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Biological Molecules
Part 1
Chemistry of Life
• All matter is composed of atoms
• There are 3 types of subatomic particles
Type Charge Location– positive charge– Neutrons no charge nucleus– Electrons charge
Isotopes
• Isotopes are atoms of the same element which differ in mass and in number of
• Atomic number = # of = # • Atomic weight/MW = # protons + #
The atom
Understanding chemical bonding between atoms and molecules is fundamental to understanding biochemistry
Biochemistry: the chemistry that takes place within living systems
1:10
Elements in the Human Body
• • Carbon• • Nitrogen• • Phosphorus• Chlorine• Silicon• • Magnesium• Iodine•
Understanding chemical bonding between atoms and molecules is fundamental to understanding biochemistry
Covalent Bonds:Strong bonds formed by the sharing of electrons between adjacent atoms
Non Covalent Bonds (interactions):Weak interactions
• Ionic bonds (electrostatic interactions)
• Hydrogen bonds• van der Waals interactions• Hydrophobic effect
What is the most abundant molecule in a cell?
1:12
Covalent vs Ionic bonds
Covalent bonds: Ionic bonds:
1:13
• Ionic bonds result from loss or gain of electrons
What do you have when an electron leaves an atom? cation with a charge
What do you have an an electron is added to an atom?anion with a charge
• Two ions are held together by electrostatic interactions
• Biochemically significanat ions:
Ionic (electrostatic) bonds
1:14
• Formed by sharing electrons between atoms
• Each atom forms a characteristic number of covalent bonds with other atoms
(depends on the number of available/outer shell electrons)
carbon can form covalent single, double and triple bonds
Covalent bonds
Organic and Inorganic Compounds
Organic compounds• Chains C, H•
• Usually large molecules
•
Inorganic compounds• Usually metal/non-
metal combinations
• Small number of atoms
Water
• Covalently bonded together
• 2H, 1O atom
• Polar molecule– H carries a net charge– O carries a net charge– Therefore, H from one water molecule has an
attraction to the O of another water molecule
Hydrogen bonds between water molecules
the extensive hydrogen bonding between water molecules accounts for many of the properties of water such as
• boiling point (degrees Celsius)• freezing temperature ( degrees Celsius)• ability to interact with many other molecules
2:13
Role of Water
• : – due to its polarity– The solvent properties of water are vital in biology,
because many biochemical reactions take place only within aqueous solutions (e.g., reactions in the cytoplasm and blood)
• :– Water resists temperature change, and so it help
maintain a constant internal temperature in licing things
• :– Joint lubrication– Digestion (moving food through the digestive track)
Properties of Water
• Water has high (cling together) – This makes it good for materials
through tubes vessels• Water absorbs much before it warms up or ,
and gives off much heat before it . This way it protects organisms from rapid temperature .
• Water has a high heat of , keeping the body when it vaporizes sweat
• Frozen water is dense than liquid water.
Acids
example:
HCl +Cl-
Compounds that dissociate in water to form H+ ions
Bases
Compounds that dissociate in water to form OH- ions
pH scale
The acidity or basicity of a solution is referred to its pH
Acids pH < 7 (more )Bases pH > 7 (less )Neutral pH = 7 (H+ = OH-)
pH scale
• Measures the H+ concentration in a solution
• Every time the pH decreases by 1, each unit has 10 times the acidity of the previous unit– Example
• pH 6 = 1.0 x 10-6 M = 0.000001M [H+]• pH 5 = 1.0 x 10-5 M = 0.00001M [H+]
pH in Biological Systems
• Cellular processes are usually governed by the pH of the medium in which the process takes place
• Most biological systems are not exactly neutral– ex: blood had the pH of
Add OH-
Add H+
7.35 ideal
death
death
Buffer
• Used in order to maintain constant pH (not necessarily neutral)
• When pH is low, buffer will ad • When pH is , buffer will add
Blood
Carbonic Acid Bicarbonate Ion
H+ + HCO3-
• When pH of blood is too high (basic), the kidneys will remove the bicarbonate ions from the blood, reducing its concentration. The equilibrium will then shift to the left to compensate for the lost bicarbonate ion, generating more H+, lowering the pH.
+ H2CO3
• When pH of blood is too low (acidic), the H+ reacts with the bicarbonate ion to create more carbonic acid, reducing the number of H+ ions, therefore, increasing the pH
H+ + HCO3-
By the end of this section you should be able to:
• Describe the role of water as a solvent, temperature regulator and lubricant
• Describe how the polarity of the water molecule results in hydrogen bonding
• Differentiate among acids, bases, and buffers
• Describe the importance of pH to biological systems in the human body