Chapter 1 Biochemistry and the Organization in Cells
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Transcript of Chapter 1 Biochemistry and the Organization in Cells
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Paul D. Adams • University of Arkansas
Mary K. CampbellShawn O. Farrellhttp://academic.cengage.com/chemistry/campbell
Chapter One Biochemistry and the Organization of
Cells
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Some Basic Themes• All living things make use of the same types of biomolecules, and all
use energy– as a result, all living things can be studied using the methods
of chemistry and physics
• The fundamental similarity of cells of all types makes it interesting to speculate on the origins of life– both cells and the biomolecules of which they are made must
have arisen ultimately from very simple molecules, such as H2O, CH4, CO2, NH3, N2, and H2
• Field of Biochemistry draws many disciplines• allows us to answer questions related to molecular nature of
life
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Biomolecules
• Organic chemistry:Organic chemistry: the study of the compounds of carbon– the cellular apparatus of living organisms is made
up of carbon compounds– biomolecules are part of the subject matter of
organic chemistry– the reactions of biomolecules can be described by
the methods of organic chemistry
• The experiment of Friedrich Wöhler in 1828
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Levels of Structural Organization in the Human Body
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Biomolecules (Cont’d)
• Functional group:Functional group: an atom or group of atoms that shows characteristic physical and chemical properties
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ATP and The Reactions for its Formation
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Origins of Life• The “big bang” theory
– all matter was originally confined in a very small space– as the result of an explosion, it started to expand with great
force; temperature approx. 15 x 109 K– the average temperature of the universe has been decreasing
ever since– in the earliest stages of the universe, the only elements present
were H, He, and Li– other elements formed by
• thermonuclear reactions in stars• explosions of stars• the action of cosmic rays outside the stars
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Relative Abundance of Important Elements
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Biomolecules (Cont’d)• Gases present in the atmosphere of the early earth included
NH3, H2S, CO, CO2, CH4, N2, H2, and H2O but not O2
• Experiments have demonstrated that important biomolecules, such as proteins and nucleic acids, could have arisen under abiotic (nonliving) conditions from reactions of these simple compounds– in the earth’s oceans– on the surface of clay particles
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Biomolecules (Cont’d)• Living cells include very large molecules, such as proteins,
nucleic acids, polysaccharides, and lipids– these biomolecules are polymers (Greek: poly + meros, many +
parts)– they are derived from monomers (Greek: mono + meros, single
+ part) --amino acids --> proteins --nucleotides --> nucleic acids --monosaccharides --> polysaccharides --glycerol and 3 fatty acids --> lipids
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Informational Macromolecules
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Biomolecules (Cont’d)
• Enzymes:Enzymes: a class of proteins that are biocatalysts– the catalytic effectiveness of a given enzyme depends on its
amino acid sequence• Genetic code:Genetic code: the relationship between the nucleotide
sequence in nucleic acids and the amino acid sequence in proteins– theories of the origin of life consider how such a coding system
might have arisen
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Biomolecules (Cont’d)
• Which came first…the chicken or the egg?• catalytic activity associated with proteins• coding associated with nucleic acids
• It has been discovered recently that certain types of RNA have catalytic activity and are capable of catalyzing their own further processing (See Figure 1.7 p.12)• RNA is now considered by many scientists to have
been the original coding material• it still serves this function in some viruses
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The “RNA World”• The appearance of a form of RNA capable of coding for
its own replication was the pivotal point in the origin of life
• This original RNA both encoded for and catalyzed its own replication
• In time, this system evolved to encode for the synthesis of protein catalysts
• Even later, DNA became the primary genetic material, and RNA took on only an intermediary role in the synthesis of proteins
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Stages in the Evolution of Self-replicating RNA Molecules
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Theories on the Origin of Life• A key point in the development of living cells is the
formation of membranes that separate cells from their environment
• Some theories of the origin of life focus on proteins– according to one model, proteinoids aggregated
to form microspheres• Double-Origin theory:Double-Origin theory: the development of a coding
system and the development of catalysis came about separately– a combination of the two later in time produced
life as we know it.
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Prokaryotes and Eukaryotes
•• Prokaryote:Prokaryote: Greek derivation meaning “before the nucleus”
– single-celled organisms– include bacteria and cyanobacteria
•• Eukaryote:Eukaryote: Greek derivation meaning “true nucleus”• contain a well-defined nucleus surrounded by a
nuclear membrane• can be single celled, such as yeasts and
Paramecium, or multicellular, such as animals and plants
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Comparison of Prokaryotes and Eukaryotes
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Comparison of Prokaryotic and Eukaryotic Cell
mainly unicellular
0.2-5m in diameter anaerobic or aerobic No
free in cytoplasm as nucleoid
RNA & protein synthesized in the same compartment
no cytoskeleton
usually haploid simple division
following DNA replication
mainly multicellular; with differentiation of many cell types
10-50m in diameter aerobic Yes, with several kinds of
organelles in nucleus, condensed with
proteins into chromosomes RNA synthesized in nucleus;
proteins in the cytoplasm cytoskeleton composed of
protein filaments
almost always diploid or polyploid
mitosis in somatic cells; meiosis in gamete formation
Prokaryotes
EukaryotesCellular Organization
Cell Size
Metabolism
Compartmentalization
DNA
RNA and Protein
Cytoplasm
Ploidy
Cell Replication
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• Important organelles listed in table 1.3
A Comparison of a typical animal cell, plant cell, and prokaryotic cell
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Mitochondria
Site of ATP production via
aerobic metabolism Key Features
outer membrane intermembrane space inner membrane matrix
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Chloroplasts Site of photosynthesis in
plants and green algae Key Features
outer membrane intermembrane space inner membrane stroma thylakoid membrane thylakoid lumen
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Lysosomes
Responsible for degrading certain cell components material internalized
from the extracellular
environment Key Features
single membrane pH of lumen 5 acid hydrolases carry
out degradation reactions
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Peroxisomes
Responsible for degrading
fatty acids toxic compounds
Key Features single membrane contain oxidases and
catalase
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Five Kingdoms, Three Domains
• 5-kingdom system takes into account differences between prokaryotes and eukaryotes
• Provides classification for eukaryotes that are neither plants nor animals
• Kingdoms are: Monera, Protista, Fungi, Plantae, and Anamilia
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Five Kingdoms, Three Domains
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What is source of energy in cells?• Light from the sun is the ultimate source of
energy for all life on earth– photosynthetic organisms use light energy to drive
the energy-requiring synthesis of carbohydrates– non-photosynthetic organisms consume these
carbohydrates and use them as energy sources• The energetics of a chemical reaction
• if the change in free energy is negative (free energy decreases), the reaction is spontaneous as written
• if the change in positive (free energy increases), the reaction will not occur as written unless energy is supplied from an external source
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How are energy changes measured?
Thermodynamics- branch of science that answers questions about processes that are energetically favorable
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Spontaneity in biochemical reactions
• Free Energy of a System G < 0 spontaneous exergonic- energy released
G= 0 Equilibrium
G > 0 Nonspontaneous endergonic- energy required
• Life and Thermodynamics G=H-TS
H is heat of a reaction at constant pressure
S is the change in entropy
G is the change in free energy
• T is the temperature