.
2.
3.
4.
5.
Temperature
pH
Salts
All of the above
None of these
Effects of Temperature and pH
• Each enzyme has an
optimal temperature in
which it can function
• Each enzyme has an
optimal pH in which it
can function
• Tertiary structure can
be radically altered by
changes in pH
In salad dressings, oil quickly separates
from vinegar because oils are
1.
2.
3.
4.
5.
heavier than water.
polar.
nonpolar.
hydrophilic.
amphiphilic.
A protein containing more than one polypeptide
chain exhibits the __________ level of protein
structure.
1.
2.
3.
4.
5.
A) primary
B) secondary
C) tertiary
D) quaternary
E) infinite
Nucleic acids
DNA, RNA, and ATP
Nucleic acids
• (Primarily)
Informational molecules
in cells
• Include DNA, RNA, and
ATP/ADP
• DNA is the code to
make a protein
• Living things are made
up of protein
Nulceotides are the monomers of
nucleic acid polymers
• Consist of a sugar, a
phosphate, and a
nitrogen-containing
base
• Sugar can be
deoxygenated
• Bases contain the
genetic information
Hydrogen bonds hold the two sides of
the DNA ladder together
• DNA bases have –OH
and –NH2 groups
• Sides of ladder are
covalently bonded
• Rungs held together
with H-bonds
There are 4 kinds of DNA bases
• Adenine and Thymine,
Cytosine and Guanine
• A, T, C, and G
• RNA has Uracil instead
of Thymine
RNA’s major task is to carry out the
instructions of DNA
• DNA is
doublestranded,
RNA single
• DNA has
thymine,
RNA has
uracil
ATP
A nucleotide-based
ATP, a single RNA nucleotide, is the
basic energy currency of all cells
LE 8-12
The Regeneration of ATP
ATP
Energy for cellular work
(endergonic, energyconsuming processes)
Energy from catabolism
(exergonic, energyyielding processes)
ADP +
What powers this cycle?
P
i