Bio 81 Exam 1

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

• Organisms are composed of matter

• An element is a substance that cannot be broken down to other substances by chemical reactions

• A compound is a substance consisting of 2 or more elements in a fixed ratio

Subatomic Particles

• Atoms are composed of subatomic particles

  • Neutrons (no charge)

  • Protons (positive charge)

  • Electrons (negative charge)

• Atomic number = number of protons in its nucleus

• Mass number = sum of protons + neutrons

Isotopes

• Same number of protons but a different number of neutrons

• Radioactive isotopes decay spontaneously, giving off particles and energy

Energy Levels of Electrons

• Energy is the capacity to cause change

• Potential energy is the energy that matter has become of its location or structure

• The electrons of an atom differ in their amounts of potential energy

• An electron’s state of potential energy is called its energy level, or electron shell

• Valence electrons are those in the outermost shell, or valence shell

• Chemical behavior of an atom is determined by valence electrons

• Elements with a full valence shell are chemically inert 

Chemical Bonding Between Atoms

• Atoms with incomplete valence shells can share or transfer valence electrons with certain other atoms

Covalent Bonds

• Sharing of a pair of valence electrons by 2 atoms

• Shared electrons count as part of each atom’s valence shell

• Electronegativity is an atom’s attraction for the electrons in a covalent bond

• Polar covalent bond: one atom is more electronegative and the atoms do not share the electron equally

Ionic Bonds

• Cation: positively charged ion

• Anion: negatively charged ion

Hydrogen Bonds

• Forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom

Van Der Waals Interactions

• Electrons are distributed asymmetrically in molecules or atoms

Molecular Shape and Function

• Shape is determined by the positions of its atoms’ valence orbitals

Chemical Reactions

• Breaking and making of chemical bonds

• Reactants → products

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

Four Emergent Properties of Water Contribute to Earth’s Suitability for Life

• Cohesive behavior

• Ability to moderate temperature

• Expansion upon freezing

• Versatility as a solvent

Cohesion of Water Molecules

• Cohesion: hydrogen bonds hold water molecules together

  • Helps the transport of water against gravity in plants

  • Surface tension is a measure of how hard it is to break the surface of a liquid

• Adhesion is an attraction between different substances (ie. between water and plant cell walls)

Moderation of Temperature by Water

• Water absorbs heat from warmer air and releases stored heat to cooler air

• Water can absorb or release a large amount of heat with only a slight change in its own temperature

• Kinetic energy is the energy of motion

• Heat is a measure of the total amount of kinetic energy due to molecular motion

• Temperature measures the intensity of heat due to the average kinetic energy of molecules

Water’s High Specific Heat

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

• Specific heat of water is 1cal/g/ºC

• Water resists changing its temperature because of its high specific heat

• Water’s high specific heat can be traced to hydrogen bonding

  • Heat is absorbed when hydrogen bonds break

  • Heat is released when hydrogen bonds form

Evaporative Cooling

• Evaporation is transformation of a substance from liquid to gas

• Heat of vaporization is the heat a liquid must absorb for 1g to be converted to gas

• As a liquid evaporates, its remaining surface cools (evaporative cooling)

• Evaporative cooling of water helps stabilize temperatures in organisms and bodies of water

Floating of Ice on Liquid Water

• Ice floats because hydrogen bonds are more “ordered”, making ice less dense

• Water reaches its greatest density at 4ºC

Water: the Solvent of Life

• Solution: a liquid that is a homogenous mixture of substances

• Solvent: the dissolving agent of a solution

• Solute: the substance that is dissolved

• Aqueous solution: one in which water is the solvent

Hydrophilic and Hydrophobic Substances

• Hydrophilic: substance that has an affinity for water

• Hydrophobic: substance that does not have an affinity for water

• Oil molecules are hydrophobic because they have relatively nonpolar bonds

• Colloid: a stable suspension of fine particles in a liquid

Acidic and Basic Conditions

• A hydrogen atom in a hydrogen bond between 2 water molecules can shift form 1 to the other

  • The hydrogen atom leaves its electron behind and is transferred as a proton, or a 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-)

• Concentrations of H+ and OH- are equal in pure water

• Adding certain solutes, called acids and bases, modifies the concentrations of H+ and OH-

• pH scale is used to describe whether a solution is acidic or basic

Acids and Bases

• Acid: substances that increases the H+ concentration of a solution

• Base: substances that reduces the H+ concentration of a solution

The pH Scale

• Aqueous solution

  • [H+][OH-] = 10^-14

• pH = -log[H+]

Buffers 

• The internal pH of most living cells must remain close to pH 7

• Buffers: substances that minimize changes in concentrations of H+ and OH- in a solution

• Most buffers consist of an acid-base pair that reversibly combines with H+

Organic Chemistry

• The study of compounds that contain carbon

Organic Molecules and the Origin of Life on Earth

• Stanley Miller’s classic experiment demonstrated the abiotic synthesis or organic compounds

• Experiments support the idea that abiotic synthesis of organic compounds, perhaps near volcanoes, could have been a stage in the origin of life

Hydrocarbons

• Organic molecules consisting of only carbon and hydrogen

• Undergo reactions that release a large amount of energy

Isomers

• Compounds with the same molecular formula but different structures and properties

  • Structural isomers: have different covalent arrangements of their atoms

  • Cis-trans isomers: have the same covalent bonds but differ in spatial arrangements

  • Enantiomers: isomers that are mirror images of each other

Chemical Groups Important in the Processes of Life

• Functional groups: 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

Macromolecules

• The Molecules of Life: 

  • All living things are made up of 4 classes of large biological molecules: 

    • Carbohydrates

    • Lipids

    • Proteins

    • Nucleic acids 

  • Macromolecules: large molecules composed of thousands of covalently connected atoms 

    • Molecular structure and function are inseparable 

• Most Macromolecules are Polymers, Built from Monomers 

  • Polymer: a long molecule consisting of many similar building blocks

    • Monomers: the small building-block molecules in a polymer

  • ¾ classes of life’s organic molecules are polymers

    • Carbohydrates

    • Proteins

    • Nucleic acids 

• The Synthesis and Breakdown of Polymers: 

  • An immense variety of polymers can be built from a small set of monomers 

  • Dehydration reaction: occurs when 2 monomers bond together through the loss of a water molecule 

  • Polymers are disassembled into monomers by hydrolysis

    • A reaction that is essentially the reverse of the dehydration reaction

• Carbohydrates Serve as Fuel and Building Material 

  • Carbohydrates: include sugar and the polymers of sugar 

    • The simplest carbohydrates are monosaccharides aka simple sugars

  • Carbohydrate macromolecules are polysaccharides, polymers composed of many sugar building blocks 

• Sugars: 

  • Monosaccharides: have molecular formulas that are usually multiples of CH2O

    • Glucose (C6H12O6): the most common monosaccharide 

  • Monosaccharides are classified by: 

    • The location of the carbonyl group (as aldose/ketose)

    • The number of carbons in the carbon skeleton 

• Disaccharide: formed when a dehydration reaction joins 2 monosaccharides 

  • This covalent bond is called glycosidic linkage

• Polysaccharides: 

  • Polysaccharides: the polymers of sugars, have storage and structural roles

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

• Storage Polysaccharides: 

  • Starch: a storage polysaccharide of plants, consists entirely of glucose monomers 

    • Plants store surplus starch as granules within chloroplasts and other plastids 

    • Amylose: the simplest form of starch 

  • Glycogen: a storage polysaccharide in animals 

    • Humans and other vertebrates store glycogen mainly in liver and muscle cells 

• Structural Polysaccharides: 

  • Cellulose: a polysaccharide that’s a major component of the tough wall of plant cells 

    • Like starch, cellulose is a polymer of glucose, but the glycosidic linkages differ

    • The difference is based on 2 ring forms for glucose: alpha (𝛼) and beta (β)

      • Polymers with 𝛼 glucose are helical

      • Polymers with β are straight 

        • Straight structures: H atoms on 1 strand can bond with OH groups on other strands 

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

• Chitin: another structural polysaccharide is found in the exoskeleton of arthropods 

  • Also provides structural support for the cell walls of many fungi 

• Lipids are a Diverse Group of Hydrophobic Molecules 

  • Lipids: the one class of large biological molecules that don’t form polymers

    • The unifying feature of lipids is having little/no affinity for water

      • Lipids are hydrophobic because they consist mostly of hydrocarbon, which form nonpolar covalent bonds

  • The most biologically important lipids are fats, phospholipids, and steroids 

• Fats: 

  • Fats: constructed from 2 types of smaller molecules: glycerol and fatty acids

    • Glycerol: 3-carbon alcohol with a hydroxyl group attached to each carbon 

    • Fatty acid: consists of a carboxyl group attached to a long carbon skeleton 

  • Fats separate from water b/c water molecules form hydrogen bonds with each other & exclude the fats 

    • In a fat, 3 fatty acids are joined to glycerol by an ester linkage, creating a triacylglycerol, or triglyceride 

• Fatty acids vary in length (# of carbons) and in # and locations of double bonds

  • Saturated fatty acids: have the maximum number of hydrogen atoms possible & no double bonds

    • Saturated fats: fats made from saturated fatty acids

      • Solid at room temp

      • Most animal fats are saturated 

  • Unsaturated fatty acids: have 1 or more double bonds 

    • Unsaturated fats/oils: fats made from unsaturated fatty acids  

      • Liquid at room temperature 

      • Plant fats and fish fats 

• A diet rich in saturated fats may contribute to cardiovascular disease through plaque deposits

  • Hydrogenation: process of converting unsaturated fats to saturated fats by adding hydrogen

  • Hydrogenation vegetable oils also creates unsaturated fats with trans double bonds

    • These trans fats may contribute more than saturated fats to cardiovascular disease 

• Certain unsaturated fatty acids aren't synthesized in the human body 

  • These must be supplied in the diet

    • These essential fatty acids include the omega-3 fatty acids, required for normal growth, and thought to provide protection against cardiovascular disease 

  • The major function of fats is energy storage

    • Humans and other mammals store their fat in adipose cells 

      • Adipose tissue also cushions vital organs and insulates the body

• Phospholipids: 

  • Phospholipid: 2 fatty acids and a phosphate group are attached to glycerol 

    • The 2 fatty acid tails are hydrophobic

    • The phosphate group and it’s attachments form a hydrophilic head

• When phospholipids are added to water, they self-assemble into a bilayer, with the hydrophobic tails pointing toward the interior

  • The structure of phospholipids results in a bilayer arrangement found in cell membranes

  • Phospholipids are the major component of all cell membranes 

• Steroids: 

  • Steroids: lipids characterized by a carbon skeleton consisting of 4 fused rings

  • Cholesterol: an important steroid that’s a component in all animal cell membranes

    • Although cholesterol is essential in animals, high levels in the blood may contribute to cardiovascular disease 

• Proteins Include a Diversity of Structures, Resulting in a Wide Range of Functions: 

  • Proteins account for more than 50% of the dry mass of most cells

  • Protein functions include: 

    • Structural support

    • Storage

    • Transport

    • Cellular communications

    • Movement 

    • Defense against foreign substances

• Enzymatic proteins: 

  • Function: selective acceleration of chemical reactions

  • Example: digestive enzymes catalyze the hydrolysis of bonds in food molecules

• Storage proteins: 

  • Function: storage of amino acids

  • Examples: casein (protein of milk) is the major source of amino acids for baby mammals 

    • Plants have storage proteins in their seeds

    • Ovalbumin is the protein of egg white - used as an amino acid source for the developing embryo 

• Hormonal proteins: 

  • Function: coordination of an organism’s activities 

  • Example: Insulin (hormone secreted by the pancreas) causes other tissues to take up glucose, thus regulating blood sugar concentration 

• Contractile and motor proteins

  • Function: movement

  • Examples: motor proteins are responsible for the undulations of cilia and flagella; actin and myosin proteins are responsible for the contraction of muscles 

• Defensive proteins: 

  • Function: protection against disease

  • Example: antibodies inactivate and help destroy viruses and bacteria 

• Transport proteins: 

  • Function: transport of substances

  • Examples: hemoglobin (the iron-containing protein of vertebrate blood) transports oxygen from the lungs to other parts of the body; other proteins transport molecules across cell membranes 

• Receptor proteins: 

  • Function: response of cell to chemical stimuli 

  • Example: receptors built into the membrane of a nerve cell detect signaling molecules released by other nerve cells  

• Structural proteins: 

  • Functions: support

  • Examples: 

    • Keratin: protein of hair, horns, feathers, and other skin appendages

    • Insects and spiders use silk fibers to make their cocoons and webs

    • Collagen and elastin proteins provide a fibrous framework in animal connective tissues 

• Enzymes: a type of protein that acts as a catalyst to speed up chemical reactions

  • Can perform their functions repeatedly, functioning as workhorses that carry out the processes of life

• Amino Acid Monomers: 

  • Amino acids: organic molecules with carboxyl and amino groups 

    • Differ in their properties due to differing side chains - R groups 

• Amino Acid Polymers: 

  • Amino acids are linked by peptide bonds

  • Polypeptide: polymer of amino acids

    • Range in length from a few to more than a thousand monomers 

    • Each polypeptide has a unique linear sequence of amino acids, with a carboxyl end (C-terminus) and an amino end (N-terminus) 

• Polypeptides: 

  • Polypeptides: unbranched polymers built from the same set of 20 amino acids

  • Protein: a biologically functional molecule that consists of 1 or more polypeptides 

• Protein Structure and Function: 

  • A functional protein consists of one or more polypeptides precisely twisted, folded, and coiled into a unique shape

  • The sequence of amino acids determines a protein’s 3D structure

  • A protein’s structure determines its function 

• Four Levels of Protein Structure: 

  • Primary structure: its unique sequence of amino acids

  • Secondary structure: consists of coils and folds in the polypeptide chain 

    • Found in most proteins

  • Tertiary structure: determined by interactions among various side chains (R groups)

• Primary structure: the sequence of amino acids in a protein - is like the order of letters in a long word

  • Determined by inherited genetic information 

  • Held together by peptide bonds 

• The coils and folds of secondary structure result from hydrogen bonds between repeating constituents of the polypeptide backbone

  • Typical secondary structures: 

    • 𝛼 helix: a coil

    • Β pleated sheet: a folded structure 

• Tertiary structure: determined by interactions between R groups, rather than interactions between backbone constituents 

  • These interactions between R groups include hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals interactions 

  • Disulfide bridges: strong covalent bonds that may reinforce the protein’s structure 

• Quaternary structure: results when 2 or more polypeptide chains form one macromolecule 

  • Collagen: fibrous protein consisting of 3 polypeptides coiled like a rope

  • Hemoglobin: a globular protein consisting of 4 polypeptides: 2 alpha and 2 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

• What Determines Protein Structure? 

  • In addition to primary structure, physical and chemical conditions can affect structure

    • Alterations in pH, salt concentration, temperature, or other environmental factors can cause a protein to unravel 

    • Denaturation: the loss of a protein’s native structure 

      • A denatured protein is biologically inactive 

• Protein Folding in the Cell: 

  • It’s hard to predict a protein’s structure from its primary structure

  • They go through several stages on their way to a stable 

    • Chaperonins: protein molecules that assist the proper folding of other proteins

      • Diseases such as Alzheimer’s, Parkinson’s, and Mad Cow Disease are associated with misfolded protein

• Nucleic Acids Store, Transmit, and Help Express Hereditary Information

  • Gene: a unit of inheritance that programs the amino acid sequence of a polypeptide 

    • Genes are made of DNA - a nucleic acid made of monomers called nucleotides

• The Roles of Nucleic Acids: 

  •  There are 2 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 

    • Occurs on ribosomes 

• The Components of Nucleic Acids: 

  • Polynucleotides: polymers that are nucleic acids 

  • Nucleotides: monomers that each polynucleotide is made of 

    • Each nucleotide consists of a nitrogenous base, a pentose sugar, and one or more phosphate groups 

    • Nucleoside: the portion of a nucleotide without the phosphate group

• Nucleoside = nitrogenous base + sugar

  • 2 families of nitrogenous bases

    • Pyrimidines (cytosine, thymine, and uracil) have a single 6-membered ring

    • Purines (adenine and guanine) have a 6-membered ring fused to a 5-membered ring

  • In DNA, the sugar is deoxyribose; in RNA, the sugar is ribose

  • Nucleotide = nucleoside + phosphate group 

• Nucleotide Polymers: 

  • Linked together to build a polynucleotide 

    • Adjacent nucleotides are joined by covalent bonds that form between -OH group on the 3’ carbon of one nucleotide and the phosphate on 5’ carbon on the next 

    • These links create a backbone of sugar-phosphate units with nitrogenous bases as appendages 

  • The sequence of bases along a DNA or mRNA polymer is unique for each gene 

• The Structure of DNA RNA Molecules: 

  • RNA molecules usually exist as single polypeptide chains 

  • DNA molecules have two polynucleotides spiraling around an imaginary axis, forming a double helix 

    • In the DNA double helix, the 2 backbones run in opposite 5’→3’ directions from each other, an arrangement referred to as antiparallel 

      • One DNA molecule includes many genes 

• The nitrogenous bases in DNA pair up and form hydrogen bonds: adenine (A) with thymine (T), guanine (G) with cytosine ©

  • Called complementary base pairing 

    • Can also occur between 2 RNA molecules or between parts of the same molecule 

      • RNA: thymine is replaced with uracil (U) so A and U pair 

Cells:

• All organisms are made of cells

  • Simplest collection of matter that can be alive

• Cell structure correlated to cellular function

• All cells are related by their descent from earlier cells

  • What is the first cell? 

• Microscopes used for studying cells 

  • Light microscope (LM): visible light passed thru a specimen & then thru glass lenses

    • Lenses refract/bend light so image is magnified 

    • Magnify effectively to abt 1000x the original size

      • Consider what kind of staining should be used to differentiate diff parts of the cell 

    • Most subcellular structures including organelles (membrane-enclosed compartments) are too small to be resolved by LM 

• 3 important parameters of microscopy

  • Magnification: the ratio of the object’s image size to its real size

  • Resolution: the measure of the clarity of the image/the minimum distance of 2 distinguishable points

    • Ex: imagine standing far away from someone holding up 2 fingers, you might see it as one until you zoom close enough to see it’s actually 2 fingers 

  • Contrast: visible differences in parts of the sample 

• 2 basic types of electron microscopes (EMs) are used to study subcellular structures

  • Scanning electron microscopes (SEMs) focus a beam of electrons onto the surface of a specimen, providing 3D images 

    • Allows to visualize surface of specimen 

  • Transmission electron microscopes (TEMs) focus a beam of electrons thru a specimen 

    • TEMs used mainly to study internal structure of cells - cross-section 

      • Anything studied by these EMs has to not be alive

• Cell fractionation: taking cells apart & separating the major organelles from one another

  • Centrifuges fractionate cells into their component parts 

  • Enables scientists to determine functions of organelles 

• Eukaryotic cells have internal membranes that compartmentalize their functions

  • The basic structural & functional unit of every organism is ½ types of cells: prokaryotic/eukaryotic 

    • Prokaryotic cells: organisms of domains Bacteria & Archaea 

    • Eukaryotic cells: protists, fungi, animals, plants 

• Comparing Prokaryotic & Eukaryotic cells 

  • Basic features of all cells 

    • Plasma membrane

    • Cytosol: semifluid substance

    • Chromosomes (DNA -  carry genes) 

    • Ribosomes (make proteins)

    • Plasma membrane: selective barrier that allows sufficient passage of oxygen, nutrients, & waste to service volume of every cell 

      • Need to have enough to allow enough O2 in cell, CO2 out, nutrients in, waste out 

      • Need enough surface area of membrane to service all volume on inside 

    • General structure of a biological membrane: double layer of phospholipids 

      • Hydrophilic & hydrophobic regions 

• Prokaryotic cells are characterized by having: 

  • No nucleus 

  • Nucleoid: DNA in unbound region

  • No membrane-bound organelles

    • Has ribosomes

  • Cytoplasm bound by plasma membrane 

    • Includes everything inside cell 

• Eukaryotic cells are characterized by having: 

  • DNA in nucleus that’s bounded by membranous nuclear envelope

  • Membrane-bound organelles 

  • Cytoplasm in the region btwn the plasma membrane & nucleus 

• Eukaryotic cells generally much larger than prokaryotic cells 

• Metabolic requirements set upper limits on size of cells

  • Surface area to volume ratio of cell is critical 

    • SA: plasma membrane inside cell; Volume: everything inside cell 

  • As SA increases by n^2, volume increases by n^3

    • Small cells have a greater surface area relative to volume 

      • Can meet their metabolic requirements easily 

• The nucleus: information central 

  • Nucleus: contains most of cell’s genes & is usually most conspicuous organelle 

  • Nuclear envelope: encloses nucleus, separating it from cytoplasm 

    • Nuclear membrane: double membrane; each membrane consists of lipid bilayer 

  • Pores regulate entry & exit of molecules from nucleus

    • Ex: prevent DNA from leaving but allow RNA to leave

  • Shape of nucleus maintained by nuclear lamina made of proteins & microfilaments 

  • DNA is organized into descrete units aka chromosomes 

    • Each chromosome is composed of a single DNA molecule associated w/ proteins 

  • Chromatin: DNA & proteins of chromosomes are together 

    • Condenses to form discrete chromosomes as cell prepares to divide

  • Nucleolus located within nucleus & is the site of ribosomal RNA (rRNA) synthesis

• Ribosomes: protein factories

  • Ribosomes: particles made of ribosomal RNA & protein

  • Carry out synthesis in 2 locations

    • Cytosol (free ribosomes) 

    • Outside of endoplasmic reticulum/nuclear envelope (bound ribosomes) 

• Endomembrane system regulates protein traffic & performs metabolic functions in the cell 

  • System of membranes inside cell important for making, packaging, distributing proteins

  • Components of endomembrane system 

    • Nuclear envelope

      • Continuous & physically connected  

    • Endoplasmic reticulum

      • Continuous & physically connected 

    • Golgi apparatus

      • Connected by little bubbles of membrane that travel from 1 to the next 

      • Still receives things from the ER thru little vesicles 

    • Lysosomes

      • Not continuous 

    • Vacuoles

      • Not continuous 

    • Plasma membrane

      • Not continuous but receives things from Golgi thru vesicles 

  • They are continuous/connected via transfer by vesicles 

• The Endoplasmic Reticulum: Biosynthetic Factory

  • The Endoplasmic reticulum (ER) accounts for more than half of total membrane in many eukaryotic cells 

  • ER membrane continuous w/ nuclear envelope 

  • 2 distinct regions of ER

    • Smooth ER: lacks ribosomes

    • Rough ER: surface studded w/ ribosomes 

• Functions of Smooth ER: 

  • Synthesizes lipids

  • Metabolizes carbohydrates

  • Detoxifies drugs & poisons

    • Found a lot in liver & muscle cells 

  • Stores calcium ions - muscle cells to contract

• Functions of Rough ER: 

  • Has bound ribosomes that secrete glycoproteins (proteins covalently bounded to carbohydrates) 

  • Distributes transport vesicles: proteins surrounded by membranes

  • Is a membrane factory for the cell 

    • Cell membranes are constantly losing pieces as they take things into cell & pinch off to form vesicles 

    • Makes more membrane that’ll go up & fuse w/ cell membrane to keep it the same size 

• The Golgi Apparatus: Shipping and Receiving Center 

  • The Golgi Apparatus consists of flattened membranous sacs called cisternae 

  • Functions: 

    • Modifies products of the ER

    • Manufactures certain macromolecules 

    • Sorts & packages materials into transport vesicles 

• Lysosomes: Digestive Compartments

  • Lysosome:  membranous sac of hydrolytic enzymes that can digest macromolecules 

    • Hydrolyze proteins, fats, polysaccharides, nucleic acids 

    • Work best in acidic envrionment inside lysosome 

  • Some types of cells can engulf another cell by phagocytosis; this forms a food vacuole 

    • A lysosome fuses w/ the food vacuole & digests the molecules 

  • Lysosomes also use enzymes to recycle the cell’s own organelles & macromolecules - process called autophagy 

• Vacuoles: Diverse Maintenance Compartments 

  • A plant cell/fungal cell may have 1 or more vacuoles, derived from ER & Golgi apparatus 

  • Food vacuoles: formed by phagocytosis 

  • Contractivle vacuoles: found in many freshwater proteins - pump XS water out of cells 

  • Central vacuoles: found in many mature plant cells - hold organic compounds & water 

• Mitochondria & Chloroplasts Change Energy From 1 Form to Another 

  • Mitochondria: sites of cellular respiration 

    • Metabolic process that uses oxygen to generate ATP 

  • Chloroplasts:  found in plants & algae - sites of photosynthesis

  • Peroxisomes: oxidative organelles 

    • Can remove electrons from diff molecules 

• Evolutionary Origins of Mitochondria & Chloroplasts 

  • Mitochondria & chloroplasts have similarities w/ bacteria

    • Double membrane

    • Contain free ribsomes & circular DNA molecules 

    • Grow & reproduce somewhat independently in cells 

• The Endosymbiont Theory 

  • An early ancestor of eurkaryotic cells ate a nonphotosynthetic prokaryotic cell (cellular respiration), which formed an endosymbiont relationship w/ its host 

  • The host cell & endosymbiont merged into a single organism, a eukaryotic cell w/ a mitochondrion

  • @ least 1 of these cells may have taken up a photosyntheitc prokaryote, becoming the ancestor of cells that contain chloroplasts 

• Mitochondria: chemical energy conversion 

  • Mitochondria are in nearly all eukaryotic cells 

  • Have a sooth outhe rmembrane & inner membrane folded into cristae 

    • Cristae present large surface area for enzymes that synthesize ATP 

  • Inner membrane creates 2 compartments: intermembrane space & mitochondrial matrix 

    • Some metabolic steps of cellular respiration are catalyzed into mitochondrial matrix 

• Chloroplasts: Capture of Light Energy 

  • Contain green pigment chlorophyll, as well as enzymes & other molecules that function in photosynthesis

  • Found in leaves & other green organs of plants & in algae 

  • Structure includes: 

    • Thylakoids: membranous sacs, stacked to form granum 

    • Stroma: internal fluid 

  • One of a group of plant organelles called plastids 

• Peroxisomes: Oxidation 

  • Peroxisomes: specialized metabolic compartments bounded by single membrane 

  • Produce hydrogen peroxide & convert it to water

  • Perform reactions w/ many diff functions 

  • How peroxisomes are related to other organelles is still unknown  

• The Cytoskeleton is a Network of Fibers That Organizes Structures and Activities in the Cell 

  • Cytoskeleton: network of fibers extending throughout cytoplasm 

  • Organizes cell’s structures & activities, anchoring many organelles 

  • Compared of 3 types of molecular structures 

    • Microtubulues

    • Microfilaments

    • Intermediate filaments

• Roles of the Cytoskeleton: Support & Motility

  • Cytoskeleton helps to support cell & maintain its shape

  • Interacts w/ motor proteins to produce motility 

  • Viesciles can travel along “monorails” inside cell provided by cytoskeleton 

  • Recent evidence esuggests that cytoskeleton may help regulate biochemical activities 

• Microtubules: hollow rods abt 25 nm in diameter & about 200 nm to 25 microns long

  • Functions:

    • Shaping the cell 

    • Guiding movement of organelles 

    • Separating chromosomes during cell division 

• Centrosomes & Centrioles: 

  • In many cells, microtubules grow out from a centrsome near the nucleus 

    • “Microtubule-organizing center” 

  • In animal cells, the centrosome has a pair of centrioles, each with 9 triplets of microtubules arranged in a ring 

• Cilia & Flagella 

  • Microtubules control the beating of cilia and flagella, locomotor appendages of some cells 

  • Cilia and flagella differ in their beating patterns 

  • Share common structure 

    • Core of microtubulues sheathed by plasma membrane 

    • Basal body anchors cilium/flagellum 

    • Motor protein called dynein - drives the bending movements of a cilium/flagellum 

• How Dynein “Walking” Moves Flagella & Cilia 

  • Dyenin arms alternately grab, move & release outer microtubules 

  • Protein cross-links limit sliding

  • Forces exerted by dynein arms cause doublets to curve, bending cilium/flagellum

• Microfilaments (actin filaments) 

  • Microfilaments: solid rods abt 7nm in diameter - built as a twisted double chain of actin subunits 

    • Structural role of microfilaments is to bear tension, resisting pulling forces within cell 

    • Form a 3D netwok called cortex just insde plasma membrane to help support cell’s shape 

    • Bundles of microfilaments make up core of microvilli of intestinal cells 

• Microfilaments that function in cellular motility contain the protein myosin in addition to actin 

  • Thousands of actin filanets are arranged parallel to one another in muscle cells 

  • Thicker filaments composed of myosin interdigitate w/ the thinner actin fibers 

• Localized contraction brought about by actin & myosin also drives amoeboid movement 

  • Pseudopodia (cellular extensions) extended & contract thru reversible assembly & contraction of actin subunits into microfilaments 

  • Cytoplasmic streaming: circular flow of cytoplasm within cells 

    • This streaming speeds distribution of materials within cell 

    • In plant cells, actin-myosin interactions & sol-gel transformations drive cytoplasmc streaming 

• Intermediate filaments 

  • Intermediate filaments range in diameter from 8-12 nanometers, larger than microfilaments but smaller than microtubules 

    • Support cell shape & fix organelles in place 

  • More permanent cytoskeleton fixtures than the other 2 classes 

• Extracellular components & connections btwn cells help coordinate cellular activities 

  • Most cells synthesize & secrete materials that’re external to plasma membrane 

  • Extracellular structures include 

    • Cell walls of plants

    • Extracellular matrix (ECM) of animal cells 

    • Intercellular junctions

• Cell walls of plants 

  • Cell wall: extracellular structure tht distinguishes plant cells from animal cells 

  • Prokaryotes, fungi, & some protists also have cell walls 

  • Protects plant cell, maintains its shape, & prevents excessive uptake of water 

  • Plant cell walls are made of cellulose fibers embedded in other polysaccharides & protein 

• Plant cell walls may have multiple layers 

  • Primary cell wall: relatively thin & flexible 

    • Has pectin & cellulose 

  • Middle lamella: thin layer between primary walls of adjacent cells 

  • Secondary cell wall (in some cells): added between plasma membrane & primary cell wall 

    • Has lignin & cellulose 

• Plasmodesmata: channels between adjacent plant cells 

• The extracellular matrix (ECM) of animal cells 

  • Animal cells lack cell walls but are covered by an elaborate extracellular matrix (ECM) 

  • ECM is made up of glycoproteins such as collagen, proteoglycans, & fibronectin 

    • ECM proteins bind to receptor proteins in plasma membrane called integrins 

  • Functions of ECM: 

    • Support 

    • Adhesion

    • Movement

    • Regulation 

• Cell junctions: 

  • Neighboring cells in tissues, organs, or organ systems often adhere, interact, & communicate thru direct physical contact 

  • Intercellular junction facilitate this contact 

  • Several types of intercellular junctions:

    • Plasmodesmata

    • Tight junctions

    • Desmosomes

    • Gap junctions

• Plasmodesmata in plant cells: 

  • Plasmodesmata: channels that perforate plant cell walls 

  • Thru plasmodesmata, water & small solutes (& sometimes proteins & RNA) can pass from cell to cell 

• Tight functions, desmosomes, & gap junctions in animal cells 

  • At tight junctions, membranes of neighboring cells are pressed tgth, preventing leakage of extracellular fluid 

  • Desmosomes (anchoring junctions) fasten cells tgth into strong sheets

  • Gap junctions (communicating junctions) provide cytoplasmic channels between adjacent cells

Membranes:

• Plasma membrane: boundary that separates living cell from surroundings 

  • Exhibits selective permeability: allows some substances to cross it more easily than others

• Membrane models: scientific inquiry

  • 1935: Hugh Davson & James Danielli proposed sandwich model in which phospholipid bilayer lies between 2 layers of globular proteins 

    • Problems w/ this model: membrane proteins have hydrophilic & hydrophobic regions 

  • 1972: S.J. Singer & G. Nicolson: membrane is mosaic of proteins dispersed within bilayer, w/ only hydrophilic regions exposed to water 

• Cellular membranes are fluid mosaics of lipids & proteins 

  • Phospholipids: most abundant lipid in plasma membrane

    • Amphipathic molecules: containing hydrophobic & hydrophilic regions

    • Fluid mosaic model: states membrane is a fluid structure w/ a “mosaic” of various proteins embedded in it  

• As temps cool, membranes switch from fluid to solid state 

  • Temp at which membrane solidifies depends on types of lipids 

  • Membranes rich in unsaturated fatty acids are more fluid than those rich in saturated fatty acids

    • Membranes must be fluid to work properly; they are usually about as fluid as salad oil

• The steroid cholesterol has diff effects on membrane fluidity @ diff temps

  • Warm temps (37C): cholesterol stops movement of phospholipids 

  • Cool temps: maintains fluidity by preventing tight packing

  • Variations in lipid composition of cell membranes of many species appear to be adaptations to specific environmental conditions 

  • Ability to change lipid compositions in response to temp changes has evolved in organisms that live where temps vary 

• Membrane proteins and their functions: 

  • Membrane: collage of different proteins, often grouped tgth, embedded in fluid matrix of lipid bilayer 

  • Proteins: determine most of membrane’s specific functions

  • Peripheral proteins: bound to surface of membrane

  • Integral proteins: penetrate hydrophobic core

    • Transmembrane proteins: integral proteins that span the membrane

    • The hydrophobic regions of an integral protein consist of 1+ stretches of nonpolar amino acids, often coiled into alpha helices 

• 6 major functions of membrane proteins:

  • Transport

  • Enzymatic activity

  • Signal transduction

  • Cell-cell recognition

  • Intercellular joining

  • Attachment to cytoskeleton and extracellular matrix (ECM)

•  The role of membrane carbohydrates in cell-cell recognition 

  • Cells recognize e/o by binding to surface molecules (often containing carbohydrates) on extracellular surface of the plasma membrane 

  • Membrane carbohydrates may be covalently bonded to lipids (forming glycoproteins) or more commonly to proteins (forming glycoproteins) 

    • Carbohydrates on external side of plasma membrane vary among species, individuals, & even cell types in an individual 

• Synthesis & sidedness of membranes 

  • Membranes have distinct inside & outside faces

    • Asymmetrical distribution of proteins, lipids, & associated carbohydrates in the plasma membrane is determined when the membrane is built by ER & Golgi apparatus

• The permeability of the lipid bilayer: 

  • Hydrophobic (nonpolar) molecules: can dissolve in the lipid bilayer and pass through the membrane rapidly (hydrocarbons)

  • Polar molecules: don’t cross the membrane easily (sugars) 

    • Transport proteins: allow passage of hydrophilic substances across the membrane 

      • Channel proteins: have a hydrophilic channel that certain molecules/ions can use as a tunnel

• Aquaporins: channel proteins that facilitate the passage of water 

  • Carrier proteins: bind to molecules and change shape to shuttle them across the membrane

    • A transport protein is specific for the substance it moves 

• Passive transport is diffusion of a substance across a membrane with no energy investment

  • Diffusion: the tendency for molecules to spread out evenly into the available space

    • Altho each molecule moves randomly, diffusion of a population of molecules may be directional 

  • @ dynamic equilibrium: as many molecules cross the membrane on 1 direction as in the other 

• Substances diffuse down their concentration gradient

  • The region along which the density of a chemical substance increases/decreases 

    • No work must be done to move substances down the concentration gradient 

  • Passive transport: the diffusion of substances across a biological membrane

    • No energy is expended by the cell to make it happen 

• Effects of osmosis on water balance: 

  • Osmosis: the diffusion of water across a selectively permeable membrane

    • Water diffuses across a membrane from a region of lower solute concentration to the region of higher solute concentration until the solute concentration is equal on both sides 

• Water balance of cells without walls 

  • Tonicity: the ability of a surrounding solution to cause a cell to gain/lose water 

    • Isontonic solution: solute concentration is the same as that inside the cell

      • No net water movement across the plasma membrane

    • Hypertonic solution: solute concentration is greater than inside the cell 

      • Cell loses water

    • Hypotonic solution: solute concentration is less than inside the cell

      • Cell gains water 

  • hypertonic/hypotonic environments create osmic problems for organisms

    • Osmoregulation: the control of solute concentrations and water balance

      • Necessary adaptation for life in such environments 

• Water balance of cells with walls: 

  • Cell walls help maintain water balance

    • Plant cell in a hypotonic solution swells until the wall opposes uptake

      • Cell is now turgid (firm) 

    • If a plant cell and its surroundings are isotonic, there’s no net movement of water into the cell 

      • Cell is now flaccid (limp) & the plant can wilt 

    • Hypertonic environment: plant cells lose water

      • Membrane eventually pulls away from the wall: plasmolysis 

• Facilitated diffusion: passive transport aided by proteins

  • Facilitated diffusion: transport proteins speed the passive movement of molecules across the plasma membrane

    • Still passive b/c the slute moves down its concentration gradient, & the transport requires no energy 

  • Channel proteins provide corridors that allow a specific molecule/ion to cross the membrane

    • Carrier proteins under a subtle change in shape that translocates the solute-binding site across the membrane 

  • Channel proteins include: 

    • Aquaporins for facilitate diffusion of water 

    • Ion channels that open/close in response to a stimulus (gated …) 

• Active transport uses energy to move solutes against their gradients:

  • Active transport: moves substances against their concentration gradients 

    • Requires energy, usually in the form of ATP

    • Performed by specific proteins embedded in the membranes

    • Allows cells to maintain concentration gradients that differ from their surroundings 

      • The sodium-potassium pump is one type of active transport system

• How ion pumps maintain membrane potential: 

  •  Membrane potential: the voltage difference across a membrane 

    • Voltage is created by differences in the distribution of positive & negative ions across a membrane 

  • 2 combined forces, collectively called the electrochemical gradient, drive the diffusion of ions across a membrane

    • A chemical force (the ion’s concentration gradient) 

    • An electrical force (the effect of the membrane potential on the ion’s movement)

• Electrogenic pump: a transport protein that generates voltage across a membrane

  • Sodium-potassium pump: the major electrogenic pump of animal cells 

  • Proton pump: the main electrogenic pump of plants, fungi, & bacteria 

  • Electrogenic pumps help store energy that can be used for cellular work 

• Cotransport: Coupled Transport by a Membrane Protein

  • Cotransport: occurs when active transport of a solute indirectly drives transport of other solutes

    • Plants commonly use the gradient of hydrogen ions generated by proton pumps to drive active transport of nutrients into the cell

• Bulk transport across the plasma membrane occurs by exocytosis and endocytosis

  • Small molecules and water enter/leave the cell through the lipid bilayer or via transport proteins

  • Large molecules, such as polysaccharides & proteins, cross the membrane in bulk via vesicles 

  • Bulk transport requires energy

• Exocytosis: transport vesicles migrate to the membrane, fuse w/ it, & release their contents 

  • Many secretary cells use exocytosis to export their products 

• Endocytosis: the cell takes in macromolecules by forming vesicles from the plasma membrane 

  • A reversal of exocytosis, involding different proteins

  • 3 diff types of endocytosis: 

    • Phagocytosis (“cellular eating”)

    • Pinocytosis (“cellular drinking”)

    • Receptor-mediated endocytosis 

• Phagocytosis: a cell engulfs a particle in a vacuole 

  • The vacuole fuses w/ a lysosome to digest the particle

• Pinocytosis: molecules are taken up when extracellular fluid is “gulped” into tiny vesicles 

• Receptor-mediated endocytosis: binding of ligands to receptors triggers vesicle formation

• Ligand: any molecule that binds specifically to a receptor site of another molecule 

Energy and Enzymes

• Overview: The Energy of Life

  • Cell: a miniature chemical factory where thousands of reactions occur

    • Extracts energy and applies energy to perform work 

• What is Metabolism? 

  • Metabolism: the totality of an organism’s chemical reactions

    • An emergent property of life that arises from interactions between molecules within the cell 

• Metabolic pathways: begin with a specific molecule and ends with a product

  • Each step is catalyzed by a specific enzyme 

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

  • Cellular respiration 

• Anabolic pathways: consume energy to build complex molecules from simpler ones

  • Example: the synthesis of protein from amino acids

  • Bioenergetics: the study of how organisms manage their energy resources

• Forms of Energy: 

  • Energy: the capacity to cause change 

    • Exists in various forms, some of which can perform work 

• Kinetic energy: energy associated with motion

  • Heat (thermal energy: kinetic energy associated with random movement of atoms/molecules 

  • Potential energy: energy that matter possesses because of its location/structure 

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

      • Energy can be converted from 1 form to another

• The Laws of Energy Transformation: 

  • Thermodynamics: the study of energy transformations

    • Isolated system: is isolated from its surroundings

    • Open system: energy and matter can be transferred between the system and its surroundings

      • Organisms are open systems 

• The First Law of Thermodynamics: the energy of the universe is constant

  • Energy can be transferred & transformed, but it cannot be created/destroyed 

    • Also called the principle of conservation of energy 

• The Second Law of Thermodynamics: 

  • During every energy transfer/transformation, some energy is unusable & is often lost as heat

  • 2nd law of thermodynamics: every energy transfer/transformation increases the entropy (disorder) of the universe 

• Living cells unavoidably convert organized forms of energy to heat

  • Spontaneous processes: occur without energy input; they can happen quickly/slowly 

    • For a process to occur without energy input, it must increase the entropy of the universe 

  • Cells create ordered structures from less ordered materials 

  • AND organisms replace ordered forms of matter and energy with less ordered forms 

• Why doesn’t the evolution of more complex organisms does violate the second law of thermodynamics? 

  • Entropy (disorder) may decrease in an organism, but the universe’s total entropy increases 

• The free-energy change of a reaction tells us whether or not the reaction occurs spontaneously 

  • A living system’s free energy: energy that can do work when temperature and pressure are uniform, as in a living cell 

• The change in free energy (ΔG) during a process is related to the change in enthalpy, or change in total energy (ΔH), change in entropy (ΔS), and temperature in Kelvin (T)

  • ΔG = ΔH - TΔS

  • Only processes with a negative ΔG are spontaneous 

    • Spontaneous processes can be harnessed to perform work 

• Free Energy, Stability, and Equilibrium

  • Free energy: a measure of a system’s instability, its tendency to change to a more stable state 

    • During a spontaneous change, free energy decreases & the stability of a system increases 

  • Equilibrium: a state of maximum stability

    • A process is spontaneous and can perform work only when it’s moving toward equilibrium 

• Exergonic and Endergonic Reactions in Metabolism

  • Exergonic reaction: proceeds with a net release of free energy and is spontaneous 

  • Endergonic reaction: absorbs free energy from its surroundings and is nonspontaneous

• Equilibrium and Metabolism 

  • Reactions in a closed system eventually reach equilibrium and then don’t do work 

  • Cells are NOT in equilibrium 

  • A defining feature of life is tht metabolism is never at equilibrium 

  • A catabolic pathway in a cell releases free energy in a series of reactions

• ATP powers cellular work by coupling exergonic reactions to endergonic reactions

  • A cell does 3 main kinds of work

    • Chemical

    • Transport

    • Mechanical 

  • To do work, cells manage energy resources by energy coupling

    • The use of an exergonic process to drive an endergonic one

      • Most energy coupling in cells is mediated by ATP 

• The Structure and Hydrolysis of ATP 

  • ATP (adenosine triphosphate): the cell’s energy shuttle

    • Composed of ribose (sugar), adenine (nitrogenous base), & 3 phosphate groups 

• The bonds between the phosphate groups of ATP’s tail can be broken by hydrolysis 

  • Energy is released from ATP when the terminal phosphate is broken 

    • This release of energy comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves 

• How the Hydrolysis of ATP Performs Work

  • The 3 types of cellular work (mechanical, transport, & chemical) are empowered by the hydrolysis of ATP 

  • In the cell, the energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction

    • Overall: coupled reactions are exergonic 

• ATP drives endergonic reactions by phosphorylation

  •  Transferring a phosphate group to some other molecule, such as a reaction

  • Phosphorylated intermediate: the recipient molecule

• Enzymes speed up metabolic reactions by lowering energy barriers 

  • Catalyst: a chemical agent that speeds up a reaction without being consumed by the reaction

  • Enzyme: a catalytic protein

• The Activation Energy Barrier 

  • Every chemical reaction between molecules involves bond-breaking and bond-forming

  • Activation energy: the initial energy needed to start a chemical reaction

    • Aka the free energy of activation

      • Often supplied in the form of thermal energy that the reactant molecules absorb from their surroundings

• How Enzymes Lower the EA Barrier 

  • Enzymes don’t affect the change in free energy (ΔG)

    • They instead hasten reactions that would occur eventually 

• Substrate Specificity of Enzymes

  • Enzyme’s Substrate: the reaction that an enzyme acts on 

  • Enzyme-substrate complex: what is formed when the enzyme binds to its substrate

  • Active site: the region on the enzyme where the substrate binds 

  • Induced fit: brings chemical groups of the active site of a substrate into positions that enhance their ability to catalyze the reaction 

• Catalysis in the Enzyme’s Active Site: 

  • Enzymatic reaction: the substrate binds to the active site of the enzyme

    • The active site can lower an EA barrier by: 

      • Orienting substrates correctly

      • Straining substrate bonds

      • Providing a favorable microenvironment 

      • Covalently bonding to the substrate

• Effects of Local Conditions on Enzyme Activity: 

  • What affects an enzyme’s activity? 

    • General environmental factors (temperature & pH)

    • Chemicals that specifically influence the enzyme

• Effects of Temperature and pH:

  •  Each enzyme has: 

    • An optimal temperature in which it can function

    • An optimal pH in which it can function

  • Optimal conditions favor the most active shape for the enzyme molecule 

• Cofactors: 

  • Cofactors: nonprotein enzyme helpers

    • May be inorganic (such as a metal in ionic form)/organic 

  • Coenzyme: an organic cofactor

    • Coenzymes include vitamins

• Enzyme Inhibitors: 

  • Competitive inhibitors: bind to the active site of an enzyme

    • Competes with the substrate

  • Noncompetitive inhibitors: bind to another part of an enzyme

    • Cause the enzyme to change shape

    • Make the active site less effective 

      • Examples of inhibitors: toxins, poisons, pesticides, antibiotics 

• The Evolution of Enzymes: 

  • Enzymes are proteins encoded by genes therefore: 

    • Changes (mutations) in genes lead to changes in amino acid composition of an enzyme 

    • Altered amino acids in enzymes may alter their substrate specificity 

    • Under new environmental conditions, a novel form of an enzyme might be favored 

• Regulation of enzyme activity helps control metabolism 

  • Chemical chaos would result if a cell’s metabolic pathways were not tightly regulated

    • A cell does this by switching on/off the genes that encode specific enzymes or by regulating the activity of enzymes

• Allosteric Regulation of Enzymes: 

  • Allosteric regulation: may either inhibit/stimulate an enzyme’s activity 

    • Occurs when a regulatory molecule binds to a protein at one site & affects the protein’s function at another site

• Allosteric Activation and Inhibition

  • Most allosterically regulated enzymes are made from polypeptide subunits

  • Each enzyme has active and inactive forms

    • Binding of an activator: stabilizes the active form of the enzyme

    • Binding of an inhibitor: stabilizes the active form of the enzyme 

• Cooperativity: a form of allosteric regulation that can amplify enzyme activity 

  • 1 substrate molecule primes an enzyme to act on additional substrate molecules more readily 

  • Allosteric b/c binding by a substrate to 1 active site affects catalysis in a different active site 

• Identification of Allosteric Regulators 

  • Allosteric regulators: attractive drug candidates for enzyme regulation because of their specificity 

    • Inhibition of proteolytic enzymes called caspases may help management of inappropriate inflammatory responses 

• Feedback Inhibition

  • What is feedback inhibition? 

    • Feedback inhibition: the end product of a metabolic pathway shuts down the pathway 

      • Prevents a cell from wasting chemical resources by synthesizing more product than is needed

• Specific Localization of Enzymes Within the Cell 

  • Structures within the cell help bring order to metabolic pathways

  • Some enzymes act as structural components of membranes 

  • In eukaryotic cells, some enzymes reside in specific organelles; for example, for cellular respiration are located in mitochondria

Circulatory System

Gas Exchange

• Organisms must exchange materials with its environment

  • Exchanges occur at the cellular level across the plasma membrane

Closed Circulatory System

• A circulatory system has

  • Circulatory fluid

  • A set of interconnecting vessels

  • A muscular pump, the heart

Organization of Vertebrate Circulatory Systems

• Humans and other vertebrates have a closed circulatory system called the cardiovascular system

• The 3 main types of blood vessels are arteries, veins, and capillaries

  • Blood flow is one way in these vessels

• Arteries and veins are distinguished by the direction of blood flow, not by O2 content

• Vertebrate hearts contain 2 or more chambers

  • Blood enters through an atrium and is pumped

• Arteries: branch into arterioles

  • Carry blood away from the heart to capillaries

• Capillary beds: sites of chemical exchange between the blood and interstitial fluid

• Venules: converge into veins

  • Return blood from capillaries to the heart

Blood Vessel Structure and Function

• Central lumen: a vessel’s cavity

• Endothelium: the epithelial layer that lines blood vessels

  • The endothelium is smooth and minimizes resistance

• Capillaries are only slightly wider than a red blood cell

• Arteries have thicker walls than veins to accommodate the high pressure of blood pumped from the heart

• Where?

  • The exchange of substances between the blood and interstitial fluid takes place across the thin endothelial walls of the capillaries

• Forces? 

  • The difference between blood pressure and osmotic pressure drives fluids out of capillaries at the arteriole end and into capillaries at the venule end

• Most blood proteins and all blood cells are too large to pass through the endothelium

Partial Pressure Gradients in Gas Exchange

• Partial pressure: pressure exerted by a particular gas in a mixture of gases

  • Partial pressures also apply to gases dissolved in liquids such as water

• Gases undergo net diffusion from a region of higher partial pressure to a region of lower partial pressure

Respiratory Media

• Animals can use air or water as the O2 source, or respiratory medium

• In a given volume, there is less O2 available in water than in air

• So obtaining O2 from water requires greater efficiency than air breathing

Mammalian Respiratory Systems: A Closer Look

• A system of branching ducts conveys air to the lungs

• Air passes through the nose, pharynx, larynx, trachea, bronchi, and bronchioles to the alveoli, where gas exchange occurs

• Cilia and mucus line the epithelium of the air ducts and move particles up the pharynx

• Gas exchange takes place in alveoli, air sacs at the tips of bronchioles

Coordination of Circulation and Gas Exchange

• Blood arriving in the lungs has a low partial pressure of O2 and a high partial pressure of CO2 relative to air in the alveoli

• In the alveoli, O2 diffuses into the blood and CO2 diffuses into the air

• In tissue capillaries, partial pressure gradients favor diffusion of O2 into the interstitial fluids and CO2 into the blood

Respiratory Pigments

• Respiratory pigments: proteins that transport oxygen, greatly increase the amount of oxygen that blood can carry

• Most vertebrates and some invertebrates use hemoglobin

  • Contained within erythrocytes

  • A single hemoglobin molecule can carry up to four molecules of O2, one molecule for each iron-containing heme group

• The hemoglobin dissociation curve: a small change in the partial pressure of oxygen can result in a large change in delivery of O2

  • CO2 produced during cellular respiration lowers blood pH and decreases the affinity of hemoglobin for O2; this is called the Bohr shift

Carbon Dioxide Transport

• Some CO2 from respiring cells diffuses into the blood and is transported in blood plasma, bound to hemoglobin

• The remainder diffuses into erythrocytes and reacts with water to form H2CO3, which dissociates into H+ and bicarbonate ions (HCO3-)

• In the lungs the relative partial pressures of CO2 favors the net diffusion of CO2 out of the blood

Digestion:

• The Need To Feed:

  • Food is taken in, taken apart, and taken up in the process of animal nutrition

  • Herbivores: plants and algae

  • Carnivores: other animals

  • Omnivores: regularly consume animals as well as plants or algae

  • Most animals are also opportunistic feeders

• Digestion: the process of breaking food down into molecules small enough to absorb

• Mechanical digestion: chewing; increases the surface area of food

• Chemical digestion: splits food into small molecules that can pass through membranes; used to build larger molecules

  • The process of enzymatic hydrolysis splits bonds in molecules with the addition of water

• Absorption: uptake of nutrients by body cells

• Elimination: the passage of undigested material out of the digestive system

Digestive Compartments

• Most animals process food in specialized compartments; which reduces risk of an animal digesting its own cells and tissues

Intracellular Digestion

• Food particles are engulfed by phagocytosis

• Food vacuoles, containing food, fuse with lysosomes containing hydrolytic enzymes

• Sponges digest their food entirely by this mechanism

Extracellular Digestion

• The breakdown of food particles outside of cells

• Occurs in compartments that are continuous with the outside of the animal’s body

• Animals with simple body plans have a gastrovascular cavity that functions in both digestion and distribution of nutrients

• More complex animals have a digestive tube with 2 openings; mouth and anus

• Digestive tube is called a complete digestive tract or an alimentary canal

• Can have specialized regions that carry out digestion and absorption in a stepwise fashion

Organs Specialized for Sequential Stages of Food Processing Form the Mammalism Digestive System

• Mammals digestive system: alimentary canal and accessory glands that secrete digestive juices through ducts

• Accessory glands: salivary glands, pancreas, liver, gallbladder

• Food is pushed along by peristalsis, rhythmic contractions of muscles in the wall of the canal

• Valves called sphincters regulate the movement of material between compartments

The Oral Cavity, Pharynx, and Esophagus

• The first stage of digestion (mechanical) takes place in the oral cavity

• Salivary glands deliver saliva to lubricate food

• Teeth chew food into smaller particles that are exposed to salivary amylase, initiating the breakdown of glucose polymers

• Saliva also contains mucus, a viscous mixture of water, salts, cells, and glycoproteins

• The tongue shapes food into a bolus and provides help with swallowing

• The throat, or pharynx, is the junction that opens to both the esophagus and the trachea

• The esophagus connects to the stomach

• The trachea (windpipe) leads to the lungs

Digestion in the Stomach

• The stomach stores food and begins digestion of proteins

• The stomach secretes gastric juice, which converts a meal to chyme

Chemical Digestion in the Stomach

• Gastric juice has a low pH of about 2, which kills bacteria and denatures proteins

  • Gastric juice is made up of HCL and pepsin

  • Pepsin is a protease, or protein-digesting enzyme, that cleaves proteins into smaller pieces

• Parietal cells secrete H and Cl ions separately into the lumen (cavity) of the stomach

• Chief cells secret inactive pepsinogen, which is activated to pepsin when mixed with HCL in the stomach

• Mucus in the stomach helps protect the stomach lining from the acid

Stomach Dynamics

• Coordinated contraction and relaxation of stomach muscle churn the stomach’s contents

• Sphincters prevent chyme from entering the esophagus and regulate its entry into the small intestine

Digestion in the Small Intestine

• The small intestine is the longest compartment of the alimentary canal

• Most enzymatic hydrolysis of macromolecules from food occurs here

• The first portion of the small intestine is the duodenum, where chyme from the stomach mixes with digestive juices from the pancreas, liver, gallbladder, and the small intestine itself

Pancreatic Secretions

• The pancreas produces proteases trypsin and chymotrypsin that are activated in the lumen of the duodenum

• Its solution is alkaline and neutralizes the acidic chyme

Bile Production by the Liver

• In the small intestine, bile aids in digestion and absorption of fats

• Bile is made in the liver and stored in the gallbladder

• Bile also destroys nonfunctional red blood cells

Secretions of the Small Intestine

• The epithelial lining of the duodenum produces several digestive enzymes

• Enzymatic digestion is completed as peristalsis moves the chyme and digestive juices along the small intestine

• Most digestion occurs in the duodenum; the jejunum and ileum function mainly in the absorption of nutrients

Absorption in the Small Intestine

• The small intestine has a huge surface area, due to villi and microvilli that are exposed to the intestinal lumen

• The enormous microvillar surface creates a brush border that greatly increases the rate of nutrient absorption

• Transport across the epithelial cells can be passive or active depending on the nutrient

• The hepatic portal vein carries nutrient-rich blood from the capillaries of the villi to the liver, then to the heart

• The liver regulates nutrient distribution, interconverts many organic molecules, and detoxifies many organic molecules

• Epithelial cells absorb fatty acids and monoglycerides and recombine them into triglycerides

• These fats are coated with phospholipids, cholesterol, and proteins to form water-soluble chylomicrons

  • Chylomicrons are transported into a lacteal, a lymphatic vessel in each villus

• Lymphatic vessels deliver chylomicron-containing lymph to large veins that return blood to the heart

Processing in the Large Intestine

• The colon of the large intestine is connected to the small intestine

• The cecum aids in the fermentation of plant material and connects where the small and large intestines meet

• The human cecum has an extension called the appendix, which plays a minor role in immunity

• The colon completes the reabsorption of water that began in the small intestine

• Feces, including undigested material and bacteria, become more solid as they move through the colon

• Feces are stored in the rectum until they can be eliminated through the anus

• 2 sphincters between the rectum and anus control bowel movements

Evolutionary Adaptations of Vertebrate Digestive Systems Correlate with Diet

• Digestive systems of vertebrates are variations on a common plan

  • Adaptions, often related to diet

• Many carnivores have large, expandable stomachs

• Herbivores and omnivores generally have longer alimentary canals than carnivores, reflecting the longer time needed to digest vegetation

Regulation of Digestion

• Each step in the digestive system is activated as needed

• The enteric division of the nervous system helps to regulate the digestive process

• The endocrine system also regulates digestion through the release and transport of hormones

Regulation of Energy Storage

• The body stores energy-rich molecules that are not needed right away for metabolism

• In humans, energy is stored first in the liver and muscle cells in the polymer glycogen

• Excess energy is stored in fat in adipose cells

• When fewer calories are taken in than expended, the human body expends liver glycogen first, then muscle glycogen and fat