Essential Cell Biology 3rd ed: Ch2 Chemical Components of the Cell

• INTRO

• One of the hardest things to wrap your head around in biology is the fact that all living creatures are just chemical systems.

• Until the 19th century it was mostly believed that animals contained a vital force, "animus", that was responsible for the behavior of living organisms. But this doesn’t mean that the chemistry of life is not a special one

• Organic chemistry

• Almost all chemical reactions take place in aqueous solutions.

• The chemistry involved is extremely complicated

• It is coordinated by polymeric molecules, whose properties enable cells and organisms to grow and reproduce and do all of the other things that they do.

• CHEMICAL BONDS

• Matter is made up of elements

• The smallest particle of an element that still retains its distinctive chemical properties is an atom. These are then grouped together to form molecules

• Cells are made of relatively few types of atoms

• Hydrogen - has an atomic number of 1 and is the lightest element.

• Carbon - atomic number of 6, can be the stable Carbon-12 (the most common) Carbon-13, and Carbon-14 also play a role in chemistry.

• The outer most electrons determine how atoms interact.

• Electrons are in constant motion and move in orbitals call electron shell. But the outermost electrons are the ones that interact with other atoms electrons to form molecules and compounds.

• The state of the outer electron shell determines the chemical properties of an element.

• Ionic bonds are formed by the gain or loss of electrons, and are a type of electrostatic attraction. While covalent bonds are formed when atoms share electrons (molecules are always covalent).  

• Electrostatic attractions help bring molecules together in cells

• In aqueous solutions, covalent bonds are between 10 and 100 times stronger than the other attractive forces between atoms, allowing their connections to define the boundaries of one molecule from another.

• Polar covalent bonds are extremely important in biology because they allow molecules to interact though electrical forces, using positively and negatively charged regions to interact with specific portions of other molecules.

• Water is held together by hydrogen bonds.

• 70% of a cell's weight is water, and most intercellular reactions occur in an aqueous environment.

 

 

• Hydrogen bonds are much weaker than covalent bonds and are broken relatively easily by random thermal motions, so each bond only lasts a short time.

• These bonds can form when a positively charged hydrogen is held in one molecule by a polar covalent bond and then comes into close proximity to a negatively charged atom- usually oxygen or nitrogen, but there are others.

• Like dissolves like is the rule of thumb. Polar will mix with polar and non polar will mix with non polar.

• Hydrophilic- water loving

• Hydrophobic- water fearing, these are uncharged and will form few if any hydrogen bonds, and will not dissolve in water.

• Hydrocarbons fall into this category

• Some polar molecules form acids and bases in water.

• Hydronium ion (H3O+) is made when a highly polar covalent bond between a hydrogen and another atom dissolves in water, then hydrogen is given up and is made into a hydronium ion when it is surrounded by water. So this will be common in the cell.

• Many of the acids that are important in the cell are weak acids.

• Many bases of biological importance are weak bases containing an amino group. (NH2) and can generate OH- by taking a hydrogen from water.

• These two concentrations are in a biological tug-a-war, in that an increase in the OH concentration forces a decrease in the other and vice versa.

• Pure water can act as a buffer: where acid and bases can react while the environment of the cell is kept relatively constant under a variety of conditions.

• Molecules in cells

• Carbon compounds make up the cell's of living things and are able to make large and complex molecules with not upper limit to their possible size.

• Functional groups are combinations of atoms that occur repeatedly and have distinct chemical and physical properties that influence the behavior of the molecule in which the group occurs.

• Methyl CH3

• Hydroxyl OH

• Carboxyl COOH

• Carbonyl C=O

• Phosphoryl PO3

• Amino NH2

• The combination of a phosphate and a carboxyl group, or two or more phosphate groups, gives an acid anhydride. (PICS !!!)

• Cells contain four major families of small organic molecules

• Sugars

• Monosaccharides (CH2O)n- the simple sugars where n is usually 3, 4, 5, or 6 make up and compose compounds called carbohydrates. Each sugar can exist in two forms, D or L, mirror images of each other (isomers)

• Glycosidic bonds = covalent bonds that hold monosaccharides together to form larger carbohydrates.

• These can then be labeled as disaccharides, trisaccharides, tetracaccharides, and so forth. The prefix "oligo-" is used for a small number of monomers, between 3 and 50, polymers would indicate more.

• The carbon that carries the aldehyde or the ketone can react with any hydroxyl group on a second sugar molecule to form a disaccharide.

• Maltose (glucose + glucose)

• Lactose (galactose + glucose)

• Sucrose (glucose + fructose) 

 

• The OH- group of one sugar can be bonded to the OH- group of another sugar through a condensation reaction (water expelled) and they can be  separated by hydrolysis (consumption of water). Because each monosaccharide has several OH groups they can link together in several different ways, and even branch making it relatively difficult to determine the arrangement of the sugars in polysaccharides.

• Glucose has a central role as the energy source for the cell. Animals will use glycogen and plants will use starch as long term storage of glucose, both of which are composed only of glucose units.

• Polysaccharides also make up cellulose, chitin (insect exoskeletons/fungal cell walls), and are the main component of slime, mucus, and gristle.

• Glycolipids- small oligosaccharides that are covalently linked to proteins. These tend to be found in cell membranes.

• These sugar side chains can be recognized selectively by other cells, (blood type)

• Fatty acids

• This molecule has two main regions; a long hydrocarbon chain that is hydrophobic and not very reactive, and a carboxyl group (COOH-) which is very hydrophilic and acts as an acid.

 

• If the hydrocarbon tail is saturated, that means that it has no double bonds between its carbon atoms, containing the maximum number of hydrogens. But there are types of fatty acids that are termed unsaturated, and may contain one or more double bond along their length. 

 

• Different fatty acids differ only in the length of the carbon chain, and the number and placement of the double bonds. 

• Amphipathic- molecules that possess both hydrophobic and hydrophilic regions.

• Triacylglycerol- a compound made of three fatty acid chains joined to a glycerol molecule.

• This compound is found in the cytoplasm, and how fatty acids are stored in many cells. When the cell needs energy, the fatty acid chains can by released and broken down into two carbon units which are identical to  those made from breaking down glucose, and will enter the same energy producing reaction pathways as well.

• Lipids- a derivative of fatty acids, typically containing long hydrocarbon chains and isoprenes (2-methyl-1,3-butadiene) or multiple linked aromatic rings.

• This class of molecules has the common feature of being insoluble in water but soluble in fat and organic solvents.

• Lipids and their derivatives can form larger aggregates help together by hydrophobic forces.

• Micelle

 

• Phospholipids- similar to triacylglycerol, but the glycerol is joined to two fatty acids here, and in the place of the third glycerol us a hydrophilic phosphate.

• This is what makes up cell membranes.

• Other lipids present in the cell membrane may contain one or more sugar instead of the phosphate (glycolipids) and play an important role in intracellular cell signaling.

• When these sheets of phospholipids are arranged tail to tail, they form what is known as the phospholipid bilayer. 

 

• Amino acids

• These are a varied class of molecules with one defining property: they all possess a carboxylic acid group and an amino group, both linked to the same carbon atom called the Alpha carbon. Their chemical variety comes from the side chain that is also attached to the alpha carbon.

• These are used to build proteins, which are polymers of amino acids joined head to tail in a long chain that is then folded into a three dimensional structure.

• Peptide bond- the covalent linkage between two adjacent amino acids in a protein chain. These are also formed through condensation reactions.

• The four atoms in the peptide bond form a rigid planar unit, so there will be no rotation around the C-N bond.

• Amino acids will always have an amino (NH2) group at one end (N-terminus) and a carboxyl group at the other end (C-Terminus)

• 20 types of amino acids are commonly found in proteins. 

 

• Similar to sugars, all amino acids, with the exception of glycine, exist as optical isomers. Proteins will only have the L-isomer, while some D-amino acids will occur in parts of bacterial cell walls and in some types of antibiotics. 

• Five of the twenty amino acids have side chains that can be positively charged, all the others are uncharged.

 

• Nucleotides

• Nucleoside- a molecules made of a nitrogen-containing ring compound linked to a five-carbon sugar, which can be either ribose of deoxyribose. A nucleoside that has one or more phosphate groups attached to the sugar is a nucleotide. 

 

• Pyrimidines- these are all derived from a six-membered pyrimidine ring; Cytosine, Thymine, and Uracil.

• Purine- these are similar to pyrimidines except they have a five-membered ring attached to the six-membered ring; Guanine and adenine.

• Adenosine triphosphate (ATP)- this is an example of how nucleotides can act as short term carriers of chemical energy.

• ATP is formed through the reactions that are driven by the energy released by the breakdown of food. The phosphates are linked in series by two phosphoanhydride bonds, when these bonds are broken, large amounts of energy are released. The terminal phosphate tends to be the one that is lost through hydrolysis, providing the energy required for biosynthetic reactions. 

 

• The most fundamental role of nucleotides though, is the storage and retrieval of biological information. When this is the case they will form long chains linked by a phosphodiester bond, between the phosphate group attached to the sugar of one nucleotide and a hydroxyl group on the sugar of the next nucleotide. (between the 5' carbon and the 3' carbon)

• As these chains are formed from nucleoside triphosphates through a condensation reaction, a phosphodiester bond will form with the release of an inorganic pyrophosphate.

• They are given names DNA or RNA depending on the sugar that is being used.

• RNA -adenine, guanine, cytosine, and uracil

• DNA - adenine, guanine, cytosine, and thymine.

• Not all compounds fit into these categories. (enzymes and macromolecules)

• Polymers grow by the addition of a monomer onto one end of the polymer chain via a condensation reaction, and are catalyzed by specific enzymes to ensure that only monomers of the appropriate type are incorporated into the polymer and in the right sequence.

• This reaction will occur over and over again to extend the length of the polymer chain. 

 

• Most of the single covalent bonds in a macromolecule allow rotation of the atoms they join, allowing the polymer chain to have a high level of flexibility and allows the macromolecule to adopt an almost unlimited number or conformations. But these shapes tend to be highly constrained because of the formation of noncovalent bonds that form in different parts of the molecule.

• While these bonds are weak, in large numbers they can cause the chain to adopt one particular conformation that is dependent on the linear sequence of monomers in the polymer chain.  These bonds will be primarily formed by electrostatic attractions and hydrogen bonds, and at times the van der Waals attraction.

• Water is also present in most if not all of the cell, and can also play a roll in the shape of these molecules. Water will force hydrophobic groups together in order to minimize the disruptive effect water will have on the hydrogen bonds. This is referred to as hydrophobic interaction, and is responsible for the globular shape that most protein molecules and is the force that pushes the phospholipid molecules together in cell membranes.

• These shapes that the polymers are forced into will effect which polymers they can interact with. This underlines all biological catalysis, making it possible for proteins to function as enzymes, and allow macromolecules to be used as building blocks for the formation of much larger structures. ( an example of this would be histones or any of the polymerase that interact and catalyze the replication/repair of DNA.

• All organic molecules are synthesized from, and are broken down into- the same set of simple compounds. Both their synthesis and their breakdown occur through sequences of simple chemical changes that are limited in variety and follow definite step-by-step rules.

summer classes

My month long calculus class starts on the 8th, I apologize in advance for all the math headaches this will cause. hopefully I will have some time for biology chapters during the summer semester, but no guaranties.

Essential Cell Biology 3rd: Ch1 Introduction to Cells

UNITS AND DIVERSITY OF CELLS

• All living things are made of cells: small membrane enclosed units, filled with an aqueous solution of chemicals, that have the ability to grow and divide into two identical copies.

CELLS UNDER THE MICROSCOPE

• Cells Vary Enormously in Appearance and Function
• Cells are not all the same size or shape
• They may be smooth, have flagella, or cilia, or a combination
• Some have only the cell membrane, while others produce a slime coating, or a hard bone like shell.
• Different cells need different chemicals to function, and will live in different environments.
• Aerobic - require air to live
• Anaerobic - do not need air, in some cases air will kill them
• Living Cells all Have a Similar Basic Chemistry
• The definition of live is "the state or quality that distinguishes living beings or organisms from dead ones and from inorganic matter, characterized chiefly by metabolism, growth, and the ability to reproduce and respond to stimuli."
• Scientists elaborate on this a bit saying that living things…. Are highly organized compared to natural inanimate objects, display homeostasis, reproduce themselves, grow and develop from simple beginnings, take energy and matter from the environment and transform it, respond to stimuli, show adaptation to their environment.
• Then though on the outside living things seem very different, on the inside they are all very similar.- covered more in ch2.
• The main similarities are that all living things contain
  DNA, which is made up of the same set of four monomers ( nucleotides) put together in different sequences. Then are then transcribed into RNA and then translated into proteins
• Protein molecules dominate the behavior of the cell. They are responsible for the structural support, chemical catalysts, molecular motors, and much more.
• These proteins are build from amino acids; and every living thing uses the same set of 20 different amino acids to make proteins.
• Because cells are the basic building unit for life, then nothing less than a cell can be considered alive.
• Viruses, compact packages of DNA or RNA, are not alive…. They are better described as chemical zombies.
• All Present-Day Cells Have Apparently Evolved from the Same Ancestor
• The cell reproduces by duplicating its DNA and dividing into two identical cells. But because of mutations, the daughter cells are not always identical to the parent cell.
• These mutations can be for the worse, the better, or have a neutral effect.
• It is these simple principles of genetic change and selection, aliped repeatedly over billions of cell generations, that is the basis for evolution.
• Evolution=" the process by which living species becomes gradually modified and adapted to their environment in more and more sophisticated ways"
• It is estimated that the ancestral cell existed between 3.5 billion and 3.8 billion years  ago, and was mechanically similar to the cells we see today.
• Genes Provide the Instructions for Cellular Form, Function, and Complex Behavior.
• A cells genome provides a genetic program that instructs the cell how to function, and how to grow into an organism with hundreds of different cells types (for plants and animals).
• Higher level organisms have cells that have differentiated into cell types to preform specific duties, or functions that all originated from one initial cell (egg). They do this by using the same DNA that is present in all of the other cells, but expressing the genes in a different way.
• Cells Under the Microscope
• Microscopes allowed us to see cells for the first time, a lot of early research was done using this tool.
• Light microscopes enable us to use visible light to illuminate specimens, and are used in many cell biology labs today.
• Electron microscopes use electrons instead of light to illuminate a specimen, this greatly enhances the clarity. Can see details down to a few nanometers, and the sections must be sliced very thin, so living cells can not be viewed.
• The Invention of the Light Microscope Led to the Discovery of Cells
• The term cell came from the scientist Robert Hook, when he reported that a piece of cork was composed of a mass of small chambers: this is what he referred to as cells. Later Hook and his contemporary Antoni van Leeuwnhoek where able to look at living cells.
• The official "birth" of cell biology is generally said to have been signaled by two publications: one by Schleiden in 1838, and the other by Schwann in 1839.
• They both investigated plant and animal tissues with the light microscope, showing that cells were the universal building blocks of all living tissue. Their research lead to the development of cell theory.
• Cell theory = cells are the basic units of structure and function in living organisms.
• the idea that living organisms do not arise spontaneously but can be generated only from existing organisms was not popular at first. 
• Cells, Organelles, and Even Molecules Can Be seen Under the Microscope.
• Cells are separated by an extracellular matrix, a dense material often made of protein fibers embedded in a polysaccharide gel. Each cells is typically about 5-20 um in diameter.
• To see the internal structure, most cells need to be stained because they are transparent and mostly colorless.
• You can see the nucleus and some other cellular structures, but anything smaller than about 0.2 um cannot be seen well in a light microscope.

THE PROCARYOTIC CELL

• Procaryotes are cells that do not have a nucleus, and include  the class bacteria and archaea.

• These cells have some of the simplest structure, with life stripped to the essentials.
• These cells are usually spherical, rod-like, or corkscrew shaped, and small. But there are some other species that are large. They tend to have a protective coat (cell wall)  surrounding a plasma membrane that contains the cytoplasm and the DNA.
• These cells can duplicate quickly, a single procaryote can give rise to more than 8 billion progeny in 11 hours if food is plentiful. This allows them to evolve quickly, acquiring the ability to use new food sources or to resist being killed by a new antibiotic.

• Procaryotes Are the Most Diverse of Cells
• Most procaryotes live as single-celled organisms, but some will join together to form chains, clusters or other organized multi-cellular structures.
• In chemical terms, procaryotes are the most diverse and inventive class of cells. Their variety outnumbers all other living organisms on earth.
• These cells contain DNA, but it is not segregated from the rest of the cell parts, this is part of the reason that transcription and translation can occur simultaneously in procaryotes ( this does not occur in eucaryotes).
• Eucaryotic cells are thought o have evolved from aerobic bacteria.
• The World of Procaryotes Is Divided into Two Domains: Bacteria and Archaea
• These two domains are very different from each other. Bacteria and archaea are found in all around us, but archaea are not only found in these environments but also in extreme conditions.
• Archaea can live in environments that we suspect existed on the primitive earth, where living things first evolved.

THE EUCARYOTIC CELL 

• These cells tend to be bigger and more complex that procaryotic cells. Some live as single celled organisms, and others live in multicellular groupings and make up all of the more complex organisms.
• All eucaryotic cells have a nucleus as well as some other main organelles.

• The Nucleus
• The nucleus tends to be the most noticeable organelle in the eucaryotic cell and is enclosed within two concentric membranes that collectively form the nuclear envelope.  

 

• The DNA is contained here, and under the light microscope the large supercoiled DNA can be visually seen in their chromosomal form. you can actually watch the chromosomes duplicate, segregate, and form a new nucleus. 

 

• Mitochondria
• The purpose of this organelle is to generate energy from food to power the cell and are present in ALMOST all eucaryotic cells. They harness the energy from the oxidation of food molecules to produce adenosine triphosphate (ATP) which is the basic chemical fuel that powers most of the cell's activities.

 

• The mitochondria consumes oxygen and releases carbon dioxide in a process called cellular respiration. This means that without the mitochondria, oxygen would be poison to the cell making it purely anaerobic.
• There are a few anaerobic eucaryotic cells, like the intestinal parasites, that lack mitochondria and live only in environments that are low in oxygen.
• These have a very distinctive structure, each appear sausage or worm shaped. Each is enclosed in two separate membranes, the inner membrane forms folds that project into the interior.
• These organelles contain THEIR OWN DNA and reproduce by dividing in two, and are thought to derive from bacteria that were engulfed by some ancestor of present day eucaryotic cells. Creating a symbiotic relationship.
• Chloroplasts
• These organelles are found only in the cells of plants and algae, and have a more complex structure than mitochondria. They contain internal stacks of membranes containing chlorophyll which allows the cell to obtain energy from sunlight through photosynthesis. 

 

• They the energy of sunlight in the chlorophyll molecules and use the derived energy to manufacture sugar molecules, releasing oxygen as a molecular by-product.
• These organelles, like the mitochondria, also have their own DNA and are also thought to have evolved from bacteria. 

 

• Internal membranes
• There are other membrane enclosed organelles in the cell, and tend to be involved with the cells ability to import raw materials as well as exporting manufactured materials out of the cell.
• Endoplasmic reticulum (ER)
• An irregular maze of interconnected spaces enclosed by a membrane, and is the area where most cell membranes components and materials for exported are made. 

 

• Stacks of the flattened membrane-enclosed sacs compose the Golgi apparatus, and is receives and, at times, chemically modifies the molecules made in the ER then directs them to the exterior of the cell or to other locations inside the cell. 

 

• Lysosomes
•  where intracellular digestion occurs, releasing nutrients from food particles and breaking down unwanted molecules for recycling or excretion.

• Made up of endosomes

 

• Peroxisomes
• A membrane enclosed vesicles that offer an enclosed environment for chemical reactions that contain hydrogen peroxide, deadly to the cell, is generated and degraded.
• Others
• There are many other vesicles involved in the transport of materials in between organelles
• Endocytosis- the cells ability to engulf very large particles or even whole cells.
• Exocytosis- vesicles have fused with the plasma membrane and release their contents into the external medium. (neurotransmitters, hormones, and other signaling molecules.
• Cytosol
• This is a concentrated aqueous gel of large and small molecules, and is in definition the part of the cytoplasm that is not partitioned off within intracellular membranes.
• The largest single compartment in the cell, is the site of many chemical reactions and is fundamental to the cell's existence.
• Early steps of breaking down nutrient molecules
•  the manufacture of proteins.
• Ribosomes are also found here
• These are responsible for the production of proteins from mRNA, and are often attached to the cytosolic face of the ER. 

 

• Cytoskeleton
• This network of filaments are what make up the cells structure, referred to as the Cytoskeleton.
• Responsible for directed cell movements. It is not structure less,  in fact the cytosol is filled with fine filamentous proteins that form a hatchet like structure. These filaments are anchored at one end to the plasma membrane or radiate out from near the nucleolus.
• The thinnest of the filaments are actin filaments, and are present in all eucaryotic cells. These are found in high numbers in muscle cells, functioning as part of the machinery involved in forming contractile forces.
• The thickest of the filaments are called microtubules. These filaments are hollow tubes, and help to pull the chromosomes apart during mitosis.
• The intermediate thick filaments are the intermediate filaments, and function to strengthen the cell.
• The cytoskeleton is not static, the interior of the cell is in constant motion.
• The filaments have the ability to assemble and disappear in a mater of minutes.
• Eucaryotic cells may have originated as predators.
• The eucaryotic cells did not obtain all their organelles at one time, rather they acquired each one at a different time. 

• Single celled eucaryotes that can pry on and "eat" other cells are called protozoans, and are some of the most complex cells known to date. 

 

THE MODEL ORGANISM

• All cells are thought to be dependents from a common ancestor, whose fundamental properties have been passed down  through evolution.

• Escherichia coli
• This is a small, rod-shaped bacterial cell that lives in the human gut and can cope with variable chemical conditions and environments.
• Most of what we know, when it comes to the fundamental mechanisms of life, has come from the study of E. coli.
• Saccharomyces cerevisiae
• A minimal model for eucaryotic cells, and is for all biological reasons is as close to animal cells as it is to plant cells.
• This organism has helped us to understand basic mechanisms in eucaryotic cells, like cell division.
• Arabidopsis thaliana
• A model organism for plants, both flowering and non-flowering.
• These plants help us to better understand the development and physiology of crop plants as well as other plant species.
• Drosophila melanogaster
• This is the model organism for insects, the largest group of all animal species.
• Play a major role in genetic research, as well as early development (HOX genes, and maternal effect genes).
• Caenorhabditis elegans
• 70% of human proteins have some form of a counterpart that is found in the worm, and they are great for studying development.
• Programed cell death research was greatly aided from studying this animal.
• Zebrafish
• Primarily research on vertebrates. Provides a good model to observe and research early development, as the fish is transparent for the first two weeks of its life.