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Biochemistry
Unit 1
Nucleus

Proton


(Positive charge)
Neutron

(Neutral charge)
Shells outside Nucleus

Electron

(Negative charge)

Arrangement of
electrons determine
reactions and nature of
bonds

Atomic Structure
Ionic Bonds



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
One or more electrons completely transferred
Receiving atom gains negative charge
Donating atom gains positive charge
ION=atom with a positive or negative charge
Attraction between charges bonds atoms
e.g. Na+ and Cl- form NaCl
Covalent Bonds



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Electrons shared between atoms
Single covalent bond shares 2 electrons
Double covalent bond shares 4 electrons
Triple covalent bond shares 6 electrons
Nonpolar covalent bond = 2 e- shared equally
Polar covalent bond = 2 e- shared differently
Larger nucleus pulls on e- stronger
 Creates charged poles in molecule

Covalent Bonds
Polar Covalent Bond
Hydrogen Bonds


Weak bond between oppositely charged poles of
different molecules
e.g. Water molecules
Properties of Water

Hydrogen bonds give water special properties
Excellent solvent
 High degree of cohesion
 Temperature is stable

Water as a Solvent


Ionic substances are soluble because of + and –
charges on water molecules’ poles
Polar covalent substances are soluble because
they have hydrogen bonding with water

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Hydrophilic = water loving
Nonpolar covalent substances do not dissolve
because the do not have charged poles

Hydrophobic = water hating
Water Cohesion

Strong surface tension

Strong capillary action
Stable Temperature of Water
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
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Relatively large amount of energy to warm (and
boil) or cool (and freeze)
Removes a lot of heat when perspiration
evaporates
Oceans provide a temperature-constant
environment
Organic Molecules


Based on Carbon (C)
Has 4 e- available for covalent bonding
Organic Molecules

Carbon chains form complex structures
Chains
Rings
Organic Molecules

Other atoms add variety
Hydrogen (H)
 Oxygen (O)
 Nitrogen (N)
 Sulfur (S)
 Phosphorus (P)


They form functional groups that give organic
molecules specific properties
Functional Groups

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Polar
Hydrophilic
Functional Groups

Weak acid
Functional Groups

Weak base
Functional Groups
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Acid
Functional Groups
Methyl

Hydrophobic
Functional Groups

Polar
Organic Molecules

Other atoms add variety
Hydrogen (H)
 Oxygen (O)
 Nitrogen (N)
 Sulfur (S)
 Phosphorus (P)


They form functional groups that give organic
molecules specific properties
Carbohydrates

Monosaccharides are simplest


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Consist of one sugar
Have formula (CH2O)n where n is between 3 and 8
Glucose and fructose: n = 6 (i.e. C6H12O6) but configuration is
different
Small changes in shape can cause dramatic chemical changes
Carbohydrates
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Disaccharides are two linked sugar molecules

Sucrose is glucose and fructose linked
Carbohydrates

Polysaccharides are a chain of monosaccharides

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Any molecule of repeating units is a polymer
Starch is a chain of thousands of α-glucose units

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Food storage in plants
e.g. Potatoes
Cellulose is a chain of thousands of β-glucose units

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Storage and structure
e.g. Wood and cell walls in plants
Lipids
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Insoluble in water, but soluble in nonpolar substances
Fats, oils, and waxes have three fatty acids attached to a
glycerol
Lipids

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Saturated fatty acids—carbons have single
bonds between them with hydrogens attached
Unsaturated fatty acids—carbons have double
bonds between them
Polyunsaturated fatty acids have multiple double
bonds
Fatty acids differ by size of chain and number of
double bonds
Lipids
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Phospholipids have
phosphate functional
groups
Structural foundation of
cell membranes
Occur in double
membrane with
hydrophilic heads
outside and hydrophobic
tails inside
Lipids

Steroids have a backbone
of four linked carbon
rings


Cholesterol
Some hormones
Proteins

A variety of functions
Structural (hair, fingernails, eggs, muscles, etc.)
 Enzymes (catalysts in biological systems)
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Polymers of amino acids
Bonds between amino acids are called peptide bonds
 Proteins are polypeptides

Proteins
Proteins
Proteins

Four levels of structure
Primary—order of amino acids
 Secondary—three-dimensional shape caused by
hydrogen bonding (α-helix or β-pleated sheet)
 Tertiary—three dimensional shape caused by
interaction of R-groups (forming globular proteins)
 Quaternary—two or more separate polypeptides
joining to form a larger protein

Proteins
Nucleic Acids


Nucleic acids store and transmit hereditary
information
Genes
Are the units of inheritance
 Program the amino acid sequence of polypeptides
 Are made of nucleotide sequences on DNA

The Roles of Nucleic Acids

There are two types of nucleic acids
Deoxyribonucleic acid (DNA)
 Ribonucleic acid (RNA)

Deoxyribonucleic Acid

DNA
Stores information for the synthesis of specific
proteins
 Found in the nucleus of cells

36
DNA Functions
Directs RNA synthesis (transcription)
 Directs protein synthesis through RNA (translation)

DNA
1
Synthesis of
mRNA in the nucleus
mRNA
NUCLEUS
CYTOPLASM
mRNA
2
3
Figure 5.25
Movement of
mRNA into cytoplasm
via nuclear pore
Ribosome
Synthesis
of protein
Polypeptide
Amino
acids
The Structure of Nucleic Acids
5’ end

Nucleic acids

5’C
Exist as polymers called
polynucleotides
O
O
3’C
O
O
5’C
O
O
O
O
3’C
(a) Polynucleotide,
or nucleic acid
OH
3’ end
Figure 5.26

Each polynucleotide
Consists of monomers called nucleotides
 Sugar + phosphate + nitrogen base

Nucleoside
Nitrogenous
base
O

O
P
5’C
O
CH2

O
O
Phosphate
group
Figure 5.26
(b) Nucleotide
3’C
Pentose
sugar
Nucleotide Monomers

Nucleotide monomers

Are made up of
nucleosides (sugar + base)
and phosphate groups
Nitrogenous bases
Pyrimidines
NH2
O
O
C
C
CH
C
3
N
CH
C
CH HN
HN
CH
C
CH
C
C
CH
N
N
O
N
O
O
H
H
H
Cytosine Thymine (in DNA) Uracil
(inRNA)
RNA)
Uracil (in
U
C
U
T
Purines
O
NH2
N C C
N C C
NH
N
HC
HC
C
CH
N C
N
NH2
N
N
H
H
Adenine
Guanine
A
G
Pentose sugars
5”
HOCH2 O OH
4’
H H
1’
H 3’ 2’ H
OH H
Deoxyribose (in DNA)
Figure 5.26
(c) Nucleoside components
5”
HOCH2 O OH
4’
H H
1’
H
H
3’ 2’
OH OH
Ribose (in RNA)
Nucleotide Polymers
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Nucleotide polymers

Are made up of nucleotides linked by the–OH
group on the 3´ carbon of one nucleotide and
the phosphate on the 5´ carbon on the next
Gene

The sequence of bases along a nucleotide
polymer

Is unique for each gene
The DNA Double Helix

Cellular DNA molecules
Have two polynucleotides that spiral around an
imaginary axis
 Form a double helix
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The DNA double helix
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Consists of two antiparallel nucleotide strands
5’ end
3’ end
Sugar-phosphate
Base pair (joined by
backbone
hydrogen bonding)
Old strands
A 3’ end
Nucleotide
about to be
added to a
new strand
5’ end
New
strands
3’ end
Figure 5.27
5’ end
3’ end
A,T,C,G

The nitrogenous bases in DNA
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Form hydrogen bonds in a complementary fashion
(A with T only, and C with G only)
DNA and Proteins as Tape
Measures of Evolution

Molecular comparisons

Help biologists sort out the evolutionary
connections among species
The Theme of Emergent Properties in the
Chemistry of Life: A Review

Higher levels of organization

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Result in the emergence of new properties
Organization

Is the key to the chemistry of life
Chemical Reactions in
Metabolic Processes

ATP provides the chemical energy for many metabolic
reactions
Chemical Reactions in
Metabolic Processes

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Reaction needs to reach activation energy
Catalyst accelerates reaction by lowering
required activation energy
Catalyst does not change during the reaction
Chemical Reactions in
Metabolic Processes

Reactions in biological systems are part of the
metabolism
Catabolism breaks down
 Anabolism or synthesis builds up
 Energy is transferred from one substance to another

Chemical Reactions in
Metabolic Processes


Net direction of reaction
is determined by
concentrations of
reactants and end
products
Chemical equilibrium
occurs when
concentrations of both
reactants and end
products are the same
Chemical Reactions in
Metabolic Processes

Enzymes are catalysts in biological reactions
Enzymes are globular proteins
 Specific to one reaction
 Enzymes are named with “ase” suffix
 Enzymes act on the substrate

Chemical Reactions in
Metabolic Processes
Induced fit model—active site of enzyme attaches
to substrate changing its shape for easier reaction
Chemical Reactions in
Metabolic Processes

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Enzymes operate at optimum temperature and
pH
If temperature or pH is off, the enzyme’s
structure can denature

If denatured, it does not revert to original structure
Chemical Reactions in
Metabolic Processes

Cofactors are nonprotein molecules that assist
enzymes in lowering the activation energy


Minerals
Organic cofactors are called coenzymes

Vitamins
Chemical Reactions in
Metabolic Processes

Reactions are regulated by
Allosteric enzymes
 Feedback inhibition
 Competitive inhibition

Chemical Reactions in
Metabolic Processes

Allosteric enzymes have
two binding sites

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
One for substrate
One for allosteric effector
Effector can either
activate or inhibit reaction
Chemical Reactions in
Metabolic Processes

Feedback inhibition


End product serves as an allosteric effector to shut
down reaction
Competitive inhibition

A substance other than the substrate occupies the
active site and keeps the reaction from happening