LIFE SCIENCE
BIOLOGICAL MOLECULES
ORGANIC compounds are those that contain carbon. These compounds, such as glucose, triacylglycerol, and guanine, are used in day-to-day metabolic processes. Many of these molecules are POLYMERS formed from repeated smaller units called MONOMERS.INORGANIC compounds are those that do not contain carbon. These make up a very small fraction of mass in living organisms, and are usually minerals such as potassium, sodium, and iron.
There are several classes of organic compounds commonly found in living organisms. These biological molecules include carbohydrates, proteins, lipids, and nucleic acids, which combined make up more than 95 percent of non-water material in living organisms.
Carbohydrates
CARBOHYDRATES, also called sugars, are molecules made of carbon, hydrogen, and oxygen. Sugars are primarily used in organisms as a source of energy: they can be catabolized (broken down) to create energy molecules such as adenosine triphosphate (ATP) or ni-otinamide adenine dinucleotide (NAD+), providing a source of electrons to drive cellular processes.
The basic formula for a carbohydrate is CH,O, and the majority of carbohydrates are multiples of this empirical formula. For example, GLUCOSE is CH,,. Carbohydrates can also bond together to form polymeric compounds. Some polymers of glucose include starch, which is used to store excess sugar, and cellulose, which i a support fiber responsible in part for the strength of plants.
Lipids
LIPIDS are compounds primarily composed of carbon and hydrogen with only a small percentage of oxygen. Lipids contain a HEAD, usually formed of glycerol or phosphate, and a TAIL, which is a hydrocarbon chain. The composition of the head, whether it's a carboxylic acid functional group, a phosphate group, or some other functional group, is usually polar, meaning it's hydrophilic. The tail is composed of carbon and hydrogen and is usually nonpolai, meaning it's hydrophobic.
The combined polarity of the lipid head and the nonpolarity of the lipid tail is a unique feature of lipids critical to the formation of the phospholipid bilayer in the cell membrane. The fatty acid tails are all pointed inward, and the heads are pointed outward. This provides a semipermeable membrane that allows a cell to separate its contents from the environment.
Figure 9.1. Free fatty acid lipid
The SATURATION of a lipid describes the number of double bonds in the tail of the lipid. The more double bonds a lipid tail has, the more unsaturated the molecule is, and the more bends there are in its structure. As a result, unsaturated fats (like oils) tend to be liquid at room temperature, whereas saturated fats (like lard or butter) are solid at room temperature.
Proteins
PRoTEINs are large molecules composed of a chain of AMINO ACIDS.
The sequence of amino acids in the chain determines the protein's structure and function. Each amino acid is composed of three parts:
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Amino group (-NH,): The amino group is found on all amino acids.
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Carboxyl group (-COOH: The carboxyl group is found on all amino acids.
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R group: The R group is a unique functional group that is different for each amino acid. For example, in the histidine amino acid seen in Figure 9.2, the R group is a cyclic imidazole group.
9.2. The amino acid histidine
The R group determines the amino acid's physiological function.
There are twenty-two amino acids used to produce proteins. It's not necessary to know each amino acid, but it's important to know that sequences of these amino acids form proteins and that each amino acid has a unique R-functional group.
Nucleic Acids
NUCLEIC ACIDS, which include DNA and RNA, store all information necessary to produce proteins. These molecules are built using smaller molecules called NUCLEOTIDES, which are composed of a
5-carbon sugar, a phosphate group, and a nitrogenous base.
DNA is made from four nucleotides: adenine, guanine, cytosine, and thymine. Together, adenine and guanine are classified as PURINES, while thymine and cytosine are classified as PYRIMIDINES.
These nucleotides bond in pairs; the pairs are then bonded in a chain to create a double helix shape with the sugar as the outside and the nitrogenous base on the inside. In DNA, adenine and thymine always bond as do guanine and cytosine. In RNA, thymine is replaced by a nucleotide called uracil, which bonds with adenine.
RNA also differs from DNA in that it often exists as a single strand.
Figure 9.3. DNA
Examples
1. Match the polymer with the correct monomer.
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DNA; nucleic acid
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RNA; amino acid
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starch; lipid
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histidine; glucose
2. Which of the following is not found in DNA?
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adenine
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uracil
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thymine
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cytosine
3. Which of the following is not a compound created from sugar?
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glycogen
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starch
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cellulose
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guanine
4. An amino acid contains an R group, an amino group, and a:
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hydroxyl group
-
carboxyl group
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phenyl group
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phosphate group
Answers: 1. A) 2. B) 3. D) 4. B)
THE HISTORY OF LIFE
Scientists believe life on Earth started around 3.8 billion years ago.
The exact time when the first living cells appeared is unknown, but observations in geology have indicated the type of environment when living cells first appeared. It's hypothesized that life began due to a sequence of events that created biological molecules and cell-like structures:
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synthesis of amino acid molecules and sugars, possibly from interaction of lightning and high temperatures near volcanic vents
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joining and interaction of these molecules in something resembling modern-day proteins
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assembly of these molecules within a membrane, which started to resemble a cell
The researchers STANLEY MILLER and HAROLD UREY had a hypothesis that the above three steps could have happened in a
primordial environment in which there was no oxygen. Note that higher concentrations of oxygen did not appear until the evolution of plants, so life must have started without a significant oxygen presence.
In the MILLER-UREY EXPERIMENT, the researchers placed a mixture of ingredients that included water, methane, ammonia, and hydrogen into an enclosed reactor bulb. The conditions were modified to simulate those that were thought to exist on Earth several billion years ago. A pair of electrodes was placed into the reactor vessel, and sparks that simulated lightning were fired through the mixture every few minutes.
Miller and Urey found that their reaction mixture turned pink in color within a day, and after two weeks, the reactor vessel contained a thick solution that included a number of important molecules. Among the compounds that formed were with some amino acids, including glycine, as well as sugars. After full charac-terization, the scientists found that the experiment created eleven of the twenty-two known amino acids.
Miller-Urey Experiment
Fossil Record
The FOSSIL RECORD is a history of species that existed throughout time that has been unearthed by archaeologists. The fossils, if well preserved, are able to show us the bone structures and the forms of animals, plants, and even cells that existed billions of years ago. The fossils can be used to understand how species evolved through time and, in some cases, even to see what they ate and the environments in which they lived.
The age of fossils is determined through a method called
RADIOMETRIC DATING, which examines the amount of radioactive carbon remaining in the sample. The radioactive carbon isotope carbon-14 has a half-life of 5,730 years, which means that this isotope can be used to reliably date fossils that are up to about ten half-lives, or 50,000 years in age. For fossils older than that, an isotope with a longer half-life is used. In some fossils, the presence of small amounts of uranium-238, with a half-life of 4.5 billion years, can aid in dating.
Timeline of Earth
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4.6 billion years ago: formation of Earth
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3.7 billion years ago: prokaryotes first came into existence
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2.6 billion years ago: oxygen is believed to be present in the atmosphere
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2.1 billion years ago: eukaryotic organisms have evolved
" S billion years ago: multicellular organisms h evolved
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800 million years ago: the first animals exist
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500 million years ago: Paleozoic Era
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260 million years ago: Mesozoic Era
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65 million years ago: Cenozoic Era
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10,000 years ago: early humans
The three eras. the Paleoroic. Mesozoic, and Cenozoic, were each characterized by an explosion of different species. Each era was responsible for the formation of a number of different species.
PALEOZOIC: The Paleozoic era was characterized by the colonization of land, with many types of plants appearing, and the diversification of fish and reptile species.
MESOZOIC: The Mesozoic era saw the first flowering plants appearing, as well as many land animals, including the dinosaurs.
However, at the end of the Mesozoic era, the extinction of the dinosaurs occurred, likely due to a catastrophic event such as a huge meteorite striking the earth.
CENOZOIC: In the Cenozoic era, many of the animals and plants that we see today started to evolve, including mammals, many different angiosperm plants, and the direct ancestors of humans.
Examples
1. A student is attempting to replicate the Miller-Urey experiment. Which of the following reagents does he not need?
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ammonia
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carbon dioxide
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oxygen
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water vapor
2. In the Miller-Urey experiment, which attempted to replicate conditions that were existent in early Earth, which of the following compounds was not created?
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amino acids
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methane
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lipid precursors
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chlorophyll
Answers: 1. C) 2. D)
THE BASICS OF THE CELL
The CELL is the most basic unit of life; all higher organisms are composed of cells. Most cells range from 20 um to 100 um in size, although some can be even larger. Cells were first discovered by
the Englishman RoBERT HooKE, the inventor of the microscope, in the 1600s. However, cell theory truly began to develop when a Dutchman named ANTONY VAN LEEUWENHOEK pioneered new developments in the field of microscopy, allowing scientists to view bacteria, protozoa, and other microorganisms.
Cell Subgroups
Cells are roughly divided into two large subgroups: prokaryotic cells and eukaryotic cells. The primary similarities and differences are listed in Table 9.1. below.
Table 9.1. Prokaryotic and eukaryotic cells
Traits unique to prokaryotic cells
Prokaryotic cells, such as bacteria, are the only types of cells that contain peptidoglycan, a sugar, and an amino acid layer that supports the cell membrane.
Prokaryotic cells do not have a nuclear membrane.
Many prokaryotic cells contain plasmids, which are circular rings of DNA that hold genetic information.
Traits shared by prokaryotic and eukaryotic cells
Both cells have cell membranes and often have cell walls.
Both types of cells contain DNA.
Both can have flagella and ribosomes.
Traits unique to eukaryotic cells
Eukaryotic cells have a nuclear membrane, and DNA is contained within the membrane.
Eukaryotic cells have a Golgi body, which is used for transport of proteins.
Some eukaryotic cells have lysosomes or peroxisomes, which are used in digestion.
Parts of the Cell
Although the cell is the smallest unit of life, there are many small bodies, called ORGANELLES, that exist in the cell. These organelles are required for the many processes that take place inside a cell.
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MITOCHONDRIA: The mitochondria are the organelles responsible for making ATP within the cell. A mitochondria has several layers of membranes used to assist the electron transport chain. This pathway uses energy provided by molecules such as glucose or fat (lipid) to generate ATP through the transfer of electrons.
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VACUOLE: A vacuole is a small body used to transfer materials within and out of the cell. It has a membrane of its own and can carry things such as cell wastes, sugars, or proteins.
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NUCLEUS: The nucleus of a eukaryotic cell contains all of its genetic information in the form of DNA. In the nucleus, DNA replication and transcription occur. In the eukaryotic cell, after transcription, the mRNA is exported out of the nucleus into the cytosol for use.
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ENDOPLASMIC RETICULUM: The ER, for short, is used for translation of mRNA into proteins and
for the transport of proteins out of the cell. The rough endoplasmic reticulum has many ribosomes attached to it, which function as the cell's machinery in transforming RNA into protein. The smooth endoplasmic reticulum is associated with the production of fats and steroid hormones.
RIBOSOME: The ribosome is a small two-protein unit that reads mRNA and, with the assistance of transport proteins, creates an amino acid.
Mitochondrion
Nucleus
(surrounded by nuclear membrane)
Lysosome
("breakdown body")
•Rough ER (studded with ribosomes)
Microtubules
(tiny tubes")
Plasma (cell) membrane
Figure 9.4. Animal cell
Golgi body
Smooth ER (no attached ribosomes)
Mitochondrion
Nucleus
(surrounded by nuclear membrane)
Microtubules
(tiny tubes")
Microfilaments. ("tiny threads")
Cell Wall (rigid)
Plasma (cell) membrane
Central vacuole•
Rough ER (studded with ribosomes)
Smooth ER (no attached ribosomes)
Golgi body
Chloroplast
(filled with chlorophyll)
Cell Membrane
The CELL MEMBRANE is a unique layer that surrounds the cell and performs numerous functions. It's composed of compounds called PHOSPHOLIPIDS, which are amphipathic, and consist of an alkane tail and a phospho-group head. The alkane lipid tail is hydrophobic, meaning it will not allow water to pass through, and the phosphate group head is hydrophilic, which allows water to pass through. The arrangement of these molecules forms a bilayer, which has a hydrophobic middle layer. In this manner, the cell is able to control the import and export of various substances into the cell.
Figure 9.6. Cell membrane bilayer
In addition to the phospholipid bilayer, the cell membrane often includes proteins, which perform a variety of functions. Some proteins are used as receptors, which allow the cell to interact with its surroundings. Others are TRANSMEMBRANE PROTEINS, meaning that they cross the entire membrane. These types of proteins are usually channels that allow the transportation of molecules into and out of the cell.
Membrane proteins are also used in cell-to-cell interaction. This includes functions such as cell-cell joining or recognition, in which a cell membrane protein contacts a protein from another cell. A good example, of this is the immune response in the human body. Due to the proteins found on the cell membrane of antigens, immune system cells can contact, recognize, and attempt to remove them.
Membrane Transport
A cell needs to be able to both import and export vital substances across the membrane while at the same time preventing harmful substances from entering the cell. Two major classes of transportation allow this process to occur: active transport and passive transport.
ACTIVE TRANSPORT uses ATP to accomplish one of two tasks: it can move a molecule against the concentration gradient (from low concentration to high), or it can be used to import or export a bulky molecule, such as a sugar or a protein, across the cell membrane.
Active transport requires the use of proteins and energy in the form of ATP. The ATP produced by the cell binds to the proteins in the
cell membrane and is hydrolyzed, producing the energy required to change the conformational structure of the protein. This change in
across the cell membrane.
the structure of the protein allows the protein to funnel molecules
PASSIVE TRANSPORT does not require energy and allows molecules such as water to passively diffuse across the cell membrane.
Facilirated diffusion is a form of passive transport that does not require energy but does require the use of proteins located on the cell membrane. These transport proteins typically have a "channel" running through the core of a protein specific to a certain type of molecule. For example, a transport protein for sodium only allows sodium to flow through the channel.
