BCEM 393 Chapter Notes - Chapter 1: Silicon Dioxide, Cytosine, Lipid Bilayer
15 May 2018
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Chapter 1 — Biochemistry and the Unity of Life
1.1 LIVING SYSTEMS REQUIRE A LIMITED VARIETY OF ATOMS AND MOLECULES
- Only 3 (oxygen, hydrogen, and carbon) of the 90 naturally occurring elements identified make
up 98% of the atoms in an organism
- The abundance of these 3 elements in life is vastly different from their abundance in Earth’s
crust. Why?
- One reason that oxygen and hydrogen are so common is the ubiquity of water, or the
matrix of life, as biochemist Albert Szent-Györgi called it. This tiny molecule consisting of
only 3 atoms make life on Earth possible
- The importance of water is so crucial that its presence is tantamount to saying that life
could be present
- Most large molecules in living systems are made up mostly of carbon
- Fuel molecules are made entirely of carbon, hydrogen, and oxygen
- Biological fuels (eg. fuels that power machinery) undergo combustion reactions1
- Carbon vs. Silicon
- Silicon
- Is more plentiful than carbon in Earth’s crust
- Can form 4 covalent bonds2
- Weaker bonds than carbon
- After combustion, silicon is essentially insoluble after reaction with oxygen. After it has
combined with oxygen, it is permanently out of circulation and is generally found as
quartz3
- Carbon
- Can form 4 covalent bonds
- Stronger bonds
- After combustion, carbon is readily soluble in water and can exist as a gas, thus, it
remains in biochemical circulation
- Difference in bond strength has 2 important consequences:
- Large molecules can be built with the use of carbon-carbon bonds as the backbone
because of the stability of these bonds
- More energy is released when carbon-carbon bonds undergo combustion than when
silicon reacts with oxygen. Therefore, carbon-based molecules are stronger construction
materials and are better fuels
1.2 THERE ARE FOUR MAJOR CLASSES OF BIOMOLECULES
- Proteins Are Highly Versatile Biomolecules
- Proteins are constructed from 20 building blocks (amino acids), which are linked by peptide
bonds to form long, unbranched polymers
1 The biological fuels react with oxygen to produce carbon dioxide and water
2 Property crucial to the construction of large molecules
3 Quartz is a common form of silicon dioxide
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- Polymers fold into precise 3D structures that facilitate a vast array of biochemical functions
- Protein function as signal molecules (eg. hormone) and as receptors for signal molecules
- Receptors convey to the cell that a signal has been received and initiates the cellular
response
- Example: Hormone, insulin, binds to its particular receptor, called insulin receptor, and
initiates the biological response to the presence of fuel in the blood
- Proteins also play structural roles, allow mobility, and provide defended against
environmental dangers
- Most prominent role of proteins is that of catalysts4, and protein catalysts are known as
enzymes
- Nucleic Acids Are the Information Molecules of the Cell
- The primary focus of nucleic acids is to store and transfer information. They contain
instructions for all cellular functions and interactions
- Similar to proteins, nucleic acids are linear molecules. However, they are constructer from
a 5-carbon sugar (either deoxyribose or a ribose), attached to a heterocyclic ring structure
called a base and at least one phosphoryl group
- There are two types of nucleic acid: DNA and RNA
- Genetic information is stored in DNA — the parts list that determines the nature of an
organism
- DNA is constructed from 4 deoxyribonucleotides, differing from one another only in
the ring structure of the bases — adenine (A), cytosine (C), guanine (G), and thymine
(T)
- The information content of DNA is the sequence of nucleotides linked together by
phosphodiester linkages
- DNA exists as a double-stranded helix, in which the bases interact with each other —
AT and CG
- RNA is a single stranded form of nucleic acid
- Some regions of DNA are copied as a special class of RNA molecules known as mRNA5
- mRNA is a template for the synthesis of proteins
- Unlike DNA, mRNA is frequently broken down after use
- RNA is similar to DNA composition with 2 exceptions: T is replaced by another base,
uracil (U), and the sugar component of the ribonucleotides contains an additional
hydroxyl (—OH) group
- Lipids Are a Storage Form of Fuel and Serve as a Barrier
- Lipids are much smaller than proteins or nucleic acids. Whereas proteins and nucleic acids
can have molecular weights of thousands to millions, a typical lipid has a molecular weight
of 1300 g/mol
- Lipids are not polymers made of repeating units, as are proteins and nucleic acids
- A key characteristic of biochemically important lipids is their dual chemical nature: a part of
the molecule is hydrophilic whereas another part (hydrocarbon chain) is hydrophobic
4 Catalysts are agents that enhance the rate of a chemical reaction without being permanently
affected themselves
5 messenger RNA
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Document Summary
Chapter 1 biochemistry and the unity of life. 1. 1 living systems require a limited variety of atoms and molecules. Only 3 (oxygen, hydrogen, and carbon) of the 90 naturally occurring elements identified make up 98% of the atoms in an organism. The abundance of these 3 elements in life is vastly different from their abundance in earth"s crust. One reason that oxygen and hydrogen are so common is the ubiquity of water, or (cid:1688)the matrix of life,(cid:1689) as biochemist albert szent-gy rgi called it. This tiny molecule consisting of only 3 atoms make life on earth possible. The importance of water is so crucial that its presence is tantamount to saying that life could be present. Most large molecules in living systems are made up mostly of carbon. Fuel molecules are made entirely of carbon, hydrogen, and oxygen. Biological fuels (eg. fuels that power machinery) undergo combustion reactions1. Is more plentiful than carbon in earth"s crust.
