Biological Molecules Part 1. Chemistry of Life All matter is composed of atoms There are 3 types of subatomic particles TypeChargeLocation –positive charge.

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

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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?

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Covalent vs Ionic bonds

Covalent bonds: Ionic bonds:

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• 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

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• 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

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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