study of the science of biology

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Biology Is The Science Of Life.

How Are Living Things Organized?

All living things live in a hierarchical order that starts on the cellular level and ends on the population level, with different properties at each level known as emergent properties.

What Are The Properties Of Life?

All living things must meet certain characteristics in order to be considered living. These include: cellular organization, order, sensitivity, growth, development and reproduction, energy utilization, evolutionary adaptation, and homeostasis.

How Can Living Things Be Hierarchically Organized?

Cellular Level

Organismal Level

Populational Level

Atoms<Molecule

<Macromolecule<

Organelle<Cell

Tissue<Organ<

Organ System<Organism

Population<Species

<Community<Ecosystem

What Are Emergent Properties?

Emergent Properties are properties that enter at each higher level of the hierarchy. These are properties that result in the way of the interaction between components.

Scientists Form Generalizations from Observations.

What Is The Nature Of Science?

The nature of science is both deductive and inductive. The corresponding forms of though and reasoning are used by scientists in order to understand the nature of science.

How Do Scientists Apply Deductive Reasoning?

Scientists apply Deductive Reasoning by using general rules and beliefs in order to predict specific results and outcomes. It is used to predict validity of general ideas and rules.

How Do Scientists Apply Inductive Reasoning?

Inductive Reasoning is the opposite of Deductive Reasoning. Rather than using general rules to predict specific results, it uses specific results to form general ideas. It is used to lead to generalizations.

How Is Science "Done"?

Scientists make observations and then make a hypothesis (a suggested/reasonable explanation) as a result based on their observations.

Although these hypotheses are based on the scientist's observations, they are always subject to rejection in the future and often reject on or more alternative hypotheses themselves in order to prove validity.

How Is A Hypothesis Tested?

Hypotheses are tested through experiments.

Experiments do not prove any hypotheses true, but rather prove alternate ones false.

How Are Controls Established?

Often scientists will conduct two experiments at the same time in order to determine how a process is affected by different variables, or factors. In one experiment, all the variables are kept constant (or the same) except one. In the other (the control experiment), that variable that was kept constant in the other experiment is left unaltered.

How Are Predictions Used?

Predictions are used to prove a hypothesis invalid or valid.

If an experiment shows results that are not shown by the hypothesis, then that hypothesis must be rejected.

If the same experiment shows the same results as the hypothesis shows, then the hypothesis is supported.

How Are Theories Developed?

A theory is a proposed explanation; it is often used/supported by general principles or relating concepts.

How Is Research Used In The Scientific Method?

After making a hypothesis and performing a series of experiments, a paper is written describing the experiment and the results; the paper is then given in for peer review. Afterwards it is given for publication in a scientific journal.

Basic research is intended to expand knowledge known about a subject and applied research is knowledge gained as a result of basic research.

Section On Charles Darwin Will Be Read And Outlined Later In The Course. Skip These Pages (8 - 14) For Now.

Four Themes Unify Biology As A Science.

How Does The Cell Theory Unite Biology?

The Cell Theory makes the basis for understanding the processes of reproduction and growth for all organisms. This also explains the organization of living things on a cellular level.

How Does The Molecular Basis Of Inheritance Unite Biology?

All living things have a mechanism for heredity (DNA). This explains the inheritance of new born organisms and how life continues.

How Does Evolutionary Change Unite Biology?

Evolutionary change unites biology by explaining diversity of different species and how they evolved to adapt to their environment.

How Does Evolutionary Conservation Unite Biology?

Evolutionary Conservation unites biology by explaining what characteristics were conserved during evolution and where certain organisms evolved from.

Chapter 2 Outline

Atoms Are Nature's Building Material.

What Is An Atom?

Everything is made of matter, and matter is made of atoms.

Matter requires mass and occupies space

Atoms are extremely small particles that make up matter

What Is The Structure Of An Atom?

An atom contains a positively charge nucleus in the center with protons and neutrons. Circling around the nucleus are electrons.

Protons=positively charged, Neutrons=neutral in charge, Electrons=negatively charged

What Is Atomic Mass?

Atomic Mass is the number of protons and neutrons within an atom.

How Are The Isotopes Different?

Isotopes are atoms that have a different amount of neutrons than a regular atom

Radioactive isotopes are unstable and therefore their nuclei break up and decay into elements with lower amounts of protons. The rate of their decay is expressed in half-lives.

What Are Electrons?

Electrons are negatively charged particles that circle the nucleus in orbitals.

How Do Electrons Determine The Chemical Behavior Of Atoms?

Electrons determine the chemical behavior of atoms by the number and arrangement of the electrons in the orbit.

Oxidation is the loss of an electron while reduction is the gain of an electron

Where Is The Energy Within The Atom Found?

Energy within the atom is found either as potential energy when in the same position. Moving an electron further from the nucleus absorbs energy while bringing it closer release energy.

The Atoms Of Living Things Are Among The Smallest.

Are There Different Kinds Of Atoms?

There are 92 different types of natural elements, each with a different type of atom.

What Is The Periodic Table?

The Periodic Table is a table invented by Dmitri Mendeleev that arranges elements in a pattern of chemical properties which elements were placed in groups of eight elements.

Chemical Bonds Hold Molecules Together.

Why Do Ionic Bonds Form Crystals?

Ionic Bonds form crystals because

Why Is Table Salt An Ionic Compound?

Table salt is an ionic compound because Na (Sodium) has one valence electron, which can be paired to another set of valence electrons, and Cl (Chlorine) has 7 valence electrons. When paired, they make 8 valence electrons, a complete set, and make Na+ and Cl- ions, or opposite electrical charges, making an ionic bond and ionic compound when joined together.

How Do Covalent Bonds Build Stable Molecules?

Covalent bonds share electrons when bonding, rather than losing or gaining like ionic bonds. The reason that the molecules are stable is because the end product has no electrical charge, has no free valence electrons, and the shared electrons orbit both nuclei, satisfying the octet rule.

Why Are Covalent Bonds So Strong?

The strength of covalent bonds is dependent on the number of shared electrons; therefore the more electrons are shared the stronger the bond will be.

Single Bond<Double Bond<Triple Bond

How Can Molecules Have Several Covalent Bonds?

An atom is able to share electrons with more than just another atom. Those atoms that require two or more electrons may achieve this by sharing electrons with two or more atoms.

How Do Chemical Reactions Take Place?

Chemical reactions are formed by making or breaking chemical bonds. These reactions can be influenced by many factors including temperature, concentration of reactants and products, and whether or not there is a catalyst involved in the reaction.

Water Is The Cradle Of Life.

Why Is Water So Unique?

Water is unique because it is able to form weak chemical associations and is the prevailing liquid on Earth, as it survives in almost any temperature and continues to be the center of life.

What Determines Water Chemistry?

Water's chemistry is determined by its simple atomic structure. It has two hydrogen molecules and one oxygen molecule in a covalent bond. It also has the ability to form weak chemical associations.

How Does Water Act Like A Tiny Magnet?

Within a water molecule, both hydrogen and oxygen have an attraction towards electrons they share in covalent bonds, this attraction is known as electronegativity. However, the oxygen atom has a greater electronegative power than the hydrogen molecules.

Water molecules are polar and have partial charges. Oxygen has a negative partial charge and hydrogen has a positive one.

Hydrogen bonds are formed once opposite charges of bridging (combining) hydrogen atoms are attracted to each other.

Why Does Water Cling To Polar Molecules?

Water molecules are attracted to other water molecules. This attraction is called cohesion. Adhesion is the attraction of other molecules to water molecules. Cohesion of water is caused by its surface tension

How Does Water Store Heat?

Water can store heat due to its high capacity of specific heat and heat of vaporization.

Specific heat is the amount of heat that must be absorbed or lost by 1 gram of any substance to change its temperature by 1°C

Heat of vaporization is the amount of heat it takes to vaporize water (turn water from a liquid to a gas)

Why Is Water A Powerful Solvent?

Water is a powerful solvent because it has the ability to form hydrogen bonds. Water can dissolve any material that has an electrical charge, whether the charge is full like an ion or partial like a polar molecule.

How Does Water Organize Nonpolar Molecules?

Water tends to exclude nonpolar molecules when nonpolar molecules are placed within it. This in turn causes all the nonpolar molecules to bond with each other, since they can't make hydrogen bonds with water, and to shrink. This process is called hydrophobic exclusion. Water also tends to nonpolar molecules to form into different molecular shapes.

Why Does Water Ionize?

Water ionizes when the covalent bond of a water molecule spontaneously breaks. When this happens, due to the lack of counterbalance for the proton or the electron, the hydrogen atom nucleus becomes a positively charged hydrogen ion, H+, and the rest of water molecule (with the electron) becomes a hydroxide ion, OH-.

How Is Ph Determined?

pH is the negative logarithm (exponent of molar concentration of H+; ex: 10^-7) of a solution's hydrogen ion concentration.

Acids have high H+ concentrations (pH<7), bases have low H+ concentrations (pH>7), and if a solution is neutral in H+ concentration, then it will have a pH of 7.

How Do Buffers Work?

Buffers are reservoirs for hydrogen ions; they either give or take H+ ions as needed. When the concentration falls, the buffers donate H+ ions and when concentration rises, the buffers accept H+ ions

Chapter 3

Molecules are the building blocks of life

Carbon: The framework of biological molecules

Carbon is predominantly contained in biological molecules. Due to Carbon's possession of only four valence electrons and its necessity for four more valence electrons to satisfy the octet rule, it often bonds to oxygen, nitrogen, sulfur, hydrogen, or even other carbon atoms. Also due to carbon's necessity of four more valence electrons, the biological molecules can often be complex.

What are Functional Groups?

Functional groups are groups that have chemical properties that are retained no matter what molecule they are in. They tend to also act in units during chemical reactions.

How are biological macromolecules built?

Biological macromolecules are extremely long chains of biological molecules containing one or more functional groups. They are also grouped into four categories, proteins, nucleic acids, lipids, and carbohydrates. These are often considered to be polymers, which are built through the combining of several, similar chemical subunits, often compared to rail cars on a train.

Proteins perform the chemistry of the cell

The many functions of proteins

The prime functions of protein include enzyme catalysis (the helping of chemical reactions), defense (through cell surface receptors), transport (of small molecules and ions), support (structural use; i.e. keratin in hair), motion (materials in cells), regulation (hormones), and storage (Calcium and Iron).

Amino Acids: The building blocks of proteins

Proteins are polymers (see "How are biological macromolecules built?") or amino acids, in this polymer there are 20 different types of amino acids, arranged in specific orders.

Why are Proteins polymers of amino acids?

Proteins are polymers of amino acids because they are composed of 20 different types of amino acids, covalently bonded together by peptide bonds (covalent bonds that link two amino acids together)

How is Protein structure determined?

Primary protein structure is determined through the sequence of the amino acids contained within the protein. Secondary protein structure is determined by the folding of the chain of amino acids by hydrogen bonding into coils and pleats. Tertiary protein structure is determined by the final folded shape of the globular protein

The function of the protein is determined by the shape of the protein.

What are the Levels of protein structure?

Primary, secondary, tertiary, and quaternary

There are also two more levels that are increasingly distinguished: motifs and domains

What is a Primary structure?

A Primary structure of a protein is its specific amino acid sequence. The sequence of amino acids is determined by the sequence of nucleotides of the gene that encodes the protein.

What is a Secondary structure?

Secondary Structure is the folding of the hydrogen-bonded, amino acid chain into coils and pleats.

What are Motifs?

Motifs ("Supersecondary structure") are the elements from the secondary structure that combine in proteins in characteristic ways.

What is a Tertiary Structure?

Tertiary Structure is the final folded from of a globular protein

What are Domains?

Domains are structurally independent functional units that contain each exon-encoded section of the protein

What is a Quaternary Structure?

Quaternary Structure is individual polypeptide subunits that form functional proteins

Contain all other parts of protein within it

Primary Structure<Secondary Structure<Motifs<Tertiary Structure<Domains<Quaternary Structure

How proteins fold into their functional shapes?

Chaperone proteins help new proteins fold correctly, which determines their functional shape.

What are Chaperone proteins?

Chaperone proteins are special proteins which help new proteins fold correctly

Many respond to high temperatures

How is Protein folding and disease related?

Protein folding and disease are related through chaperone protein deficiencies. This is thought to be because if chaperone proteins can't facilitate the folding of key proteins, this could cause disease. It has also been speculated that chaperone deficiency could be the cause of protein clumping in brain cells in Alzheimer disease.

How do proteins unfold?

Protein unfolding occurs during the process of denaturation. This process also occurs when proteins change shape. This process can be caused by pH, temperature, or ionic concentration.

Nucleic acids store and transfer genetic information

Information molecules

DNA (Deoxyribonucleic acid) is considered to be a heredity material

It holds the information used to make proteins

Cells use RNA (Ribonucleic acid) to find the information needed for protein synthesis from DNA and use this information to direct protein synthesis

How are we "Seeing" DNA?

We are "seeing" DNA through a scanning-tunneling microscope.

This type of microscope uses a beam of electrons rather than a beam of light in order to magnify a substance

What is the structure of nucleic acids?

Nucleic acids are polymers of five-carbon sugar, phosphate, and nitrogen-containing base

DNA

Deoxyribonucleic acid is a heredity material that holds information used for protein synthesis

It takes the shape of a double helix

It requires a scanning-tunneling microscope to "see" it

RNA

Ribonucleic acid is what cells use to obtain information for protein synthesis from DNA

It takes the shape of a single-stranded molecule

Which came first, DNA or RNA?

The DNA is simply used to store information on how to synthesize proteins. Cells use an RNA transcript to direct protein synthesis. This is speculated to be a safety precaution, protecting the DNA from wear and tear. Though now the process of protein synthesis starts in the DNA, then the RNA, then synthesizes a protein. However the DNA is speculated to have evolved from the RNA.

ATP

ATP (adenosine triphosphate) is the energy currency of the cell.

Lipids make membranes and store energy

How do Phospholipids form membranes?

Phospholipids (made of glycerol, fatty acids, and a phosphate group) form membranes when aggregated in water. Their tails move inward (since they are nonpolar) and their polar heads move outward, these two parts are at the core of all biological membranes. When this happens, they form a lipid bilayer.

What are the types of Fats and other kinds of lipids?

Triglyceride is a fat because it contains a glycerol molecule attached to three fatty acids

Terpenes, Steroids, and Prostaglandins are other forms of lipids

How do Fats act as energy storage molecules?

Fats act as energy storage molecules because a high concentration of C-H bond, which leads them to be efficient energy-storage molecules

Carbohydrates store energy and provide building materials

Sugars

Carbohydrates are a group of molecules that contain carbon, hydrogen, and oxygen in a 1:2:1 ratio

What are Monosaccharides?

Monosaccharides are simple sugars, the simplest form of carbohydrates. These may contain as little as three carbon atoms, however only those with major roles have six carbon atoms

The most important of these for energy storage is glucose; it has six carbon atoms and has seven C-H bonds.

What are Disaccharides?

Disaccharides are "double sugars" (two monosaccharides that are covalently bonded)

These often play a role in transport of sugars

What are Polysaccharides?

Polysaccharides are macromolecules which are made up of monosaccharides are subunits.

Starch and Cellulose are examples of polysaccharides

Special enzymes are required to break the links between polysaccharides

What are Sugar isomers?

Sugar isomers are alternate forms of the same empirical formula (such as glucose, fructose, and galactose). These are arranged differently by structure. These structural differences often make functional differences between them.

Transport and storage carbohydrates

What are Transport disaccharides?

Transport disaccharides are sugars that are transported within an organism's body.

These are usually glucose for humans and plants

These forms of transport change with the monosaccharides that are linked

What are Storage polysaccharides?

Storage polysaccharides are long insoluble polymers of disaccharides that hold metabolic energy. For plants, these are called starches. The animal version this is called glycogen.

Structural carbohydrates

What is Cellulose?

Cellulose is a structural carbohydrate that is a chain of glucose molecules

This resists digestion because most organisms lack the necessary enzymes

This is the prime component of a cell wall

What is Chitin?

Chitin is a structural carbohydrate that is made up of the glucose units from cellulose plus a nitrogen group.

This is used often as a hard exoskeleton of anthropods, such as that of lobsters

Chapter 4

The Origin and Early History of Life

Why Do All Living Things Share Key Characteristics?

What Is Life?

All organism on earth share several properties in order to be classified as living or nonliving. In order to determine what life is, we must first determine how to classify something as living or nonliving.

What Are The Fundamental Properties Of Life?

The Fundamental Properties of Life are properties which classify something as living. All living organisms share these properties. These properties include: Cellular organization (consistence of one or more cells), sensitivity (the response to stimuli), growth (the assimilation of energy and usage to grow- metabolism), development (the systematic, gene-directed change through growth), reproduction (creation of new individuals for the next generation), regulation (coordination of internal processes), and homeostasis (the maintenance and keeping constant of internal conditions).

How Does Heredity Play A Key Role?

Heredity plays a key role by adding that all organisms must have a genetic system, which has the capability to evolve over time.

Why Is There Considerable Disagreement About The Origin Of Life?

It is very difficult to observe and there are no witnesses. Also it is difficult to tell through prehistoric rocks.

What Are The Hypotheses About The Origin Of Life?

There are three hypotheses about the origin of life

Special Creation- the creation of life by God

Extraterrestrial origin (Panspermia)- life may have came from extraterrestrial organic materials on a meteor or cosmic dust

Spontaneous origin- life evolved from inanimate matter as molecular associations reached higher complexity

Why Do Scientists Disagree About Where Life Started?

Scientists disagree about where life started because there are many theories, most have some issues or with little evidence.

Did Life Originate In A Reducing Atmosphere?

Life may have originated in a reducing atmosphere if there were little oxygen in the environment, with carbon dioxide and nitrogen gas.

A problem with this theory is the fact that if this occurred, there would be a lack of an ozone layer and that if the carbon dioxide was locked up in the atmosphere, then it would not be considered a reducing atmosphere.

Where On Earth Could Life Have Originated?

Other possible locations for the origin of life could be: the ocean's edge, under frozen seas, deep in the earth's crust, within clay, and at deep-sea vents.

What Was The Miller-Urey Experiment?

The Miller-Urey experiment was an attempt in 1953 by Stanley L. Miller and Harold C. Urey to reproduce the Earth's possible reducing atmosphere in order to make complex organic molecules.

How Is Each Of The Chemical Evolutions Different?

Each of the chemical evolutions is different. One supports RNA as being the first organic molecule, one supports protein, and one supports a peptide-nucleic acid.

An RNA World

In this theory, scientists believe that without a heredity material, no other molecule could have been made with consistency. Also they believe that the ribosomes in the RNA act as an enzyme and that since RNA has hereditary capabilities, it could pass down information.

A Protein World

This theory suggests that protein came first and that without protein as an enzyme, no other molecule could replicate. This theory also states that RNA is too complex and unstable to be made spontaneously and that proteins are easier to synthesize.

A Peptide - Nucleic Acid World

This theory suggests that PNA was used rather than RNA or protein, as this is a combination of both, it is easier to synthesize than RNA, its more stable and simpler, and has the capability to self-replicate.

What Is Unique About Each Of The Hypotheses About The Origin Of Cells?

How Are "Bubbles" Important?

There are many hypotheses that suggest that chemical evolution may have occurred within bubbles; however whether these bubbles were lipid or protein remains a mystery.

What Was Oparin's Bubble Hypothesis?

Oparin's Bubble hypothesis was that our current atmosphere is incompatible with the creation of life. He suggested that life must been created in a much different atmosphere and that in order for cells to evolve they must have been isolated themselves from the environment using a cell membrane. He called this structure protobionts.

What Is The Host Of Bubble Hypothesis?

The Host of the Bubble Hypothesis is their contents and whether their membrane is made out of. These include what characteristics of cells they have.

What Is The Bubble Scenario?

The Bubble Scenario is that bubbles from the ocean that contained amino acids and side groups that could catalyze growth -promoting reactions survived long enough, they would carry out metabolic reactions and evolve. This would eventually lead to them turning into bubbles that could make "daughter" cells, beginning heredity and beginning life.

How Does The Current Thinking Differ From Past Ideas?

Current thinking differs from past ideas because now we can question the possibility if neither lipid nor protein came first, but rather RNA and then a lipid or protein improved stability later.

How Did Cells Become Progressively More Complex As They Evolved?

What Are The Microfossils?

Microfossils are fossilized forms of microscopic life. These are thought to be fossils of prokaryotes, stemming from rocks from 2.5 billion years ago.

Why Are The Archaebacteria The Most Ancient Organisms?

Archaebacteria are the most ancient because they grow only in environments that are unchanging and resemble Earth's early environment. These also grow only without oxygen, which is speculated to been lacking in Earth's original atmosphere.

What Are Some Unusual Cell Structures?

Some unusual cell structures are the cell wall in archaebacteria, which seems to be lacking in peptidoglycan. They also have unusual lipids in their cell membrane.

What Were Earth's First Organisms?

Earth's first organisms are speculated to be thermophilic archaebacteria, archaebacteria that live in 230°F. This is because that is thought to be a similar temperature at which Earth's early oceans where at.

Why Are The Bacteria Important In The Evolution Of Life?

Bacteria are important in the evolution of life because there are only two forms of prokaryotes: archaebacteria and bacteria. Most prokaryotes are bacteria. These have strong cell walls and simpler gene architecture. Bacteria are also photosynthetic, a property which is commonly seen in plants and algae. Cyanobacteria are one type of bacteria that is important to the history of the world because it has been producing oxygen from photosynthesis since it first appeared 2 billion years ago. This in turn greatly helped increasing oxygen concentration in Earth's atmosphere.

When Did The First Eukaryotic Cells Appear?

The first eukaryotic cells appeared about 1.5 billion years ago. They seemed to be different from prokaryotes in that they were larger and had internal membranes and thicker cell walls.

How Did The Nucleus And ER Originate?

The nucleus and ER are thought to have evolved from infoldings of the plasma membrane.

How Did The Mitochondria And Chloroplasts Originate?

Mitochondria and Chloroplasts are thought to have originated from endosymbiotic bacteria, which lived in larger bacteria and performed the photosynthesis and produced energy for the larger bacteria. They then evolved into the organelles Mitochondria and Chloroplasts.

Why Is Sexual Reproduction Important To Eukaryotic Life?

Sexual reproduction is important to eukaryotic life because it produces the diversity that is important to the evolution of a species.

Why Has Multicellularity Had A Huge Impact On The History Of Life?

Multicellularity had a huge impact on the history of life because it has encouraged the development of diversity.

How Is The Domain System Representative Of The Diversity Of Life?

The domain system categorizes the diversity of life into separate categories. The three domains are bacteria, archaea, and eukarya. There are 6 kingdoms under the eukarya domain which include: protista, fungi, plantae, and animalia.

Why Are Scientists Beginning To Take The Possibility Of Extraterrestrial Life Seriously?

Is It Possible That Live Evolved Elsewhere?

Since at least 10% of stars have planetary systems, it is theoretically possible that life may have evolved multiple times.

Why Are Ancient Bacteria On Mars Significant?

Ancient bacteria on Mars are significant because the environmental conditions of ancient Mars was similar to that of ancient Earth. This could imply that life may have once existed on Mars and since the rock we discovered this from is nearly 4.5 billion years old, life on Earth may have started through extraterrestrial origin.

What about Life on Other Planets?

Life on other planets is theoretically a possibility, although the evidence for life on Mars is not compelling, Europa may be a good candidate for extraterrestrial life, considering it has liquid water beneath its layer of ice. The conditions that exist on Europa are also less hostile to life than that of ancient Earth.

Cell Structure

Chapter 5 Outline

All organisms are composed of cells

What are some characteristics of cells?

Some characteristics of all cells are a nucleoid or nucleus (to store the DNA), cytoplasm, and a plasma membrane (cell membrane).

Where is the genetic material?

In prokaryotes the DNA is within the nucleoid and in eukaryotes the DNA is within the nucleus.

What is the function of the cytoplasm?

The cytoplasm fills the interior of the cell, excluding the nucleus. It also contains sugars, amino acids, and proteins. In eukaryotes, the cytoplasm also contains organelles.

Where is the plasma membrane?

The plasma membrane is on the outside of the cell. It acts as a barrier between the cell's contents and its environment. It is a phospholipid bilayer and contains its own proteins.

How was the cell theory developed, and why is it important?

The cell theory was developed through study of cells under microscope. General rules were not applied until the 1800s by Matthias Schleiden and Theodor Schwann. The cell theory eventually came down to three basic principles: all organisms are composed of 1 or more cells, cells are the smallest living things, and cells only "come from" other cells (through the process of division). It is important because all life on Earth descended from cells.

Why is cell size limited?

Cells size is limited because the larger the cell is, the longer time it would take for a substance to enter a cell. Also because the volume increases much more rapidly in a cell than does the surface area. The volume increases by a thousand times in proportion to the cell's surface area increasing by a hundred times.

How do we visualize cells?

We visualize cells by using light microscopes to increase and achieve high magnification and resolution (the minimum distance two point can be apart and still be distinguished), these microscopes magnify up to just above 100 nm. Electron microscopes can also be used which magnify up to the size of 1 hydrogen atom, which is just above .1 nm.

Why is there a resolution problem?

There is a resolution problem because when two objects are closer than a few hundred nanometers, the light beams that reflect off both objects begin to overlay. To solve this problem, an electron microscope must be used.

How can resolution be increased?

Resolution can be increased by using a beam of electrons rather than a beam of light, in other words, by using a transmission or scanning electron microscope.

When are stains used?

Stains are used during the process of histology, the analysis of tissue samples, and immunocytochemistry, the binding of specific molecules through antibiotics. It is used to examine specific molecular molecules.

Eukaryotic cells are more structurally complex than prokaryotic cells

What is a prokaryotic cell?

A prokaryotic cell is the simplest form of an organism. They have only a cell wall, plasma membrane, with cytoplasm and no organelles.

Why do prokaryotes have strong cell walls?

Prokaryotes have strong cell walls because this protects the cell, maintains its shape, and prevents excessive water intake.

What is the function of a flagellum?

A flagellum is used by many prokaryotes for locomotion (movement). They do so by rotating this flagellum, creating a wave that launches the prokaryote forward.

How are the prokaryotes "organized"?

Prokaryotes have no organelles, so cytoplasm has access to all parts of the cell. The DNA is also accessible via the cytoplasm due to a lack of a nuclear envelope or nucleus.

Why are the interiors of eukaryotic cells more complex?

The interiors of eukaryotic cells are more complex because they have organelles within the cytoplasm that carry out the cell's functions. All of these organelles are also surrounded by a membrane, separating them from the cytoplasm.

Take a tour of a eukaryotic cell

What is the role of the nucleus?

The nucleus is used for storage of the genetic information of the cell (DNA). It has its own membrane called the nuclear envelope that is made by two phospholipid bilayers (similar to the plasma membrane). The DNA is kept in chromosomes in the nucleus.

What is the function of the nuclear envelope?

The nuclear envelope is protects the nucleus and prevents or allows passage of substances into the nucleus.

How is the hereditary material "packaged"?

The hereditary material is "packaged" into chromosomes in the nucleus. These become threadlike when dividing and are called "chromatin".

What is the endomembrane system?

How does the endoplasmic reticulum (ER) compartmentalize the cell?

Endoplasmic reticulum compartmentalizes the cell by making folded sheets of itself throughout the cell; this makes channels between the folds.

What is the role of the rough ER?

Rough ER is coated with ribosomes. This helps in protein synthesis, these proteins are usually secreted from the cell.

How does the smooth ER differ from the rough ER?

Smooth ER does not have any ribosomes bound to it and does not carry out protein synthesis but rather synthesizes lipids and carbohydrates.

How does the Golgi apparatus function as a delivery system?

The Golgi apparatus functions as a delivery system for the cell by packaging, modifying, and distributing molecules to and from the cell. For example: when rough ER secretes proteins , they fuse with the Golgi apparatus on the cis face, where it is packaged and distributed to the trans face where it is secreted from the cell.

Why are vesicles enzyme storehouses?

What is the primary role of a lysosome?

Lysosomes are primarily used for catalyzing the quick breakdown of proteins, nucleic acids, carbohydrates, and lipids through digestive enzymes that it contains. Old organelles are something that is often digested by lysosomes.

How do microbodies aid in cell function?

Microbodies contain enzymes and absorb lipids and proteins in order to maintain the cell's metabolism. They also often convert different substances. I.e. glyoxysome converts fats into carbohydrates.

Why are the ribosomes crucial to cell survival?

Ribosomes are crucial to cell survival because they are the sites for protein synthesis. They take the information for protein synthesis from a form of RNA called messenger RNA (mRNA) and direct protein synthesis using it.

What is the role of the nucleolus?

The nucleolus produces both subunits of ribosomes. When these two units join together, they form a complete ribosome, which are the sites of protein synthesis.

Organelles that contain DNA

Why are mitochondria critical to the survival of organisms?

Mitochondria are critical to the survival or organisms because they have their own set of DNA which has information on how to create essential proteins, which is important to the cell's metabolism.

Why are the chloroplasts one of the most "important" organelles?

Chloroplasts are one of the most "important" organelles because it is the site of photosynthesis; it has its own set of DNA for this, and has information on the proteins necessary for photosynthesis.

How does endosymbiosis explain the origin of the eukaryotic cell?

Endosymbiosis supports the idea that eukaryotic cells came to be about by small prokaryotes being engulfed by larger prokaryotes. After this, the prokaryotes that were engulfed provided metabolic benefits to the larger prokaryote. Eventually this would lead to the smaller prokaryotes becoming organelles and thus giving birth to eukaryotic cells.

What makes the cytoskeleton unique?

The cytoskeleton is unique because it is a network of protein fibers within the cytoplasm of a cell that helps keep the organelles in position and maintain the shape of the cell. It has three different types of protein fibers: actin filaments, microtubules, and intermediate filaments.

What is the role of actin filaments (microfilaments)?

The role of actin filaments is responsible for movement of the cell including: contracting, crawling, "pinching" during division, and formation of the cells extensions.

What is the role of microtubules?

Microtubules are used for the organization of the cell's metabolism, transport of materials inside the cell, and they help to keep the cell's structure stable.

What is the role of intermediate filaments?

Intermediate filaments are used for the stability of the cell's structure.

How do the centrioles play a role cell function?

Centrioles help to assemble microtubules. They often occur in pairs near the nuclear membrane.

How do microtubules help move material within the cell?

Microtubules help move material within the cell by using the actin filaments to contract the cytoskeleton, which causes the movement of the cell. Microtubules are also used like train tracks by motor molecules when vesicles or organelles need to be transported further in a cell.

How do cells "move"?

Cells usually "move" in two different ways: crawling and swimming. They crawl by actin filaments combining and extending; this extension causes the edge of the cell to move forward, then the myosin motors in the actin filaments contract, causing the whole cell to move to the location of the edge. Other cells swim using flagella and cilia. Flagella have 9 microtubules surrounded by 2 central microtubules which act like a tail that spins the flagella, causing the whole cell to project forward. Cilia have the same setup of flagella, however their function is different, and they are often used for a cell's sensory capabilities such as hearing.

Not all eukaryotic cells the same

What is the function of a vacuole?

Vacuoles are used for storage of water, sugars, ions, and pigments. It also helps to increase the surface area of the cell by applying pressure on the plasma membrane, forcing it to expand.

Why do plants need cell walls?

Plants need cell walls because of protection. Primary cell walls are laid down during the youth of the plant and sometimes secondary cell walls follow.

How does the extracellular matrix (ECM) function in cell communication?

The ECM functions in cell communication by secreting various glycoproteins, which help coordinate cell behavior by creating "signaling highways" that connect between the ECM and the cytoskeleton.

Chapter 6 Outline

Advanced Placement Biology

Membranes

Biological membranes are fluid layers.

What is the phospholipids bilayer?

Phospholipid bilayers are the components of biological membranes. They contain polar heads that are hydrophilic (attracted to water) while the tails are made of fatty acids, are nonpolar, and are hydrophobic (detracted to water). When in water, the heads face outwards (towards water) and the tails point inwards (away from water).

What are phospholipids?

Phospholipids are the molecules that that form into the phospholipid bilayers. They individually are glycerol attached to 2 fatty acids and phosphorylated alcohol.

How do phospholipids form bilayer sheets?

When in water, the heads face outwards (towards water) and the tails point inwards (away from water). When two phosphoplipid molecules form, no tails come in contact with water and they form a phospholipid bilayer.

What evidence supports that the lipid bilayer is a fluid?

The lipid bilayer is a fluid because of water's tendency to make hydrogen bonds, since this process is never halted; the hydrogen bonds hold the bilayer in a liquid state.

Proteins embedded within cell membranes determine their characteristics.

Who developed the fluid mosaic model?

Davson Danielli developed the Davson Danielli model in 1935; however this model stated that the bilayer would dissolve. In 1972, S. Singer and G.J. Nicolson created the fluid mosaic model by revising Danielli's model to include that the nonpolar ends of the phospholipids are on the interior of the bilayer and the polar heads are on the exterior, with proteins inserted into the bilayer.

What are the components of the cell membrane?

There are 4 components of the cell membrane: phospholipid bilayer (the barrier for permeability and flexibility), transmembrane proteins (provide means of transportation for substances going in and out of the membrane), interior protein network (support of membranes shape and to keep proteins in specific places), and cell surface markers (used to identify certain cells).

How do we examine cell membranes?

We examine cell membranes by use of electron microscopes for structural examination. We also use procedures like embedding tissue in hard matrixes and freeze-fracturing.

What are the different types of membrane proteins and their functions?

There are 6 different types of membrane proteins. These include:

Transporters-determines what substances enter or leave the cell.

Enzymes-carry out chemical reactions inside the cell

Cell surface receptors-detect chemical messages

Cell surface identity markers- used to identify cells with each other (like ID tags)

Cell adhesion proteins-used to connect cells to other cells

Attachments to the cytoskeleton- used to link the cytoskeleton to surface proteins

What are the structures of membrane proteins?

How are proteins anchored in the bilayer?

Proteins are anchored in the bilayer by nonpolar segments of the protein.

How do proteins extend across the bilayer?

Proteins extend across the bilayer by single-pass anchors, multiple-pass channels and carriers, and pores.

Single-pass anchors work by extending spectrin and attaching it to liner proteins on the side of the cytoskeleton. This creates a network of spectrin.

Multi-pass channels and carriers work by creating spirals of helical segments (which act like channels) in which a retinal chromophore pumps molecules and ions out of the channels.

Pores work by creating a large tunnel made with 16 beta-plated sheets. This allows the passage of water and other materials through the cell membrane.

Passive transport across membranes moves down the concentration gradient.

What is diffusion?

Diffusion is the movement of substances from areas of high to low concentration. This process continues until both side/regions have equal concentration.

How is membrane transport selective?

Membrane transport is selective because each transport protein is selectively permeable (only allows a certain type of substance to enter it), it causes only certain molecules to be able to diffuse.

How does diffusion of ions take place through channels?

Diffusion of ions takes place through ion channels, since their charge would conflict with different molecules. These channels are separate from the nonpolar tails and are also specific to only specific ions.

How does facilitated diffusion use carriers?

Facilitated diffusion is the movement of molecules from concentrations of higher to lower through specific carriers. This is accomplished by the carriers mounting the molecules from one side of the membrane and then releasing them on the other side.

How does facilitated diffusion take place in red blood cells?

Facilitated diffusion occurs in red blood cells by the shape change of transmembrane proteins. In order to transport glucose, for example, the protein binds to the glucose, changes its shape, and then is able to take the glucose through the membrane and into the cell.

How does saturation of transport take place via carriers?

Saturation of transport via carriers takes place by exceeding the concentration gradient to a certain point. When the concentration gradient is high enough and all the carriers are in use, then the transport system becomes saturated.

What is osmosis?

Osmosis is the transport of water through the membrane and into a solution with a higher solute concentration.

Why do molecules diffuse down their concentration gradient?

Molecules diffuse down their concentration gradient because if they didn't, then cells would either have to much or too little of a substance that they mixed with.

What is osmotic pressure?

Osmotic pressure is the pressure that must be applied to stop the osmotic movement of water across a membrane. In contrast hydrostatic pressure is the pressure hat must be applied to increase the osmotic movement across a membrane.

How do organisms maintain osmotic balance?

Organisms maintain osmotic balance by many methods. These include:

Extrusion-the use of contracting vacuoles to remove water. These vacuoles then remove the water from themselves through a pore that they have on the cell's surface.

Isosmotic solutions-the use of solutions within a cell to match the concentration of water internally to that of the environment.

Turgor-the use of internal hydrostatic pressure, turgor pressure, in order to press the cell membrane outwards onto the cell wall.

Bulk transport utilizes endocytosis.

What is endocytosis?

Endocytosis is the engulfing of food particles by the plasma membrane and transport of the food molecules to the interior of the cell.

What are phagocytosis and pinocytosis?

Phagocytosis is the digestion of a material that is particulate (made of discrete molecules); these are usually other cells or organic matter.

Pinocytosis is the digestion of a material that is in liquid form.

What is receptor mediated endocytosis?

Receptor mediated endocytosis is the transport of a molecule through the binding to specific receptors in the plasma membrane. This is specific only to molecules that fit properly within the receptors.

What is exocytosis?

Exocytosis is the reverse procedure of endocytosis. This is the release of material from vesicles at the cell surface.

Active transport across membranes requires energy.

What is active transport?

The movement of a solute through a membrane when going against the concentration gradient. This requires the use of protein carriers and the use of ATP.

How does the Sodium-Potassium pump function?

The Sodium-Potassium pump functions through the use of ATP and the active transport of Na+ out of the cell and K+ into the cell.

When does coupled transport occur?

Coupled transport occurs when the gradient of one molecule being transported inside the cell is great enough to transport a second molecule. The sodium-potassium pump is often used in this scenario because the gradient for the Na+ to reenter the cell is often great enough to bring glucose back in with it.

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