total unit 1 notes - biology

Biological Science I Tuesdays and Thursdays 8:00-9:15, HWC 2100

Wednesdays 5:15-6:15, KIN 1024 Tota l Unit 1

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THEMES IN THE STUDY OF LIFE 1. New properties emerge at each level in the biological hierarchy

a. Life can be studied at different levels from molecules to the entire living planet b. The study of life can be divided into different levels of biological organization

2. Emergent Properties

a. Emergent properties result from the arrangement and interaction of parts within a system b. Emergent properties characterize nonbiological entities as well

i. A functioning bicycle emerges only when all of the necessary parts connect in the correct way ii. Ringo Starr emerges as one of the most influential melodic drummers in rock history when

connected with John, Paul, and George in the correct way

3. The Power and Limitations of Reductionism a. Reductionism is the reduction of complex systems to simpler components that are more manageable

to study i. For example, the molecular structure of DNA

b. An understanding of biology balances reductionism with the study of emergent properties i. For example, new understanding comes from studying the interactions of DNA with other

molecules

4. Systems Biology a. A system is a combination of components that function together b. Systems biology constructs models for the dynamic behavior of whole biological systems c. The systems approach poses questions such as:

i. How does a drug for blood pressure affect other organs? ii. How does increasing CO2 alter the biosphere?

5. Approaches to study biology (or really anything)

a. Reductionist b. Emergent properties c. Systems Biology



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6. What are the levels at which we study life • Biosphere • Ecosystem • Community • Population • Organism • Organ system • Organ • Tissue • Cell • Organelle • Molecule • Atom

7. The cell can perform all activities required for life

a. Homeostasis : Regulation of the internal environment to maintain a constant state; for example, electrolyte concentration or sweating to reduce temperature.

b. Organizat ion: Being structurally composed of one or more cells, which are the basic units of life. c. Metabol ism: Transformation of energy by converting chemicals and energy into cellular components

(anabolism) and decomposing organic matter (catabolism). Living things require energy to maintain internal organization (homeostasis) and to produce the other phenomena associated with life.

d. Growth: Maintenance of a higher rate of anabolism than catabolism. A growing organism increases in size in all of its parts, rather than simply accumulating matter.

e. Adaptat ion: The ability to change over a period of time in response to the environment. This ability is fundamental to the process of evolution and is determined by the organism's heredity as well as the composition of metabolized substances, and external factors present.

f. Response to st imul i : A response can take many forms, from the contraction of a unicellular organism to external chemicals, to complex reactions involving all the senses of multicellular organisms. A response is often expressed by motion, for example, the leaves of a plant turning toward the sun (phototropism) and by chemotaxis.

g. Reproduction: The ability to produce new individual organisms, either asexually from a single parent organism, or sexually from two parent organisms.

8. Cells are an organism’s basic units of structure and function

a. The cell is the lowest level of organization that can perform all activities required for life b. All cells:

i. Are enclosed by a membrane ii. Use DNA as their genetic information

c. The ability of cells to divide is the basis of all reproduction, growth, and repair of multicellular organisms

9. Cells and the domains of life

a. A eukaryotic cell has membrane-enclosed organelles, the largest of which is usually the nucleus b. By comparison, a prokaryotic cell is simpler and usually smaller, and does not contain a nucleus or

other membrane-enclosed organelles c. Bacteria and Archaea are prokaryotic; plants, animals, fungi, and all other forms of life are eukaryotic



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10. The continuity of life is based on heritable information in the form of DNA

a. Chromosomes contain most of a cell’s genetic material in the form of DNA (deoxyribonucleic acid) b. DNA is the substance of genes c. Genes are the units of inheritance that transmit information from parents to offspring

11. DNA Structure and Function

a. Each chromosome has one long DNA molecule with hundreds or thousands of genes b. DNA is inherited by offspring from their parents c. DNA controls the development and maintenance of organisms d. Each DNA molecule is made up of two long chains arranged in a double helix e. Each link of a chain is one of four kinds of chemical building blocks called nucleotides f. Genes

i. Genes control protein production indirectly ii. DNA is transcribed into RNA then translated into a protein iii. An organism’s genome is its entire set of genetic instructions

12. Biology - The Study of Life

a. How do we study life: i. Discovery Science – observe and describe some aspect of the world and use inductive

reasoning to draw general conclusions ii. Hypothesis-Based Science – based on observations, scientists propose hypothesis that lead to

predictions. If a hypothesis is correct and we test it, we can expect a certain outcome



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CONCEPTS TO UNDERSTAND FOR CHAPTER 2 • Matter consists of chemical elements in pure form and in combinations called compounds • An element’s properties depend on the structure of its atoms • The formation and function of molecules depend on chemical bonding between atoms • Chemical reactions make and break chemical bonds 1. Overview: A Chemical Connection to Biology

a. Biology is a multidisciplinary science b. Living organisms are subject to basic laws of physics and chemistry c. One example is the use of formic acid by ants to maintain “devil’s gardens,” stands of Duroia trees

2. Matter consists of chemical elements in pure form and in combinations called compounds

a. Organisms are composed of matter b. Matter is anything that takes up space and has mass c. Elements and Compounds

i. Matter is made up of elements ii. An element is a substance that cannot be broken down to other substances by chemical

reactions iii. A compound is a substance consisting of two or more elements in a fixed ratio iv. A compound has characteristics different from those of its elements

d. Essential Elements of Life i. About 25 of the 92 elements are essential to life ii. Carbon, hydrogen, oxygen, and nitrogen make up 96% of living matter iii. Most of the remaining 4% consists of calcium, phosphorus, potassium, and sulfur iv. Trace elements are those required by an organism in minute quantities

3. An element’s properties depend on the structure of its atoms

a. Each element consists of unique atoms b. An atom is the smallest unit of matter that still retains the properties of an element c. Subatomic Particles

i. Atoms are composed of subatomic particles ii. Relevant subatomic particles include:

1. Neutrons (no electrical charge) 2. Protons (positive charge) 3. Electrons (negative charge)

iii. Neutrons and protons form the atomic nucleus iv. Electrons form a cloud around the nucleus v. Neutron mass and proton mass are almost identical and are measured in daltons

d. Atomic Number and Atomic Mass i. Atoms of the various elements differ in number of subatomic particles ii. An element’s atomic number is the number of protons in its nucleus iii. An element’s mass number is the sum of protons plus neutrons in the nucleus iv. Atomic mass, the atom’s total mass, can be approximated by the mass number

e. Isotopes i. All atoms of an element have the same number of protons but may differ in number of

neutrons ii. Isotopes are two atoms of an element that differ in number of neutrons



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iii. Radioactive isotopes decay spontaneously, giving off particles and energy iv. Some applications of radioactive isotopes in biological research are:

1. Dating fossils 2. Tracing atoms through metabolic processes 3. Diagnosing medical disorders

f. The Energy Levels of Electrons i. Energy is the capacity to cause change ii. Potential energy is the energy that matter has because of its location or structure iii. The electrons of an atom differ in their amounts of potential energy iv. An electron’s state of potential energy is called its energy level, or electron shell

g. Electron Distribution and Chemical Properties i. The chemical behavior of an atom is determined by the distribution of electrons in electron

shells ii. The periodic table of the elements shows the electron distribution for each element iii. Valence electrons are those in the outermost shell, or valence shell iv. The chemical behavior of an atom is mostly determined by the valence electrons v. Elements with a full valence shell are chemically inert

h. Electron Orbitals i. An orbital is the three-dimensional space where an electron is found 90% of the time ii. Each electron shell consists of a specific number of orbitals

4. The formation and function of molecules depend on chemical bonding between atoms

a. Atoms with incomplete valence shells can share or transfer valence electrons with certain other atoms b. These interactions usually result in atoms staying close together, held by attractions called chemical

bonds c. Covalent Bonds

i. A covalent bond is the sharing of a pair of valence electrons by two atoms ii. In a covalent bond, the shared electrons count as part of each atom’s valence shell iii. A molecule consists of two or more atoms held together by covalent bonds iv. A single covalent bond, or single bond, is the sharing of one pair of valence electrons v. A double covalent bond, or double bond, is the sharing of two pairs of valence electrons vi. The notation used to represent atoms and bonding is called a structural formula

• For example, H–H vii. This can be abbreviated further with a molecular formula

• For example, H2 viii. Covalent bonds can form between atoms of the same element or atoms of different elements ix. A compound is a combination of two or more different elements x. Bonding capacity is called the atom’s valence xi. Electronegativity is an atom’s attraction for the electrons in a covalent bond xii. The more electronegative an atom, the more strongly it pulls shared electrons toward itself xiii. In a nonpolar covalent bond, the atoms share the electron equally xiv. In a polar covalent bond, one atom is more electronegative, and the atoms do not share the

electron equally xv. Unequal sharing of electrons causes a partial positive or negative charge for each atom or

molecule d. Ionic Bonds

i. Atoms sometimes strip electrons from their bonding partners



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ii. An example is the transfer of an electron from sodium to chlorine iii. After the transfer of an electron, both atoms have charges iv. A charged atom (or molecule) is called an ion

1. A cation is a positively charged ion 2. An anion is a negatively charged ion

v. An ionic bond is an attraction between an anion and a cation vi. Compounds formed by ionic bonds are called ionic compounds, or salts vii. Salts, such as sodium chloride (table salt), are often found in nature as crystals

e. Weak Chemical Bonds i. Most of the strongest bonds in organisms are covalent bonds that form a cell’s molecules ii. Weak chemical bonds, such as ionic bonds and hydrogen bonds, are also important iii. Weak chemical bonds reinforce shapes of large molecules and help molecules adhere to each

other 1. Hydrogen Bonds

a. A hydrogen bond forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom

b. In living cells, the electronegative partners are usually oxygen or nitrogen atoms 2. Van der Waals Interactions

a. If electrons are distributed asymmetrically in molecules or atoms, they can result in “hot spots” of positive or negative charge

b. Van der Waals interactions are attractions between molecules that are close together as a result of these charges

c. Collectively, such interactions can be strong, as between molecules of a gecko’s toe hairs and a wall surface

f. Molecular Shape and Function i. A molecule’s shape is usually very important to its function ii. A molecule’s shape is determined by the positions of its atoms’ valence orbitals iii. In a covalent bond, the s and p orbitals may hybridize, creating specific molecular shapes

5. Chemical reactions make and break chemical bonds

a. Chemical reactions are the making and breaking of chemical bonds b. The starting molecules of a chemical reaction are called reactants c. The final molecules of a chemical reaction are called products d. Photosynthesis is an important chemical reaction e. Sunlight powers the conversion of carbon dioxide and water to glucose and oxygen

i. 6 CO2 + 6 H20 → C6H12O6 + 6 O2 f. Some chemical reactions go to completion: all reactants are converted to products g. All chemical reactions are reversible: products of the forward reaction become reactants for the

reverse reaction h. Chemical equilibrium is reached when the forward and reverse reaction rates are equal



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WATER – THE MEDIUM OF LIFE Water:

• appears to be unique to our earth • covers three-fourths of its surface • constitutes 60-70 wt % of the living world • regenerates and is redistributed through evaporation (water cycle) • exists in all three states (ice, water, steam) in the natural environment • absolutely essential to life (dehydration kills quickly)

Develop our understanding of water on three fronts:

II. Hydrogen Bonding III. Emergent properties IV. Acid Base chemistry

I. Hydrogen Bonding

A. The structure of water is simple – you must be able to draw water 1. One O covalently bonded to two H 2. Bond angle is 105O 3. O is electronegative – it attracts electrons. 4. The electrons of the H spend more time closer to the O 5. Unequal electron distribution gives water a polarity

a. O region is ha a slight “-” charge b. H ends have a slight “+” charge

B. The polar nature allows for interactions 1. Liquid

a. Fragile disorganized hydrogen bonds b. Last few trillionths of a second c. Constantly reforming

2. Solid a. Organized hydrogen bonds – four neighbors in 3D space b. Crystal is more spacious than disorganized liquid – Ice floats

3. Gas a. Single molecules liberated from others by the addition of energy



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II. Emergent properties that make water great for sustaining life on earth A. Cohesion, adhesion, and surface tension

1. Collectively, hydrogen bonds hold water molecules together, a phenomenon called cohesion 2. Cohesion helps the transport of water against gravity in plants 3. Adhesion is an attraction between different substances, for example, between water and plant

cell walls 4. Surface tension is a measure of how hard it is to break the surface of a liquid - Surface tension

is related to cohesion B. Ability to moderate temperature

1. Heat and Temperature a. Water absorbs heat from warmer air and releases stored heat to cooler air b. Water can absorb or release a large amount of heat with only a slight change in its own

temperature c. The behavior of water is the basis for the metric temperature scale

a. The Celsius scale is a measure of temperature using Celsius degrees (°C) b. A calorie (cal) is the amount of heat required to raise the temperature of 1 g of

water by 1°C c. The “calories” on food packages are actually kilocalories (kcal), where 1 kcal =

1,000 cal d. The joule (J) is another unit of energy where

1 J = 0.239 cal, or 1 cal = 4.184 J 2. The high specific heat of water

a. The specific heat of a substance is the amount of heat that must be absorbed or lost for 1 g of that substance to change its temperature by 1ºC

b. The specific heat of water is 1 cal/g/ºC c. Water resists changing its temperature because of its high specific heat d. Water’s high specific heat can be traced to hydrogen bonding

a. Heat is absorbed when hydrogen bonds break b. Heat is released when hydrogen bonds form

e. The high specific heat of water minimizes temperature fluctuations to within limits that permit life

C. Evaporative cooling 1. Evaporation is transformation of a substance from liquid to gas 2. Heat of vaporization is the heat a liquid must absorb for 1 g to be converted to gas 3. As a liquid evaporates, its remaining surface cools, a process called evaporative cooling 4. Evaporative cooling of water helps stabilize temperatures in organisms and bodies of water

D. Expansion upon Freezing/Insulation of bodies of water 1. Ice floats in liquid water because hydrogen bonds in ice are more “ordered,” making ice less

dense 2. Water reaches its greatest density at 4°C 3. If ice sank, all bodies of water would eventually freeze solid, making life impossible on Earth

E. Universal solvent 1. Definitions

a. solution = solvent + solute b. Hydration shell

a. Water is a versatile solvent due to its polarity, which allows it to form hydrogen bonds easily



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b. When an ionic compound is dissolved in water, each ion is surrounded by a sphere of water molecules called a hydration shell

c. Water can also dissolve compounds made of nonionic polar molecules d. Even large polar molecules such as proteins can dissolve in water if they have

ionic and polar regions 2. Hydrophilic and Hydrophobic substances

a. A hydrophilic substance is one that has an affinity for water b. A hydrophobic substance is one that does not have an affinity for water c. Oil molecules are hydrophobic because they have relatively nonpolar bonds d. A colloid is a stable suspension of fine particles in a liquid

3. Solute concentrations and Molarity a. Most biochemical reactions occur in water b. Chemical reactions depend on collisions of molecules and therefore on the

concentration of solutes in an aqueous solution c. Molecular mass is the sum of all masses of all atoms in a molecule d. Numbers of molecules are usually measured in moles, where 1 mole (mol) = 6.02 x

1023 molecules e. Avogadro’s number and the unit dalton were defined such that 6.02 x 1023 daltons = 1

g f. Molarity (M) is the number of moles of solute per liter of solution

III. Acid Base chemistry • Water is in a state of dynamic equilibrium in which water molecules dissociate at the same rate at

which they are being reformed • Though statistically rare, the dissociation of water molecules has a great effect on organisms • A hydrogen atom in a hydrogen bond between two water molecules can shift from one to the other:

- The hydrogen atom leaves its electron behind and is transferred as a proton, or hydrogen ion (H+) - The molecule with the extra proton is now a hydronium ion (H3O+), though it is often

represented as H+ - The molecule that lost the proton is now a hydroxide ion (OH–) - Changes in concentrations of H+ and OH– can drastically affect the chemistry of a cell

A. The pH scale pH was originally written by Dr. Søren Sørensen in 1909 as PH, and it stands for pondus hydrogenii which means "potential hydrogen". The terminology refers to acidity being due to a predominance of hydrogen ions in an aqueous (water containing) solution.

1. In any aqueous solution at 25°C the product of H+ and OH– is constant and can be written [H+][OH–] = 10–14

2. The pH of a solution is defined by the negative logarithm of H+ concentration, written as pH = –log [H+]

3. For a neutral aqueous solution [H+] is 10–7 = –(–7) = 7

4. Acidic solutions have pH values less than 7 5. Basic solutions have pH values greater than 7

B. Acids and Bases 1. What causes an imbalance in H+ and OH- concentrations? Acids and Bases 2. Acids increases the hydrogen ion concentration 3. Hydrochloric Acid = HCl 4. HCl -> H+ + Cl- (single arrow = complete dissociation = STRONG)



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5. Bases reduce the hydrogen ion concentration two ways a. Accepting a H+

Ammonia: NH3 + H+ <-> NH4+

b. Providing and OH- (which ultimately makes another molecule of water) Sodium Hydroxide: NaOH -> Na+ + OH-

C. Buffers 1. The internal pH of most living cells must remain close to pH 7 2. Buffers are substances that minimize changes in concentrations of H+ and OH– in a solution 3. Most buffers consist of an acid-base pair that reversibly combines with H+ 4. The weak acid, carbonic acid, is formed when CO2 reacts with H2O in blood plasma

H2CO3 ßà HCO3- + H+

H+ donor H+ acceptor H ion (acid) (base) CARBON – THE BACKBONE OF LIFE Carbon:

• Enters the biosphere through plants (convert CO2 to sugar and biological macromolecules) • Unique in its ability to form molecules that are large complex and diverse • Forms bonds with H, N, O, P, and S to make biological macromolecules (DNA, RNA, and proteins)

Develop our understanding of carbon on three fronts:

I. The study of carbon compounds II. Carbon makes four bonds III. A small number of chemical groups are key to molecular diversity

I. The study of carbon compounds – Organic chemistry

A. Organic compounds = carbon containing compounds B. Range from small molecules (CH4) huge macromolecules (chromosomes) C. Think of C as the coolest, tiny-est LEGO ever

II. Carbon bonds to four other atoms A. Carbon has 6 electrons

1. 2 in first shell 2. 4 in second shell (4 valence electrons)

B. Completes outer shell by sharing its 4 valence electrons with other atoms C. Tetravalence is what makes carbon so versatile D. Single and double bond geometry – Shape and function intertwined in biology

1. Hybrid orbitals and tetravalence give methane a tetrahedral geometry – Bond angles of 109.5 2. Hybrid orbitals of double bonds create a trigonal planar molecule – Bond angles of 120

III. Carbon backbones can connect diverse molecules A. Carbon Backbone variation

1. Length 2. Branching 3. Double bonds



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4. Circularization • The electron configuration of carbon gives it covalent compatibility with many different elements • The valences of carbon and its most frequent partners (hydrogen, oxygen, and nitrogen) are the “building

code” that governs the architecture of living molecules B. Hydrocarbons

1. Hydrocarbons are organic molecules consisting of only carbon and hydrogen 2. Many organic molecules, such as fats, have hydrocarbon components 3. Hydrocarbons can undergo reactions that release a large amount of energy

C. Isomers 1. Structural isomers have different covalent arrangements of their atoms 2. Geometric isomers have the same covalent arrangements but differ in spatial arrangements 3. Enantiomers are isomers that are mirror images of each other

IV. A small number of chemical groups make biological molecules KNOW FIGURE 4.9

• Functional groups are the components of organic molecules that are most commonly involved in chemical reactions

• The number and arrangement of functional groups give each molecule its unique properties A. Hydroxyl B. Carbonyl C. Carboxyl D. Amino E. Sulfhydrol F. Phosphate G. Methyl



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CARBON – THE BACKBONE OF LIFE Carbon:

• Enters the biosphere through plants (convert CO2 to sugar and biological macromolecules) • Unique in its ability to form molecules that are large complex and diverse • Forms bonds with H, N, O, P, and S to make biological macromolecules (DNA, RNA, and proteins)

Develop our understanding of carbon on three fronts:

IV. The study of carbon compounds V. Carbon makes four bonds VI. A small number of chemical groups are key to molecular diversity

V. The study of carbon compounds – Organic chemistry

A. Organic compounds = carbon containing compounds B. Range from small molecules (CH4) huge macromolecules (chromosomes) C. Think of C as the coolest, tiny-est LEGO ever

VI. Carbon bonds to four other atoms A. Carbon has 6 electrons

1. 2 in first shell 2. 4 in second shell (4 valence electrons)

B. Completes outer shell by sharing its 4 valence electrons with other atoms C. Tetravalence is what makes carbon so versatile D. Single and double bond geometry – Shape and function intertwined in biology

1. Hybrid orbitals and tetravalence give methane a tetrahedral geometry – Bond angles of 109.5 2. Hybrid orbitals of double bonds create a trigonal planar molecule – Bond angles of 120

VII. Carbon backbones can connect diverse molecules A. Carbon Backbone variation

1. Length 2. Branching 3. Double bonds 4. Circularization

• The electron configuration of carbon gives it covalent compatibility with many different elements • The valences of carbon and its most frequent partners (hydrogen, oxygen, and nitrogen) are the “building

code” that governs the architecture of living molecules B. Hydrocarbons

1. Hydrocarbons are organic molecules consisting of only carbon and hydrogen 2. Many organic molecules, such as fats, have hydrocarbon components 3. Hydrocarbons can undergo reactions that release a large amount of energy

C. Isomers 1. Structural isomers have different covalent arrangements of their atoms 2. Geometric isomers have the same covalent arrangements but differ in spatial arrangements 3. Enantiomers are isomers that are mirror images of each other

VIII. A small number of chemical groups make biological molecules KNOW FIGURE 4.10

• Functional groups are the components of organic molecules that are most commonly involved in chemical reactions: hydroxyl, carbonyl, carboxyl, amino, sulfhydrol, phosphate, methyl



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BIOLOGICAL MACROMOLECULES Biological Macromolecules are polymers built from monomers 1. All living things are made up of four classes of large biological molecules

a. Carbohydrates b. Lipids c. Proteins d. nucleic acids

2. Within cells, small organic molecules are joined together to form larger molecules a. Macromolecules are large molecules composed of thousands of covalently connected atoms b. Molecular structure and function are inseparable

A polymer is a long molecule consisting of many similar building blocks 1. These small building-block molecules are called monomers

a. An immense variety of polymers can be built from a small set of monomers b. Three of the four classes of life’s organic molecules are polymers

i. Polysaccharides are built from monosaccharides ii. Nucleic Acids (DNA and RNA) are built from nucleotides (A, T/U, C, and G) iii. Proteins are built from amino acids (A, R, N, D, C, E, Q, G, H, I, L, K, M, F, P, S, T, W, Y, and V)

2. Polymers are formed by dehydration synthesis a. A dehydration synthesis occurs when two monomers bond together through the loss of a water

molecule b. Enzymes are macromolecules that speed up the dehydration process

3. Polymers are disassembled to monomers by hydrolysis a. Hydrolysis is essentially the reverse of the dehydration reaction

CARBOHYDRATES

• Carbohydrates include sugars and the polymers of sugars • The simplest carbohydrates are monosaccharides, or single sugars • Carbohydrate macromolecules are polysaccharides, polymers composed of many sugar building blocks

called monosaccharides IV. Monosaccharides

A. have molecular formulas that are usually multiples of CH2O B. Numbering of monosaccharide carbons (from functional group) C. Glucose (C6H12O6) is the most common monosaccharide D. Monosaccharides are classified by

1. The location of the carbonyl group (as aldose or ketose) 2. The number of carbons in the carbon skeleton 3. Spatial arrangement of carbons

a. Though often drawn as linear skeletons, in aqueous solutions many sugars form rings E. Monosaccharides serve as a major fuel for cells and as raw material for building molecules F. Monosaccharides may be linear chains or ring structures

V. Disaccharides A. A disaccharide is formed when a dehydration reaction joins two monosaccharides B. This covalent bond is called a glycosidic linkage

VI. Polysaccharides A. Polymers of sugars



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B. The structure and function of a polysaccharide are determined by its sugar monomers and the positions of glycosidic linkages

C. Roles of polysaccharides 1. Energy storage roles

a. Starch – amylose (unbranched and amylopectin) i. Storage polysaccharide of plants ii. consists entirely of glucose monomers a. Plants store surplus starch as granules within chloroplasts and other plastids

b. Glycogen (more branched than amylopectin) a. Glycogen is a storage polysaccharide in animals b. Humans and other vertebrates store glycogen mainly in liver and muscle cells

2. Structural roles a. Cellulose

a. The polysaccharide cellulose is a major component of the tough wall of plant cells

b. Like starch, cellulose is a polymer of glucose, but the glycosidic linkages differ c. The difference is based on two ring forms for glucose: alpha (α) and beta (β) d. Structure function relationships

1. Polymers with α glucose are helical 2. Polymers with β glucose are straight

e. In straight structures, cellulose, H atoms on one strand can bond with OH groups on other strands

f. Parallel cellulose molecules held together this way are grouped into microfibrils, which form strong building materials for plants

g. Enzymes that digest starch by hydrolyzing α linkages can’t hydrolyze β linkages in cellulose

h. Cellulose in human food passes through the digestive tract as insoluble fiber i. Some microbes use enzymes to digest cellulose j. Many herbivores, from cows to termites, have symbiotic relationships with these

microbes b. Chitin

a. Chitin, another structural polysaccharide, is found in the exoskeleton of arthropods

b. Chitin also provides structural support for the cell walls of many fungi c. Used to make “dissolving stitches”

LIPIDS • Share one important trait: mix poorly with water • Are not true polymeric macromolecules • Some polar parts, but generally hydrocarbons (non-polar) • We will focus on Fats, Phospholipids and Steroids

1. Fats

a. Fats are constructed from two types of smaller molecules: glycerol and fatty acids i. Fatty acids

1. Think about the name fatty acid (Hydrocarbon + Carboxyllic acid) 2. A fatty acid consists of a carboxyl group attached to a long carbon skeleton



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ii. Glycerol 1. three-carbon alcohol with a hydroxyl group attached to each carbon

iii. Three fatty acids are joined to glycerol by an ester linkage, creating a triacylglycerol, or triglyceride

iv. Fatty acids vary in 1. length (number of carbons) 2. number and locations of double bonds

a. Saturated fatty acids i. have the maximum number of hydrogen atoms possible and no double

bonds (They are saturated with hydrogens) ii. solids at room temperature iii. animal fats (except for fish)

b. Unsaturated fatty acids i. have one or more double bonds ii. liquids at room temperature iii. plant and fish fats

b. Some points on hydrogenation i. A diet rich in saturated fats may contribute to cardiovascular disease through plaque deposits ii. Hydrogenation is the process of converting unsaturated fats to saturated fats by adding

hydrogen iii. Hydrogenating vegetable oils also creates unsaturated fats with trans double bonds iv. These trans fats may contribute more than saturated fats to cardiovascular disease

c. Functions in biology i. The major function of fats is energy storage

1. A gram of fat stores twice as much energy as a gram of carbohydrate (Remember my gasoline analogy last Thursday??)

2. Plants don’t have to move so they can store carbohydrates, animals move so need a more efficient energy storage solution.

ii. Humans and other mammals store their fat in adipose cells iii. Adipose tissue also cushions vital organs and insulates the body

2. Phospholipids a. Two fatty acids and a phosphate group are attached to glycerol

i. Hydrophobic tail: The two fatty acids ii. hydrophilic head: the phosphate group and its attachments

b. Formation into bilayers i. When phospholipids are added to water, they self-assemble into a bilayer, with the

hydrophobic tails pointing toward the interior ii. The structure of phospholipids results in a bilayer arrangement found in cell membranes iii. Phospholipids are the major component of all cell membranes

3. Steroids a. Steroids are lipids characterized by a carbon skeleton consisting of four fused rings b. Cholesterol

i. component in animal cell membranes ii. synthesized in the liver iii. essential in animals, but high levels in the blood may contribute to cardiovascular disease iv. Precursor from which other steroids are formed (estradiol, testosterone)

c. Very important biological molecules that signal gene expression



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PROTEINS

• Proteins account for more than 50% of the dry mass of most cells • Protein functions include structural support, storage, transport, cellular communications, movement, and

defense against foreign substances • Polypeptides are polymers built from the same set of 20 amino acids • A protein consists of one or more polypeptides • Amino acids are organic molecules with carboxyl and amino groups • Amino acids differ in their properties due to differing side chains, called R groups

1. Proteins have several roles in the cell

a . Enzymes i. Enzymes are a type of protein that acts as a catalyst to speed up chemical reactions ii. Enzymes can perform their functions repeatedly, functioning as workhorses that carry out

the processes of life

2. Amino Acid Polymers a. Amino acids are the building blocks

i. All have a common chemical structure with differing radical (“R”) groups ii. R-groups give specific chemical properties

1. Non-polar – equal distribution of electrons 2. Polar – Unequal distribution of electrons 3. Charged – Acidic or Basic

b. Amino acids are linked by peptide bonds c. A polypeptide is a polymer of amino acids d. Polypeptides range in length from a few to more than a thousand monomers e. Each polypeptide has a unique linear sequence of amino acids f. A functional protein consists of one or more polypeptides twisted, folded, and coiled into a

unique shape

3. Structure Function Relationships a. The sequence of amino acids determines a protein’s three-dimensional structure b. A protein’s structure determines its function – 4 levels of structure

i. The primary structure of a protein is its unique sequence of amino acids ii. Secondary structure, found in most proteins, consists of coils and folds in the polypeptide

chain iii. Tert iary structure is determined by interactions among various side chains (R groups) iv. Quaternary structure results when a protein consists of multiple polypeptide chains

c. Primary structure i. Primary structure, the sequence of amino acids in a protein, is like the order of letters

in a long word ii. Primary structure is determined by inherited genetic information

d. Secondary Structure i. The coils and folds of secondary structure result from hydrogen bonds between

repeating const ituents of the polypeptide backbone ii. Typical secondary structures are:



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1. a coil called an a hel ix 2. and a folded structure called a b pleated sheet

e. Tertiary Structure i. Tertiary structure is determined by interact ions between R groups, rather than

interactions between backbone constituents ii. These interactions between R groups include:

1. hydrogen bonds 2. ionic bonds 3. hydrophobic interactions 4. van der Waals interactions

iii. Strong covalent bonds called disulfide bridges may reinforce the protein’s structure f. Quaternary Structure

i. Quaternary structure results when two or more polypeptide chains form one macromolecule

ii. Collagen is a fibrous protein consisting of three polypeptides coiled like a rope iii. Hemoglobin is a globular protein consisting of four polypeptides: two alpha and two

beta chains Sickle Cell Disease - A Change in Primary Structure

• A slight change in primary structure can affect a protein’s structure and ability to function • Sickle-cell disease, an inherited blood disorder, results from a single amino acid substitution in the protein

hemoglobin

4. Other Factors Play a Role in Protein Structure a. In addition to primary structure, physical and chemical conditions can affect structure b. Alterations in pH, salt concentration, temperature, or other environmental factors can cause a

protein to unravel c. This loss of a protein’s native structure is called denaturation d. A denatured protein is biologically inactive

5. Protein Folding in a Cell

a. It is hard to predict a protein’s structure from its primary structure b. Most proteins probably go through several states on their way to a stable structure c. Chaperonins are protein molecules that assist the proper folding of other proteins

1. Protein Structures

a. Scientists use X-ray crystal lography to determine a protein’s structure b. Another method is nuclear magnetic resonance (NMR) spectroscopy, which does not

require protein crystallization c. Bioinformatics uses computer programs to predict protein structure from amino acid

sequences



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NUCLEIC ACIDS - Store and transmit hereditary information

• The amino acid sequence of a polypeptide is programmed by a unit of inheritance called a gene • Genes are made of DNA, a nucleic acid • There are two types of nucleic acids:

- Deoxyribonucleic acid (DNA) - Ribonucleic acid (RNA)

• DNA provides directions for its own replication • DNA directs synthesis of messenger RNA (mRNA) and, through mRNA, controls protein synthesis • Protein synthesis occurs in ribosomes

2. Nucleic Acid Structure

a. Nucleic acids are polymers called polynucleotides b. Each polynucleotide is made of monomers called nucleotides c. Each nucleotide consists of:

i. a nitrogenous base ii. a pentose sugar iii. and a phosphate group

d. The portion of a nucleotide without the phosphate group is called a nucleoside

3. Nucleotide Monomers a. Nucleoside = nitrogenous base + sugar b. There are two families of nitrogenous bases:

i. Pyrimidines (cytosine, thymine, and uracil) have a single six-membered ring ii. Purines (adenine and guanine) have a six-membered ring fused to a five-membered ring

c. The sugars between DNA and RNA differ: i. DNA, the sugar is deoxyribose ii. RNA, the sugar is ribose

d. Nucleotide = nucleoside + phosphate group

4. Nucleotide Polymers a. Nucleotide polymers are linked together to build a polynucleotide b. Adjacent nucleotides are joined by covalent bonds that form between the –OH group on the 3’

carbon of one nucleotide and the phosphate on the 5’ carbon on the next c. These links create a backbone of sugar-phosphate units with nitrogenous bases as appendages d. The sequence of bases along a DNA or mRNA polymer is unique for each gene

5. The DNA Double Helix

a. A DNA molecule has two polynucleotides spiraling around an imaginary axis, forming a double helix

b. In the DNA double helix, the two backbones run in opposite 5’ → 3’ directions from each other, an arrangement referred to as antiparallel

c. The nitrogenous bases in DNA pair up and form hydrogen bonds: i. adenine (A) always with thymine (T) (two hydrogen bonds) ii. guanine (G) always with cytosine (C) (three hydrogen bonds)



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YOU SHOULD NOW BE ABLE TO:

• List and describe the four major classes of molecules • Describe the formation of a glycosidic linkage and distinguish between monosaccharides, disaccharides, and

polysaccharides • Distinguish between saturated and unsaturated fats and between cis and trans fat molecules • Describe the four levels of protein structure • Distinguish between the following pairs: pyrimidine and purine, nucleotide and nucleoside, ribose and

deoxyribose, the 5’ end and 3’ end of a nucleotide



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1. CELLS – The Fundamental Unit of Life

A. All organisms are made of cells B. The cell is the simplest collection of matter

that can live C. Cell structure is correlated to cellular function D. All cells are related by their descent from earlier cells E. Though usually too small to be seen by the unaided eye, cells can be complex

2. Microscopy

A. Scientists use microscopes to visualize cells too small to see with the naked eye B. The quality of an image depends on

i. Magnification, the ratio of an object’s image size to its real size ii. Resolution, the measure of the clarity of the image, or the minimum distance of two

distinguishable points iii. Contrast, visible differences in parts of the sample

C. Resolution is inversely related to the wavelength used to visualize (Light, electron) D. Light Microscopes

i. In a light microscope (LM), visible light passes through a specimen and then through glass lenses, which magnify the image

ii. LMs can magnify effectively to about 1,000 times the size of the actual specimen iii. Various techniques enhance contrast and enable cell components to be stained or labeled iv. Most subcellular structures, including organelles (membrane-enclosed compartments), are too

small to be resolved by an LM E. Electron Microscopes

i. Two basic types of electron microscopes (EMs) are used to study subcellular structures ii. Scanning electron microscopes (SEMs) focus a beam of electrons onto the surface of a

specimen, providing images that look 3-D 1. Surface covered with a film of Gold, beam excites gold really looking at the energy

given off by gold iii. Transmission electron microscopes (TEMs) focus a beam of electrons through a specimen

1. TEMs are used mainly to study the internal structure of cells 2. Sample stained with a heavy metal (Urinyl Acetetate)

iv. By the way, FSU is one of the world leaders in electron microscopy (TITAN Krios)



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3. Cell Fractionation A. Cell fractionation takes cells apart and separates the major organelles from one another B. Ultracentrifuges fractionate cells into their component parts - (Other methods include

chromatography, organic extractions, precipitation) C. Cell fractionation enables scientists to determine the functions of organelles D. Biochemistry and cytology help correlate cell function with structure

4. There are two types of cells:

A. The basic structural and functional unit of every organism is one of two types of cells: prokaryotic or eukaryotic

i. Only organisms of the domains Bacteria and Archaea consist of prokaryotic cells ii. Protists, fungi, animals, and plants all consist of eukaryotic cells

B. Basic characteristics of all cells (Prokaryotic or Eukaryotic): i. Plasma membrane

1. a selective barrier that allows sufficient passage of oxygen, nutrients, and waste to service the volume of every cell

2. The general structure of a biological membrane is a double layer of phospholipids ii. Cytosol - semifluid interior substance cytosol iii. Chromosomes (carry genes) iv. Ribosomes (make proteins)

C. Basic characteristics of Prokaryotic cells i. No nucleus ii. DNA in an unbound region called the nucleoid iii. No membrane-bound organelles iv. Cytoplasm bound by the plasma membrane

D. Basic characteristics of Eukaryotic cells i. DNA in a nucleus that is bounded by a membranous nuclear envelope ii. Membrane-bound organelles iii. Cytoplasm in the region between the plasma membrane and nucleus

5. Cell size

A. Eukaryotic cells are generally much larger than prokaryotic cells B. The logistics of carrying out cellular metabolism sets limits on the size of cells C. The surface area to volume ratio of a cell is critical D. As the surface area increases by a factor of n2, the volume increases by a factor of n3 E. Small cells have a greater surface area relative to volume



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ORGANELLES Groups

a. Endomembrane system i. Nucleus - Information central ii. Endoplasmic Reticulum - Factory iii. Golgi Apparatus - Shipping and Receiving iv. Lysozomes - Digestive Compartments, Disassembly v. Vacuoles - Maintenance compartments vi. [Plasma Membrane] vii. The membranes of this system are either directly connected connected or connected by

transport vesicles b. Energy conversion

viii. Mitochondria ix. Chloroplasts x. Peroxisomes

1. The Nucleus

1. The nucleus contains most of the cell’s genes and is usually the most conspicuous organelle 2. The nuclear envelope encloses the nucleus, separating it from the cytoplasm 3. The nuclear membrane is a double membrane; each membrane consists of a lipid bilayer 4. Pores regulate the entry and exit of molecules from the nucleus 5. The shape of the nucleus is maintained by the nuclear lamina, which is composed of protein filaments 6. In the nucleus, DNA and proteins form genetic material called chromatin 7. Chromatin condenses to form discrete chromosomes 8. The nucleolus is located within the nucleus and is the site of ribosomal RNA (rRNA) synthesis

2. Ribosomes - responsible for the conversion of genetic material to protein

1. Ribosomes are particles made of ribosomal RNA and protein 2. Ribosomes carry out protein synthesis in two locations:

i. In the cytosol (free ribosomes) - generally make proteins for use in the cytosol ii. On the outside of the endoplasmic reticulum or the nuclear envelope (bound ribosomes) - generally

make proteins for transport through a membrane (lysozomes, nucleus, plasma membrane) 3. Endoplamic Reticulum

i. The endoplasmic reticulum (ER) accounts for more than half of the total membrane in many eukaryotic cells

ii. The ER membrane is continuous with the nuclear envelope iii. There are two distinct regions of ER:

1. Smooth ER, which lacks ribosomes a. Synthesizes lipids b. Metabolizes carbohydrates c. Detoxifies poison d. Stores calcium

2. Rough ER, with ribosomes studding its surface a. Has bound ribosomes, which secrete glycoproteins (proteins covalently bonded to

carbohydrates) b. Distributes transport vesicles, proteins surrounded by membranes



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c. Is a membrane factory for the cell

4. Golgi Apparatus i. The Golgi apparatus consists of flattened membranous sacs called cisternae ii. Functions of the Golgi apparatus:

1. Modifies products of the ER 2. Manufactures certain macromolecules 3. Sorts and packages materials into transport vesicles

5. Lysozymes

i. A lysosome is a membranous sac of hydrolytic enzymes that can digest macromolecules ii. Lysosomal enzymes can hydrolyze

1. proteins 2. fats 3. polysaccharides 4. nucleic acids

iii. Some types of cell can engulf another cell by phagocytosis; this forms a food vacuole iv. A lysosome fuses with the food vacuole and digests the molecules v. Lysosomes also use enzymes to recycle the cell’s own organelles and macromolecules, a process called

autophagy 6. Vacuoles

i. A plant cell or fungal cell may have one or several vacuoles 1. Food vacuoles are formed by phagocytosis 2. Contractile vacuoles, found in many freshwater protists, pump excess water out of cells 3. Central vacuoles, found in many mature plant cells, hold organic compounds and water



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Changing energy from one form to another • Mitochondria are the sites of cellular respiration, a metabolic process that generates ATP • Chloroplasts, found in plants and algae, are the sites of photosynthesis • Peroxisomes are oxidative organelles • Mitochondria and chloroplasts

o Are not part of the endomembrane system o Have a double membrane o Have proteins made by free ribosomes o Contain their own DNA

3. Mitochondria

i. Are in nearly all eukaryotic cells ii. They have a smooth outer membrane and an inner membrane folded into cristae iii. The inner membrane creates two compartments: intermembrane space and mitochondrial matrix iv. Some metabolic steps of cellular respiration are catalyzed in the mitochondrial matrix v. Cristae present a large surface area for enzymes that synthesize ATP

4. Chloroplasts

i. The chloroplast is a member of a family of organelles called plastids (closely related plant organelles) ii. Chloroplasts contain the green pigment chlorophyll, as well as enzymes and other molecules that

function in photosynthesis iii. Chloroplasts are found in leaves and other green organs of plants and in algae iv. Chloroplast structure includes:

i. Thylakoids, membranous sacs, stacked to form a granum ii. Stroma, the internal fluid

5. Peroxisomes

i. Peroxisomes are specialized metabolic compartments bounded by a single membrane ii. Oxygen is used to break down different types of molecules iii. Peroxisomes produce hydrogen peroxide - transfer hydrogens to 02 iv. Convert H2O2 (which is toxic) to water

total unit 1 notes - biology

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