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UNIT 1:  CELLULAR FUNCTIONS

The “Work” of Cells

Life on Earth depends on a constant supply of solar energy.  If the sun’s energy were to stop, life would cease to exist within a matter of hours.  All forms of life are either directly or indirectly dependent on the sun.  Photosynthesis is the process that plants, some bacteria, and some protists use to capture the sun’s energy and produce carbohydrates.  The remaining life forms, like animals, some bacteria, and some protists acquire their energy by eating photosynthetic organisms.  The harnessing of sunlight energy, and converting it into organic molecules, balanced with the consumption of this stored chemical energy, is the basis life.

A.  The Energy Involved in Cellular Processes

·           the sum of all activities that take place in a cell are called metabolism

·           metabolic processes can either be anabolic – “building” or catabolic – “breaking down”, and they are crucial to providing cells with energy

·           one very important endergonic (meaning “energy in”) biochemical reaction is photosynthesis – the process whereby electrons of chlorophyll molecules are excited by photonic energy (light), and are not allowed to fall back down to the original energy level

·           the energy gained in the “jump” eventually goes into “fixing” 6 carbon atoms (of gaseous CO₂) into one molecule of organic glucose

·           this process requires energy and stores it in the covalent bonds of glucose

·           one very important exergonic (meaning “energy out) biochemical reaction is  cellular respiration – the process whereby the chemical potential energy stored in the bonds of organic molecules (typically glucose) is “realized” and used to do work for the cell

·           the energy “freed up” is used to help make ATP – the “energy currency” of all living cells

·           this process releases energy

ATP – The Cell’s Power Pack

·         ATP is a nucleotide made of an adenosine nucleoside (pentose ribose sugar +  adenine base) and a triphosphate tail

·         Figure 4.3, p. 89, shows how adenosine diphosphate (ADP) is phosphorylated into adenosine triphosphate (ATP)

·         The reason why cells go through the trouble of making ATP, and using it, as opposed to anything else, as an energy source to drive metabolic processes, is because of ATP’s chemical character:

·         ATP is well suited to its role as any energy molecule

·         it contains high energy bonds between its phosphate groups

·         each phosphate of the triphosphate “tail” of the molecule is negative in charge, therefore repels the other two phosphates

·         this repulsive condition within the ATP structure makes the last phosphate bond is extremely unstable

·         therefore, the last phosphate readily breaks off of the molecule, freeing up energy that is stored in the bond

·         this is why the bond between the second and third phosphate is called a “high energy bond”

·         whenever an ATP is dephosporylated it releases a particular quantity of energy that is efficiently used to power metabolic activities

·         typical metabolic reactions usually require the amount of energy available when one ATP is dephosphorylated

·         if the cell used the entire molecule of glucose, for example, it would be like using a forest fire to light a cigarette!

·         therefore, the most efficient, effective energy source for all metabolic processes is ATP

·         when ATP is used, an ADP and a free phosphate result:

ATP  ®  ADP  +  P_i  +  ENERGY

·         cellular respiration is the process where the ADP molecule is converted back into ATP

·           to view the process of phosphorylation click on http://student.ccbc.cc.md.us/biotutorials/energy/adpan.html

Homework:            1-7, p. 89

B.  Enzymes

·           enzymes are specialized protein molecules that function as biological catalysts to facilitate chemical reactions

·           catalysts allow reactions to proceed sometimes 1 billion times faster than they would if they were absent

·           the survival of living organisms depends on the proper functioning of its enzymes

·           without enzymes, essential biochemical reactions would not occur fast enough sustain life

·           in biological processes, when a reactant molecule needs to become a product, it will bind to its specific enzyme

·           the molecule that the enzyme binds to is called a substrate

·           the substrate molecule actually “fits” its enzyme perfectly and binds to it in a “lock-and-key” manner

·           the perfect-fitting “notch” on the globular enzyme is called the active site of the enzyme

·           at the point when the substrate molecule is becoming  a product, the substrate and enzyme are bound together to form an enzyme-substrate complex

·           to view an animation of how an enzyme “fits” its substrate click on http://scholar.hw.ac.uk/site/biology/activity6.asp

·           Figure 4.4, p. 90 demonstrates how an enzyme helps a substrate become products in catabolic enzyme activity

·           each enzyme catalyzes only one chemical reaction – this means that each enzyme is specific in function

·           the shape of the “notch” or groove is important since this will dictate whether or not the substrate will bind to the enzyme

·           this means that the structure or shape of the enzyme is extremely important to its function since a less than perfect fit means enzyme inactivity or dysfunction

·           there are two ways that an enzyme can be inhibited:

1.        competitive inhibition:  a molecule occupies the active site of an enzyme thereby “blocking” the substrate and preventing the enzyme-substrate complex from forming – examples of such inhibitors are cyanide and arsenic – these substances compete bind to active sites on vital biological enzymes and prevent the intended substrates reacting with the enzyme

2.        non-competitive inhibition:  a molecule binds to the enzyme at a location other than the active site, which effectively alters the enzyme shape, making it dysfunctional

·           most biological processes involve the successful collision between reactant molecules in order for products to form

·           not all collisions are successful

·           to ensure the success of such collisions, and in order for the transition complex to occur, thus the product molecules to be produced, enzymes need to become involved

·           in living systems, enzymes actually hold reactant molecules in place, in the correct 3-dimensional orientation in space, so collisions age successful, and products are made

·           Figure 4.5, p. 91 illustrates the effect that enzymes have on the ease with which a reaction takes place

·           note that enzymes have no effect on the total amount of energy that goes into or is released in any reaction – the ball’s change in position is the same if an enzyme is involved or if it isn’t

·           enzymes only lower the activation energy, thereby allowing more reactant molecules to possess the minimum amount of energy necessary to collide successfully and make products

·           to view an example of how enzyme activity affects a substrate click on http://web.ukonline.co.uk/webwise/spinneret/other/anenz.htm

Homework:            1-7, p. 92

C.  The Synthesis of Proteins

·           recall that proteins have many different functions:

1.        form the cytoskeleton of cells for structure and support

2.        act as enzymes to catalyze chemical reactions

3.        intrinsic proteins within cell membranes can function as chemical receptors and transport substances

4.        chemical communication between cells

·            given the importance of proteins to the survival of cells, it is essential for living cells to continuously produce a new supply of them wherever they are required

·            the process of producing proteins is called protein synthesis

·            Figure 4.6, p. 93, illustrates the two major steps of protein synthesis:

1.  Transcription:           -  takes place in the nucleus

-  the specific section of DNA , that codes for a specific desired protein, is copied into a molecule of  

   messenger RNA (mRNA)

-  mRNA is brought out of the nucleus to ribosomal RNA (rRNA) on the endoplasmic reticulum

2.  Translation:              -  takes place in the cytoplasm

-  at the rRNA, a third kind of RNA, transfer RNA (tRNA), brings the required amino acid one

   at a time to build the primary structure of the protein according to the instructions on the mRNA strand

-  the rRNA assemble the amino acids in the order at which they are brought to it

·            once the polypeptide has been assembled at the ribosome it enters the RER

·            in the RER the protein molecule assumes its final shape by assuming the necessary shapes – secondary, tertiary, or quaternary

·            the RER sends the protein out by way of a vesicle to the Golgi complex, where they are either stored or packaged for export via exocytosis

·            for a detailed view of protein synthesis, click on http://www.eolas.ca/Micro_2.htm

·            an analogy for protein synthesis:

Imagine you come home and realize that you have a long message on your answering machine.  You press the play button, but all you here is a muffled, fragmented sound.  You call over your friend, who is an audio expert, to transcribe the message for you onto a piece of paper.  As clear as the script on this paper may be, it doesn’t make any sense to you because it is in a form of hieroglyphics.  You bring the script to an archeologist, who specializes in hieroglyphics.  Each time he reads a word from the message, he calls out to one of his 20 assistants, who go down numerous corridors of shelves and retrieve the translated words from the shelves.  Each assistant brings the word to the archeologist, who then staples the pages together.  Once the stapling is complete, he gives you the stapled package.  You look at the message, and it reads, “you have just constructed your first polypeptide chain….the secondary, tertiary, and quaternary steps will follow”.

Description of Analogy:

-     the message on the answering machine represents the section on the DNA strand that codes for the construction of a particular protein

-     your finger represents the protein that enters the nucleus and initiates protein synthesis

-     your friend, the audio expert, represents the protein responsible for creating the mRNA strand

-     the transcribed message, in hieroglyphics represents the mRNA

-     bringing out to an archeologist is reflective of the mRNA leaving the nucleus and going into the cytoplasm

-     the archeologist is the rRNA that translates the mRNA and helps string the amino acids together by stapling them

-     the 20 assistants represent the 20 different tRNAs that bind to their own specific amino acid and carry it to the amino acid linking site at the rRNA

-     the corridors of shelves represent the endoplasmic reticulum, along which the tRNAs move

-     the staples represent the polypeptide bonds that link amino acids together

-     the final message represents the primary polypeptide sequence of amino acids

Homework:        1-4, p. 95

D.  Making Fuel – Photosynthesis and Food Production

·           the process of changing sunlight energy into chemical potential energy, stored in covalent bonds, is called photosynthesis

·           organisms that can do this are called “self-feeders” or autotrophs

·           they are able to “fix” six carbons of gaseous CO₂ into a six carbon sugar called glucose -- this source of potential energy is the fuel that will be burned and used to make ATP

·           the other products of photosynthesis, other than glucose, are six oxygen molecules

·           the process occurs in organelles called chloroplasts – p. 96, Figure 4.9

·           each chloroplast contains an elaborate internal membrane system of connected disc-shaped structures called thylakoids

·           thylakoids stack up to form grana (singular granum)

·           inside each thylakoid membrane are many pigment molecules

·           the major pigment is called chlorophyll a

·           the unique molecular structure of chlorophyll a, as well as all the other kinds of pigments,  makes it effectively capture photonic energy from the visible light and use this energy to fix CO₂ into glucose

·           the two main stages of photosynthesis are:

1.  light-dependent reactions

·         water molecules are split into O₂ and H₂ – the oxygen is released as a product

·         light energy goes into making ATP and other energy forms to power the process of fixing CO₂ into glucose

2.  light-independent reactions

·         the CO₂ is “fixed” into glucose as the H₂ from water is added to it

·         it is called light-independent because the “fixing” of CO₂ does not need light in order to take place

·       organisms that use light as the energy source to fix CO₂ are called photoautotrophs

·           organisms that can convert inorganic substances from their external environments, such as hydrogen sulphide, carbon dioxide, or iron-containing compounds, into organic macromolecules, like carbohydrates, lipids, proteins, and nucleic acids, are called chemoautotrophs – examples of such organisms are chemoautotrophic bacteria that live in extreme conditions like volcanoes, sulphur springs, etc.

·           scientists believe that the chemoautotrophic bacteria are related to the first life forms on Earth

·           these cells would have been well-suited to the conditions that probably existed on the young, developing planet

Homework:       1-5, p. 97

E.  Making Usable Energy – Cellular Respiration

·           cellular energy is necessary for any metabolic process to occur

·           the most useful form of cellular energy is the ATP molecule – its particular chemical character makes it the most efficient source of energy to drive biochemical processes

·           the process of making ATP from nutrient molecules is called cellular respiration

·           any carbohydrate, lipid, protein, or nucleic acid can be used as a nutrient source to make ATP, however, the fastest, and most efficient pathway begins with glucose

·           Figure 4.11, p. 99 illustrates how other molecules, other than glucose, can be used as sources of fuel to make ATP

·           the entire process consists of 4 stages:

1.        Glycolysis

2.        Pyruvate Oxidation

3.        Kreb’s Cycle

4.        Electron Transport Chain and Chemiosmosis

·            in a nutshell, the cell takes a glucose molecule through this process so it can extract energy from it – the covalent bonds in glucose are slowly broken down in a series of reactions (about 20 of them) that are over all exergonic

·            the over all purpose of these “domino” reactions is to take the potential energy, stored in the bonds of glucose, and free it up to phosphorylate ADP molecules to make ATP molecules

·            Figure 4.10, p. 98, summarizes the entire process:  C₆H₁₂O₆  +  O₂  →  6CO₂  +  6H₂O  + free energy

·            the first stage, called glycolysis, occurs in the cytoplasm of the cell

·            glycolysis means “glucose-splitting” – in this stage, each 6-carbon glucose molecule is split into two 3-carbon molecules of pyruvic acid, and two ATP molecules are made

·            this process does not involve oxygen, and occurs in all types of cells

·            in eukaryotic cells, if oxygen is present, the pyruvic acid enter the mitochondrion where the next 3 stages occur, and 34 more ATP molecules are made

·            if oxygen is not present, the process of making ATP does not stop -- two alternative pathways of cellular respiration may occur (i.e. two “plan Bs”)

·            because both of these alternative pathways occur in the absence of oxygen, the process is referred to as anaerobic respiration

·            in plants, the anaerobic respiration is called alcoholic fermentation

• instead of the pyruvic acid entering the mitochondrion, it gets consumed in the cytoplasm
• each pyruvic acid releases a CO₂, and becomes alcohol (ethanol), thus the name alcoholic fermentation
• this fermentation causes a necessary coenzyme to be regenerated, which helps continue glycolysis, and make 2 more ATP molecules
• this process can be used by humans to make yeast-bread dough rise (utilizing the CO₂ product), or to make alcoholic beverages (utilizing the ethanol product)

·             in animals, the anaerobic respiration is called lactic acid fermentation

• instead of the pyruvic acid entering the mitochondrion, it stays in the cytoplasm where it gets converted to lactic acid, which regenerates necessary enzymes to help continue the glycolytic pathway, and as a result, 2 more ATP are made in the cytoplasm
• the downfall to this process is that lactic acid build-up is toxic
• for example, lactic acid causes muscles to cramp and feel fatigued – it needs to be changed back to pyruvic acid in the presence of oxygen
• this explains why panting takes place after rigorous exercise – you owe your body the oxygen necessary to break down the lactic acid
• this pay back is called oxygen debt

·           for detailed animations that illustrate the molecular processes of anaerobic and aerobic respiration, click on  http://www.sp.uconn.edu/~terry/Common/respiration.html

Homework:       1-7, p. 101