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B IOL OGY 130 I N T R O D U C T O R Y C E L L B I O L O G Y

L E C T U R E N O T E S

Course Author: Dr. N.C. BolsInstructor: M. PinheiroDepartment of BiologyUniversity of Waterloo

Fall, 2012

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BIOL 130 LECTURE NOTES Fall, 2012 b

BIOLOGY 130 COURSE OUTLINE

INTRODUCTORY CELL BIOLOGY

Course Description: Introduction to the concepts of cell biology with an emphasis on(1) the structural organization of the cell and (2) the function of critical molecularprocesses that are characteristic of living organisms.Course Objectives: At the end of the course you should be able to:Explain some of the big concepts in cell biology, such as the difference between virusesand cells, and the flow of genetic information.Know in moderate detail several key pathways of energy metabolism and of signaltransduction.Understand the vast vocabulary of cell biology so that the introductions will be easy tomany life science disciplines, such as biochemistry, molecular biology, genetics, andphysiology.+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++Related Course: BIOL 130L LAB 0.25 Cell Biology Laboratory. This course is run byDr. D. Miskovic (Ext. 35330) in ESC 357E ([email protected]). The

course could be taken concurrently with Biol 130, after Biol 130, or not at all.+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

ORDER OF MATERIAL TO BE COVERED AND EXAMINED ON

Modules (6) Subject (pages in Course Text )

Module 1: Introduction to Cells and Cellular Chemistry

1a Introduction to Cell Biology (1-30) 1

1b Chemical Basis of Life (31-39) 2

1c Lipids (39-41; 46-49) 31d Carbohydrates (42-46) 4

1e Nucleic acids (74-76; 386-390) 5

1f Proteins (49-63) 6

Module 2: Enzymes and Energy Metabolism

2a Bioenergetics (84-92; 107; 182; 185-188) 7

2b Enzymes (92-103; 112-116) 8

2c Metabolism (105-116) 9

---------------------------------- Midterm on modules 1 & 2-------------------------------------------------

Module 3: Membranes and Energy Metabolism

3a Membranes (117-141; 250-258) 10

3b Membrane transport (143-155; 158-161) 11

3c Cellular uptake of particles & macromolecules (301-309) 12

3d ATP formation & the mitochondria (173-200) 13

3e Photosynthesis & the chloroplast (206-223) 14

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BIOL 130 LECTURE NOTES Fall, 2012 d

PURCHASES TO MADE FROM UNIVERSITY BOOKSTORE FOR BIOLOGY 130:

Course text book Cell and Molecular Biology: concepts and experiments (2010 6thedition) by G. Karp. The publisher is John Wiley & Sons Inc and the book is availablein the bookstore in two forms, listed below with ~ price.i. Regular Bound Text (ISBN-13 978-0-470-48337-4). ~$149

The book will have resale value.ii. Binder Ready version (ISBN 9780470556559) (Looseleaf) ~$97

This version might have little resale value.

The recommended readings from this text are listed in the course outline and in thelecture notes.

used booksEarlier editions of the textbook can be used but they will have some disadvantages. Thepages in the course notes will not match precisely the pages in the older editions. Theolder editions likely will have little subsequent resale value. The older editions will be

missing a few recent discoveries.

General Instructions about Tutorial AssignmentsTutorials for Biol 130 have been designed to help you develop and practice the skills that youwill need to use through your years of study at the University of Waterloo and not just in Biol130. Some examples of these skills are:

to build up glossary and create concept maps

to efficiently use the Library

to read with understanding scientific journal articles

to write concisely and effectively

to orally present information on chosen relevant topics

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BIOL 130 LECTURE NOTES Fall, 2012 e

University Policies to be aware of and sites to check

Academic Integrity: In order to maintain a culture of academic integrity, members of theUniversity of Waterloo community are expected to promote honesty, trust, fairness, respectand responsibility. [Check www.uwaterloo.ca/academicintegrity/ for more information.]

Grievance: A student who believes that a decision affecting some aspect of his/her universitylife has been unfair or unreasonable may have grounds for initiating a grievance. Read Policy70, Student Petitions and Grievances, Section 4,www.adm.uwaterloo.ca/infosec/Policies/policy70.htm. When in doubt please be certain tocontact the departments administrative assistant who will provide further assistance.

Discipline: A student is expected to know what constitutes academic integrity [checkwww.uwaterloo.ca/academicintegrity/] to avoid committing an academic offence, and to takeresponsibility for his/her actions. A student who is unsure whether an action constitutes anoffence, or who needs help in learning how to avoid offences (e.g., plagiarism, cheating) orabout rules for group work/collaboration should seek guidance from the course instructor,

academic advisor, or the undergraduate Associate Dean. For information on categories ofoffences and types of penalties, students should refer to Policy 71, Student Discipline,www.adm.uwaterloo.ca/infosec/Policies/policy71.htm. For typical penalties check Guidelinesfor the Assessment of Penalties,www.adm.uwaterloo.ca/infosec/guidelines/penaltyguidelines.htm.

Appeals: A decision made or penalty imposed under Policy 70 (Student Petitions andGrievances) (other than a petition) or Policy 71 (Student Discipline) may be appealed if thereis a ground. A student who believes he/she has a ground for an appeal should refer to Policy 72(Student Appeals) ww.adm.uwaterloo.ca/infosec/Policies/policy72.htm.

Note for Students with Disabilities: The Office for Persons with Disabilities (OPD), locatedin Needles Hall, Room 1132, collaborates with all academic departments to arrangeappropriate accommodations for students with disabilities without compromising the academicintegrity of the curriculum. If you require academic accommodations to lessen the impact ofyour disability, please register with the OPD at the beginning of each academic term.

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BIOL 130 LECTURE NOTES Fall, 2012 f

Table of Contents for Biology 130 notes

Modules: Subject (Pages in Course Text)

Module 1: Introduction to Cells and Cellular Chemistry1a Introduction to Cell Biology (1-30)1b Chemical Basis of Life (31-39)1c Lipids (38-41; 46-49)1d Carbohydrates (42-46)1e Nucleic acids (74-76; 386-390)1f Proteins (49-63)

Module 2: Enzymes and energy metabolism

2a Bioenergetics (84-92; 107; 182; 185-188)2b Enzymes (92-103; 112-116)

2c Metabolism (105-116)

Module 3: Membranes and energy metabolism

3a Membranes (117-141)3b Membrane transport (143-155; 158-161)3c Cellular uptake of macromolecules and particles (301-309)3d ATP formation and the mitochondria (173-200)3e Photosynthesis and the chloroplast (206-223)

Module 4: Flow of genetic information

4a Flow of information in cells (379-381; 386-390, 419-422; 455-457; 481-487)

4b Transcription and translation (422-455; 461-468)4c Control of gene expression (503-531; 448-451)4d DNA replication and repair (533-548; 552-554)4e Cell cycle (560-571; 585-588; 590-591)

Module 5: Signal Transduction pathways

5a Cell signaling and cAMP (605-614; 618-6320)5b Other 2ndmessengers: lipids, calcium and nitric oxide (614-617; 634-638; 640-642)5c Receptor Tyrosine Kinases, Cell Proliferation and Death (623-630; 638-640; 642-646)

Module 6: Biology of Cancer

6a Regulation of cell proliferation gone wrong (650-671)6b Regulation of cellular social behavior gone wrong (230-258; 675-676)

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BIOL 130 MODULE 1 1

Module 1 outline and notes: Introduction to Cells and Cellular Chemistry

1a Introduction to Cell Biology

1a1) Discovery and Properties of cells1a2) Exceptions to the Cell Theory1a3) Two fundamentally Different Classes of Cells

1a4) Eukaryotes vs. Prokaryotes1a5) Common Features of Eukaryotes and Prokaryotes1a6) Organisms from all species are made of cells1a7) Types of Eukaryotic Cells

1b Chemical Basis of Life

1b1) Chemical Bonds1b2) Polar Molecules1b3) Ionization1b4) Free Radicals1b5) Biologically Important Weak Bonds

1b6) Nature of Biological Molecules1b7) Water

1c Lipids

1c1) Introduction to four macromolecules1c2) Lipids1c3) Biological Roles of Lipids1c4) Fatty acids1c5) Triacylglycerols1c6) Phosphoglycerides1c7) Steroids

1d Carbohydrates

1d1) Introduction to Carbohydrates1d2) Monosaccharides1d3) !Glucose and "glucose1d4) Disaccharides1d5) Nutritional Polysaccharides1d6) Structural Polysaccharides

1e Nucleic acids

1e1) Introduction to Nucleic Acids

1e2) Nitrogen Bases1e3) Nucleosides1e4) Nucleotides1e5) Ribonucleic Acid (RNA)1e6) Deoxyribonucleic Acid (DNA)

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BIOL 130 MODULE 1 2

1f Proteins

1f1) Protein functions1f2) Amino Acids1f3) Peptide bond1f4) Primary Structure of Proteins1f5) Protein confirmation

1f6) Secondary Structure of Proteins1f7) Tertiary Structure of Proteins1f8) Motifs vs. Domains1f9) Quaternary Structure of Proteins1f10) Covalent Modifications of Proteins1f11) Other Structural Features of Proteins1f12) Multiprotein Complexes

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BIOL 130 MODULE 1 3

1a: Introduction to Cell Biology: Unit #1

1a 1) Discovery and properties of cells (Karp: pp. 1-30)

History of cell theory

1. Robert Hooke 16652. Leuwenhoek 1673-17003. Schleiden 1838-18394. Schwann 1838-18395. Rudolf Virchow 1858

Cell theory or cell doctrine

1. All living things are composed of one or more units called cells.2. Each cell is capable of maintaining its vitality independent of the rest

(i.e. Smallest clearly defined unit of life is the cell.)3. Cells can arise only from other cells.

Basic Properties of Cells (living matter)(Karp: pp. 3-6)

1.

Cells are highly complex and organized but all are enclosed by a physical barriercell membrane.

2. Blue print DNA (genetic program).3. Cells acquire and utilize energy.4. Cells carry out a variety of chemical reactions.5. Cells are capable of producing more of themselves.

6.

Cells engage in numerous mechanical activities.7. Cells are able to respond to stimuli.8. Cells are capable of self-regulation.

1a 2) Exceptions to the cell theory

Crossroads between living and non living matter

viruses(Karp: Figs. 1.20. 1.21, 1.22)1. Viruses are bits of nucleic acids that have a protein coat

2. Inert outside the cells3. Reproduce only in cells

viroids circular RNA without protein coat

prions proteinaceous infectious particles

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BIOL 130 MODULE 1 4

1a 3) Two fundamentally different classes of cells

Prokaryotes before nucleus (Karp: p. 7 Fig. 1.8; p. 9 Table 1.1)

Always single cell organisms. Prokaryotes 1-10 !m (recently, rare exceptions have been found to be larger)

DNA lies free in cell or sometimes in an area called nucleoid region. DNA is associated with fewer proteins and so is sometimes called 'naked'.

Eukaryotes true nucleus(Karp: p. 9 Table 1.1, p. 10 Fig. 1.10)

All cells of multicellular organisms are eukaryotes. Eukaryotes 10-100 !m

(exception, Caulerpa = largest single-cell organism) DNA is organized into a nucleus. Nucleus is an organelle. DNA is associated with a characteristic set of proteins.

1a 4) Eukaryotes vs. Prokaryotes

Eukaryotes have but prokaryotes do not havethe following:

1. Organelles: Some examplesMitochondria produce energy in form of ATP.Lysosomes membrane bound sacs containing digestive enzymes.Microbody (peroxisomes) oxidation of fatty acids and detoxification of

certain toxic compounds (hydrogen peroxide).

2. Network of internal membranes:Endoplasmic reticulum (e.r.)

rough e.r. ribosomes are bound to the membrane network.smooth e.r. stores calcium

3. Cytoskeletonmicrotubules pipe-like cylinders about 20-25 nm in diameter.microfilaments cylinders about 5 nm in diameter.intermediate filaments cylinders or fibers 10 nm in diameter.

4. Complex cilia and flagella

5. Capacity for endocytosis and phagocytosis

1a 5) Common features of Eukaryotes and Prokaryotes(Karp: pp. 3-6)

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BIOL 130 MODULE 1 5

1a 6) Organisms from all species are made of cells

Organisms can be divided into 6 kingdoms(5 kingdoms if prokaryotes is considered just one).

Two prokaryote kingdoms (types of prokaryotic cells)

Archae (Archaebacteria) often live in extreme environments.

e.g. thermophiles all have cell walls.

Bacteria (Eubacteria) (Monera)

all have cell walls except mycoplasma. mycoplasma are smallest cells (0.2 m)

Four eukaryote kingdoms

Protista (Figs. 1.16)

one celled and some colonial eukaryotic organisms.Includes algae, water molds, slime molds and protozoa.

Fungi Includes both multicellular organisms (e.g. mushrooms) and single-celled

organisms (e.g. yeast). All have cell walls and are heterotrophs (depend on an external source of

organic compounds).

Plantae Always multicellular and always have cell walls Most carry on photosynthesis.

Animalia Always multicellular and hetertrophs(depend on an external source of organic

compounds).

1a 7) Types of eukaryotic cells

A. Most complex single-celled (unicellular) protists (Fig. 1.16)

B. Plant vs. Animal Cells (Karp: p. 8 Fig. 1.8)

Plants have1. Cell walls made of cellulose and lignin2. Plastids organelles bound by 2 membranes

concerned with energy metabolism e.g. chloroplast3. Large vacuoles

C. Cell specialization in multicellular organisms (differentiation) (Fig 1.17)

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BIOL 130 MODULE 1 6

1b: Chemical Basis of Life: Unit #2(Karp: p. 31-39)

1b 1) Chemical bonds

Hold two or more atoms together in an aggregate

Covalent bonds

The important strong bond in biological systems. A chemical bond that results from sharing of electron pairs between atoms. Covalent bonds can be formed between similar or even identical atoms. An atomic aggregate linked together by covalent bonds is called a molecule. Convention is to indicate a single covalent bond by a solid line between bonded

atoms. H-O-H

Common elements and their covalent bonding ability

1. principal is that an atom is most stable when its outermost electron shell is filled.

2. number of bonds depends on number of electrons needed to fill its outer shell.(Karp: p. 32 Fig. 2.1)

C = carbon 4 covalent bonds or their equivalent in double and triple bondsH = hydrogen 1 bondO = oxygen 2 bondsS = sulfur 2 bonds in organic moleculesN = nitrogen 3 bonds

P = phosphorus 5 (3) bonds

1b 2) Polar molecules

1. Certain atoms attract the shared electron pairs to a greater extent than other atoms.2. This property of attracting electrons is called electronegativity.3. When a covalent bond has an uneven distribution of charge, it is called a polar bond.4. If molecule is appropriately shaped, a polar bond may result in a polar molecule or

dipole.

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BIOL 130 MODULE 1 7

Polar and nonpolar molecules

Examples:

1. H2O because of the angles of its bonds the H2O molecule is not a linear molecule

but, instead, has an angular shape.

2. This gives H2O molecule a partially negative end and two partially positive wings

so H2O is a polar molecule.

3. Molecules in which there is little or no separation of negative and positive chargesare nonpolar e.g. O2.

1b 3) Ionization

One atom loses electrons and another atom gains them. Occurs because at least one partner is very electronegative.

Results in charged atoms or ions. Negatively charged, anions.

(has extra electron relative to number of protons in nucleus) Positively charged, cations.

(has extra proton relative to number of electrons)

Na+and Cl-ions are stable because they possess filled outer shells

1b 4) Free radicals

Atoms or molecules that have orbitals containing a single unpaired electron.

Example is superoxide radical: O2.-

Highly reactive and damaging. Might contribute to the process of aging. Reactive oxygen species (ROS) are important free radicals.

1b 5) Biologically important weak bonds(i.e. noncovalent bonds)

1. Ionic bonds

2. Hydrogen bonds3. Hydrophobic bond or hydrophobic interactions

Ionic bonds

Electrostatic attraction between fully charged components.An example is table salt.

Attraction between positively charged Na+and negatively charged Cl-.

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BIOL 130 MODULE 1 8

Hydrogen bond (Karp: p. 36 & 37 Figs. 2.3, 2.7)

1. A bond between an electronegative atom and a hydrogen atom that is alreadycovalently linked to another electronegative atom.

2. Hydrogen commonly bonds with highly electronegative atoms such as O and N.3. Thus the pair of shared electrons is closer to the electronegative atom.

4. The positively charged nucleus of H atoms is readily attracted to unshared pair ofelectrons of a second electronegative atom.

5. The noncovalent associations resulting from such electrostatic forces are calledhydrogen bonds.

Hydrophobic bonds(water-fearing) (Karp: p. 36 Fig. 2.5)

Tendency of nonpolar groups to aggregate when in the presence of H2O.

Nonpolar molecules are essentially insoluble in water because they lack the chargedregions that would attract them to the poles of water molecules.

In water, the nonpolar molecules are forced to aggregate.

1b 6) Nature of biological molecules

1. Organic molecules: carbon-containing molecules.2. Hydrocarbons: contain only carbon and hydrogen.3. Most organic molecules in biology: are hydrocarbons with certain of the hydrogen

atoms replaced by various functional groups.

Functional groups:

1. Particular groupings of atoms that often behave as a unit and give organicmolecules their properties.

2. Common functional groups (Karp: p. 41 Table 2.3 structural formula)Examples: CH3, OH, COOH, NH2(these are condensed structural form.)

3. Common linkage between functional groups.Ester bonds formed between carboxylic acid and alcohols.Amide bonds formed between carboxylic acid and amines.

1b 7) Water: Life-supporting properties of water Fluid matrix around which insoluble fabric of cell is constructed.

Important because forms weak interactions with so many different chemical groups.

Water as a solvent

Dipolar nature of H2O makes it an ideal solvent for a variety of substances.

1. Salts dissolve readily in H2O. e.g. NaCl (Karp: p. 35 Fig. 2.2)

2. Covalent compounds with weakly polar properties

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BIOL 130 MODULE 1 9

Readily dissolved in H2O.

Compounds such as sugars have OH groups and carbonyl groups. These dissolve because H2O molecules form hydrogen bonds with these polar

groups.

3. Nonpolar covalent molecules insoluble in water. Such as benzene, ether, and chloroform are readily miscible only with one

another or with other nonpolar solvents.

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BIOL 130 MODULE 1 10

1c: Lipids:Unit #3(Karp: pp. 39-41; 46-49)

1c 1) Introduction to four macromolecules

Macromolecules huge, highly organized molecules that form the structure and carryout the activities of cells.

Macromolecules can be divided into 4 major categories(Karp: p. 42 Fig. 2.11)1. Lipids2. Carbohydrates3. Nucleic acids4. Proteins

Carbohydrates, nucleic acids and proteins are polymers. Polymers are composed of a large number of low-molecular-weight building

blocks, or monomers.

1c 2) Lipids

1. Small, diverse organic molecules that are insoluble in H2O but soluble in nonpolar

organic solvents. e.g. chloroform or benzene.2. Hydrophobic or contain significant hydrophobic regions.

1c 3)_Biological roles of lipids

1. Source of energy in the diet and serve to store energy in the body.e.g. fats and oils

2. Some hormones (chemical messengers) are lipids.e.g. steroids and prostaglandins.Prostaglandins usually act in an autocrine and paracrine fashion whereas steroidhormones act in an endocrine fashion

3. Many vitamins are lipids.e.g. vitamins A, D, E

4. The basic structural elements of biological membranes.e.g. phospholipids

1c 4) Fatty acids(Karp: p. 47 Fig. 2.19b)

Unbranched hydrocarbon chains with a carboxyl group at one end.

Chains are typically 14 to 20 carbons. Chain is hydrophobic. Carboxyl group is hydrophilic. Therefore fatty acids are amphipathic. They can form micelles in water (Karp: p. 47 Fig. 2.20). They may be saturated or unsaturated.

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Saturated vs. unsaturated fatty acids

When all carbon atoms of a fatty acid chain are joined by single covalent bonds, thecompound is saturated.

O##

CH3- (CH2) n - C - OH

If one or more double bonds are present between carbons in the chain, thecompound is unsaturated.

O##

CH3- C = C - (CH2) n - C - OH

# #

H H

1c 5) Fats and oils(triacylglycerols) (Karp: Fig. 2.19a, c & d)

Major compound for storing energy in both animals and plants. Consist of glycerol esterified to three fatty acids. The fatty acids can be identical. If fatty acids are different, it is a mixed fat. Fats that are liquid at room temperature are oils. Oils contain unsaturated fatty acids.

1c 6) Phosphoglycerides(Karp: p 47 Fig. 2.22; p.123 Fig. 4.6)

Major component of membranes of all types. Consist of glycerol esterified to two fatty acids. The 3rdOH group of glycerol is bonded covalently to a phosphate group. This is the parent compound, phosphatidic acid. Several different, small polar groups can be linked to the phosphate.

ex. choline. This would be phosphatidyl choline. All phosphoglycerids are phospholipids. All phospholipids are amphipathic.

1c 7) Steroids(Karp: p. 48 Fig. 2.21; p.123 Fig. 4.7)

Includes cholesterol which is found in membranes. Cholesterol needed for synthesis of sex hormones. Male androgens (e.g. testosterone) and female estrogens (estrogen)

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1d: Carbohydrates:Unit #4(Karp: pp. 42-46)

1d 1) Introduction to Carbohydrates

Have general formula (CH2O)n

Includes simple sugars (monosaccharides) and all larger molecules constructed ofsugar building blocks.

1. Monosaccharides (simple sugars)

2. Oligosaccharides 2 to 10 monosaccharide units linked together.Attached to lipids: forms glycolipids.Attached to proteins: forms glycoproteins

3. Polysaccharides very long chains of monosaccharide units.

1d 2) Monosaccharides

Energy source and source of carbon for other cellular compounds. Carbon chain containing one aldehyde or ketone Plus (-OH) groups at the other carbons

aldehyde ketone

H C = O R1# #

R C = 0

#R2

Aldehyde carbon is numbered #1. Classified according to the number of C in the molecule. Generally 3 to 7 carbon atoms.

Heptose has 7 carbons. Hexose has 6 carbons. Pentose has 5 carbons.

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1d 5) Nutritional polysaccharides: glycogen and starch

Except at branch points, the repeating disaccharide is maltose.

Glycogen(Karp: p. 45 Fig. 2.17a)

Principal food reserve in animals and fungi: usually stored in liver and muscle ofanimals.

!-glucose units, mostly linked 1-4, but highly branched via frequent 1-6 linkages

Starches(Karp: p. 45 Fig. 2.17b)

Principal food reserve in plants. Comes in 2 forms: amylose and amylopectin.

Amylose is an unbranched !1,4 polymer of glucose. Amylopectin has same structure but is slightly branched. Amylopectin is not as highly branched as glycogen.

1d 6) Structural polysaccharides

Cellulose(Karp: p. 45 Fig. 2.17c)

Linear polymer of several hundred to thousand "glucose units. An insoluble, rigid structural polymer. Makes up cell wall of plants. Cellobiose is the repeating unit of cellulose. We cannot hydrolyze "1,4 linkage

Chitin(Fig. 2.18)

Unbranched polymer of the sugar N-acetylglucosamine. N-acetylglucosamine like glucose except has acetylamino group at position 2. Outer covering of insects, spiders and crustaceans.

Glycosaminoglycans(GAGs) (Karp, p. 46)

Made up of repeating dissacharide in which the two sugars are different. One of the two sugar residues is always an amino sugar,

Either N-acetylglucosamine or N-acetylgalactosamine. GAGs are found in extracellular matrix (ECM) of animal tissues.

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1e: Nucleic AcidsUnit #5(Karp p. 74-76; 386-390)

1e 1) Introduction to Nucleic acids

Macromolecules constructed as a long chain (strand) of monomers, called nucleotides. Either deoxyribonucleic acid (DNA) or ribonucleic acid (RNA).

Both are information molecules

Nucleotides(Karp: p. 75 Fig. 2.53a)

Consist of 3 units: A nitrogen base A pentose sugar A phosphate group

1e 2) Nitrogen bases(Karp: p. 75 Fig. 2.54)

Organic compounds composed of C, N, H and in some cases O There are two broad types:Pyrimidinebases

three main bases1. cytosine2. uracil3. thymine

Purinebasestwo main bases1. adenine2. guanine

1e 3) Nucleosides

Pentose sugar 5 carbon sugar

Can be either ribose or deoxyribose

Purine or pyrmidine nucleosides

A purine or pyrimidine attached to a sugar. IF the pentose is ribose, compound is a ribonucleoside. e.g. adenosine

IF pentose is deoxyribose, compound is deoxyribonuceloside. e.g. deoxyadenosine

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1e 4) Nucleotides(Karp: p 75 Fig. 2.53a; p 386 Fig. 10.9b)Nucleoside and phosphoric acid

Some examples:Adenosine Monophosphate (AMP) deoxyadenosine monophosphate (dAMP)Adenosine Diphosphate (ADP) deoxyadenosine diphosphate (dADP)

Adenosine Triphosphate (ATP) deoxyadenosine diphosphate (dATP)

3', 5' cyclic adenosine monophosphate (cAMP)

Nucleotides are involved in three major cellular functions

1. Nucleotides are monomeric units from which DNA and RNA are made.2. Second messengers in cell signaling e.g. cAMP.3. They act as agents in energy-transferring reactions during metabolism.

a. Cleaving off phosphate groups releases energy e.g. ATPb involved as coenzymes in energy-transferring reactions e.g. NAD

Nucleotide coenzymes Coenzymes are nonprotein substances that are required for enzyme action. Coenzymes usually are adenosine nucleotides combined with vitamins of B complex. Nicotinamide is B vitamin niacin.

NAD = nicotinamide adenine dinucleotide (Karp: p. 110 Fig. 3.27)NADP = nicotinamide adenine dinucleotide phosphateFAD = flavin adenine dinucleotideCoenzyme - A = ATP plus B vitamine pantothenic acid

1e 5) Ribonucleic acid (RNA) (Fig. 2.53b) Chain of ribonucleotides.

Joined by 3'-5' phosphodiester linkage or bond. Sugar phosphate backbone:

Phosphate atom is esterified to 2 oxygen atoms on adjoining sugarsSugar is always ribose.

Base can be:1. Adenine2. Guanine3. Cytosine4. Uracil

but NOT thymine Usually single stranded:

one end is the 5' end.the other end is the 3' end

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1e 6) Deoxyribonucleic acid (DNA)(Karp: pp. 386-388 Figs. 10.9, 10.10)

Chain of deoxyribonucleotides.Joined by 3'-5' phosphodiester linkage or bond.

Sugar phosphate backbone:

Phosphate atom is esterified to 2 oxygen atoms on adjoining sugarsSugar is always deoxyribose.

Base can be:1. adenine2. guanine3. cytosine4. thymine

but NOT uracil

DNA is double stranded(Karp: p. 388 Fig. 10.10)

Double-stranded helix with the two strands lying antiparallel Two strands are held together by hydrogen bonds between bases. Hydrogen bonds are between complementary pairs of purines and pyrimidines. Rules of base pairing:

Adenine pairs with Thymine (AT)Guanine pairs with Cytosine (GC)

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1f: Proteins: Unit #6(Karp: pp. 49-63)

1f 1) Protein Functions

Proteins in brief

Consist of one or more polypeptide chains. A polypeptide is a polymer of amino acids linked together by peptide bonds. Our cells may have as many as 100,000 different proteins. Proteins have a diverse array of functions.

Some general functions of proteins

1. Enzymes protein catalysts2. Structural elements e.g. tubulin3. Contractile elements e.g. myosin

4. Control activity of genes e.g. transcription factors5. Transport material across membranes e.g. glucose transporter6. Carriers e.g. hemoglobin7. Hormones e.g. insulin8. Antibodies

1f 2) Amino Acids(Figs. 2.24, 2.26)

Building blocks of proteins.

Organic acids that contain an amino group

general structure

H H O# # ##

H N C! C OH#

Ramino group carboxyl group

!carbon = first carbon after the carboxyl group

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R groupsFig 2.26

R = side chains of variable structure.= any of 20 different groups

Differences in R groups accounted for different properties of amino acids and

proteins.

R groups can be broadly classified as:1. Polar charged2. Polar uncharged3. Nonpolar4. R groups with unique properties.

1f 3) Peptide bond or Amide linkage(Karp: p. 50 Fig. 2.24)

links !-amino group of one amino acid with !-carboxyl group of adjoining amino acid.

the linkage in dipeptides and in polypeptides. R groups are not involved.

1f 4) Primary Structure of protein

The sequence of amino acids in a polypeptide. Most polypeptides contain over 100 amino acids. In a polypeptide chain, amino acids are residues. N-terminus is the end of a polypeptide with a free !amino group. C-terminus is the end of a polypeptide with a free !carboxyl group.

1f 5) Protein confirmation

Three dimensional structure of a protein. Secondary, tertiary, and quaternary structure describes confirmation. Primary structure determines secondary, tertiary, and quaternary structures of proteins.

1f 6) Secondary structure of protein

Results from hydrogen bonding between the oxygen of one peptide group and the

nitrogen of another peptide group. Secondary, tertiary, and quaternary structure describes confirmation. R groups are not involved. Fixed configuration of the polypeptide backbone. Secondary structure is limited to a small number of conformations. Two common secondary structures.

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helix (Karp: p. 55 Fig. 2.30)

Cylindrical, twisting spiral Each amino acid is hydrogen bonded to its fourth neighbor on both sides.

pleated sheets or -pleated sheets(Karp: p. 55 Fig. 2.31)

Polypeptide chains of pleated sheets are stretched out and lie side by side, either

parallel or anti-parallel to one another. Bonded groups may be portions of same chain folded back on itself or bonded

groups may be on separate chains.

Unorganized portions of protein

60% of the polypeptide chain in an average protein exists as !helices and "sheets. Remainder is in random coils and turns. Do not get continuous helix or pleated sheet for two reasons:

1. Juxtaposition of two bulky or similarly charged side chains.2. Proline 'helix breaker'

Depiction of secondary structure(Karp: p. 56 Fig. 2.32) !helices are represented by helical ribbons. "strands as flattened arrows. Unorganized connecting segments are thin strands in loops and turns.

1f 7) Tertiary Structure

The way that regions of secondary structure are oriented with respect to each other. Tertiary structure predominates in globular proteins. Monomeric proteins consist of a single polypeptide chain folded into its tertiary

structure. Tertiary structure results from side chain interactions (Karp: p. 58 Fig. 2.35).

These are:1. Hydrogen bonds2. Hydrophobic bonds3. Ionic bonds4. Disulfide bond (Karp: p. 53)

covalent bond between two cysteines

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1f 8) Motifs vs. Domains

Motifs(Karp: p. 510-511 Figs 12.37, 12.38)

A substructure found among many different proteins. Recurring combinations of secondary structure.

Characteristic combinations of !helices, "sheets and loops found in a variety of proteins. Usually associated with a particular function.

e.g. Zinc finger (see section 4c4 and Karp p 521) Bundle of three secondary structures: an !helix and a pair of anti-parallel "

strands. This motif generally is present in proteins that bind DNA.

Domains(Karp: p. 58 Fig. 2.36)

Found often in large proteins. A region within a protein that folds and functions in a semi-independent manner.

Domains are modules of tertiary structure. Different domains of a polypeptide often represent parts that function in a semi

independent manner. e.g. bind different factors Some polypeptides containing more than 1 domain are thought to have arisen

during evolution by fusion of genes.

1f 9) Quaternary Structure(Karp: p. 60 Fig. 2.38)

Most proteins are made up of more than 1 polypeptide chain. Each chain is a subunit.

A protein with 2 identical subunits = homodimer A protein with 2 non-identical subunits heterodimer Often the subunits can be independently folded. Quaternary structure is the spatial arrangement of these subunits. The bonds involved are the same as in tertiary structure.

1f 10) Covalent Modifications of Proteins

Modifications made by additions to the amino acid R groups. An example is placement of a phosphate on serine, threonine and tyrosine residues.

(Karp p. 607; Fig. 15.3)

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1f 11) Other structural Features of Proteins

Fibrous vs. globular proteins On basis of overall confirmation.

Fibrous:

Has highly elongated shape. Found outside living cells.

Globular: A compact shape. Most proteins within a cell are globular.

1f 12) Multiprotein complexes(Karp: p. 61 Fig. 2.41)

Physical association of different proteins, each with a specific function, to coordinate

a larger function.e.g. pyruvate dehydrogenase complex

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Module 2 outline and notes: Enzymes and energy metabolism

2aBioenergetics2a1) Introduction to Bioenergetics2a2) The Laws of Thermodynamics2a3) Free Energy

2a4) ATP and Coupled Reactions2a5) Oxidation-reductions and making of ATP2a6) Three General Processes of ATP Formation2a7) Utilization of Free Energy of ATP

2b Enzymes

2b1) Introduction to Enzymes2b2) Active site and Molecular Specificity2b3) Denaturation and enzyme activity2b4) Enzyme inhibitors2b5) Naming enzymes

2b6) Metabolic regulation2b7) Feedback principle

2c Metabolism

2c1) Introduction to Metabolism2c2) Glycolysis2c3) Reducing Power2c4) Equilibrium vs. Steady State Metabolism and Regulation2c5) Separating Catabolic and Anabolic Pathways2c6) Separating and regulating glycolysis and gluconeogenesis2c7) Regulating ATP levels

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2a: Bioenergetics:Unit #7(Karp: pp. 84-92; 107; 182; 185-188)

2a 1) Bioenergetics Study of various types of energy transformations that occur in living organisms.

Energy: Capacity to do work. Work is to change or move something

Thermodynamics: Study of changes in energy that accompany events in the universe. Predict direction that events will take. Predict whether or not an input of energy is required to cause the event to happen.

2a 2) The Laws of Thermodynamics

First Law of Thermodynamics

Energy can neither be created nor destroyed. However, energy can be converted from one form to another.

e.g. conversion of sunlight into chemical energy

Second Law of Thermodynamics

Events in the universe have direction. Events proceed from a state of higher energy to a state of lower energy.

Such events are spontaneous. They are thermodynamically favorable and can occurwithout input of external energy.

The amount of useable energy is reduced.

2a 3) Free energy($ G)

1. $G is a change during a process in the energy available to do work.2. A negative free energy ( $G) means that the energy transformation may proceed

spontaneously.a. This is thermodynamically favorable and is an exergonic process.

b. Energy is available for use in another process.3. A positive free energy (+ $G) means that the energy transformation may not

proceed.a. This is thermodynamically unfavorable and is an endergonic process.b. Energy must be added for process to proceed.

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Standard-free energy difference ($ G %)

Describes difference in free energy when one mole of each reactant is converted toone mole of each product at 25C and 1 atm of pressure.

Free-energy changes in metabolic reactions

Cells can carry out many reactions with positive $G%.

1. Ratio of the reactant to product is maintained above that defined by equilibriumconstant by other cellular reactions.

2. Couple endergonic and exergonic reactions. Coupling occurs when an endergonic reaction and an exergonic reaction are

catalyzed by same enzyme.

2a 4) ATP and coupled reactions(Karp: pp. 90-91)

Link between exergonic and endergonic reactions is ATP. Hydrolysis of ATP drives endergonic reactions.

ATP + H2O &ADP + phosphate $G%= -7.3 kcal/mole

glutamic acid + NH3&glutamine + H2O $G%= 3.4 kcal/mole

glutamic acid + ATP + NH3&glutamine + ADP + HPO $G%= -3.9 Kcal/mole

ATP acts as a common intermediate in biological-energy transfer.

2a 5) Oxidation reduction (or redox) reactions and making of ATP

Loss of Electrons from a substance is Oxidation (LEO). Gain of Electrons by a substance is Reduction (GER). Oxidations and reductions always occur together. Substance that is oxidized (donates electrons) is reducing agent. Substance that is reduced (gains electrons) is the oxidizing agent.

Oxidation state of carbon atom (Karp: p. 107 Fig. 3.23)

1. Is not obvious but here are 2 helpful rules.a. Oxidized = O2added or hydrogen removed.

b. Reduced = O2removed or hydrogen added.

2. Degree of reduction of a compound is a measure of its ability to perform chemicalwork within the cell.

3. Carbohydrates are rich in chemical energy because they contain strings of|H-C-OH

|e.g. glucose

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Oxidation-Reduction potential(Karp: pp. 106; 182, 186, Fig 5.14)1. The tendency of a substance to accept or to donate electrons in a chemical reaction

with another substance is defined by its oxidation-reduction potential or redoxpotential.

2. This is expressed in volts._________________________________________________

-0.6 -0.4 -0.2 0 +0.2 +0.4 +0.63. When compound has a negative value, it readily donates electrons.4. When compound has a positive value, it readily accepts electrons.5. Electrons can be transferred spontaneously from a compound to another compound

that has a more positive redox potential.6. The greater the gap in redox potential between the donor and the acceptor, the

greater the standard free-energy change.7. This energy can be used for the phosphorylation of ADP to ATP.

Electron-transport chain

1. Electron carriers are capable of existing in either an oxidized or reduced state.2. Electrons are passed from 1 carrier to next until final acceptor becomes reduced.3. Each electron carrier along chain has a more positive redox potential than previous one.4. With each successive transfer, electrons loose additional free energy.5. Free energy released by electron transfer is utilized to generate a proton gradient.6. Proton gradient is utilized to drive formation of ATP.

2a 6) Three General Processes of ATP Formation

Oxidative phosphorylation

Formation of ATP in electron transport chain of mitochondria.

Photophosphorylation Formation of ATP in electron transport chain of chloroplast.

Substrate-level phosphorylation(Fig. 3.28) ATP formation is coupled to the hydrolysis of phosphate compounds with a higher $Go'.

e.g. glycolysis

2a 7) Utilization of free energy of ATP (Karp: p. 91-92 Fig. 3.6; Fig. 3.7)

1. Separate charges across a membrane. e.g. function of nerves and muscle2. Concentrate a particular solute within the cell e.g. active transport3. Drive an otherwise unfavorable reaction e.g. protein synthesis4. Slide filaments across one another. e.g. cell movement

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Overcoming Activation Energy Barrier

1. Even thermodynamically favorable reactions do not proceed on their own atrelatively rapid rates in absence of enzymes ( p. 93 Table 3.3).e.g. glucose is kinetically stable even if thermodynamically unstable.

2. Chemical reactions require that certain covalent bonds be broken within reactants.

3. Reactants must contain sufficient kinetic energy that they overcome a barrier,activation energy. (Fig. 3.8)

4. enzymes catalyze reactions by decreasing magnitude of activation energy barrier.

2b 2) Active site and Molecular Specificity (Figs. 3.10, 3.11, 3.12, 3.14)Enzymes: Accelerate bond-breaking and bond-forming processes. Do this by forming a complex with reactants (enzyme-substrate complex). Bind substrates by noncovalent interactions at active site.

Active or catalytic site of enzymes: Part of enzyme directly involved in binding substrate. Typically buried in cleft or crevice of the enzyme. Accounts for specificity of enzymes.

Each enzyme exhibits a very great specificity for a particular reaction.

2b 3) Denaturation and enzyme activity(Karp: p. 62 Fig. 2.43)

Denaturation is unfolding or disorganization of a protein.

Destroying secondary and higher structure is called denaturation. Specificity and catalytic properties of enzymes are a result of their 3 dimensional

structure. Therefore, denaturation destroys enzyme activity.

2b 4) Enzyme Inhibitors(Karp: pp. 102-103) Molecules that bind to an enzyme and decrease its activity. Can be of two types: irreversible or reversible.Irreversible inhibitors Bind very tightly to an enzyme Often form a covalent bond to one of enzyme's amino acid residues.

Often man made reagents. e.g. organophosphate pesticides Made in nature as part of chemical warfare. e.g. penicillin

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Reversible inhibitors Bind loosely to an enzyme and can be readily displaced. Can be of two types.

Competitive inhibitors(Karp: p. 102 Fig. 3.20) Compete with substrate for active site.

Structurally resemble substrate But cannot be transformed into product. Can be overcome if substrate/inhibitor ratio is great enough.

Noncompetitive inhibitors Does not bind at same site as substrate. Inhibitor acts at a site other than active site. Level of inhibition depends only on concentration of inhibitor. Concentration of substrate cannot overcome it (Karp: p. 104 Fig. 3.21a)

2b 5) Naming enzymes

Informal or trivial names Named by tacking -ase onto end of substrate

A few hints.Kinase usually involves ATP

e.g. hexokinase and pyruvate kinasedehydrogenase usually involves coenzyme NADH

e.g. glyceraldehyde phosphate dehydrogenasesome exceptions to -ase ending

e.g. trypsin and pepsin

2b 6) Metabolic Regulation(Karp: pp. 112-116)

Enzymes are regulatory elements in metabolism. Metabolism is sum total of all chemical changes in cells. Metabolism can be controlled by:

1. Controlling concentrations of enzymes (long term control)discussed later under gene regulation

2. Changing an enzyme's activity

Two important ways:a. Covalent modificationb. Allosteric modulation

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Covalent modification (Karp: p. 112-113; p. 607 Fig 15.3; p. 619 Fig. 15.12)

1. Many enzymes exist in active and inactive forms.e.g. glycogen phosphorylase (gp)

glycogen phosphorylase a activeglycogen phosphorylase b inactive

2. Active and inactive forms are interconverted by covalent modifications.Addition of 1 phosphate on a specific serine residue makes gp active.Removal of this phosphate makes gp inactive.

3. These are catalyzed by other enzymes.Protein kinases puts phosphate groups onto proteins.Protein phosphatases removes phosphates from proteins.

Allosteric modulation(Karp: p. 113)

1. Activity is modulated through noncovalent binding of a specific metabolite at a siteon the protein other than active site.

2. There can be negative or positive modulators.3. They change the conformation of the enzyme.4. Positive modulators stabilize a conformation that has a high affinity for substrate.5. Negative modulators stabilize a conformation that has a low affinity for substrate.

2b 7) Feedback principle(Karp: p. 113 Fig. 3.30)

1. Allosteric enzymes are often first enzyme in a metabolic pathway.2. They are subject to feedback inhibition.3. intracellular level of a substance regulates the rate of its own synthesis.

4. Controls activity of one or more enzymes within pathway that produces it.

E1 E2 E3

A ' B ' C ' D

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2c: Metabolism: Unit #9(Karp: pp. 105-116)

2c 1) Introduction to Metabolism

Sum total of all chemical changes that occur in cells. Made up of interconnected metabolic pathways.

Pathways are sequence of chemical reactions. Each reaction is catalyzed by a specific enzyme. Compounds formed in each step along the pathway are metabolites. Pathway leads to an endproduct. Endproduct has a particular role in the cell. Two broad types of metabolic pathways.

Catabolic pathways Breaking of chemical bonds in large, complex molecules to form small simple molecules. These molecules can be used to synthesize other molecules. Catabolic reactions are exergonic.

Provide chemical energy for cell

Anabolic pathways Synthesis of large molecules by chemically bonding together small molecules. Anabolic reactions are endergonic. Require energy.

The two are interconnected. Catabolic pathways provide energy and small molecules for anabolic pathways.

2c 2)Glycolysis(Karp: p. 108 Fig. 3.24)

1. A universal catabolic pathway.2. Breakdown of glucose.3. Ten-step reaction sequence (glucose to pyruvate).4. Occurs in presence or absence of O2.

5. Occurs in cytosol.

Glycolytic products for 1 molecule of glucose

1. Uses 2 ATP and produces 4 ATP

ATP formed by substrate-level phosphorylation2. Yields 2 pyruvates

pyruvate stands at junction of anaerobic vs. aerobic

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3. Yields 2 NADHa. Fermentationb. Electron transport chain in mitochondriac. Make NADPH

2c 3) Reducing Power

1. A cell's reservoir of NADPH.2. Formation of complex biological molecules requires reduction of precursors.3. Accomplished by transfer of high-energy electrons from NADPH.4. NADPH is coenzyme for enzymes having reductive role in anabolic pathways.

e.g. C3cycle in photosynthesis

e.g. fat

5. NADPH is interconvertible with NAD+.

6. NAD+is coenzyme for dehydrogenases in catabolic pathways.e.g. glyceraldehyde dehydrogenase in glycolysis

2c 4) Equilibrium versus steady state metabolism(Karp: p. 92 Fig. 3.7)

Many reactions in a metabolic pathway may be near equilibrium. However, several reactions in a pathway are poised far from equilibrium. These are essentially irreversible and keep pathway going in a single direction. Cellular metabolism can maintain itself at irreversible nonequilibrium conditions

because the cell is an open system. An open system because materials are continually flowing in and out of the cell. Cellular metabolism is said to exist in a steady state.

In a steady state, the concentrations of reactants and products remain essentiallyconstant, even though individual reactions are not necessarily at equilibrium.

Driving force for glycolysis

When concentration of metabolites in the cell are measured, Three reactions are far from equilibrium (Figs. 3.24, 3.25, 3.31):

1. Hexokinase2. Phosphofructokinase3. Pyruvate kinase

These 3 are essentially irreversible and keep pathway going in a single direction.

All subject to feedback inhibition by ATP.

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2c 5) Separating Catabolic and Anabolic Pathways

1. e.g. glycolysis and gluconeogensisGlycolysis (catabolic) breakdown of glucoseGluconeogenesis (anabolic) formation of glucose

2. Thermodynamic problem cannot proceed simply by reversal of reactions.

Glycolytic pathway contains 3 thermodynamically irreversible reactions. (Fig. 3.31)3. Regulatory problem two pathways could not be controlled independently of one

another.

2c 6) Separating and regulating glycolysis and gluconeogenesis(Fig. 3.31)

1. Solved by using different enzymes to catalyze 3 key reactions in 2 opposing pathways.e.g. Step between fructose-6-phosphate and fructose 1,6-bisphosphate

2. Other reactions are identical, although they run in opposite directions.

Phosphofructokinase in glycolysis

fructose 6-phosphate + ATP 'ADP + fructose 1, 6-bisphosphate This is an allosteric enzyme.

positive modulators: ADP, AMP, fructose 2, 6-bisphosphatenegative modulator: ATP

When cell has ample ATP, the enzyme is inhibited. If ATP is being used up, the enzyme is stimulated.

Fructose 1,6-bisphosphatase in gluconeogenesis

fructose 1,6-bisphosphate + H2O 'fructose 6-phosphate + pi Allosterically inhibited by high levels of AMP. Competitively inhibited by fructose 2, 6-bisphosphate.

2c 7) Regulating ATP levels

Generally ATP levels do not fluctuate ATP must be maintained high relative to that of ADP and AMP. In this way, -$G of ATP hydrolysis remains large enough to drive endergonic reactions.

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Here are some sample midterm questions.

1. Which one of the following specific compounds is correctly matched with the generalclass of compound to which it belongs?A. insulin / carbohydratesB. testosterone / protein

C. cellulose / nucleic acidD. insulin / lipidE. estrogen / lipid

2. Which one of the following molecules would be considered macromolecules?A. polypeptidesB. organic acidsC. purinesD. hexosesE. oligosaccharides

3. Which one of the following statements about enzymes is nottrue?A. Enzymes are proteins.B. Enzymes regulate metabolism.C. Enzymes change the direction of a chemical reaction.D. Enzymes can be covalently modified.E. If all (A to D) are true, answer E.

4. What is the repeating disaccharide in cellulose?A. maltoseB. cellobioseC. lactose

D. sucroseE. none of the above

5. Which one of the following completions is correct? Eukaryotic cells . . .A. include only cells that have cell walls.B. have their DNA organized into a nucleus.C. have no organelles.D. have their DNA organized into a nucleoid region.E. are found only in multicellular organisms.

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ANSWERS TO SAMPLE MIDTERM QUESTIONS on previous page.

1. E2. A3. C

4. B5. B6. C7. E8. D9. E10. B

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Module 3 outline and notes: Membranes and energy metabolism

3aMembranes3a1) Introduction to Membranes3a2) Overview of Plasma Membrane Structure3a3) Membrane Lipids3a4) Plasma Membrane Carbohydrates

3a5) Membrane Proteins3a6) Motility of Membrane Proteins and Cell Polarity3a7) Specialized membrane structures: intercellular junctions

3bMembrane transport3b1) Movement of Substances Across Plasma Membranes3b2) Diffusion3b3) Solute Transport Mechanisms3b4) Diffusion through Lipid Bilayer3b5) Diffusion of Ions Through Membranes3b6) Facilitated Diffusion

3b7) Active Transport3b8) Na+-K+ATPase3b9) Coupling Active Transport to Existing Ion Gradients3b10) Membrane Potentials

3c Cellular uptake of particles and macromolecules

3c1) Introduction to Cellular Uptake of Particles and Macromolecules3c2) Endocytosis3c3) Pathways in receptor-mediated endocytosis3c4) LDLs and cholesterol metabolism3c5) LDL and HDL in heart disease3c6) Phagocytosis

3c7) Some bacteria circumvent being killed by macrophages3d ATP formation and the mitochondria

3d1) Fermentation: Anaerobic Oxidation of Pyruvate3d2) Aerobic Oxidation of Pyruvate3d3) TCA or Krebs Cycle3d4) Mitochondria Structure3d5) Electron Transport Chain3d6) ATP formation3d7) Overall Products from oxidizing glucose

3ePhotosynthesis and the chloroplast3e1) Heterotrophs vs. Autotrophs

3e2) Chloroplasts3e3) Absorption of Light3e4) Reaction-Center Chlorophyll3e5) Photophosphorylation3e6) CO2Fixation and Formation of Carbohydrates

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3a3) Membrane Lipids

All are amphipathic. Except for glycolipids and cholesterol, all contain phosphate group.

These are phospholipids. Phospholipids have a glycerol backbone.

These are phosphoglycerides.

Phosphoglycerides(Karp: p. 48 Fig. 2.22; p. 123 Fig. 4.6)

Diglycerides often one saturated and one unsaturated fatty acid.

3rdOH group has phosphate plus either:

1. Choline phosphatidyl choline.2. Ethanolamine phosphatidylethanolamine.3. Serine phosphatidylserine.

4. Inositol phosphatidylinositol.

Sphingolipids(Karp: p. 123 Fig. 4.6b)

Sphingosine-based lipids.Sphingosine is an amino alcohol with a long hydrocarbon chain.

Two additions:1. Always a fatty acid to amino group of sphingosine. This is a ceramide.2. Additional groups esterified to terminal OH.

a. If phosphorylcholine, molecule is sphingomyelin.

b. If carbohydrate, molecule is glycolipid.

glycolipids

1. If carbohydrate is a monosaccharide, glycolipid is a cerebroside.2. If carbohydrate is an oligosaccharide, glycolipid is a ganglioside.

Cholesterol(Karp: p. 124 Fig. 4.7)

May constitute up to 50% of lipid molecules in plasma membrane of certain animalcells.

Is absent from plasma membranes of all bacterial cells. Cholesterol increases fluidity of bilayer.

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3a 4) Plasma membrane carbohydrates

All of carbohydrate faces outward into extracellular space. Covalently linked to either protein or lipid.

glycoproteins (Karp: p. 126 Fig. 4.11; p. 127 Fig. 4.12)

Carbohydrate is present in short, branched oligosaccharides (

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1. Integral proteins

Penetrate into lipid bilayer. Usually pass right through. Have segments protruding into extracellular space.

Have segments protruding into cytoplasm.

Transmembrane segments Pass through lipid bilayer. Usually consist of nonpolar amino acids organized in an !-helical conformation.

Some integral membrane proteins can form aqueous channel through lipid bilayer.

2. Peripheral membrane proteins

Located entirely outside of lipid bilayer. Either on extracellular or cytoplasmic surface. Associated with membrane surface by noncovalent bonds. Weak electrostatic bonds to hydrophilic head groups of phospholipids or

hydrophilic portion of integral proteins. Peripheral proteins on cytoplasmic surface function in transmembrane signal transduction.

3. Lipid-anchored membrane proteins

Covalently linked to lipid molecules within bilayer.

Two types of lipid anchors:a. Glycophosphatidyl inositol in outer leaflet

proteins linked to this by short oligosaccharide chainb. Long hydrocarbon chains in inner leaflet

A G protein called Ras is linked this way.G proteins are involved in transmembrane signal transduction.

3a6) Motility of Membrane Proteins and Cell Polarity

Control over membrane motility

1. Integral membrane proteins are not totally free to drift in lipid sea.2. Restraints as a result of:

a. Interactions occurring within membrane.

b. Links to materials on inner or outer surface of membranes. (Karp: p. 142 Fig. 4.27)3. Leads to membrane domains

Regions in which a protein may travel (Karp: p. 142 Fig. 4.27)

Membrane Domains and Cell polarity (Karp 140)

e.g. Epithelial cells lining inner surface of intestine. ( Fig. 4.30)

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Highly polarized cells whose different surfaces carry out different functions.1. Apical plasma membrane

Faces lumen of intestine Selectively absorbs substances from lumen.

2. Lateral plasma membrane surface

Interacts with neighboring epithelial cells.3. Basal plasma membrane

Adheres to underlying extracellular substrate (basement membrane) Functions in exchange of substances with bloodstream.

3a7) Specialized membrane structures: intercellular junctions

Nonjuctional

Space between neighboring cells ~20-30 nm.

No specialized structures are seen in space or in cells.

Specialized cell-cell junctions

Specialized regions of close-range contact between adjacent cells.1. Adherens junctions

2. Desmosomes

3. Tight junctions

4. Gap junctions Often occur together as intercellular junctional complex.

Adherens Junctions and Desmosomes: anchoring cells to other cells

Adherens junctions(zonulae adherens) (Karp: p. 252; Fig. 7.25; p. 252 Fig. 7.26)

Sites where cadherins are concentrated. Space between cells is 20-35 nm. In cytoplasm, structures called plaques seen. Cadherins connected to actin filaments by catenin. Very common in epithelia, such as gut epithelium. Occur as 'belt' that encircles each of cells near its apical surface

Binds that cell to its neighbors.

Desmosomes(Karp: p. 253 Fig. 7.27 & 7.28)

Sites where cadherins (desmogleins and desmocollins) are concentrated. Space (desmoglea) between cells is 20-35 nm. Desmolgea contains collagenous glue. Opposite desmoglea are dense cytoplasmic plaques. Intermediate filaments run out of plaques across cell. Desmosome abundant in epithelia.

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Occur basal to adherens junctions. 'spot welding'.

Tight Junctions (TJ): sealing extracellular space(Karp: p. 254 Fig. 7.30)

No space between two neighboring epithelial cells.

Two membranes together are ~12 nm thick rather than ~14 nm. Appear to involve fusion of outer leaflets of adjacent membranes 5 layered structure as seen in TEM. Claudins are the proteins of tight junctions. TJ occur at very apical end of junctional complex Serve to seal space between cells. In intestine, tight junctions form a ring or zone completely around each cell. This forces material to go through cells rather than between cells.

Gap junctions: mediate cell-to-cell communication(Karp: p. 257; Fig. 7.32; 7.33)

Space between adjacent cells is 2-4 nm. 7 layered structure as seen in TEM. Extremely small channels (connexons) span the gap. Connexons allow for cytoplasmic continuity between adjacent cells. Only low molecular weight material can pass between cells. Gap junctions act as molecular sieves. Integrate activities of individual cells of a tissue.

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3b: Membrane Transport: Unit #11(Karp: p. 143-155; 158-161)

3b1) Movement of substances across plasma membranes

1. Plasma membrane is selectively permeable.

a i.e. somesolutes are more permeable than others.b. This allows cells to concentrate substancesc. Influx movement of substance into cells.d. Efflux movement of substances out of cells.e. Net flux one exceeds the other.

2. Plasma membrane is semipermeable.a. i.e. freely permeable to H2O (solvent), while allowing much slower passage to

small ions and polar solutes.

3b2) Diffusion

Continual movement of molecules among each other in liquids or gases Greater the concentration difference the greater is the rate of diffusion. Ability of an ion to diffuse between two compartments depends on 2 gradients:

1. Chemical gradient determined by concentration difference of substance.2. Electric potential gradient determined by difference in charge.3. Together these differences are combined to form an electrochemical gradient.

Diffusion of Water through Membranes

Osmosis Is movement of water through a semi-permeable membrane in response to aconcentration gradient of H2O.

Osmotic pressure is proportional to the number of particles in solution Osmolarity is a calculated quantity of a solution. Units are milliosmoles.

Tonicity Is an observed property that depends on permeability of the cell membraneand is relative to another cell or solution (Figs. 4.35).

1. If cell swells, the solution is hypotonic relative to cell.a. animal cells swell and eventually burst.

If these are red blood cells, this is hemolysis.b. plant cells push against surrounding cell wall.

This is turgor pressure. (Karp: p. 146 Fig. 4.36)

2. If cell shrinks, the solution is hypertonic relative to cell.Plant cell pulls away from surrounding cell wall.This is plasmolysis.

3. If cell neither shrinks or swells, the solution is isotonic.

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3b3) Solute transport mechanisms(Karp: p. 143 Fig. 4.33)

1. Passive diffusionAll driven by concentration gradient.a. Simple diffusion through lipid bilayerb. Simple diffusion through an aqueous channel

c. Facilitated diffusion solute binds specifically to a membrane protein carrier.2. Active energy coupled transport

Uses protein carrier but driven by ATP hydrolysis.

3b4) Diffusion through Lipid Bilayer

1. Greater the lipid solubility, faster the diffusion into the cell. (Karp: p. 145 Fig. 4.34)

Partition coefficient is a measure of lipid solubility or hydrophobicity or nonpolarity.

partition coefficient = concentration in oil

concentration in H2O

2. The smaller the molecule, the greater is the rate of diffusion. Very small, uncharged molecules penetrate very rapidly.

e.g. O2& CO2appear to slip between adjacent phospholipids

3. Ions and lager polar molecules, such as sugars and amino acids, cannot diffusethrough lipid bilayer.

3b5) Diffusion of ions through membranes

Ion channels: Permeable to specific ions. Each formed by integral membrane proteins that surround an aqueous pore. Highly selective Only one type of ion passes through pore. Bidirectional. Net flux depends on electrochemical gradient.

Gated channels

1. Most ion channels exist in either an open or a closed conformation.2. Such channels are termed gated.

3. Voltage-gated channelsConformation state depends on difference in ionic charge on two sides of membrane.

e.g. K+channel (Karp: p. 150-151 Fig. 4.41; Fig. 4.43)4. Chemical-gated channels

Conformational state depends upon binding of a particular substance.e.g. Acetylcholine (neurotransmitter) acts on outer surface of certain cation channels.

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Na+-K

+ATPasetransport cycle(Karp: p. 153 Fig. 4.46)

1. Na+ions bind to protein on inside of membrane.2. ATP is hydrolyzed.

3. Conformation of Na+-K+ATPase is changed.

4. Na+ions are expelled to external space.

5. K+ions bind on outside of membrane.6. Phosphate group on protein is removed.7. Protein snaps back to its original conformation.

8 K+ions move to inside of cell.

3b9) Coupling active transport to existing ion gradients

1. Na+that has been pumped out is driven back in by concentration gradient.

2. Membrane almost impermeable to Na+.3. Therefore transport protein is required.4. Transport protein does not work unless it binds another molecule (e.g. glucose).5. Glucose is driven into cell against its concentration gradient.6. This is cotransport and driven by secondary active transport.7. Symport two solutes are moved in same direction.

(i.e. glucose and Na+)8. Antiport two solutes moved in opposite direction.

(i.e. Na+and H+)

Secondary transport in intestine(Karp: p. 140 Fig. 4.30; p. 158 Fig. 4.49)

Uptake of glucose by cotransport occurs at apical plasma membrane. Glucose diffuses through cytoplasm of intestinal epithelial cell. At basal plasma membrane glucose is transported out of cell and into bloodstream

by facilitated diffusion.

3b10) Membrane potentials

All cells have a voltage gradient across their membrane or a membrane potential. By convention, inside is negative with respect to outside (Fig. 4.51 & 4.52). Magnitude varies between -15 and -100 mV.

Membrane potential arises from:1. Passive properties of the membrane (semi-permeable)

2. Active transport in Na+/K+ATPase

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3c: Cellular Uptake of Macromolecules and Particles: Unit #12(Karp: pp. 301-309)

3c 1) Introduction to Cellular Uptake of macromolecules and particles How cells take in materials too large to penetrate plasma membrane. Uptake of extracellular materials into cytoplasmic vesicles without breaking

continuity of plasma membrane.Two different mechanisms:

1. Endocytosis uptake of fluid, dissolved solutes and suspended macromolecules.2. Phagocytosis uptake of particulate matter. > 0.5 m

3c 2) Endocytosis

Can be divided into 2 categories.a. Bulk-phase endocytosis

Brings about uptake of extracellular fluids without recognition by surface ofplasma membrane.

Any molecules that happen to be present in enclosed fluid gain entry intocells.

Occurs in a continual manner in many types of cells.

b. Receptor-mediated endocytosis (RME) Brings about uptake of specific macromolecules (ligands) following their

binding to receptors on plasma membrane.(ligand any molecule that can bind a receptor)

Material taken up by endocytosis is delivered to a network of tubules andvesicles.

These are collectively known as endosomes.

Two main types of receptors in receptor-mediated endocytosis (RME)

(Fig. 8.42)1. house keeping receptors

- often bind nutrients and deliver them to cytoplasme.g. LDL receptor

2. signal receptors- binds ligands that are hormones or growth factors.- endocytosis of these leads to destruction of receptor.- a process called "receptor down regulation".

Endosomes

Network of cytoplasmic membrane vesicles and tubules.- Early endosomes are located near peripheral region of cell.

(act as first sorting station) Late endosomes are in interior part of cell. (main sorting station) Late endosomes receive material from:

a. Early endosomesb. Golgi apparatus

Late endosomes can be thought of as a prelysosomal compartment.

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Coated pits(Karp: p. 302-304 Figs. 8.37 & 8.38)

Sites on membrane where receptors for receptor-mediated endocytosis areconcentrated.

Surface is indented.

Indentation is covered on its cytoplasmic side by a bristly electron-dense material.

Proteins of the coated pits(Figs. 8.39, 8.40 & 8.41)1. clathrin

- main structural protein- composed of 3 heavy and 3 light chains organized into a triskelion.- forms scaffold for the pit or cage or basket.

2. adpatins-link ligand to clathrin cage-adaptins organize into adaptors.Adaptors bind

1. Clathrin on one side and2. Cytoplasmic tails of specific membrane receptors on other side.

3. dynamin-large GTP-binding protein.-releases clathrin-coated vesicle from the membrane.

3c3) Pathways in receptor-mediated endocytosis(Karp: p. 306 Fig. 8.42)

1. common stepsa. Clathrin coat is removed from coated vesicle to yield uncoated vesicle.

b. Uncoated vesicle fuses with early endosome.2. house keeping receptors.

a. ligand and receptor are separated from each other in early endosome.b. Receptors bud off into recycling vesicles to be taken back to membrane.c. Endosomal carrier vesicle buds off with ligands and fuses with late endosome.d. From late endosome, ligand moves to lysosome for ultimate delivery to

cytoplasm.3. signaling receptors

a. ligand and receptor bud off into endosomal carrier vesicle.b. Endosomal carrier vesicle fuses with late endosome.c. Ligand and receptor are transferred to lysosome for destruction.

3c4) LDLs and cholesterol metabolism

An example of receptor-mediated endocytosis delivering nutrients. Cells need cholesterol for membrane assembly or metabolic processes (e.g. steroid

metabolism). Cholesterol is synthesized by liver. Hydrophobicity of cholesterol prevents transport in blood as free cholesterol.

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LDL particles carry cholesterol in blood from liver to body's cells. LDL = low density lipoprotein

LDL particles(Karp: p. 307 Fig. 8.43)

Consists of a central core of cholesterol esterified to long-chain fatty acids.

Core is surrounded bya. Coat of phospholipids and unesterified cholesterol.b. A single molecule of apolipoprotein B.

Apolipoprotein B interacts with LDL receptors.

LDL receptors

Cells contain a variable number of LDL receptors on plasma membrane. Concentrated in coated pits. Once LDL binds receptors:

a. Pit invaginates to form a coated vesicle.

b. Clathrin coat is disassembled.c. LDL receptors are recycled back to plasma membraned. LDL particles are delivered to lysosomes.e. Protein of LDL is digested and cholesterol is released.

3c5) LDL and HDL in heart disease

LDL and heart disease

High blood levels of LDL are associated with increased risk of heart disease.(e.g.) atherosclerosis.

Atheroscleoris is characterized by LDL-containing plaques (atheroscleroticplaques). Plaques form on inner walls of blood vessels. This causes the narrowing of major arteries and reduced blood flow. Plaques also act as sites for formation of blood clots. Blood clots that block coronary arteries are leading cause of myocardial infarction

(heart attack).

LDL and atherosclerotic plaque formation(Fig. 8.44)

1. Initiated by:

i. Injury to endothelial cells lining blood vessels.ii. Reactive oxygen species (ROS) chemically alter LDL-cholesterol.2. Macrophages are attracted to injured endothelium and

i. Ingest LDL oxidized by ROS.ii. Accumulate cholesterol-rich fatty droplets in cytoplasm.iii. Are referred to as macrophage foam cells.

3. Smooth muscle cells around blood vessel are:i. Stimulated to proliferate by foam cells andii. Produce fibrous cap that bulges into arterial lumen.

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3c6) Phagocytosis 'cell eating' (Karp: p. 308; Fig. 8.45)

Uptake of particulate material and delivery to a lysosome. Delivery done via a phagosome. Lysosome is cell's digestive organelle. (Karp p. 297) Phagosome fuses with primary lysosome to form secondary lysosome.

Fusion activates lysosomal enzymes. ~50 different hydrolytic enzymes in lysosome. (Karp: p. 298; Table 8.1) Contents digested providing:

a. Nutrition products move into cytoplasm.b. Defense microorganisms are killed.

Macrophages and neutrophils (Karp p. 308-309)

are professional phagocytes in animals. have mechanisms for killing ingested microorganisms:

1. lysosomes contains lysozyme, an enzyme that degrades bacterial cell walls.

2. Acidic pH of lysosome kills some.3. oxygen free radicals generated within phagosome kill some bacteria.

a. hydrogen peroxide yields superoxide radical. (Karp p. 34)b. nitric oxide (NO) yields peroxynitrite (Karp p. 640-641)

3c7 Some bacteria circumvent being killed by macrophages (Karp p 308-309)

1.Mycobacterium tuberculosis causes tuberculosis- engulfed into phagosome but prevents fusion of phagosome with

lysosome.2. Coxiella burnetii - causes Q fever.

- this bacteria is not killed by either lysosomal enzymes or acidic pH.3.Listeria monocytogenes causes meningitis

- produced proteins that destroy the integrity of the lysosomal membraneallowing the bacteria to escape into the cytoplasm.

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3d: ATP Formation and the Mitochondria: Unit #13(Karp: p. 173-209)

3d1) Fermentation: Anaerobic oxidation of pyruvate(Karp: p. 111 Fig 3.29; p 177 Fig. 5.5)

1. Glycolysis glucose to pyruvate

a. In cytosolb. Presence or absence of O2

c. Net of 2 ATP/glucose

2. Fermentationa. In cytosolb. Absence of O2

c. Regenerates NAD+to support glycolysisd. Muscle

i. Lactate dehydrogenase

ii. Lactatee. Yeasti. Alcohol dehydrogenaseii. Ethanol

3d2) Aerobic Oxidation of Pyruvate(Fig. 5.5)

1. When O2is present, pyruvate enters mitochondria.

2. Completely oxidized to CO2.

a. Pyruvate dehydrogenase

b. TCA or Krebs cycle3. Get up to 36 ATP/glucose

Oxidation of pyruvic acid to Acetyl CoA

1. Catalyzed by pruvate dehydrogenase complex2. One CO2is evolved.

3. NADH is formed

3d3) TCA or Krebs cycle(Karp: p. 179 Fig. 5.7)

1. 2-carbon acetyl group condenses with 4-carbon oxaloacetate to form 6-carbon citrate.2. One turn of cycle evolves 2 CO2.

3. his completes oxidation of pyruvate.

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4. Free energy is conserved in.a. 3 NADH and 1 FADH2.

Will be used in electron-transport chain to form ATP.b. 1 GTP energetically equivalent to ATP

TCA or Krebs cycle: Central pathway of cell(Karp: p. 180 Fig. 5.8)

1. Metabolites of other catabolic pathways enter TCA cyclee.g. breakdown of proteins

2. TCA cycle metabolites can be used to synthesize larger molecules (anabolism).e.g. amino acids for protein synthesis

3. Amphibolic pathway used in both catabolism and anabolism.

3d4) Mitochondria structure(Karp: p. 176 Fig. 5.3; Fig. 5.4)1. Outer membrane

a. Porins

Integral proteins that form large, nonselective membrane channels.2. Intermembrane space3. Inner membrane

a. Electron transport chainb. ATP synthase

4. Matrixa. TCA cycleb. DNA (genes for ~13 polypeptides)c. Ribosomes

3d 5) Electron transport chain (or respiratory chain) (Karp: p. 188 Fig. 5.17)1. Sequential transfer of electrons from one electron carrier to another.2. All carriers are associated with the inner mitochondrial membrane.3. Five types of electron carriers

Components of electron transport chain(Karp: p. 185 Fig. 5.12)1. Flavoproteins

Prosthetic groups are derived from riboflavin. (FAD or FMN)e.g. NADH dehydrogenase

2. Cytochromes Proteins that contain heme groups.

Iron of heme undergoes reversible transition between Fe3+and Fe2+.3. Ubiquinone (or coenzyme Q)

Lipid-soluble molecule4. Iron-sulfur proteins

Iron is closely linked to inorganic sulfur.5. copper in cytochrome oxidase

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Function of Electron Transport Chain

1. Free energy released from oxidation/reductions of electron transport chain moves

H+from matrix to intermembrane space.

2. This sets up a H+gradient.3. Ionic gradient across a membrane represents a form of energy.

4. Energy is used to form ATP. This is oxidative phosphorylation.

Proton-motive force

1. Two components to H+gradient across inner mitochondrial membrane.a. pH gradient (chemical gradient)b. Voltage gradient (electrical gradient)

Therefore, this is an electrochemical gradient.2. Proton-motive force ($()

Expression of energy present in electrochemical gradient. ~220 mV

Voltage component ~80 %; pH component ~20 %3. Maintenance requires inner mitochondrial membrane be highly impermeable to H+.

Electron transport is uncoupled from ATP formation by 2,4 dinitrophenol.

Makes inner mitochondrial membrane permeable to H+.4. $(also drives ADP, phosphate and Ca++into matrix.

3d 6) ATP formation

1. Chemiosmotic mechanism Energy stored in proton gradient drives phosphorylation of ADP.

2. Catalyzed by ATP synthase.

3. ATP synthase (Karp: p. 194 Fig. 5.23)a. F1headpiece projects into matrix.b. F0basepiece embedded in lipid bilayer contains H

+ channel.4. Controlled movement of H+through channel induces:

a. Conformation changesb. These drive ATP formation.

3d7) Overall Products from oxidizing glucose

Overall products of electron transport chain

1. ATPEach NADH = 3 ATPEach FADH2= 2 ATP

2. H2OFormed by O2finally accepting electrons.

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Return from complete oxidation of 1 molecule of glucose

Glycolysis &glucose to pyruvate = 2 ATP(also two NADH2)

Pyruvate &acetyl CoA

(do twice) = 2NADH2 = 6 ATP

Two turns of Krebs cycle6 NADH = 18 ATP2 FADH2 = 4 ATP2 GTP = 2 GTP

2NADH from glycolysis = 4 ATP(glycerol phosphate shuttle; Karp 181; Fig. 5.9)

Total = 36

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3e: Photosynthesis and the Chloroplast: Unit #14(Karp: p. 206-223)

3e1) Heterotrophs vs. Autotrophs

Heterotrophs:

Depend on an external source of organic compounds. Earliest life forms must have been heterotrophs.

Earliest life forms would have utilized organic molecules that had formed abiotically.(see Fig 1.9 on p 9 Karp)

Autotrophs:

Utilize CO2to manufacture their organic molecules.

Chemoautotrophs Utilize the energy stored in inorganic molecules (e.g. hydrogen sulfide) to

convert CO2into organic compounds.

Phototrophs Utilize the radiant energy of sun to convert CO2into organic compounds.

Photoautotrophs include

1. Higher plants2. Eukaryotic algae3. Various flagellated protists.4. A variety of prokaryotes (e.g. green bacteria)

All carry out photosynthesis

Photosynthesis

Sunlight is transformed into chemical energy and utilized to form carbohydrates.Light

CO2+ H2O ' (CH2O) + O2

Photosynthesis in higher plants will be examined.

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3e2) Chloroplast1. Organelle in which photosynthesis takes place.2. Located predominantly in mesophyll cells of leafs.3. Semi autonomous and self replicating.4. Bound by 2 membranes separated by a narrow space.5. Thylakoids flattened membranous sacs within chloroplast.

a. Lumen space inside a thylakoidb. Grana orderly stacks of thylakoids.

6. Stroma space surrounding thylakoids.

Overview of photosynthesis

light6CO2+ 12 H2O ' C6H12O6+ 6O2+ 6H2O

2 series of reactions.

1. Light reaction (light-dependent reaction)

a. Energy from sunlight is converted to chemical energy.b. Products.

i. ATPii. NADPH

c. Occurs in thylakoid membranes.2. Dark reaction (light-independent reaction)

a. ATP and NADPH are used to synthesize carbohydrates.b. Occurs in stroma.

3e3) Absorption of light

Energy comes from sun in form of electromagnetic radiation. These radiations travel in discrete packets called photons. When a photon is absorb, compound is converted to a higher energy state (excited state). Ground state may be re-established in three different ways:

1. Energy may be dissipated as heat.2. Energy may be reemitted in form of longer wavelength, fluorescence.3. Energy may be transferred to another molecule.This is what happens with photosynthetic pigments.

Photosynthetic Pigments

Pigments are molecules that contain a chromophore.

Chromophore chemical group capable of absorbing light of particular wavelengths ()). Absorption spectrum plot of intensity of light absorbed vs. ). Action spectrum plot of physiological response vs. ). Action spectrum of photosynthesis (Fig. 6.8).

Follows absorption spectrum of the chlorophylls and carotenoids.

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1. Chlorophylls: major light capturing molecules

Absorb light of blue and red )(Karp: p. 212 Fig. 6.6) Reflects green )(we see) Two parts (Fig. 6.6):

a. Porphyrin ring functions in light absorption

Magnesium atom in center of ring Different side groups on ring. This gives different kinds of chlorophyll (a b c & d)

b. Phytol side-chain Inserts chlorophyll in lipid bilayer of thylakoid membrane.

2. Carotenoids: an accessory pigment (Karp p. 212)

Long hydrocarbon chains containing alternating double bonds. Increase efficiency by absorbing light in those regions where chlorophyll absorbs

light inefficiently.

Absorb light of blue and green )(400-550nm) . Reflects yellow, orange and red ). Protect photosynthetic machinery from damage caused by reactive oxygen species.

3e4) Reaction-center chlorophyll(Karp: p. 213 Fig. 6.9)

Specific chlorophylls capable of transferring electrons to an electron acceptor. Other pigments act as a light-harvesting antenna system. Absorb light at other )and transfer energy to reaction center chlorophyll. Reaction-center chlorophylls are organized into 2 photosystems.

These linked by a chain of electron carriers. All within thylakoid membranes.

Photosystem II (PSII)(Karp: p. 215 Fig. 6.11 but not all details)

1. Reaction center chlorophyll is referred to as P680.P = pigment680 = )of light that this chlorophyll molecule absorbs most strongly.

2. When P680 absorbs photons, it gives up electrons to a primary electron acceptor(pheophytin) of higher reducing potential.

3. P680 replenishes its electrons from H2O.

4. As H2O becomes oxidized, O2is released.

Pheophytin eventually transfers electrons to a chain of electron carriers.

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Photosystem I (PSI) (Karp: p. 218 Fig. 6.15 but not all details)

Reaction center chlorophyll is P700. P700 accepts electrons from last member of electron transport chain of PSII. P700 is raised to an excited state by absorbing light. In this state electrons are transferred to primary electron acceptor A0.

A0has a high reducing potential.

Electrons have two fates. They can pass down:

a. A short electron transport chain to NADP+to form NADPH.b. To P700 to form ATP (cyclic photophosphorylation). (Fig. 6.17)

Z scheme or pathway(Karp: p. 214 Fig. 6.10; p. 217 Fig. 6.14)

1. Two photosystems acting in series.2. Electron flow occurs in 3 steps:

a. Between H2O and PSII.

b. Between PSII and PSI. Electron transport chain(Fig. 6.16 but not all details)

c. Between PSI and NADP+.

3. As electrons flow along Z-pathway, H+ions are moved from stroma to innercompartment of thylakoids.

4. Important end result is proton gradient.Proton concentration:a. High in lumen of thylakoid.b. Low in stroma.

3e 5) Photophosphorylation(Karp: p. 219 Fig. 6.16)

1. Formation of ATP as result of electrons moving through photosystems I and II.2. As in mitiochondria:

a. Proton gradient drives ATP formation.b. Enzyme is ATP synthase.

3. ATP synthase embedded in thylakoid membranes.4. Two types of photophosphorylation

a Noncyclic photophosphorylationb. Cyclic photophosphorylation

Noncyclic photophosphorylation(Karp: p. 214 Fig 6.10; p. 219 Fig. 6.16)

1. Electrons move in linear path from H2O to NADP+

2. Uses photosystems I and II3. Formation of ATP, NADPH and O2

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Cyclic photophosphorylation(Karp: p. 221 Fig. 6.17)

1. Electrons move from P700 to ferredoxin and back to P7002. Involves photosystem I only.3. Formation of ATPRelative amount of noncyclic vs. cyclic photophosphorylation is regulated.

3e 6) CO2fixation and formation of carbohydrate

Done in all photosynthetic plants by C3cycle.

C3or Calvin cycle(Karp: p. 222 Fig. 6.19; p. 223 Fig. 6.20)

1. Carboxylationa. CO2combines with ribulose -1, 5-bisiphosphate.

b. Forms a transient 6 carbon compound.c. This breaks down to form 2 molecules of 3-phosphoglycerate (PGA).

d. Catalyzed by ribulose -1, 5-bisphosphate carboxylase ("Rubisco").2. ATP is used to form 1, 3 bisphosphyglycerate .3. NADPH is used to reduce above to glyceraldehyde 3-phosphate (GAP)

GAP has a number of fates:

1. Remain in chloroplast.a. Regenerate RuBPb. Converted to starch

2. Exported to cytosol.a. Converted to sucrose.

b. Oxidized in glycolysis and TCA cycle to provide ATP

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Module 4 outline and notes: Flow of Genetic Information

4aFlow of information in cells4a1) The Gene as an Abstract Concept4a2) Chromosomes: Physical Carriers of the Genes4a3) How do genes determine a characteristic of an organism?4a4) What is the chemical nature of the gene

4a5) How does DNA direct synthesis of proteins?4a6) Central Dogma of Molecular Biology4a7) Genetic Code4a8) Modern attempts to define a gene4a9) Genome4a10) Organization of nuclear genome: chromatin and chromosomes4a11) Biochemistry of Chromatin4a12) Nucleosomes4a13) Jumping genes4a14) Reversing the normal flow of genetic information: reverse transcription

4bTranscription and translation

4b1) Basic Transcription Process4b2) DNA sequences critical for starting and stopping transcription4b3) Proteins responsible for transcription4b4) Describing RNAs4b5) RNA processing4b6) Mature mRNAs4b7) Tra

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