Unit 1: Chemistry of Life

Structure of Water and Hydrogen Bonding

Chemistry Review

• Matter: anything that takes up space and has mass

• Elements: a substance that cannot be broken down into other substances by chemical reactions

  • 92 elements occur naturally in nature

• Compounds: a substance consisting of two or more different elements combined in a fixed ratio

  • H2O

  • NaCl

• CHOPN: Carbon, Hydrogen, Oxygen, Phosphorous, Nitrogen; makes up 92% of living matter

• Essential Elements: of the 92 naturally occurring elements, 20-25% are essential to survive and reproduce

• Trace Elements: of the 92 naturally occurring elements, these are required by an organism in very small quantities

• Atomic Number: number of protons (and electrons)

• Atomic Mass: sum of protons and neutrons averaged over all isotopes

• Group: vertical columns on Periodic Table; elements in the same group have the same amount of valence electrons

• Period: horizontal rows on Periodic Table; elements in the same period have the same total number of shells

• Bohr Model: shows electrons orbiting the nucleus of an atom

  • Electrons are placed on shells outside the nucleus

  • Each shell has a different energy level and can hold up to a certain number of electrons (formula to find e- on each shell is 2n^2, where n is the shell number)

    • 1st shell: 2 e- (electrons); ex. 2(1)^2

    • 2nd shell: 8 e- (electrons); ex. 2(2)^2

    • 3rd shell: 18 e- (electrons); ex. 2(3)^2

• Lewis Dot Model: simplified Bohr’s diagram

  • Does not show energy levels

  • Only shows electrons in the valence shell (outermost shell)

  • Electrons as dots are placed around the element symbol in N/S/E/W directions

  • First time around the element symbol is single dots then the second time around you pair the dots

Types of Bonds:

• Elements want to be stable

  • achieve this by forming chemical bonds with other elements

  • Octet rule: elements will gain, lose, or share electrons to complete their valence shell (8 electrons) and become stable (like a noble gas)

• Chemical Bonds: an attraction between two atoms, resulting from the sharing or transferring of valence electrons

• Electronegativity: the measure of an atom’s ability to attract electrons to itself

  • electronegativity decreases as you go down the Periodic Table

  • electronegativity increases as you go to the right of the Periodic Table

• Covalent Bonds: when two or more atoms share electrons (usually between two nonmetals)

  • forms molecules and compounds

    • Single bond: 1 pair of shared e-

    • Double bond: 2 pairs of shared e-

    • Triple bond: 3 pairs of shared e-

  • There are two types of covalent bonds…

    • Nonpolar covalent: electrons are shared equally between two atoms (e.g. O2)

    • Polar covalent: electrons are not shared equally between two atoms (e.g. H2O)

      • unequal sharing of electrons results in partial charges on oxygen and hydrogen

• Ionic Bonds: the attraction between oppositely charged atoms (ions)

  • usually between nonmetal and metal (metal transfers electrons (e-) to nonmetal)

  • forms ionic compounds and salts

    • NaCl (Sodium Chloride)

    • LiF (Lithium Chloride)

  • occurs when there is a transfer of electrons from one atom to another atom forming ions

    • cation: positively charged ion

    • anion: negatively charged ion

• Hydrogen Bonds: the partially positive hydrogen atom in one polar covalent molecule will be attracted to an electronegative atom in another polar covalent molecule

  • Intermolecular Bond: bond that forms between molecules

• Why does this happen?

  • when a hydrogen atom is bonded to an Oxygen or Nitrogen, the electrons are drawn mostly away from the Hydrogen and toward the electronegative atom (Don’t forget that this is a polar covalent bond)

    • this causes the hydrogen to have a partial positive charge and the electronegative atom (N or O) to have a partial negative charge

Properties of Water

• Polarity: unequal sharing of the electrons makes water a polar molecule

• Cohesion: attraction of molecules for other molecules of the same kind (H2O molecules stick to each other)

  • hydrogen bonds between H2O molecules hold them together and increase cohesive forces

  • allows for the transport of H2O and nutrients against gravity in plants

  • responsible for surface tension (property of allowing liquid to resist external force)

• Adhesion: the clinging of one molecule to a different molecule (H2O molecules stick to something else—like a cell wall)

  • because of the polarity of H2O

    • in plants, this allows water to cling to the cell walls to resist the downward pull of gravity

• Capillary Action: the upward movement of water due to the forces of cohesion, adhesion, and surface tension (moves water upwards)

  • occurs when adhesion is greater than cohesion

    • important for the transport of water and nutrients in plants

• Temperature Control:

  • High specific heat: H2O resists changes in temp. by…

    • hydrogen bonds

      • heat must be absorbed to break hydrogen bonds, but heat is released when hydrogen bonds are formed

    • Importance of High Specific Heat:

      • moderates air temp

        • large bodies of water can absorb heat in the daytime and release heat at night

      • stabilizes ocean temp

        • benefits marine life

      • organisms can resist change in their own internal temp

  • Evaporative Cooling: water has a high heat of vaporization

    • the molecules with the highest kinetic energy leave as a gas

    • Importance of Evaporative Cooling:

      • Moderates Earth’s climate

      • Stabilizes temp in lakes and ponds

      • Prevents terrestrial organisms from overheating (e.g. sweating in humans)

      • Prevents leaves from becoming too hot in the sun

• Density (floating ice): as water solidifies it expands and becomes less dense

  • due to the hydrogen bonds:

    • when cooled, H2O molecules move too slowly to break the bonds

      • allows marine life to survive under floating ice sheets

    • with lower temps, hydrogen bonds cause water molecules to form a crystalline structure

• Solvent: dissolving agent in a solution

  • water is a versatile solvent (could also be referred to as a universal solvent)

    • the polar molecules are attracted to ions and other polar molecules water can form hydrogen bonds with

  • water can interact with sugars or proteins containing many oxygens and hydrogens

  • water will form hydrogen bonds with the sugars or proteins to dissolve it

• Ionic Compounds: dissolves ions

  • partially negative oxygen in water will interact with a positive atom

  • partially positive hydrogen in water will interact with a negative atom

Elements of Life:

• Organic Chemistry: the study of compounds with covalently bonded carbon

• Organic Compounds: compounds that contain carbon and hydrogen

Carbon: can form single, double, or triple covalent bonds

• a single carbon can form up to 4 covalent bonds

  • can form long chains

• most commonly formed with hydrogen, oxygen, and nitrogen

  • the type and number of covalent bonds carbon forms with other atoms affects the length of the carbon shape and the shape of the molecule

Carbon Chains: carbon can use its valence electrons to form covalent bonds to other carbons

• this links the carbons into a chain

• Hydrocarbons: organic molecules consisting of only hydrogen and carbon (simple framework for more complex organic molecules)

• Carbon chains form the skeletons of most organic molecules

  • skeletons can vary in length, branching, double bond position, and presence of rings

• many regions of a cell’s organic molecules contain hydrocarbons

Functional Groups: chemical groups attached to the carbon skeleton that participate in chemical reactions

• Hydroxyl group: -OH

• Carbonyl group: -C=O

• Carboxyl group: —COOH

• Amino group: -NH2

• Sulfhydryl group: -SH

  H

• Methyl group: -C-H

  H

• Phosphate group: -OPO²-_{3 (2 of the 3 Oxygens are negative)}

Introduction to Biological Macromolecules

Molecular Diversity due to Carbon

• variations in carbon skeletons allow for molecular diversity

• carbon can form large molecules known as macromolecules

  • four classes of macromolecules (molecules made of smaller subunits)

    • Carbohydrates (Polymer): CHO; Carbon, Hydrogen, Oxygen

    • Proteins (Polymer): CHONS; Carbon, Hydrogen, Oxygen, Nitrogen, Sulfur

    • Nucleic acids (Polymer): CHOPN; Carbon, Hydrogen, Oxygen, Phosphorus, Nitrogen

      • along with carbon, nitrogen is an important element for building proteins and nucleic acids

    • Lipids (doesn’t include true polymers and are hydrophobic molecules): CHONP; Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorus

      • phosphorus is important for building nucleic acids and some lipids

Formation and Breakdown of Macromolecules

• Monomers: the repeating units that make up a polymer

• Polymers: chain-like macromolecules of similar or identical repeating units that are covalently bonded together (multiple monomers covalently bonded together)

• Dehydration reaction: bonds 2 monomers with the loss of H2O

  • the -OH of one monomer bonds to the -H of another monomer forming H2O, which is then released

    • Ex. glucose and sucrose lose an H2O molecule and then bind together to form sucrose (a polymer, polysaccharide)

• Hydrolysis: breaks the bonds in a polymer by adding H2O

  • One of the -H of the H2O bonds to one monomer and the remaining -OH of the H2O attaches to the other monomer

    • Ex. adding water to sucrose splits it into glucose (a monomer, monosaccharide) and fructose (a monomer, monosaccharide)

Biological Macromolecules

Carbohydrates: includes sugars and polymers of sugars (CHO)

• contains a carbonyl group (-C=O) and many hydroxyl groups (-OH)

• Monosaccharides: simple sugars

  • molecular formulas with multiples of the unit CH2O

  • most common is glucose

    • nutrients and fuel for cells

    • used in cellular respiration

  • can serve as building blocks for amino acids, or as monomers for disaccharides and polysaccharides

• Disaccharides: 2 monosaccharides joined together by covalent bonds

  • most common is sucrose

    • monomers of sucrose: glucose and fructose

    • plants transfer carbohydrates from leaves to other parts of the plant in the form of sucrose

• Polysaccharides: polymer with many sugars joined via dehydration reactions

  • storage polysaccharides

    • plants store starch (polymer of glucose monomers)

      • allows plants to store excess glucose

    • animals store glycogen (polymer of glucose)

      • stored in liver and muscle cells

  • structural polysaccharides:

    • cellulose: tough substance that forms plant cell walls

    • chitin: forms exoskeleton of arthropods

Protein: molecule consisting of polypeptides (polymer of amino acids) folded into a 3D shape (CHONS)

• Formation: amino acids→peptide→polypeptide→protein

• shape determines function

• Amino Acids: molecules that have an amino group and a carboxyl group (—COOH)

  • 20 different amino acids

  • general structure: amino group on the left side, R group (variable side chain) in the middle, and carboxyl group on the right side

  • each amino acid (AA) has a unique side chain

    • unique aspects of the AA are based on the side chain’s physical and chemical properties

    • side chains can be grouped as

      • nonpolar (hydrophobic)

      • polar (hydrophobic)

      • charged/ionic (hydrophilic)

    • side chains interact, which determines the shape and function of the protein

• Formation of peptide bonds: to form a peptide bond, the carboxyl group of one AA must be positioned next to the amino group of another AA

• Polypeptides: many AA linked by peptide bonds

  • each polypeptide has a unique sequence of AAs and directionality

    • each end is chemically unique

      • one end is a free amino group (N-terminus)

      • one end is a free carboxyl group (C-terminus)

    • the sequence of AAs determines the 3D shape (shape determines function)

      • when a polypeptide twists and folds (b/c of R group interaction) it forms a protein

• Functions of Proteins:

  • Antibody: help protect the body from disease

  • Enzyme: carry out chemical reactions or assist in creating new molecules

  • Messenger: transmit signals (ie hormones)

  • Structural: provide structure and support

  • Transport/storage: bind to and carry small atoms and molecules through the body

• Levels of Protein Structure:

  • Primary: linear chain of AA

    • determined via genes

    • dictates secondary and tertiary forms

  • Secondary: coils and folds due to hydrogen bonding within the polypeptide backbone

    • pleated sheet: hydrogen bonds between polypeptide chains lying side by side

    • helix: hydrogen bonding between every 4th AA

  • Tertiary: 3D folding due to interactions between the side chains of the AAs

    • reinforced by hydrophobic interactions and disulfide bridges of the side chains

    • the covalent bond formed between sulfur atoms and two cysteine monomers

  • Quaternary: association of 2+ polypeptides

    • found in only some proteins

Nucleic Acids: polymers made of nucleotide monomers (CHONP)

• Function to: store, transmit, and express hereditary information

  • 2 forms:

    • DNA: deoxyribonucleic acid

    • RNA: ribonucleic acid

• Components: nucleotides→polynucleotides→nucleic acids

• Nucleotide: each nucleotide is comprised of a…

  • Nitrogenous base: 2 types…

    • pyrimidines: one ring with 6 atoms

      • cytosine

      • thymine (only found in DNA)

      • uracil (only found in RNA)

    • purines: one ring with 6 atoms bonded to one ring with 5 atoms

      • adenine and guanine

  • Five Carbon Sugar: a sugar is bonded to the base

    • DNA: sugar is deoxyribose (b/c one less OH in the base)

    • RNA: sugar is ribose (b/c one more OH than DNA in the base)

      • they both differ in structure and function

  • Phosphate Group: added to the 5’ carbon of the sugar (which is attached to the base) to form a nucleotide

    • nucleoside: portion w/o phosphate group

• Polynucleotides: phosphate groups link adjacent nucleotides

  • phosphodiester linkage

  • directionality: 5’ phosphate end to 3’ hydroxyl (-OH) end (nucleotides get added to 3’)

  • sequence of bases along the DNA or mRNA is unique for each gene

    • dictates AA sequence

      • dictates primary structure of protein

        • dictates 3D structure of a protein

  • DNA: consists of 2 polynucleotides

    • forms a double helix

      • strands are antiparallel (5’ to 3’ and 3’ to 5’)

      • held together by hydrogen bonds between bases (adenine to thymine, cytosine to guanine)

  • RNA: single-stranded polynucleotide

    • variable in shape

      • due to base pairing within RNA

        • adenine bonds to uracil

        • cytosine bonds to guanine

Lipids: class of molecules that do not include true polymers (CHOP)

• generally small in size

• often not considered to be a macromolecule

• lipids are nonpolar-hydrophobic

• types of lipids:

  • fats: composed of glycerol (alcohol, hydroxyl groups) and fatty acids (long carbon chains, carboxyl groups at one end)

    • 3 fatty acids join to a glycerol via ester linkage

    • bond between a hydroxyl and carboxyl group

      • classified as either a:

        • saturated fatty acid: no double bonds between carbons in the carbon chain = more hydrogen (saturated w/ hydrogen)

        • an unsaturated fatty acid: contains one or more double bonds

• phospholipids major component of cell membranes

  • 2 fatty acids attached to a glycerol and a phosphate

  • assembles as a bilayer in H2O

    • tails (fatty acids) are hydrophobic

    • head (phosphate and glycerol) is hydrophilic

• steroids: lipids that have four fused rings

  • unique groups attached to the ring determine the type of steroid

Unit 2a: Cell Structure and Function

Subcellular Components and Compartmentalization

Cells:

• the basic structural and functional units of every organism

  • all cells:

    • are bound by a plasma membrane

    • contain cytosol

    • contain chromosomes

    • contain ribosomes

• 2 types of cells:

  • Prokaryotes:

    • domains bacteria and archaea

    • DNA is in the nucleoid region

    • generally smaller in size than eukaryotes

  • Eukaryotes:

    • protists, fungi, plants, animals

    • DNA is in the nucleus

    • contains membrane-bound organelles

Organelles & Other Features:

• Organelles: membrane-bound structures in eukaryotes; there are 2 categories

  • Endomembrane organelles:

    • nuclear envelope

    • endoplasmic reticulum

    • golgi complex

    • lysosomes

    • vesicles/vacuoles

    • plasma membrane

  • Energy organelles:

    • mitochondria

    • chloroplasts

• Other features: not membrane-bound but critically important in both prokaryotes and eukaryotes

  • ribosomes: distinct differences between prokaryotes and eukaryotes

  • cytoskeleton:

    • microtubules

    • microfilaments

    • intermediate filaments

Organelles:

• Compartmentalization: in organelles allows for different metabolic reactions to occur in different locations

  • increases surface area for reactions to occur

  • prevents interfering reactions from occurring in the same locations

• Unique cell components: plant cells and animal cells have certain organelles that only belong to either the plant or animal cell

  • Plants:

    • chloroplasts

    • central vacuole

    • cell wall plasmodesmata (or plasmodesma)

  • Animals:

    • lysosomes

    • centrosomes

    • flagella

Endomembrane Organelles:

• Nucleus: contains chromosomes (genetic information)

  • enclosed by the nuclear envelope

    • double membrane

  • has pores

    • pores regulate entry and exit of materials from the cell

  • contains a nucleolus

    • dense region of the nucleus where ribosomal RNA (rRNA) is synthesized

      • rRNA is combined with proteins to form large and small subunits of ribosomes

      • subunits exit via nuclear pores

        • assembles into ribosomes

          • ribosomes translate messages found on mRNA (messenger RNA) into the primary structure of polypeptides

• Ribosomes: compromised of ribosomal RNA and protein (some texts don’t classify them as organelles because they are not membrane-bound)

  • functions: synthesize proteins

  • can be found in 2 locations:

    • cytosol

      • proteins produced here generally function only within the cytosol (ex. enzymes)

      • known as free ribosomes (not bound to anything)

    • bound to the endoplasmic reticulum or nuclear envelope

      • proteins produced here can be secreted from the cell

        • leave via transport vesicles

• Endoplasmic Reticulum: a network of membranous sacs and tubes

  • Functions:

    • synthesizes membranes

    • compartmentalize the cell to keep proteins formed in the rough ER separate from those of free ribosomes

  • 2 types:

    • rough ER:

      • contains ribosomes bound to the ER membrane

    • smooth ER:

      • contains no ribosomes

      • synthesizes lipids, metabolizes carbohydrates, and detoxifies the cell

• Golgi Complex: contains flattened membranous sacs called cisternae

  • separate the sacs from the cytosol

  • each cisternae is not connected

  • has directionality

    • cis face: receives vesicles from the ER

    • trans face: sends vesicles back out into the cytosol to other locations or to the plasma membrane for secretion

  • Functions:

    • receives transport vesicles with materials from the ER

    • modifies the materials

      • ensures newly formed proteins are folded correctly or modified correctly

    • sorts the materials

    • adds molecular tags

    • packages materials into new transport vesicles that exit the membrane via exocytosis

• Lysosomes: membranous sacs with hydrolytic enzymes

  • functions:

    • hydrolyzes macromolecules in animal cells

    • Autophagy: lysosomes can recycle their own cell’s organic material

      • allows the cell to renew itself

• Peroxisomes: similar to lysosomes

  • membrane-bound metabolic compartment

    • catalyze reactions that produce H2O2 (hydrogen peroxide)

      • enzymes in peroxisomes then break down H2O2 into water

• Vacuoles: large vesicles that stem from the ER and Golgi

  • selective in transport

  • Types:

    • Food vacuole: form via phagocytosis (cell eating) and then are digested by lysosomes

    • Contractile vacuole: maintains water levels in cells

    • Central vacuole: found in plants

      • contains inorganic ions and water

      • important for turgor pressure

Energy Organelles:

• Endosymbiont theory: the theory that explains the similarities mitochondria and chloroplasts have to a prokaryote

  • theory states that an early eukaryotic cell engulfed a prokaryotic cell

    • prokaryotic cell became an endosymbiont (cell that lives in another cell)

      • became one functional organism

  • evidence:

    • double membrane

    • ribosomes

    • circular DNA

    • capable of functioning on their own (they still can’t survive on their own)

• Mitochondria: site of cellular respiration

  • structure of the double membrane:

    • outer membrane is smooth

    • inner membrane has folds called cristae

      • divides the mitochondria into two internal compartments and increases the surface area

  • Intermembrane: space between inner and outer membrane

  • Mitochondrial matrix: enclosed by inner membrane

    • location for the Krebs cycle

    • contains:

      • enzymes that catalyze cellular respiration and produce ATP

      • mitochondrial DNA

      • ribosomes

  • the number of mitochondria in a cell correlates with metabolic activity

    • cells with high metabolic activity have more mitochondria

      • ex. cells that move/contract

• Chloroplasts:

  • specialized organelles in photosynthetic organisms

    • site of photosynthesis

    • contains the green pigment chlorophyll

  • inside of its double membrane:

    • thylakoids

      • membranous sacs that can organize into stacks called grana

        • light-dependent reactions occur in grana

  • Stroma: fluid around thylakoids

    • locations for the Calvin cycle

    • contains

      • chloroplast DNA

      • ribosomes

      • enzymes

The Cytoskeleton:

• network of fibers throughout the cytoplasm

  • gives structural support (especially for animal cells) and mechanical support

    • anchor organelles

    • allow for movement of vesicles and organelles and/or the whole cell

      • movement occurs when the cytoskeleton interacts with motor proteins

  • 3 types of fibers in cytoskeleton:

    • microfilaments: thin solid rods made of the protein actin

      • Functions: maintain cell shape

        • bear tension

      • assist in muscle contraction and cell motility

        • actin works with another protein called myosin to cause a contraction

      • division of animal cells

        • contractile ring of the cleavage furrow

    • microtubules: hollow rod-like structures made of the protein tubulin

      • grows from the centrosome

        • assist in microtubule assembly

      • functions:

        • serve as structural support for the movement of organelles that are interacting with motor proteins

        • assist in the separation of chromosomes during cell division

        • cell motility (ex. cilia and flagella)

    • intermediate filaments:

      • fibrous proteins made up of varying subunits

      • permanent structural elements of cells

      • Functions:

        • maintain cell shape

        • anchor nucleus and organelles

        • form the nuclear lamina

          • lines the nuclear envelope

Unit 2b: Membrane Structure and Function

Plasma Membranes and Membrane Permeability

Plasma Membrane: separates internal cell environment from external environment

• compromised primarily of phospholipids

• phospholipids are amphipathic

  • hydrophobic tails and hydrophilic head

  • forms a bilayer

Selective Permeability: the ability of membranes to regulate the substances that enter and exit

• Hydrophilic head oriented towards aqueous environment

• Hydrophobic tails are facing inwards away from aqueous environment

Fluid Mosaic Model:

• a model to describe the structure of cell membranes

  • Fluid: membrane is held together by weak hydrophobic interactions and can therefore move and shift

    • temperature affects fluidity

    • unsaturated hydrocarbon tails help maintain fluidity at low temps

      • kinked tails prevent tight packing of phospholipids

    • cholesterol helps maintain fluidity at high and low temps

      • high temp: reduces movement

      • low temp: reduces tight packing of phospholipids

  • Mosaic: compromised of many macromolecules

Membrane Proteins:

• 2 major categories of proteins in the membrane:

  • integral proteins: proteins that are embedded into the lipid bilayer

    • aka transmembrane proteins

    • amphipathic

  • peripheral proteins: proteins that are not embedded into the lipid bilayer

    • loosely bonded to the surface

Membrane Carbohydrates:

• important for cell-to-cell recognition

  • glycolipids: carbohydrates bonded to lipids

  • glycoproteins: carbohydrates bonded to proteins; most abundant

Plant Cells:

• plants have a cell wall that covers their plasma membranes

  • extracellular structure (not found in animal cells)

    • provides:

      • shape/structure

      • protection

      • regulation of water intake

  • cell wall is composed of cellulose

  • thicker than plasma membranes

  • contain plasmodesmata

    • hole-like structures in the cell wall filled with cytosol that connect adjacent cells

Membrane Transport and Facilitated Diffusion:

Selective Permeability:

• some substances can cross the membrane more easily than others

• easy passage across the membrane:

  • small nonpolar, hydrophobic molecules

    • ex. hydrocarbons, CO2, O2, N2

• difficult passage or protein assisted passage:

  • hydrophilic, polar molecules, large molecules, ions:

    • ex. sugars, water

Transport across the membrane:

• there are two main types of transport across a membrane: passive and active

  • Passive transport: Transport of a molecule that does not require energy from the cell because a solute is moving with its concentration/electrochemical gradient

    • involved in import of materials and export of waste

    • ex.

      • diffusion: spontaneous process resulting from constant motion of molecules; substances move from high to low concentration (down the concentration gradient)

        • occurs directly across membrane; different rates of diffusion for different molecules

      • osmosis: diffusion of water down its concentration gradient across a selectively permeable membrane (diffusion of water from low solute concentration to high solute concentration)

      • facilitated diffusion: diffusion of molecules through the membrane via transport proteins (down gradient)

        • increases rate of diffusion for small ions, water, and carbohydrates

        • 2 types of transport proteins (each is specific for their substances)

          • channel: channel for molecules and ions to pass; hydrophilic; many are gated channels, that only allow passage when there’s a stimulus

            • Aquaporins: specific channel protein for water

          • carrier: undergo conformational changes for substances to pass

  • Active transport: transport of a molecule that requires energy (ATP); usually energy’s required b/c it moves a solute against concentration gradient

    • types of active transport:

      • pumps: moves substances against concentration gradient and use ATP for the energy to do so; aka “primary active transport”; involved in membrane potential (unequal concentrations of ions across membrane that results in an electrical charge (electrochemical gradient)

        • sodium potassium pumps: animal cells will regulate their relative concentration of Na+ and K+ (3 NA+ get pumped out of cell, 2 K+ gets pumped into cell—> +1 net charge to extracellular fluid)

        • proton pump: integral membrane protein; builds up proton gradient across membrane; aka hydrogen ion gradient/hydrogen ion pump

      • cotransport: coupling of a favorable movement of one substance with an unfavorable movement of another substance; favorable movement (downhill diffusion), unfavorable movement (uphill diffusion)

      • exocytosis: secretion of molecules via vesicles that fuse to the plasma membrane; once fused, contents of vesicle are released to the extracellular fluid

      • endocytosis: the uptake of molecules from vesicles fused from the plasma membrane

        • phagocytosis: when a cell engulfs particles to be later digested by lysosomes

        • pinocytosis: nonspecific uptake of extracellular fluid containing dissolved molecules

        • receptor mediated endocytosis: specific uptake of molecules via solute binding to receptors on the plasma membrane

Unit 3a: Energy and Enzymes

Metabolism

metabolism: all of the chemical reactions in an organism

Metabolic pathways: series of chemical reactions that either build or break down complex molecules; two types of pathways

• Catabolic pathways: pathways that release energy by breaking down complex molecules into simpler compounds

• Anabolic pathways: pathways that consume energy to build complicated molecules from simpler compounds

Energy:

• Energy: the ability to do work

• organisms need energy to survive and function

  • a loss in energy flow results in death

• Kinetic energy: energy associated with motion

  • thermal energy: energy associated with the movement of atoms or molecules

• Potential energy: stored energy

  • Chemical energy: potential energy available for release in a chemical reaction

Laws of Thermodynamics:

The study of energy transformations in matter is called thermodynamics; the laws apply to the universe as a whole

• 1st Law:

  • energy cannot be created or destroyed

  • energy can be transferred or transformed

• 2nd Law:

  • energy transformation increases the entropy (disorder) of the universe

  • during energy transfers or transformations, some energy is unusable and often lost as heat

Free Energy: scientists use this concept to determine the likelihood of reactions in organisms, or determine if the reactions are energetically favorable

• ΔG = ΔH - TΔS

  • ΔG (delta G): change in free energy

  • ΔH: total change in energy

  • T: absolute temp. (K)

  • ΔS: change in entropy

• free energy change reactions determine whether or not the reaction occurs spontaneously (no outside input of energy is required)

• based on free energy changes, chemical reactions can be classified as exergonic or endergonic

  • exergonic reactions: reactions that release energy; ΔG<0

    • ex. cellular respiration

  • endergonic reactions: reactions that absorb energy; ΔG>0

    • ex. photosynthesis; reaction is not spontaneous, absorbs free energy

Cells and Energy:

• living cells have a constant flow of materials in and out of the membrane

  • cells are not at equilibrium

• cells perform 3 kinds of work:

  • mechanical: movement; ex, beating cilia, movement of chromosomes, contraction of muscles)

  • transport: pumping substances across membranes against spontaneous movement

  • chemical: synthesis of molecules; ex, building polymers from monomers

ATP:

• Adenosine triphosphate: molecule that organisms use as a source of energy to perform work

• ATP couples exergonic reactions to endergonic reactions to power cellular work

  • exergonic process drives the endergonic process

• organisms obtain energy by breaking the bond between the 2nd and 3rd phosphate in a hydrolysis reactions

  • ATP —> ADP

• phosphorylation: the released phosphate moves to another molecule to give energy

• hydrolysis of ATP: water + ATP = ADP + Pi

• ADP can be regenerated to ATP via the ATP cycle:

  • ATP +H2O +energy from cellular work —> ADP + Pi

  • ADP + Pi + energy from exergonic process —> ATP + H2O

Rate of Metabolic Reactions:

• laws of thermodynamics tells us if a reaction is spontaneous, but it doesn’t describe the rate of the reaction

Enzymes:

• macromolecules that catalyze (speed up) reactions by lowering the activation energy

  • aren’t consumed by the reaction

  • type of protein

  • all enzyme names end in -ase

Enzyme Structure:

• the enzyme acts on a reactant called a substrate

  • active site: area substrate binds to

Enzyme Function:

• Induced Fit: enzymes change shape of their active site to allow the substrate to bind better

• enzyme catabolism: helps break down complex molecules

• enzyme anabolism: helps build complex molecules

Effects on Enzymes:

• Efficiency can be affected by different factors such as (change in shape = change in function):

  • temperature: rate of enzyme activity increases with temperature up to a certain point, after that point, the enzyme will denature

  • pH levels: enzymes function best a specific pH; varies upon location; pH level outside or normal level can cause hydrogen bonds to break (changing the shape of enzyme)

  • chemicals

Enzyme Cofactors:

• Cofactors: non protein molecules that assist enzyme function

  • inorganic cofactors: metals

  • Holoenzyme: an enzyme with a the cofactor attached

• Coenzyme: organic cofactors, such as vitamins

Enzyme Inhibitors:

• Competitive Inhibitors: reduce enzyme activity by blocking substrates from binding to active site

  • can be reversed with increased substrate concentration

• Noncompetitive inhibitors: bind to allosteric site, which changes shape of active site, preventing substrates from binding

  • type of allosteric inhibition

Regulation of Chemical Reactions:

• cells must be able to regulate its metabolic pathways

  • control where and when enzymes are active

  • switch gene that code enzymes on or off

Allosteric Regulation:

• Allosteric enzymes have 2 binding sites:

  • 1 active site

  • 1 allosteric site (regulatory site/other than the active site)

  • Molecules bind (noncovalent interactions) to an allosteric site which changes shape and function of active site

    • can result in inhibition (by inhibitor) or stimulation (by activator) of enzymes activity

Allosteric Regulation: Activator;

• Allosteric activator: it binds to allosteric site and stabilizes shape of enzyme so the active sites remain open

Allosteric Regulation: Inhibitor;

• Allosteric inhibitor: binds to allosteric site and stabilizes enzyme shape so the active sites are closed (inactive form)

Allosteric Regulation: Cooperativity;

• cooperativity: substrate binds to one active site (on an enzyme with >1 active site) which stabilizes active form

Unit 3b: Cellular Respiration

Cellular Respiration

Cells harvest chemical energy stored in organic molecules and use it to generate ATP;

• chemical equation: organic molecules + O2 —> CO2 + H2O + energy

Glycogen is the major source of fuel for animals (starch for plants)

• breaks down into glucose

  • catabolic breakdown: C6H12O6 + 6O2 —> 6CO2 + 6H2O + energy (ATP and Heat)

    • C6H12O6 is oxidized to 6CO2

      • oxidation: loss of electrons; becomes more positive

    • 6O2 is reduced to 6H2O

      • reduction: gain of electrons; becomes more negative

  • oxidation of glucose transfers e- ‘s to a lower energy state, releasing energy to be used in ATP synthesis

Path of Electrons in Energy Harvest:

Most electrons will follow this downhill exergonic path (for cellular respiration):

glucose (typical starting point) —> NADH (high energy electron carrier) —> ETC (Electron Transport Chain) —> oxygen (final electron acceptor)

• glucose is broken down in steps to harvest energy

  • electrons are removed from glucose at different steps

  • each e- removed also has a H+ removed with it

  • e- must be taken up by specific acceptors (oxidizing agents) such as NAD+ (turns into NADH) and FAD (turns into FADH2)

  • example:

    • 2e- and 1 proton are transferred to coenzyme NAD+, reducing it to NADH (stores the energy)

    • other proton is released into surrounding solution as H+ (hydrogen ion)

    • NADH carries and transfers the 2 high energy e- ‘s to the ETC and releases another proton

• Electron Transport Chain (ETC): sequence of membrane proteins that shuttle electrons down a series of oxidation-reduction reactions (redox reactions)

  • releases energy used to make ATP

  • ETC transfers e-’s to oxygen (final electron acceptor) to make H2O

    • releases energy

3 Stages of Cellular Respiration:

• Stage 1: Glycolysis; starting point of cellular respiration (in both eukaryotes and prokaryotes)

  • occurs in the cytosol (in both types of cells)

  • splits glucose (6C) into 2 pyruvates (3C)

  • glycolysis is an aerobic process (requires no oxygen)

  • 2 stage process:

    • Energy investment stage: cell uses 2 ATPs to phosphorylate compounds of glucose

    • Energy payoff stage: energy is produced by substrate level phosphorylation & makes 4 ATPs (however 2 are used, so net yield of 2)and 2 NADHs

      • net energy yield per 1 glucose:

        • 2 ATP

        • 2 NADH

      • Summary:

        • Energy Investment: 2 ATP —> 2 ADP + Pi

        • Energy Payoff: 4 ADP + Pi —> 4 ATP

          • 2 NAD+ + 4 e- + 4H+ —> 2 NADH + 2 H+

        • Net: 2 ATP, 2 NADH + 2 H+, 2 Pyruvates

• Stage 2a: Pyruvate Oxidation; when oxygen is present, pyruvate enters the mitochondria (eukaryotes) (this stage in prokaryotes still occurs in the cytosol)

  • pyruvate is oxidized into Acetyl CoA

    • Acetyl CoA is used to make citrate in the citric acid cyle (next stage)