Download Organic Molecules

Biochemistry

Organic compounds - Contain carbon & hydrogen,
are covalently bonded

Inorganic compounds

Water, salts, and many acids and bases

acid HCl --> H+ (proton donor) + Cl- pH below 7

base NaOH --> Na+ (cation) + OH- , proton
acceptor, pH above 7

salt NaCl --> Na+ (cation) + Cl- (anion), pH 7
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Figure 2.14
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Organic Compounds

Carbohydrates

Lipids

Proteins

Nucleic Acids
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Carbohydrates

Contain carbon, hydrogen, and oxygen

Function: source of cellular food

Examples: Monosaccharides or simple sugars

6-carbon structural isomers
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Figure 2.14a
Figure 2.16
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Figure 2.15a
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Figure 2.17
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Figure 2.15b
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Carbohydrates

Disaccharides or double sugars
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Figure 2.14b
Carbohydrates

Polysaccharides or polymers of simple sugars
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Figure 2.14c
Starch vs. Cellulose (fiber)
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Lipids

Contain C, H, and O, but the proportion of oxygen
in lipids is less than in carbohydrates

Examples:

Neutral fats or triglycerides

Phospholipids

Steroids
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Neutral Fats (Triglycerides)

Composed of three fatty acids bonded to a glycerol molecule

Neutral fats – found in subcutaneous tissue and around organs
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Figure 2.15a
Figure 2.19
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Other Lipids


Phospholipids – modified triglycerides with two
fatty acid groups and a phosphorus group
Phospholipids – chief component of cell
membranes
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Figure 2.15b
Figure 2.20
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Other Lipids


Steroids – four interlocking hydrocarbon rings
cholesterol, bile salts, vitamin D, sex hormones,
and adrenal cortical hormones
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Figure 2.15c
Amino Acids

Building blocks of protein, containing an amino
group, NH2 and a carboxyl (acid) group COOH
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Figure 2.23a
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Protein

Macromolecules composed of combinations of 20
types of amino acids bound together with peptide
bonds
Peptide bond
H
H
R
O
N
C
C
OH
H
Amino acid
+
H
H
R
O
N
C
C
OH
H
Amino acid
Dehydration H O
2
synthesis
Hydrolysis
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H
H2O
H
R
O
H
R
O
N
C
C
N
C
C
H
H
OH
Dipeptide
Figure 2.17
Structural Levels of Proteins

Primary

Secondary

Tertiary

Quaternary
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Structural Levels of Proteins
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Figure 2.18a–c
Structural Levels of Proteins
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Figure 2.18b,d,e
Protein Denaturation

Reversible unfolding of proteins due to drops in
pH and/or increased temperature
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Figure 2.19a
Protein Denaturation

Irreversibly denatured proteins cannot refold and
are formed by extreme pH or temperature changes
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Figure 2.19b
Characteristics of Enzymes

Most are globular proteins that act as biological
catalysts

Holoenzymes consist of an apoenzyme (protein)
and a cofactor (usually an ion)

Enzymes are chemically specific

Frequently named for the type of reaction they
catalyze

Enzyme names usually end in -ase

Lower activation energy
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Characteristics of Enzymes
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Figure 2.20
Mechanism of Enzyme Action

Enzyme binds with substrate

Product is formed at a lower activation energy

Product is released
Active site
Amino acids
+
Enzyme (E) Substrates (S)
H2O
Enzyme-substrate
complex (E-S)
Free enzyme (E)
Peptide bond
Internal rearrangements
leading to catalysis
Dipeptide product (P)
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Nucleic acids are polymers of monomers called nucleotides.
Each nucleotide consists of three parts: a nitrogen base, a pentose sugar, and a
phosphate group
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Nucleic Acids
Composed of carbon, oxygen, hydrogen, nitrogen, and phosphorus
Their structural unit, the nucleotide composed of
N-containing base
pentose sugar
phosphate group


Five nitrogen bases contribute to nucleotide structure – adenine (A), guanine
(G), cytosine (C), thymine (T), and uracil (U)
Two major classes – DNA and RNA
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Deoxyribonucleic Acid (DNA)
 Double-stranded helical molecule found in the
nucleus of the cell

Replicates itself before the cell divides, ensuring
genetic continuity

Provides instructions for protein synthesis
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Structure of DNA
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Figure 2.22b
Ribonucleic Acid (RNA)

Single-stranded molecule found in both the nucleus and the
cytoplasm of a cell

Uses the nitrogenous base uracil instead of thymine

Three varieties of RNA: messenger RNA, transfer RNA, and
ribosomal RNA
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Adenosine Triphosphate (ATP)

Source of immediately usable energy for the cell

Adenine-containing RNA nucleotide with three
phosphate groups
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Figure 2.29
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Energy

The capacity to do work (put matter into motion)

Types of energy


Kinetic – energy in action
Potential – energy of position; stored (inactive)
energy
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Forms of Energy

Chemical – stored in the bonds of chemical substances

Electrical – results from the movement of charged particles

Mechanical – directly involved in moving matter



Radiant or electromagnetic – energy traveling in waves (i.e., visible light,
ultraviolet light, and
X-rays)
Energy is easily converted from one form to
another (First Law of Thermodynamics)
During conversion, some energy is “lost” as heat
( Second Law of Thermodynamics - Entropy)
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
Chemical reactions can be classified as either
exergonic (exothermic) or endergonic (endothermic)

An exergonic reaction - release of free energy
lower potential energy in endproduct
Fig. 6.6a
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
An endergonic reaction is one that absorbs free
energy from its surroundings.

Endergonic reactions store energy greater potential
energy in endproduct

Sunlight- source of energy for photosynthesis
Fig. 6.6b
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
ATP couples exergonic reactions to
endergonic reactions

ATP (adenosine triphosphate) is a type of nucleotide consisting of the
nitrogenous base adenine, the sugar ribose, and a chain of three phosphate
groups.
Fig. 6.8a
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
The bonds between phosphate groups can be broken
by hydrolysis.
ATP is regenerated by adding a phosphate group to ADP.
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Enzymes speed up metabolic reactions by
lowering energy barriers

A catalyst is a chemical agent that changes the rate
of a reaction without being consumed by the reaction.

An enzyme is an organic catalyst.
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
Exergonic reaction requiring Activation energy

Activation energy is the amount of energy necessary
to push the reactants over an energy barrier.
Fig. 6.12
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Figure 2.26
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
Enzyme speed reactions by lowering EA.

The transition state can then be reached even at
moderate temperatures (body temperature).

Enzymes hasten reactions that would occur
eventually.

enzymes are selective
they determine
which chemical
processes will
occur at any time.
Fig. 6.13
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Enzymes are substrate specific

A substrate is a reactant which binds to an enzyme
at its active site.
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