1 the atoms of life h, o, c, n constitute 99% of the atoms in the human body. why? ( s and p are...
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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
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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
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