1 The Atoms of Life H, O, C, N constitute 99% of the atoms in the human body. Why? ( S and P are also important in biomolecules) Ability to form covalent.

1

The Atoms of Life H, O, C, N constitute 99% of the atoms in the human body.

Why?(S and P are also important in biomolecules)

Ability to form covalent bonds by sharing electrons - covalent bonds are strongerLightest atoms capable of forming such bondsstrength of covalent bonds is inversely proportional to atomic weights of atoms so they form the strongest covalent bonds.C, N, O can form double bonds, C and N can form triple bonds

1s

2s

2p

H

1s

2s

2p

C

1s

2s

2p

N

1s

2s

2p

O

1 bondno lone pairs

4 bondsno lone pairs

3 bonds3 pairs

2 bonds2 lone pairs

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Biomolecules are Carbon Compounds

All biomolecules contain carbonvery versatile in forming covalent bonds - can form the most - 4four covalent bonds arranged tetrahedrally - adds to versatilitycan bond to N, O, and Hcan form single bonds to itself stably - unlike N and O - N-N and O-O

single bonds are very unstable

Atoms other than carbon are called heteroatomsin organic and biochemistry.

1s

2s

2p

C

C

HHH

H

C

HHH

OH

C

HHH

NHH

C

H

H

H

H C

O

H

H

H

H

C

N

H

H

H

H H

CH4

CH3OH CH3NH2

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Functional Groups Determine Physical and Chemical PropertiesOver 18 million organic molecules can be classified into 14 families. Classificationdepends on the functional groups present in the molecule. Below are the mostimportant functional groups in biochemistry.

The reactive part of the molecule (the part that has

a functional).

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Biological macromolecules have a “Sense” or Directionality

They have “Structural Polarity” - they are not symmetricalMonomers have a “head” and a “tail” - joining occurs in a head-to-tail

fashion“My favorite class is Biochemistry not P. E.” “P.E. not Biochemistry is

class favorite my”

Properties of Biomolecules

H3N CH C

CH3

O

O

H3N CH C

CH2

O

O

CH2

C

OH

O

H3N CH C

CH3

O

O

NH

CH C

CH2

O

O

CH2

C

OH

OOR

HN CH C

CH3

O

O

H3N CH C

CH2

O

O

CH2

C

OH

O

Amino terminus

Amino terminus

Carboxy terminus

Carboxy terminus

Ala-Glu and Glu-Ala will havedifferent reactive properties

Ala-Glu

Glu-Ala

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More Properties of Biomolecules Biological macromolecules are informational

Reading some biological macromolecules in the proper direction can specify information - like reading words in the proper direction gives information

DNA read in the proper direction codes for genesMust have some mechanism for recognizing and deciphering the

information, though.

Biomolecules have unique and characteristic 3D shapes

HIV-1 Protease with InhibitorPDB code 1A30

What gives biomolecules their unique and characteristic shapes?

Deoxygenated Human HemoglobinPDB code 2HHB

6

Biomolecules interact through “structural complementarity”

Life is dependent on the ability of millions of biomolecules to recognize and interact withone another in very specific ways.

HIV-1 Protease with inhibitor

Enzyme-substrate, DNA strands, receptor-ligand, antibody-antigen, sperm-egg, protein subunits, enzyme-inhibitors

What determines structural complementarity?

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May the Weak Forces Be with You Weak forces direct and maintain biological structure

covalent bonds hold atoms together to form moleculesIntramolecular - occur between different parts of same moleculenon-covalent forces determine the 3D shape of molecules (e.g. they

determine the characteristic shape of proteins)

Weak forces determine structural complementarity

Intermolecular - occur between different molecules

non-covalent forces direct enzyme-substrate interactions, hold 2 strands of DNA together and subunits of proteins, help ligands find the correct receptor

(also partly responsible for physical properties)

Weak forces permit transient interactionsbiomolecular interactions should be transient - ligands must come off

receptors, DNA strands must separate for replication

Weak forces demand certain environmental conditions

weak forces are destroyed if a narrow range of conditions are not present

pH, ionic strength, and temperature must be kept semi-constant or biological structure is destroyed (called denaturation)

If structure is destroyed, so is function

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There are 4 Major Types of Weak Forces in Biochemistry

Van der Waals Interactionsoccurs between nuclei of one atom and electron cloud of anotheroperates only over a limited inter-atomic distancevery weak - many must add to be significant

Atoms of Gln 121 from lysozyme fit neatly into a pocket on an antibody against lysozyme.The atoms of Gln 121 and those of the antibody are of the correct distance apart to havefavorable van der Waals interactions. These interactions stabilize the binding of lysozymeto its antibody.

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Hydrogen bondsoccur between a hydrogen covalently bound to an electronegative

atom (O or N) and the lone pair of a second electronegative atom (O or N)

hydrogen bond donor - the hydrogen bound to the electronegative atom

hydrogen bond acceptor - the second electronegative atomstronger than van der Waalshydrogen bonds are highly directional - form straight bonds between

donor, hydrogen, and acceptor atoms.Very important in nucleic acid and protein structure

GC base pair

AT base pair

The base pairs of nucleic acids such as DNA interactthrough hydrogen bonds and other weak chemicalforces. It is largely the hydrogen bonds that direct DNA replication and transcription.

O

HO

H

O

HO H

linear H-bond non-linear H-bond

donor

acceptor

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Ionic Interactions (Salt Bridges)occur between a positively charged atom (like NH4

+) and a negatively charged atom (like COO-) like nonmetal cations and metal anions to form salts

can also have repulsive electrostatic interactions

Protein strand

Intramolecular ionic bonds betweenoppositely charged groups on aminoacid residues in a protein

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Hydrophobic InteractionsWarning: Many textbook descriptions of the “hydrophobic effect” are

incorrect or incomplete

driving force for DNA strand association, for protein folding, and for membrane formationhydrophobic - “water hating” - nonpolarhydrophilic - “water loving” - polarnonpolar molecules don’t “prefer” to interact - it is the water that prefers non-ordered

interaction with itself and excludes nonpolar molecules in the process.Water molecules would have to be ordered around a non-polar molecule (entropically

disfavored). The aggregation of nonpolar requires less water to be ordered than if each nonpolar molecule were surrounded by water by itself.

Non-polar amino acids are buried inside a protein and DNA bases are buried inside the helix.

Related Application: The Power of SoapHydrophobic interactions allow dirt and grease (nonpolar substances) to be washed away in water. Through the formation of micelles, the long, nonpolar, and hydrophobic tails of soap surround the particles of grease and dirt. The polar head groups of soap interact favorably with water.

water

Sodium oleate - amphiphilic

Na+

Polar headgroup

Nonpolar hydrocarbontail