Download Molecules - Chapter 2

Molecules
Chapter 2
Introduction to
Biochemistry and
Review
Covalent Bonds - SPONCH
 Non
polar – Equal sharing of the
electrons
 Polar
– Unequal sharing of the
electrons
Water and Hydrogen
Hydrogen Bonds
Water
 Water
contains polar covalent
bonds
 Oxygen and hydrogen do not
share electrons equally
 Oxygen exerts a greater pull on
the electrons and gains a
negative charge
 Hydrogen as a result has a
positive charge
Dipole
 As
a result – the water
molecule has a positive end the
Hydrogens
 The oxygen is slightly negative
 This forms a dipole – a polar
covalent molecule
Hydrogen bonds

One of the
most significant
consequences
of the polar
covalent bond is
the production
of inter
molecular bonds
with other
water molecules
Water as the universal
solvent
 Water
is able to dissolve small
non polar covalent molecules,
ionic compounds, and other
polar covalent molecules
 Water soluble molecules are
described as hydrophilic
 Those molecules that are not
soluble in water are
hydrophobic
Properties
Adhesion- water molecules stick to
unlike surfaces such as glass or
plastic( -) Meniscus
 Cohesion – water molecules stick to
each other – “ sticky Mickeys” –
drop of water
 Water exists in three states on
Planet earth ( Liquid – aquatic
environment outside us and inside
us)
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More

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Specific heat – Water does not
change temperature as rapdily as
air- high specific heat
Density of water = 1g/ml
Surface tension –
Solutions – universal solventDissolves – salts( ionic bonds),
sugar( non polar covalent), and polar
covalent( unequal sharing)
Molecules in water polar
Yea or Nay
 Hydrophilic
– water loving
 Hydrophobic – water hating or
fearing
Polar molecule?
Water and hydrogen
ions
 http://www.biology.arizona.edu
/biochemistry/problem_sets/p
h/ph.html
Acid and Base
 Acids
are hydrogen donors or
proton donors
COOH
COO- +
H+
 Bases are hydrogen acceptors
or proton acceptors
NH2
NH3+
Acids and Bases
pH
 pH
= The concentration of H+
ions
 The negative logarithm of the
hydrogen ion concentration in
an aqueous solution.
 pH
= - log[ H30+]
pH and measurementpHydrion paper
pH measurement – pH
meter
Carboxylic acids
( Organic acids)
The acidic functional group in organic
acids is the carboxl group
 The carboxyl group is a proton donor
 COOH
COO- in water solution

Buffering capacity
Organic bases
 Proton
acceptors – gain a
hydrogen and become positively
charged in water solution
 The amino group - NH2
becomes NH3+
Amino acids
 Contain
both an amino group
and a carboxyl group
 They are amphoteric
 “zwitterions”
Amino acids
Amino Acid Structure
 Alanine
Amino acids
 http://www.johnkyrk.com/amin
oacid.html
Formulas



Structural
formulas show the
atoms and the
arrangement of
the atoms in the
compound
Molecular
formulas tell the
number of each
type of atom in
the compound,
C6H12O6
Structural formula and
condensed


Complete Structural Formula
H H H
| | |
H-C-C-C-H
| | |
H H-C-H H
|
H

Condensed Structural Formula
CH3CHCH3CH3
or
CH(CH3)3
Isomers

These
molecules have
the same
structural
formula but a
different
arrangement of
the atoms
Macromolecules
 Proteins
 Lipids
 Carbohydrates
 Nucleic
acids
p
a
c
e
G
r
o
u
p
2
1
2
1
2
1
Protein Facts
Proteins: Polymers of Amino Acids
Proteins are polymers of amino
acids. They are molecules with
diverse structures and functions.
 Each different type of protein has
a characteristic amino acid
composition and order.
 Proteins range in size from a few
amino acids to thousands of them.
 Folding is crucial to the function of
a protein and is influenced largely
by the sequence of amino acids.


Proteins are polymers
 Proteins
are polymers of amino
acids. They are molecules with
diverse structures and
functions.
 Polymers are made up of units
called monomers
 The monomers in proteins are
the 20 amino acids
Proteins: Polymers of
Amino Acids
Each
different type of protein
has a characteristic amino acid
composition and order.
Proteins range in size from a
few amino acids to thousands of
them.
Folding is crucial to the
function of a protein and is
influenced largely by the
sequence of amino acids.
Polar side chains
Non Polar Hydrophobic
side chains
Electrical charged
hydrophilic
Functions of proteins
Hormones – Growth hormone
Receptors – to Receive information
so that cell can communicate with
other cells
 Neurotransmitters – messenger
molecules – to send information
between neurons
 Cytoskeleton – actin, myosin, and
collagen – the structure of
connective tissue and muscles
 Antibodies – Immunoglobulins to
fight disease


Function of Proteins continued
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Enzymes – Biological catalysts
Transport of small molecules –
Albumin and haptoglobin
Transport of oxygen – hemoglobin
and myoglobin
Membrane proteins – to assist in
support
Channels in membranes – to allow
the passage of molecules or ions
Electron carriers in electron
transport in the production of ATP
Functions( continued)i

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Clotting proteins
Immune proteins to fight infectious
agents
Histones – DNA binding proteins
Toxins to repel or kill other
organisms
Bacteriocins – molecules produced
by bacteria against bacteria
Biochemical Reactions
 Polymerization
reactioncondensation and dehydration
synthesis – involves the loss of
water between two amino acids
and the formation of a peptide
bond ( OH is lost from the
carboxyl group and H is lost
from the hydroxyl) requires
energy
 Hydrolysis – the addition of
water causes the peptide bond
Polymerization
Hydrolysis
Four levels of Protein
Structure
There are four levels of protein
structure: primary, secondary,
tertiary, and quaternary.
 The precise sequence of amino acids
is called its primary structure.
 The peptide backbone consists of
repeating units of atoms: N—C—C—
N—C—C.
 Enormous numbers of different
proteins are possible.

The causes of Tertiary
structure
Carbohydrates
 Diverse
group of compounds
based on the general formula
CH2O
 Range in moleclular mass from
less than 100 to hundreds of
thousands of daltons
 Energy
 Energy storage
 Structural
Monosaccharides
( Hexoses)
 CH2O
– Molecular formula
C6H12O6
 Simple sugars ( hexoses)
 Glucose – blood sugar
 Galactose
 Fructose – fruit sugar
Hexoses
D isomers
 Optical isomers

Isomers

These monosaccharides have the
same molecular formula but a
different arrangement of C, H , and
O
Glyceraldehyde – the
simplest sugar
Monosaccharides(
Pentoses)
Ribose
 Deoxyribose

Disaccharides
 Glucose
Lactose
 When
+ Galactose
two monosaccharides are
combined they form a
disaccharide.
 The bond that connects the
two sugars is an alpha
glycosidic linkage
Disaccharides
Dehydration synthesis to
form disaccharides
Glucose + Glucose
Maltose
alpha
beta
 This forms an alpha glycosidic
linkage

Beta glycosidic linkages
Glucose + Glucose
Cellobiose
beta
beta
 This combination forms a beta
glycosidic linkage.

Polysaccharides
 Macromolecules
 Amylose
– giant molecule
formed by thousands of glucose
molecules connected by an
alpha glycosidic linkage
Amylose
Plant starch
 Stores energy
 Found in tubers,
grains, seeds
 Hydrolysis
releases sugar
molecules for
glycolysis

Glycogen
Animal starch
 Found in muscle
and liver in the
human body
 Glycogen
hydrolysis
produces
glucose for the
blood stream

Glycogen has energy
storage for musclesprovides sugars for
mitochondria
Cellulose
 Formed
by glucose molecules
 Forms the cell walls of plants
 Connected by beta glycosidic
linkages
 Bond cannot be broken down or
degraded
 Energy stored in bonds – not
released during digestion
Derivative sugars
 These
are derivative
carbohydrates
 Carbon 6 in glucose may be
oxidized from CH2OH to a
carboxyl group producing
glucuronic acid
Glucose + O2
Glucuronic acid
Phosphorylated sugars
Phosphate
group attached
to glucose
 Glycolytic
pathway
intermediate
 Release of
energy

Amino group added to
basic glucose molecule

Basic molecules for chondroitin
sulfate and hyaluronic acid the
foundation of connective tissue
Chitin
Chitin forms the basis of the insect
exoskeleton
 Hard outer covering – prevents
dehydration and holds the water
inside and protects the organism

Lipids
 Chemically
diverse group of
molecules
 Non polar molecules
 Hydrophobic
 Not really macromolecules
because they are not polymers
constructed from monomers
Lipids have diverse cellular
roles
 Energy
production
 Energy storage
 Hormones
 Carotenoids help to capture
light energy
 Structural – forming cell
membranes
Phospholipids
 Form
the basis of cell
membranes
 Formed from phosphate groups
that are hydrophilic joined to
 Two long chain non polar fatty
acid chains
Fatty acids( fats and
oils)
Saturated and
unsaturated
Saturated fatty
acids have all
single bonds and
have a
maximized
number of
hydrogens
attached to the
carbons
 Unsaturated
fatty acids have
a double bond

Molecular structure
Saturated fatty
acids are linear
[inflexible]
 Unsaturated
fatty acids have
a kink
[flexible]

Cis and Trans Fatty
Acids
When plants
and animals
build fatty
acids they make
the cis forms
 Food
manufacturers
found that
foods like chips
with the trans
form have a
longer “shelf

Cis fatty acids
 Natural
 However
they turn rancid and
spoil
 The cis form is used by the
body.
 When the trans form is eaten
in foods the body tries to use
it for the same functions
 Cis are flexible and trans are
not flexible which causes them
adhere to surfaces
Polyunsaturated
 These
molecules have more
than one double bond
 Kinks - prevent stacking – lend
flexibility
Triglycerides
 Glycerol
+ 3 fatty acid chains =
a triglyceride
 Triglycerides are fat storage
molecules
 Provide slow release of energy
Steroids
 Family
of organic molecules
 Made of multiple rings
 Important constituent of
membranes
 They are hormones – signaling
molecules and messenger
molecules
Cholesterol
 Synthesized
in the liver
 Basis for the formation of sex
hormones
 Used in cell membranes
 Cause a problem when it is
deposited in the lining of blood
vessels
 May lead to arteriosclerosis
and heart attacks
Nucleic Acids
 Informational
molecules
 Information storage
 Transmission of information
 Linear polymers
 Catalytic properties( RNA)
 Gene Expression
Regulation(RNA)
 Structural( Ribosomes)
DNA
 Deoxyribonucleic
 Giant
acid
polymer
 Basis of heredity
 Purines( Adenine and guanine)
 Pyrimidines( Cytosine and
Thymine)
 Sugar – Deoxyribose
 Phosphate group
Nucleotides
Bases
 Bases
form hydrogen bonds in
the middle of the helix
DNA
 The
backbone of DNA is made
from sugar and phosphates
 The sugar and phosphates are
connected by phosphodiester
bond or linkage
 One end has an end with an
OH-this is called the 3’ end
 The other end has a PO4- this
is called the 5’end
DNA
 The
molecule is made of two
strands
 They are antiparallel
 3’------------------5’
 5’------------------3’
 The molecule is linear with
purine and pyrimidines in a
sequence
 The purines are bonded to the
pyrimidines with hydrogen
RNAs
RNAs are made complementary to
DNA
 Single stranded molecules
 Vary in function
Transfer RNA
Ribosomal RNA
Nc RNAs( noncoding RNAs)
Transcriptional regulators
Translational regulators
RNAi
Anti sense
