Basic Biology I: Cells

How organisms work

Outline

• Chemistry (pp. 8-10): atoms, molecules and bond, polar bonds, water

• Biochemistry (pp. 11-17): four basic macromolecules

• Cells (pp. 20-29): membrane, osmotic pressure, organelles, endosymbiosis, cell division, gene expression

• Enzymes and energy generation (pp. 57-58 and 64-69)

Chemistry

• Name the components of atoms and their role in determining the atom’s identity and in forming chemical bonds.

• Distinguish between the 3 main types of chemical bond

• Understand the relationship between water, polar and non-polar, and hydrophilic and hydrophobic

Chemistry• At the bottom, biology is nothing but applied chemistry

• All matter is composed of atoms

• Elements such as carbon and oxygen are a group of atoms of the same type. For instance, a nail made of iron is just a large group of iron atoms.

• There are 92 naturally occurring elements, plus about 25 artificially-created elements.

• Living things are mainly composed of the elements carbon, hydrogen, oxygen, and nitrogen. Another dozen or so elements are also used: phosphorus, iron, magnesium, sodium, potassium, chlorine, to name a few.

Atoms • Atoms have 3 components: protons, neutrons, and electrons

– The type of element (carbon, iron, etc. ) is entirely determined by how many protons are in the nucleus.

• protons and neutrons are in the nucleus – Protons have a +1 charge

– Neutrons have no charge

• Electrons circle around the nucleus, in a series of shells.

– Electrons have a -1 charge

– Chemical bonds are created by movements of the electrons between atoms

• The number of protons determines which element the atom is.

– Hydrogen: 1 proton, carbon = 6 protons, oxygen = 8 protons.

– Biological and chemical processes never change the number of protons in any atom.

• Normally, the number of electrons is equal to the number of protons, so the atom has no electrical charge: it is neutral.

Chemical Bonds• Atoms can combine with each other to form molecules.

• A molecule is a defined number of atoms grouped into a defined spatial relationship. For example, water, H2O, is 2 hydrogen atoms connected to an oxygen atom. The oxygen is in the middle, and the hydrogens are attached at an angle to it.

• A large group of the same molecule is called a compound (just as a large group of the same atom is called an element).

• Molecules are held together by chemical bonds. Chemical bonds are formed by the movement of electrons.

• Chemical bonds are the result of 2 forces:• 1. The octet rule, which means that atoms want to have 8 electrons in

their outer shell (2 in the case of hydrogen).• 2. The attraction between atoms of opposite electrical charge.

• The three main types of chemical bond are; ionic bond, covalent bond, and hydrogen bond.

Ionic Bonds

• In an ionic bond, one atom gives an electron to another atom. This makes both atoms ions, and they are held together because their opposite charges attract each other.

↑ In sodium chloride (table salt), sodium starts out with 1 electron in its outer shell. The next shell down has 8 electrons, so by giving 1 electron away, the sodium atom gets a full outer shell. It then has a +1 charge.

• Chlorine starts out with 7 electrons in its outer shell. By gaining one more electron, it gets 8 in the outer shell, and a -1 charge.

↑ The + charged sodium and the – charged chlorine attract each other, and they pack together in salt crystals.

Covalent Bonds• Covalent bonds occur when 2 atoms

share a pair of electrons. The electrons spend part of their time with both atoms, so the octet rule is satisfied sufficiently.

• A molecule of hydrogen gas, H2, has 2 hydrogen atoms. Each atom provides 1 electron, so in the bond each atom shares 2, a complete shell for hydrogen.

• The bond is symbolized as a line connecting the 2 H’s: H-H

↑ In water (H2O), the oxygen has 6 electrons in its outer shell, and it shares one with each of the 2 hydrogens, giving 8 shared electrons for oxygen and 2 for each hydrogen.

• Covalent bonds are the most common type in biological molecules.

Polar Covalent Bonds• Sometimes the electrons in a covalent bond aren’t

shared equally, because one atom attracts electrons more strongly than the other. When this happens, the electrons spend more time with one atom, and that atom becomes slightly negatively charged. The other atom becomes slightly positively charged. This is a polar covalent bond, because the atoms form positive and negative poles.

• Water is a polar compound, because the oxygen is slightly negative and the hydrogens slightly positive.

– Oxygen attracts electrons more than hydrogen

• Note that the total charge on the molecule is balanced, same number of electrons as protons, but within the molecule the charges are slightly separated.

(Bonds where the electrons are shared equally are called non-polar.)

• Polar molecules attract each other: the opposite charges attract.

Hydrogen Bonds• The slight + and – charges in polar

bonds attract each other. In biological molecules, it is common for the partial + charge on a hydrogen to attract the partial – charge on a nearby oxygen or nitrogen. This attraction is called a hydrogen bond. A hydrogen bond is the attraction between a hydrogen atom and the small negative charge on another atom.

↑ Hydrogen bonds are very weak compared to covalent bonds, but large numbers of them can add up to a strong bond. The strands of DNA are held together by hydrogen bonds.

• Hydrogen bonds also form between different parts of the same molecule, and between water and other molecules.

Water

• All life occurs in water. Most molecules are dissolved in water: an aqueous solution.

• Water, H2O, is a polar compound. The 2 hydrogens are held at an angle to each other, and so the oxygen end of the molecule is partially negative and the hydrogen end is partially positive.

• Water forms many hydrogen bonds with other water molecules and with other polar substances. This causes water molecules to stick together (causing surface tension) and stick to other things (causing capillary action, how water gets from the roots to the top of trees).

Water• Polar substances dissolve in

water, because water forms hydrogen bonds with the polar molecules. Thus, polar substances are called hydrophilic, or “water-loving”.

• Non-polar substances don’t dissolve in water because they can’t form hydrogen bonds, so they are called hydrophobic, or ‘water-fearing”. Oils and fats are examples of non-polar substances.

• Cells are surrounded by a hydrophobic membrane. Keeps the cell’s contents separated from the outside world.

Hydrophilic coating reduces friction by trapping a thin layer of water next to the boat’s hull.

Biochemistry

• Name the 4 types of macromolecule, their subunits, and their functions in the cell.

• Distinguish between different sub-types of carbohydrate, lipid, and nucleic acid in terms of their structure and role in the cell.

• Understand how protein folding is related to enzyme activity.

Organic Compounds• It used to be thought that only living

things could synthesize the complicated carbon compounds found in cells

• German chemists in the 1800’s learned how to do this in the lab, showing that “organic” compounds can be created by non-organic means.– Raw materials: coal and oil

• Today, organic compounds are those that contain carbon. (with a few exceptions such as carbon dioxide and diamonds)

Four Basic Types of Macromolecule

• Most organic molecules in the cell are long chains of similar subunits. Because they are large, these molecules are called macromolecules. Each macromolecule has a different type of subunit.

• The four types of macromolecule are:1. carbohydrates (sugars and starches), Subunit = simple sugar.2. lipids (fats). Subunits = fatty acids and glycerol3. proteins, Subunits = amino acids4. nucleic acids (DNA and RNA). Subunits = nucleotides

• The cell also contains water, inorganic salts and ions, and other small organic molecules.

• Plants often produce secondary metabolites: special compounds that attract pollinators, inhibit microorganisms, deter grazing animals, etc. We have found uses for many of these secondary metabolites as medicines, spices, and drugs.

Carbohydrates

• Sugars and starches: “saccharides”.• The name “carbohydrate” comes from

the approximate composition: a ratio of 1 carbon to 2 hydrogens to one oxygen (CH2O). For instance the sugar glucose is C6H12O6.

• Carbohydrates are composed of rings of 5 or 6 carbons, with –OH groups attached. This makes most carbohydrates water-soluble.

• Carbohydrates are used for energy production and storage (sugar and starch), and for structure (cellulose).

Sugars• Monosaccharides, or simple sugars, like glucose

and fructose, are composed of a single ring. • Glucose is the primary food molecule used by

most living things: other molecules are converted to glucose before being used to generate energy. Glucose can also be assembled into starch and cellulose.– Fructose is a another simple sugar found in plants,

It is sweeter than glucose and is used to sweeten may food products.

• Disaccharides are two simple sugars joined together. Most of the sweet things we eat are disaccharides: table sugar is sucrose, glucose joined to fructose. Plants use photosynthesis to make glucose, but convert it to sucrose for ease of transport. – Maltose, malt sugar, consists of two glucoses

joined together. It is a breakdown product of starch, which yeast converts to ethanol when beer is brewed.

Complex Carbohydrates• = polysaccharides (many sugars linked

together).– Can be linear chains or branched.

• Some polysaccharides are used for food storage: starch.– Starch is a glucose polymer, we have

enzymes that easily digest starch. – Starch is a convenient way to store

glucose in both plants and animals. • Some polysaccharides are structural: the

cellulose of plant cell walls and fibers is a polysaccharide composed of many glucose molecules, but linked together differently than starch.– We don’t have enzymes that can digest

these polymers. Cows and termites depend on bacteria in their guts to digest cellulose, producing methane as a byproduct.

Lipids• Lipids are the main non-polar component

(hydrophobic) of cells. Mostly hydrocarbons—carbon and hydrogen.

• They are used primarily as energy storage and cell membranes.

• 4 main types: fats (energy storage), phospholipids (cell membranes), waxes (waterproofing), and steroids (hormones).

• Waxes: waterproof coating on plants and animals. Composed of fatty acids attached to long chain alcohols. – The ability of plant to coat themselves in waxes

was crucial to the ability to live on dry land.

• Steroids have carbon atoms arranged in a set of 4 linked rings.– Cholesterol is steroid; it is an essential

component of cell membranes (along with the phospholipids).

– Many human hormones are steroids

Triglycerides and Phospholipids• Triglycerides are the main type of

fat. A triglyceride is composed of 3 fatty acids attached to a molecule of glycerol.– Fatty acids are long hydrocarbon

chains with an acid group at one end.

• Fats store about twice as much energy per weight as carbohydrates like starch.

• Phospholipids are the main component of cell membranes.

– they have a glycerol with 2 fatty acids attached, plus a phosphate-containing “head” group instead of a third fatty acid.

• The head group is hydrophilic, while the fatty acids are hydrophobic.

• Cell membranes are 2 layers, with the head groups facing out and the fatty acids forming the interior of the membrane.

Proteins• The most important type of

macromolecule. Roles: – Enzymes: all chemical reactions in the

cellsare catalyzed by enzymes, which are proteins: building up, rearranging, and breaking down of organic compounds,, generating energy

– Structure: collagen in skin, keratin in hair, crystallin in eye. Also, movement of materials inside the cell.

– Transport: everything that goes in or out of a cell (except water and a few gasses) is carried by proteins.

• All organisms contain protein, but animals have much more protein than plants: most of the animal body is composed of protein, while most of the plant body is carbohydrate.– Proteins are 1/3 nitrogen. Acquiring

this nitrogen and getting rid of nitrogenous waste is a big problem animals face.

Amino Acids• Amino Acids are the subunits of

proteins. • Each amino acid contains an amino

group (-NH2) and an acid group (COOH). Proteins consist of long chains of amino acids, with the acid group of one bonded to the amino group of the next.

• There are 20 different kinds of amino acids in proteins. Each one has a functional group (the “R group”) attached to it.

• Different R groups give the 20 amino acids different properties, such as charged (+ or -), polar, hydrophobic, etc.

• The different properties of a protein come from the arrangement of the amino acids.

Protein Structure• A polypeptide is one linear chain of

amino acids. A protein consists of one or more polypeptides, and they sometimes contain small helper molecules such as heme.

• After the polypeptides are synthesized by the cell, they spontaneously fold up into a characteristic conformation which allows them to be active. The proper shape is essential for active proteins. For most proteins, the amino acids sequence itself is all that is needed to get proper folding. – The joining of polypeptide subunits into a

single protein also happens spontaneously, for the same reasons.

• Denaturation is the destruction of the 3-dimensional shape of the protein. This inactivates the protein, and makes it easier to destroy. Heat is the easiest way to denature proteins: this is the effect of cooking foods.

Nucleic Acids• Nucleotides are the subunits of nucleic

acids.• Nucleic acids store and transmit genetic

information in the cell. • The two types of nucleic acid are RNA

(ribonucleic acid) and DNA (deoxyribonucleic acid).

• Each nucleotide has 3 parts: a sugar, a phosphate, and a base.

• The sugar, ribose in RNA and deoxyribose in DNA, contain 5 carbons. They differ only in that an –OH group in ribose is replaced by a –H in DNA.

• The main energy-carrying molecule in the cell is ATP. ATP is an RNA nucleotide with 3 phosphate groups attached to it in a chain. The energy is stored because the phosphates each have a negative charge. These charges repel each other, but they are forced to stay together by the covalent bonds.

DNA and RNA• DNA uses 4 different bases: adenine

(A), guanine (G), thymine (T), and cytosine (C). The order of these bases in a chain of DNA determines the genetic information.

• DNA consists of 2 complementary chains twisted into a double helix and held together by hydrogen bonds. DNA is a stable molecule which can survive thousands of years under proper conditions– The DNA bases pair with each other:

A with T, and G with C.

• RNA consists of a single chain that also uses 4 bases: however, the thymine in DNA is replaced by uracil (U) in RNA. RNA is much less stable than DNA: it is used to convey information for immediate use by the cell.

Cells• List the tenets of the cell theory.• Know the essential difference between prokaryotes and eukaryotes, and

which types of organism belong to which group. • Understand how the cell membrane allows only certain molecules in and out

of the cell. • Explain what osmotic pressure is, and describe the function of the cell wall in

resisting osmotic pressure.• Explain the endosymbiotic theory for the origin of mitochondria and

chloroplasts. • Know the functions of these organelles: nucleus, mitochondria, chloroplast,

endoplasmic reticulum, Golgi body, lysosome• Understand the relationship between chromosomes, DNA, and genes.• Understand the purpose of mitosis (but not the steps involved). • List the steps of gene expression and the molecules involved in each step.• Know the purpose of the genetic code and transfer RNA

The Cell Theory

• Use of the microscope for 150 years or so led to these basic beliefs about cells:

• 1. All living things are composed of cells.

• 2. The cell is the smallest unit of life.

• 3. All cells arise from pre-existing cells.

Basic Cell Organization

• All cells contain:– 1. cell membrane that keeps the

inside and outside separate.– 2. DNA-containing region that

holds the instructions to run the processes of life.

– 3. Cytoplasm: a semi-fluid region containing the rest of the cell’s machinery.

• Prokaryotes: (bacteria): simple cells with DNA loose in the cytoplasm. No nucleus or other internal membrane-bound organelles.

• Eukaryotes (plants, animals, fungi, protists): complex cells with DNA in a nucleus separated from the cytoplasm by a membrane.

Cell Membrane• Composed of phospholipids, with a

polar (and therefore hydrophilic) head group, and 2 non-polar (hydrophobic) tails. A bilayer with the polar heads on the outsides and hydrophobic tails inside satisfies all of the molecule. The membrane is a “phospholipid bilayer”.

• The membrane also contains cholesterol and various proteins. The proteins act as sensors, attachment points, cell recognition, or they transport small molecules through the membrane.

• Only water, a few gasses, and a few other small non-polar molecules can move freely through a pure phospholipid membrane. Everything else must be transported into the cell by protein channels in the membrane.

Transport Across the Cell Membrane• Each type of molecule that crosses the membrane needs its

own transporter protein: the transporters are very specific.

• Basic rule: things spontaneously move from high concentration to low concentration (downhill). This process is called diffusion.

• To get things to move from low to high (uphill), you need to add energy. In the cell, energy is kept in the form of ATP.

• Three basic transport mechanisms: passive transport for downhill, active transport for uphill, and bulk transport for large amounts of material in either direction.

• Also need to deal with excess water entering the cell.

Passive and Active Transport• Passive transport uses protein

channels through the membrane that allow a particular molecule to go through it, down the concentration gradient. Glucose is a good example: since cells burn glucose for energy, the concentration inside is less than the concentration outside.

• Active transport uses proteins as pumps to concentrate molecules against the concentration gradient. The pumps use ATP for energy. One example is the calcium pump, which keeps the level of calcium ions in the cell 1000 times lower than outside, by constantly pumping calcium ions out. The balance of sodium and potassium ions is maintained with potassium high inside and sodium low inside, using a pump. Up to 1/3 of all energy used by the cell goes into maintaining the sodium/potassium balance.

Water in the Cell• Water also moves down the concentration

gradient. Since the cell is full of other molcules, water wants to moves into the cell to dilute them. This process is called osmosis, and it exerts a pressure that can cause cells to swell up and burst.

• We say that pure water is hypotonic relative to the inside of a cell: pure water has fewer particles in it, so the water moves into the cell. A plant cell in pure water swells up against the cell wall: a nice crisp vegetable, for example.

• Conversely, if cells are put into a concentrated salt solution, water will leave the cells, moving to dilute the water outside. The concentrated salt solution is hypertonic: has more particles in it than the inside of the cell. The cell shrinks away from the cell wall: the plant wilts.

• Normal body fluids are isotonic, having the same concentration of particles as the inside of the cell.

• The most important function of the plant cell wall is to defend against osmotic pressure.

Mitochondria and Chloroplasts• The mitochondria are the site where most of the

cell’s ATP is generated, when organic compounds are broken down to carbon dioxide and water, using oxygen.

• All eukaryotes have mitochondria. The number in a cell depends on that cell’s energy needs.

• Mitochondria have their own circular DNA, the same kind found in bacteria. This and other evidence has led to the theory of endosymbiosis: that mitochondria were once free-living bacteria that developed a mutually beneficial relationship with a primitive eukaryotic cell.

• Chloroplasts are the organelles where photosynthesis occurs. They are also the result of endosymbiosis: chloroplasts are descended from free-living photosynthetic bacteria.

• Several types of algae have had 2 rounds of endosymbiosis: The first event got the chloroplasts established in the cells (creating red and green algae). The second endosymbiosis event occurred when another single-celled organism (a protist) swallowed one of these algae to create brown algae.

Endosymbiont Hypothesis

Nucleus• The main components of the nucleus are

the chromosomes. A chromosome is composed of a single very long DNA molecule plus the proteins that support it and control it.

• The DNA carries the genes, which are instructions needed to build and maintain the cell, respond to changes in the environment, and to divide into 2 cells.

• Each gene is a short region of the chromosome’s DNA. There are several thousand genes on each chromosome.

• What genes do: the nucleotide sequence of each gene codes for a single polypeptide, the chain of amino acids that make up proteins.

• Most eukaryotes have a small number of chromosomes: humans have 46 chromosomes, corn plants have 20. The number is fixed within a species: all humans have 46 chromosomes except for some genetic oddities.

Cell Division and Genes• Cells divide to make more cells. The

chromosomes must be precisely divided so that each daughter cell gets exactly the same DNA.– All the other organelles are just

randomly separated into the daughter cells,

• Key points about genes:– All cells within an organism have the

same genes.– What makes cells different from each

other is that different genes are turned on and turned off in different cells.

• Before a cell can divide, it must replicate its DNA, so there are 2 copies of each chromosome (=2 DNA molecules), attached at the centromere.

• Once the DNA has been replicated, the cell is ready to divide, using the process of mitosis.

Summary of Mitosis• Mitosis is normal cell division, which goes on throughout

life in all parts of the body. – Meiosis is the special cell division that creates the sperm and

eggs, the gametes. We will discuss meiosis separately.

• Prophase: • Chromosomes condense• Nuclear envelope disappears• centrosomes move to opposite sides of the cell• Spindle forms and attaches to centromeres on the chromosomes

• Metaphase• Chromosomes lined up on equator of spindle• centrosomes at opposite ends of cell

• Anaphase• Centromeres divide: each 2-chromatid chromosome becomes

two 1-chromatid chromosomes• Chromosomes pulled to opposite poles by the spindle

• Telophase• Chromosomes de-condense• Nuclear envelope reappears• Cytokinesis: the cytoplasm is divided into 2 cells

Gene Expression• Each gene is a short section of a

chromosome’s DNA that codes for a polypeptide.

• Different genes are active (expressed) in different cells

• Genes are expressed by first making an RNA copy of the gene called messenger RNA,(transcription) and then using the information on the RNA copy to make a protein (translation).

• Transcription occurs in the nucleus, but translation occurs in the cytoplasm. The messenger RNA needs to be transported out of the nucleus.

Transcription

• Transcription is the process of making an RNA copy of a single DNA gene.– The RNA copy is messenger RNA

• The copying is done by an enzyme: RNA polymerase.

• The bases of RNA pair with the bases of DNA: A with T (or U in RNA), and G with C. The RNA copy of a gene is just a complementary copy of the DNA strand.

• RNA polymerase attaches to a signal at the beginning of the gene, then it moves down the gene, adding new bases to the RNA copy, until it reaches a termination signal at the end of the gene.

Genetic Code• There are only 4 bases in DNA and

RNA, but there are 20 different amino acids that go into proteins. How can DNA code for the amino acid sequence of a protein?

• Each amino acid is coded for by a group of 3 bases, a codon. 3 bases of DNA or RNA = 1 codon.

• Since there are 4 bases and 3 positions in each codon, there are 4 x 4 x 4 = 64 possible codons.

• This is far more than is necessary, so most amino acids use more than 1 codon.

• 3 of the 64 codons are used as STOP signals; they are found at the end of every gene and mark the end of the protein.

• One codon (AUG) is used as a START signal: it is at the start of every protein.

Transfer RNA• Transfer RNA molecules act as adapters

between the codons on messenger RNA and the amino acids. Transfer RNA is the physical manifestation of the genetic code.

• Each transfer RNA molecule is twisted into a knot that has 2 ends.

• At one end is the “anticodon”, 3 RNA bases that matches the 3 bases of the codon. This is the end that attaches to messenger RNA.

• At the other end is an attachment site for the proper amino acid.

• A special group of enzymes pairs up the proper transfer RNA molecules with their corresponding amino acids.

• Transfer RNA brings the amino acids to the ribosomes, which are RNA/protein hybrids that move along the messenger RNA, translating the codons into the amino acid sequence of the polypeptide.

Translation• First step: initiation. The messenger RNA binds to a

ribosome, and the transfer RNA corresponding to the START codon binds to this complex– The ribosome has 2 sites for binding transfer

RNA. The first tRNA with its attached amino acid binds to the first site, and then the transfer RNA corresponding to the second codon bind to the second site.

– The ribosome then joins the two amino acids together.

• Step 2 is elongation: the ribosome moves down the messenger RNA a distance of one codon. – The old, empty tRNA is removed.– A new transfer RNA, matching the new codon,

binds– The ribosome attaches the new amino acid to the

growing polypeptide– The process repeats: the ribosome moves down

the messenger RNA, adding new amino acids to the growing polypeptide chain.

• The final step in translation is termination. When the ribosome reaches a STOP codon, there is no corresponding transfer RNA. Instead, the whole complex falls apart, releasing the new polypeptide.

Internal Membrane System

• The internal membrane system is a group of organelles that has 3 basic functions: 1. to manufacture new lipids and

membranes, 2. to synthesize membrane-bound

proteins, 3. to package proteins for export out

of the cell.

• Proteins that span the membrane are very hydrophobic. They need to be synthesized directly into the membrane.

• We will talk about 4 organelles as part of this system: the endoplasmic reticulum (ER), the Golgi bodies, the lysosomes, and the peroxisomes.

Endoplasmic Reticulum

• “Reticulum” means network; the ER is a network of tubules in the cytoplasm, composed of membranes just like the cell membrane. It provides a membrane channel from the nucleus to the cell membrane.

• Two types, connected together: rough ER and smooth ER

• Rough ER looks rough because it is studded with ribosomes, the cellular machines that synthesize proteins. Ribosomes on the rough ER make the proteins that are inserted into the membrane, using the instructions from messenger RNA. Other ribosomes, not attached to the ER, make the non-membrane-bound proteins.

• Smooth ER has no ribosomes. It is used to synthesize the lipids of the membrane.

Golgi Body and Secretion• Proteins that are going to be secreted

out of the cell are synthesized in the rough ER. They get finished in the Golgi body: sugar molecules are attached to some of the amino acids. The sugars help protect the exported proteins from degradation.

• Golgi looks like a series of stacked plates.

• Vesicles are small, membrane-bound organelles. Vesicles carry proteins from the ER to the Golgi, and then from the Golgi body to the cell membrane. Secretion to the outside world occurs by exocytosis: the vesicle fuses with the cell membrane, releasing its contents.

• Proteins synthesized into the membrane of the ER end up in the cell membrane by the same mechanism

Lysosomes and Peroxisomes

• Lysosomes are intracellular stomachs: they are full of digestive enzymes that operate at low pH. You can think of them as little acid vats. Vesicles transport materials to the lysosomes, and the lysosomes digest them.

• Peroxisomes are membrane-bound sacs used to break down fatty acids and some other molecules. They generate hydrogen peroxide, a poisonous molecule, in the process, which is the source of the name peroxisome.

Enzymes and Energy

• State the two laws of thermodynamics.• Understand how enzymes catalyze chemical reactions.• Diagram the relationship between glucose, carbon

dioxide, electrons, oxygen, and water in the generation of energy.

• Distinguish between glycolysis, the Krebs cycle, and electron transport: what the starting and ending molecules are, where they occur, under what conditions do they occur

Energy in the Cell• All life needs energy. Cells convert

the chemical bond energy in food molecules to chemical bond energy stored in ATP molecules.– ATP energy is then used to run

metabolism and all other bodily processes.

• Food molecules contain potential energy in their chemical bonds. We are going to examine how this energy is transferred to ATP.

• “calories” are a measure of energy.– We are ignoring the difference between

“calorie” and :”Calorie” • Some foods contain more energy

per gram than others, because their chemical bonds store more energy. For instance, carbohydrates and proteins store 4 calories per gram, while fats store 9 calories per gram.

Thermodynamics• First Law: the total mount of energy in the

Universe is constant. Energy is neither created not destroyed, it just changes form.

– When energy is expended, part of it goes to do useful work, and the rest ends up as waste heat. None of it is lost, but it changes forms.

• Second Law: disorder (entropy) increases. Energy goes from useful forms to useless heat.

– Every energy transformation step is inefficient (as a consequence of the Second Law), meaning that some of the energy is converted to waste heat at every step, and the amount of useful work decreases with every step.

• Life is very orderly compared to non-living things. Living things are able to locally reverse the overall direction of entropy by using a lot of energy.

• The energy of living cells comes from the Sun, and it ends up as waste heat.

• In general, only about 10% of the total energy in food gets used to do something useful. The other 90% is lost as heat.

ATP• In living cells, energy is carried in

molecules of ATP, adenosine triphosphate. – When the energy is used, one of the

phosphates attached to ATP is released, giving ADP, adenosine diphosphate.

– ATP is made by adding a phosphate to ADP.

– ATP is constantly being generated, and it is used almost as soon as it is made.

• How energy is stored in the ATP molecule: The 3 phosphates each have a negative charge, and so they repel each other. When the bond holding them together is broken, the phosphates fly apart, like a spring being released.

Metabolic Reactions• A metabolic reaction is the

conversion of one chemical compound into another one inside a living cell. Each different reaction is catalyzed by a different enzyme.

• For every metabolic reaction, you start with reactants and convert them to products.

• The basic rule: reactions run downhill: more energetic reactants are converted to less energetic products.

• If a reaction needs to run uphill, creating products that contain more energy than the reactants, energy in the form of ATP must be added.

• Reactants are also called substrates.

Enzymes• Enzymes are proteins that cause

specific chemical reactions to occur.• Enzymes act as catalysts: they help

the reaction occur, but they aren’t used up in the reaction.

• All reactions require an input of energy to get them started: the activation energy. Think of touching a match to a piece of paper to start a fire: the match is supplying the activation energy.

• Enzymes work by lowering the activation energy for a reaction. The reaction occurs thousands or millions of times faster than without the enzyme. The little bit of activation energy needed is supplied by the collision of the molecules involved.

• Enzymes are very specific for their substrates: they work on only a very limited number of similar molecules.

Oxidation of Glucose• The basic food molecule is glucose, a simple sugar that has 6 carbon atoms.• Energy from chemical bonds is transferred in the form of electrons. Oxidation

means removing electrons. Its opposite is reduction, which is gaining electrons. LEO = Lose Electrons Oxidation; GER = Gain Electrons Reduction.

• Cells oxidize glucose to form carbon dioxide and water. The cell removes high energy electrons from glucose (in a series of steps), which converts it to carbon dioxide. The energy stored in the electrons is used to make ATP. The electrons (now low energy) are given to oxygen molecules, converting them to water.

• By passing the electrons through a series of steps before their final destination in water, the cell can harvest the energy efficiently. In contrast, burning releases the energy all at once, so it can’t be captured easily.

– Some common forms of oxidation: burning and rusting.

Respiration: Three Steps• Respiration is generating energy by breaking down food molecules,

converting the energy in their chemical bonds to ATP energy.– All cells respire, including plants.

1. Glycolysis: The anaerobic breakdown of glucose into the 3-carbon sugar pyruvate. – Long ago, before oxygen was present in the atmosphere, all cells used

anaerobic respiration, which means generating energy in the absence of oxygen.

– Many bacteria only have anaerobic respiration. – Plants and animals perform glycolysis in the cytoplasm, not in any organelle. – When no oxygen is present, yeast converts the pyruvate into ethanol.

2. Krebs cycle: removes high energy electrons from pyruvate, converting it into carbon dioxide. – Most eukaryotes also use aerobic respiration, generating energy with the use

of oxygen. We use anaerobic respiration to start the process, but finish it with aerobic. Aerobic respiration is much more efficient than anaerobic.

– The Krebs cycle occurs in the mitochondria. 3. The electron transport chain is considered separately from the Krebs

cycle, but it is also part of aerobic respiration. It uses the energy from the high energy electrons generated in the Krebs cycle to make ATP.

Glycolysis• Occurs in the cytoplasm, not in mitochondria• Does not use oxygen.• Almost all living things use this pathway.• Basic process: add phosphates (from ATP) to

each end of the glucose, then split it in half, using that chemical bond energy to generate 4 ATPs.

– Final 3-carbon products = pyruvate.– Net yield: 2 ATPs per glucose

• Glycolysis also releases 2 electrons. These electrons can be converted to energy if oxygen is present, but they cause problems if not.

• What to do with excess electrons? Give them back to pyruvate in some way:

– In yeast, the pyruvate gets converted to ethanol when the electrons are added back. Ethanol is the alcohol in alcoholic beverages like beer, wine, and vodka.

– In humans and many bacteria, pyruvate gets converted to lactic acid. Causes muscle pain during intense exercise when not enough oxygen gets to the muscle cells.

Krebs Cycle• Requires oxygen, occurs in the

mitochondria• Conversion of pyruvate (from

glycolysis) to carbon dioxide, with generation of high energy electrons and ATP.

– Pyruvate and pyruvic acid are the same thing.

• Preliminary steps before starting the Krebs cycle: 3 carbon pyruvate to 2 carbon acetyl CoA; third carbon lost as carbon dioxide. Generates high energy electrons carried by NADH and FADH2

• Krebs cycle: add 2 carbon acetyl CoA to 4 carbon sugar, producing citric acid. Then remove the 2 extra carbons one at a time as carbon dioxide, generate several high energy electrons (NADH in the diagram) plus some ATP.

Electron Transport• The final stage in aerobic respiration• The Krebs cycle generates many high

energy electrons. Also some from glycolysis. These need to be converted to ATP so the cell can use them.

• Electron transport pumps H+ ions from the inner compartment to the outer compartment of the mitochondria.

– This is uphill pumping, against the concentration gradient.

– Uses energy from high energy electrons to run the pumps.

• The final protein pump adds the electrons (plus hydrogen) to oxygen, producing water.

• The H+ level builds up between the membranes. It flows back into the inside through a special protein channel called ATP synthase, which uses the energy of their flow to combine ADP and Pi into ATP. This is the main way energy is generated in the cell.