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Chapter 1 Principles of Biochemistry

Chapter 1. Principles of Biochemistry
1.1 What Is Biochemistry?
1.2 The Chemical Basis of Life:
A Hierarchical Perspective
1.3 Storage and Processing of
Genetic Information
1.4 Determinants of
Biomolecular Structure and
1.1 What Is Biochemistry?
§ Biochemistry aims to explain biological processes at the
molecular and cellular levels.
§ It is a core discipline in life sciences.
§ It is at the interface of biology and chemistry.
§ It relies heavily on the quantitative analysis of data.
§ It often studies in vitro (outside a living cell) systems.
It All Started with Fermentation…
§ Fermentation is the conversion of rotting fruit or grain into
alcohol solutions through the action of yeast.
§ Yeast was determined to be the catalyst.
§ Used to produce wine and beer from yeast
Alcoholic Fermentation
§ This reaction has been around
since 2000 B.C.
§ Buchner demonstrated that
CO2 and CH3CH2OH were
produced in vitro from sugar
using brewer’s yeast in 1897.
§ Buchner is credited with
proposing that “enzymes”
helped speed up this reaction.
§ Biomolecules that increase the rate (catalyze) of biochemical
reactions dramatically
§ Found in all living cells
§ Responsible for the following reactions:
• Aerobic respiration
• Fermentation
• Nitrogen metabolism
• Energy conversion
• Programmed cell death
§ Examples:
• Proteins or ribonucleic acid (RNA)
Biochemistry: An Applied Science
§ Biochemistry uses advanced experimental methods to develop in
vitro conditions for exploiting cellular processes and enzymatic
1.2 The Chemical Basis of Life: A Hierarchical Perspective
§ The foundation of this
hierarchy includes
chemical elements and
functional groups.
§ Chemical elements:
Percent dry
weight (percent)
Additional trace
elements (less
than 0.1 percent),
Additional trace
elements (less
than 0.1 percent),
Upper M, n
Upper C
Upper N
Upper F, e
Upper O
Upper C, o
Upper H
Upper C, u
Upper C, a
Upper Z, n
Upper P
Upper S, e
Upper K
Upper M, o
Upper S
Upper C, l
Less than 1
Upper F
Upper N a
Less than 1
Upper C, r
Upper M, g
Less than 1
Upper S, n
Organizational Hierarchy of Biochemistry
Chemical Bonding Observed in Biochemistry
§ The most common carbon bonds are C—C, C=C, C—H, C=O,
C—N, C—S, and C—O.
Number of unpaired electrons
Upper H, one unpaired atom
Upper O, four paired and two unpaired atom.
Upper N, two paired and three unpaired atom.
Upper C four unpaired atom.
Molecular Geometry Revisited
§ A carbon atom can bind up to four single bonds to form a
§ The rotation around a single bond is very easy due to its sigma
bond, whereas a carbon–carbon double bond includes a pi bond
and rotation is not possible without breaking this pi bond.
Trace Elements
§ In addition to the elements observed in Table 1.1, trace elements
are used as cofactors in proteins and are required for life.
§ These elements are required in smaller (“trace”) amounts.
§ These elements include:
• Zinc
• Iron
• Manganese
• Copper
• Cobalt
Essential Ions
§ Play a key role in cell signaling and neurophysiology
§ Include:
• Calcium
• Chloride
• Magnesium
• Potassium
• Sodium
Functional Groups
§ Play an important role in structure and function of biomolecules
Biomolecules, Part 1
§ Four major types:
• Amino acids
• Nucleotides
• Simple sugars
• Fatty acids
Biomolecules, Part 2
Primary cellular function
Amino acid
Protein function
Nitrogen metabolism
Energy conversion
Nucleic acid function
Energy conversion
Signal transduction
Enzyme catalysis
Simple sugar
Energy conversion
Cell wall structure
Cell recognition
Nucleotide structure
Fatty acid
Cell membranes
Energy conversion
Cell signaling
Amino Acids
§ Nitrogen-containing
molecules that function
primarily as the building
blocks of protein
§ Covalently linked into a linear
chain to form polypeptides
§ Differ from each other by the
side chain attached at the
central carbon
§ Include the nucleic acids, DNA
and RNA
§ Consist of the following:
• Nitrogenous base
• Five-membered sugar
• 1–3 phosphate groups
§ Examples include:
• Cytosine
• cAMP
• NAD+
Simple Sugars
§ Carbohydrates
• Contain C, H, and O atoms
§ Have a 2:1 ratio of hydrogen
atoms to oxygen atoms
§ Include:
• Monosaccharides
• Disaccharides
Fatty Acids
§ Amphipathic molecules
§ Act as components of plasma
membrane lipids
§ Act as a storage form of
energy (i.e., fats)
§ Consist of:
• Carboxyl group attached to
a hydrocarbon chain
Saturated vs. Polyunsaturated Fatty Acids
§ Saturated fatty acids contain no C=C double bonds in the
hydrocarbon chain.
§ Polyunsaturated fatty acids contain multiple C=C double bonds
in the hydrocarbon chain.
§ Higher-end structural form of biomolecules
§ Include:
• Chemical polymers such as:
– Proteins—amino acid polymers
– Nucleic acids—nucleotide polymers
– Polysaccharides—polymers of glucose molecules
Polymers in Macromolecules: Nucleic Acids
§ Covalently linked
§ Include DNA and
§ Nucleotides are
linked together by
Polymers in Macromolecules: Proteins
§ Covalently linked amino acids
§ Also known as polypeptides
• R = different amino acid side chains
Polymers in Macromolecules: Polysaccharides
§ Consist of mixtures of simple sugars of repeating units of glucose
§ Covalent linkage between glucose units (i.e., glycosidic bond) is
key to the identification and chemical properties of the
Various Examples of Polysaccharides
Metabolic Pathways
§ Enable cells to coordinate and control complex biochemical
processes in response to available energy
§ Function within membrane-bound cells
§ Examples include:
• Glycolysis and gluconeogenesis (glucose metabolism)
• Citrate cycle (energy conversion)
• Fatty acid oxidation and biosynthesis (fatty acid metabolism)
Metabolic Pathway Terminology
§ Metabolites
• Small biomolecules that serve as both reactants and products
in biochemical reactions within cells
• Frequently observed in reactions that are essential in lifesustaining processes
§ Metabolic flux
• The rate at which reactants and products are interconverted in
a metabolic pathway
Metabolic Pathway Example: The Urea Cycle
Metabolic Pathway Formats
Cellular Structures
Key Cellular Structure Functions, Part 1
§ Genome
• All encoded genes and other DNA elements specifying genetic
composition of prokaryotic and eukaryotic cells
§ Nucleolus
• Site of ribosome assembly
§ Ribosomes
• Location of protein synthesis
Key Cellular Structure Functions, Part 2
§ Mitochondria
• Responsible for ATP production
§ Peroxisomes and lysosomes
• Involved in macromolecule degradation and detoxification
§ Endoplasmic reticulum
• Sequester ribosomes for protein synthesis
§ Golgi apparatus
• Involved in protein translocation and protein secretion in the
plasma membrane
Cell Specialization
§ A higher level of organizational complexity
§ Allows multicellular organisms to exploit their environment
through signal transduction
Signal Transduction
§ A complex organization level that consists of specialized cells
§ Allow multicellular organisms to respond to environmental
§ Can adapt to change through signal transduction mechanisms
that facilitate cell–cell communication
The Circulatory System
§ Highest level of hierarchical organization
§ Include cohabitation of different organisms in the same
environmental niche
§ Involve a shared use of resources and waste management
Ecosystem Examples
§ This is the top rung of the hierarchal ladder of life.
§ This is how organisms interact with their environment and each
1.3 Storage and Processing of Genetic Information
§ 1952 – DNA was determined
to be sufficient to promote
viral replication.
§ Rosalind Franklin collected Xray diffraction data to
determine the structure of
Watson and Crick’s Discovery
§ 1953 – Watson and Crick determined that DNA is a double helix.
§ This discovery explained how DNA was used to pass on genetic
§ 1962 – The duo were awarded the Nobel Prize in Physiology or
Deoxyribonucleotides vs. Ribonucleotides
§ Deoxyribonucleotides are
monomeric units of DNA that
lack an OH group on the C-2'
of the ribose sugar.
§ Ribonucleotides are
structurally similar to
deoxyribonucleotides, except
they contain an OH at the C-2'
position in the ribose sugar.
Nucleotide Base Pairs
§ The complimentary base pairs are as follows:
• in DNA: G-C and A-T
• in RNA: G-C and A-U
Nucleotide Base Pairs in the Helix
Central Dogma
§ Describes how information
is transferred between
DNA, RNA, and protein
Relationship between DNA and Protein
“-ome” Biochemistry
§ Genome
• Collection of genes
§ Transcriptome
• Collection of DNA transcripts (RNA products) generated by
DNA transcription
§ Proteome
• Collection of proteins produced by mRNA translation either in
the entire organism or under special conditions
1.4 Determinants of Biomolecular Structure and Function
§ Structure determines function for DNA.
Mutant Genes
§ Proteins acquire a bounty of molecular structures through
random mutations.
§ Can be germ-line cell
• Passed from parents to offspring
• Result in inherited genetic diseases
§ Can be in somatic cells
• Not inherited by the offspring
• Limited to the individual organism
Random Mutation and Natural Selection
Gene Duplications