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.