Chapters 3, 5, 6, 7 Lecture Notes PDF

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These were my lecture notes for chapters 3,5,6 and 7. My professor was Dr. Fletcher....

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Chapter 3: Macromolecules Part 1: Synthesis -

Name the 4 macromolecules of life

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Describe the difference between polymers and monomers and which macromolecules are classified as polymers Identify the processes of how polymers are created and broken down

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Molecules of Life -

Another level of hierarchy in biological organization - Creates macromolecules

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Macromolecules have emergent properties: - Ability to form into large structures -

Catalyze chemical reactions

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Signal (receptors, hormones, etc…) and record information (recorded in the DNA) Large molecules composed of smaller molecules

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Complex structures

4 Major Biological Classes: 1. Carbohydrates 2. Proteins 3. Nucleic Acids 4. Lipids -

ALL organic molecules (contain carbon)

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Polymers: built from monomers linked by covalent bonds - Organisms share the same limited numbers of monomer types (40-50 common monomers) -

- Same building blocks but not always the same result Diversity comes from the arrangement of monomers into polymers Carbs, Proteins, and Nucleic Acids are three classes of life’s organic macromolecules - LIPIDS ARE THE EXCEPTION

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Dehydration Synthesis: condensation reaction (taking water out) -

Monomers → Polymers (the hydrogen of a polymer interacts with the hydroxyl group of the unlinked monomer to link the monomer to the polymer and water on the side)

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Hydrolysis: disassembly of polymers to monomers -

Water is a reactant: one monomer receives an H+ ion while another receives an OHion

Catalyzing Macromolecules Chemical Reactions - Enzymes: biological molecules that speed up reactions -

Speed up hydrolysis and dehydration synthesis Specific enzymes exist for each macromolecule class -

Carbs: broken down by amylase, sucrase, maltase, and lactase Proteins: broken down by pepsin and peptidase Nucleic Acids: ribonuclease, deoxyribonuclease, and polymerases

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Lipids: broken down by lipases

Carbohydrates: -

Explain how carbohydrates are formed from their respective subunits

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Explain the structural and functional properties of carbohydrates Explain the benefits of carbohydrates Describe the three different classes of carbohydrates

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Name important monosaccharides, disaccharides, and polysaccharides

Carbohydrates -

Found in grains, fruit, and veggies Provide energy in the form of glucose General formula: (CH2O)n with the ratio of carbon:hydrogen:oxygen 1:2:1

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Main types: monosaccharides, disaccharides, polysaccharides

Monosaccharides (sugars): - Monomers - Simple sugars (3-7 carbons) - Fuel that can be converted into other organic molecules and combined into polymers - Ex. glucose has the formula C6H12O6 - Contain carbonyl group (C=O) -

Can be linear, but found as rings in aqueous solutions (energy) Names end in -ose (ex. glucose) -

Trioses (3) Pentoses (5) Hexoses (6) - glucose

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Aldoses: carbonyl group at the end of the carbon chain Ketoses: carbonyl group in the middle of the carbon chain

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Structural Isomers -

Glucose → important source of energy

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Galactose → part of lactose/milk sugar

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Fructose → part of sucrose/fruit

Disaccharides: -

2 monosaccharides (glucose + fructose = sucrose)

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Joined by dehydration (glycosidic linkage → the type of covalent bond describing a link between two monosaccharides)

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Broken by hydrolysis (1 monomer receives an H+ ion and the other receives an OH- ion) Maltose (grain sugar: glucose + glucose)

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Lactose (milk sugar: galactose + glucose)

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Sucrose (table sugar: glucose + fructose)

Polysaccharides: - Long chains of monomers -

branched/unbranched

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Colossal molecules (greater than daltons: LARGE) lots of monosaccharides

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POLYMERS - Storage: -

STARCH (plants): a polymer consisting entirely of glucose monomers - Amylose (unbranched includes alpha bonds)

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Amylopectin (branched includes alpha bonds)

GLYCOGEN (animals): consists of glucose molecules (alpha bonds)

Structural:

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CELLULOSE: polymer of glucose, beta bonds, a major component of plant wall cells - Every other glucose monomer is flipped (hydroxyl group flipped every

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other monomer - creates spiraling shape) CHITIN: found in the exoskeleton of arthropods (ex. Shrimp shell) and fungal cell walls - Contains nitrogen (big difference between cellulose and chitin), can be used as a surgical thread (dissolvable stitches)

Differences between structural and storage polymers: -

Starch and cellulose are both glucose polymers BUT they differ in bonding linkages, which require different enzymes for hydrolysis Most organisms cannot digest cellulose (cows have microbes in their stomachs can facilitate this process to break down beta linkages)

Proteins -

Explain how proteins are formed from its respective subunits Explain the structural and functional properties of proteins

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Identify each of the 4 functional groups of an amino acid Explain the relationship between protein sequence and structure

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Compare and contrast alpha helices and beta strands Compare and contrast the concept of polarity in the context of chemical bonds and proteins

Most abundant organic molecule of life - Diverse range of functions: -

Regulatory Structural Protective Transport Enzymes Toxins

Creation of new proteins through RNA

ENZYMES: -

Catalysts in biochemical reactions Specific enzyme for a specific substrate

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Types: - Catabolic: breaks down substrates -

Anabolic: builds more complex molecules

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Catalytic: affect the rate of reaction

AMINO ACIDS: specific protein monomers (building blocks) - Everything is bounded by a central carbon group (the “alpha carbon”)

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Amino group (NH2) Carboxyl group (COOH)

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Hydrogen

- Sidechain (R-group) We have 20 different amino acids -

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Essential amino acids that must be supplied in the diet (are not made in the body!!!): isoleucine, leucine, cysteine

Each one has a different R-group (variant group) - Determine the chemical nature of each amino acid - Nonpolar: aliphatic chains and aromatic rings (lots of hydrocarbons that are hydrophobic - CH2)

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Polar: charged (positive or negative), lots of functional groups (which are polar)

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The sequence and number of amino acids determine protein shape, size, and functions Polypeptides: - Polymers of amino acids, linked by peptide bonds (covalent bond) by -

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Charged amino acids are hydrophilic

dehydration synthesis One or more polypeptide to create protein

PROTEINS: - Four levels of structure: - Primary Structure: a string of amino acids, most crucial (folding cannot happen without the primary structural sequence) - The sequence determines the 3D structure, which determines the -

function Secondary Structure: the folding or coiling of the polypeptide into a repeating configuration (alpha helixes and beta-pleated she sheets ets → develop by hydrogen bonding) -

Alpha Helix: hydrogen bond between the oxygen in the carbonyl group and amino acid 4 positions down the chain (creating a helix

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shape) Beta Pleated Sheet: hydrogen bonding between atoms on the backbone

of the polypeptide chain Tertiary Structure: after developing the secondary structure, overall unique 3D shape of a polypeptide resulting from chemical interactions between amino acids and R groups - Hydrophobic interactions and van der Waals interactions -

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Quaternary Structure: - Doesn’t happen for all proteins -

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DIFFERENT CHEMICAL REACTIONS: hydrophobic interactions, ionic, hydrogen, disulfide linkages

Two or more polypeptides

What determines protein conformation? - The physical and chemical conditions of the environment (ex. Ramen noodles) -

pH (ex. Pepsin in the stomach cannot harm the rest of the body because when the enzyme leaves the stomach, the pH levels increase and cause the enzyme to lose function)

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Temperature (incorrect temperatures can change the shape which changes the function, causing the enzyme to not be functional and break down → denaturation)

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Denaturation: when a protein unravels and loses its native/stable conformation and functionality (ex.

Cooking an egg → clear to white egg DENATURATION “you can’t uncook an egg”) -

Sickle Cell Anemia: change in a single amino acid (occurs in the beta chain of hemoglobin) - Results in crescent-shaped blood cells that decreases the oxygen-carrying capacity

NUCLEIC ACIDS: - Explain how nucleic acids are formed from their respective subunits -

Explain the structural and functional properties of nucleic acids Compare and contrast the concept of polarity in the context of chemical bonds and nucleic acids

Genes: units of inheritance - Encodes the amino acid sequence of polypeptides - Made of nucleic acids -

Unique for each gene Two types: the only difference is the MISSING OXYGEN ON DNA

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DNA: stores information in the sequences of bases for the synthesis of specific proteins (THYMINE) -

Found in the nucleus (eukaryotes), mitochondria, chloroplasts (prokaryotes) Directs RNA synthesis

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Indirectly directs protein synthesis through mRNA

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RNA: less stable, transcribed to make polynucleotides (URACIL) - Found in the nucleus, cytoplasm

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Polymers: polynucleotides: made up of nucleotides linked by OH- group on the 3’ carbon of one nucleotide and the phosphate on the 5’ of the next nucleotide

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Monomers: nucleotides (sugar + nitrogenous base)

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Pyrimidines: Cytosine ©, thymine (T), uracil (U) Purines: adenine (A), guanine (G)

DNA Double Helix -

2 polynucleotides that spiral around in a double helix 2 antiparallel

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Sugar and phosphate BACKBONE is on the outside of the helix Nitrogenous bases stacked and hydrogen-bonded with a base from the opposite strand A and T (have 2 hydrogen bonds between) C and G (have 3 hydrogen bonds between)

RNA -

Primarily involved in protein synthesis Types: - Messenger RNA (mRNA) - Transfer RNA (tRNA) - Ribosomal RNA (rRNA) - Uracil in place of thymine

LIPIDS -

Explain how lipids are formed from their respective subunits Explain the structural and functional properties of lipids Compare and contrast the structure of a triglyceride with a phospholipid

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Explain how the presence of double bonds or changes in the length of fatty acids affect the physical properties of triglycerides

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Recall and define the terms hydrophilic and hydrophobic. Relate these to and define amphipathic

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A diverse group of hydrophobic molecules Do not consist of polymers

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Dominated by nonpolar covalent bonds including hydrocarbon regions - Carboxyl group on the hydrocarbon regions

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Functions: long-term energy stores, insulation from the environment from both plants and animals (blubber on whales), building blocks for some hormones (testosterone and estrogen), an important component of cell membranes

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Types: fats, oils, waxes, phospholipids, steroids

Fats: -

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1 glycerol + 3 fatty acids (attached together via ester linkages) - 3 molecules of water released in the reaction (dehydration synthesis) - Hydroxyl group of the glycerol Fatty acids: vary in double bond (number of double bonds and where they are) and length - Saturated Fatty Acids: maximum number of hydrogen atoms possible

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No double bonds between carbons SOLID at room temp (tightly packed at room temperature)

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Bad fat leading to heart disease → plaque buildup

Unsaturated Fatty Acids: have more or one double bond between carbons -

Monounsaturated fat: only one double bond Polyunsaturated fat: many double bonds LIQUID at room temperature (loose packing of the fatty acids)

→ Trans-Fats: each double bond of an unsaturated fat may be in one of two positions -

Cis configuration: hydrogens are on the same side of the chain, have a kink in the chain Trans configuration: hydrogens are on opposite sides of the chain, do not have kinks in the chain

Waxes: long fatty acid chains (ester-linked to a long chain of alcohol) - HYDROPHOBIC Phospholipids: only have 2 fatty acids, phosphate group instead of 3rd fatty acids -

Hydrophilic head Hydrophobic tail AMPHIPATHIC (hydrophobic and hydrophilic parts)

Steroids: carbon skeleton consisting of 4 fused rings -

Hydrophobic Different from other lipids Cholesterol (most common steroid) -

Found in the cell membrane Synthesized in the liver

Chapter 5: Structure & Function of Plasma Membranes Part 1: Components and Structure -

Sketch a cell membrane according to the fluid mosaic model Indicate positions and orientations of phospholipids, cholesterol, and integral and peripheral membrane proteins

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Explain why membranes are asymmetrical Describe at least 3 different factors that affect membrane fluidity

Membranes: a collage of different proteins embedded in the fluid matrix of the lipid bilayer (ex. Balloon rather than plastic bag) Flexible but not TOO flexible to lose structural component Plasma Membrane: separates the living cell from its nonliving surroundings -

SELECTIVELY PERMEABLE: allows some substances to cross “the border” more easily than others Functions: defines the outer border, gatekeeper (manages what enters and exits), receives external signals and initiates cell response, adheres to neighboring cells

Fluidity of the Membrane - Cell membranes are fluid mosaics of lipids and proteins -

Phospholipid: most abundant in the plasma membrane, can move within the bilayer, hydrophilic heads, hydrophobic tails Changes in the type of hydrocarbon tails affect the fluidity of the plasma membrane

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Lipid composition changes in response to temperature change (more viscous in cold (membranes rigid) and less viscous in hot (membranes more fluid)) for PLANTS

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Animals have cholesterol (steroid) to uphold the viscosity of the membrane (buffer)

Fluid Mosaic Model: a membrane is a fluid structure with a mosaic of various proteins embedded in it -

Phospholipids, cholesterol, proteins, and carbohydrates

Components of Plasma Membrane: - Phospholipids: MAIN ASPECT of plasma membrane - 2 fatty acids (nonpolar and hydrophobic) - saturated or -

unsaturated A glycerol molecule - hydrophilic

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Phosphate group (polar and hydrophilic)

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Bilayer: sphere polar heads outwards, nonpolar tails inwards

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Proteins: drift within the bilayer - Transporters - Receptors - Enzymes - Binding and adhesion - Integral Proteins: integrated into bilayer, one or more hydrophobic regions but all others are hydrophilic - Some amino acids are hydrophobic - Location and number of these regions determine how they arrange within the bilayer - Peripheral Proteins: occur only on the surface - Receptor Proteins Carbohydrates: on the exterior surface of the plasma membrane - Oligosaccharide carbs - Bound to either proteins (glycoproteins) or to lipids (glycolipids) - Cell to cell recognitions and attachment

Plasma membranes are asymmetric -

Inner surface differs from outside Ex. interior proteins anchor fibers of the cytoskeleton to the membrane, exterior proteins bind to the extracellular matrix

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Endomembrane system: group of membranes and organelles - Membrane proteins and lipids are synthesized, modified, packaged, and transported using the: - endoplasmic reticulum - Golgi apparatus - Nuclear envelope - Plasma membrane - Lysosomes

Selectively Permeable: - Cell must exchange materials with its surroundings

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Hydrophobic molecules (lipid soluble, can pass through RAPIDLY) Polar and charged molecules -

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Do not cross membrane rapidly because the polarity: nothing to attract them across the nonpolar membrane

- Transport proteins: allow passage of hydrophilic substances across membrane Passage across a synthetic phospholipid bilayer is dependent on size and solubility in lipid Charged molecules rarely cross a lipid bilayer no matter the size

Part 2: Transport -

Learning

Molecule Transport: - Permeability of the membrane allows cytosol (inside) solutions to differ from extracellular -

(outside) fluids - asymmetrical membrane Passive Transport:three ways, requires no energy

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- Simple Diff usion - Osmosis: movement of water (NOT SOLUTE MOVEMENT) - Facilitated Diffusion Active Transport: one way, requires ATP

SIMPLE DIFFUSION -

The tendency for molecules of any substance to spread out evenly into the available space (ex. Candles, perfume)

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Passive transport of solute molecules moving from areas of high concentration to areas of low concentration NO ENERGY (ex. Food coloring in water) Substances move down their concentration gradient (the difference in concentration of a

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substance from one area to another) - Ex. through lipid bilayer in membranes -

Net movement STOPS once equilibrium is achieved Nonpolar molecules can diffuse easily through biological membranes (O2, CO2, lipid hormones)

OSMOSIS -

Special type of diffusion Movement of water across semi permeable membrane

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Water is moving from areas of low concentration to high concentration Affected by the concentration gradient of dissolved substances

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Differences in water concentration occur when a solute cannot pass through the selectively permeable membrane

TONICITY: the ability of a solution to cause a cell to gain or lose water - Changes the volume in the cell by osmosis - Has a great impact on cells without cell walls (animal cells) -

3 conditions: isotonic, hypotonic, hypertonic Live in a hypotonic/hypertonic environment, but prefer isotonic

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Have special adaptations for osmoregulations controlling water flow

Isotonic Solution: the concentration of solutes in the same inside and outside of the cell -

No net movement of water Water flows both directions at an equal rate

Hypotonic Solution: concentration of solutes is less outside the...