Chapter 1: Fundamentals of Biology

• Biology is the scientific study of life

• Life is recognizable by what living things do

There are 5 unifying themes within biological sciences: organization, information, energy and matter, interactions, and evolution.

Emergent Properties

• Emergent properties result from the arrangement and interaction of parts within a system

  ▪Emergent properties characterize non-biological entities as well (ex: a bike only works when all of the necessary parts connect in the right ways.)

• emergent properties= the whole is greater than the sum of the parts.

• Reductionist approach= studying isolated components of the living system (think geneticists and molecular biologists)

• ▪systems biology=analysis of the interactions among the parts of a biological system

• Systems biology can be used to study life at all levels

• Technology gains of the past 30 years has facilitated the growth of systems biology approaches

The Cell

• The cell is the smallest unit of organization that can perform all activities required for life

• Every cell is enclosed by a membrane(a thin sheet of tissue or layer of cells acting as a boundary, lining, or partition in an organism) that regulates passage of materials between the cell and its environment

• Bacterial and archaean cells = prokaryotic

• Cells of all other forms = eukaryotic cells

• A eukaryotic cell has membrane-enclosed organelles, the largest of which is usually the nucleus

• A prokaryotic cell is simpler and smaller than a eukaryotic cell. It does NOT contain a nucleus or other membrane enclosed organelles.

DNA, the Genetic Material

• Chromosomes contain genetic material in the form of one long DNA strand.

• Genes are units of inheritance and encode information for building the molecules synthesized within the cell.

• For most genes the sequence makes the blueprint for the production of protein.

• Genes are encoded into DNA. DNA turns into RNA. RNA turns into a protein. This is gene expression

Genomics

• A Genome is a organisms library of genetic instructions

• Genomics is the study of sets of genes in one or more species. The approach depends on “High-throughput” technology which provides enormous amounts of data.

• Proteomics is the study of whole sets of proteins and their properties

• The entire set of proteins expressed by a given cell, tissue, or organ is called a proteome

• Bioinformatics is the use of computational tools to process a large volume of data

Molecules: Interactions Within Organisms

• Many biological processes can Self regulate. The process is called feedback.

• In feedback regulation, the output, or product of a process, regulates that very process

• Negative feedback is a form of regulation that occurs by the output reducing the initial stimulus (More common)

• Positive feedback is when an end product speeds up it’s own production.(Less common)

Ecosystems: An Organism’s Interactions with Other Organisms and the Physical Environment

• Interactions between organisms at the ecosystem level may hurt or help both organisms.

• Organisms are divided into 3 domains, bacteria, archaea, and Eukarya.

• The prokaryotes include the domains Bacteria and Archaea 

• Domain Eukarya includes all eukaryotic organisms

• Domain Eukarya includes the protists and three kingdoms 

  ▪Plants, which produce their own food by photosynthesis

  ▪Fungi, which absorb nutrients

  ▪Animals, which ingest their food

• The most numerous and diverse eukaryotes are the protists which are mostly single-celled organisms

  ▪They are classified into several groups and sometimes are more related to plants, animals, and fungi more than other protists.

• DNA is the universal genetic language common to all organisms

• Recorded observations are called data

• Qualitative data often take the form of recorded descriptions

• Quantitative data are expressed as numerical measurement, organized into tables and graphs

• Biology is marked by “discoveries,” while technology is marked by “inventions”

Chapter 2: Chemistry of Biology

The Chemistry of Biology

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

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

• Molecules are two or more atoms chemically joined together (ex. molecular oxygen)

• ▪About 20–25% of the 92 natural elements are required for life (essential elements)

  ▪Carbon, hydrogen, oxygen, and nitrogen make up 96% of living matter

  ▪Most of the remaining 4% consists of calcium, phosphorus, potassium, and sulfur

  ▪Trace elements are required by an organism in only minute quantities

• Each element consists of unique atoms

• An atom is the smallest unit of matter that still retains the properties of an element

• Atoms are composed of subatomic particles

• Relevant subatomic particles include

  ▪Neutrons (no electrical charge)

  ▪Protons (positive charge)

  ▪Electrons (negative charge)

• Neutrons and protons form the atomic nucleus

• Electrons form a “cloud” of negative charge around the nucleus

• Neutron mass and proton mass are almost identical

• Atoms of the various elements differ in number of subatomic particles

• An element’s atomic number is the number of protons in its nucleus

• An element’s mass number is the sum of protons plus neutrons in the nucleus

• Atomic mass, the atom’s total mass, can be approximated by the mass number

Isotopes

• All atoms of an element have the same number of protons but may differ in number of neutrons

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

• Radioactive isotopes decay spontaneously, giving off particles and energy

Radiometric Dating

• A “parent” isotope decays into its “daughter” isotope at a fixed rate, expressed as the half-life (Carbon-14 🡪 Nitrogen-14)

  ▪In radiometric dating, scientists measure the ratio of different isotopes and calculate how many half-lives have passed since the fossil or rock was formed

  ▪Half-life values vary from seconds or days to billions of years

• Energy is the capacity to cause change

• Potential energy is the energy that matter has because 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

• The chemical behavior of an atom is determined by the distribution of electrons in electron shells

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

• The chemical behavior of an atom is mostly determined by the valence electrons

• Elements with a full valence shell are chemically inert

• An orbital is the three-dimensional space where an electron is found 90% of the time

• Each electron shell consists of a specific number of orbitals

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

• These interactions usually result in atoms staying close together, held by attractions called

• A covalent bond is the sharing of a pair of valence electrons by two atoms

• In a covalent bond, the shared electrons count as part of each atom’s valence shell

• A molecule consists of two or more atoms held together by covalent bonds

• A single covalent bond, or single bond, is the sharing of one pair of valence electrons

• A double covalent bond, or double bond, is the sharing of two pairs of valence electrons

• Bonding capacity is called the atom’s valence

• Covalent bonds can form between atoms of the same element or atoms of different elements

• A compound is a combination of two or more different elements

• Atoms in a molecule attract electrons to varying degrees

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

• The more electronegative an atom is, the more strongly it pulls shared electrons toward itself

• in a nonpolar covalent bond, the atoms share the electron equally

• In a polar covalent bond, one atom is more electronegative, and the atoms do not share the electron equally

• Unequal sharing of electrons causes a partial positive or negative charge for each atom or molecule

• ▪Atoms sometimes strip electrons from their bonding partners

  ▪An example is the transfer of an electron from sodium to chlorine

• After the transfer of an electron, both atoms have charges

• A charged atom (or molecule) is called an ion

• A cation is a positively charged ion

• An anion is a negatively charged ion

• An ionic bond is an attraction between an anion and a cation

• Compounds formed by ionic bonds are called ionic compounds, or salts

• Salts, such as sodium chloride (table salt), are often found in nature as crystals

• Most of the strongest bonds in organisms are covalent bonds that form a cell’s molecules

• Many large biological molecules are held in their functional form by weak bonds

• The reversibility of weak bonds can be an advantage

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

• In living cells, the electronegative partners are usually oxygen or nitrogen atoms

• A molecule’s size and shape are key to its function

• A molecule’s shape is determined by the positions of its atoms’ orbitals

• Molecular shape determines how biological molecules recognize and respond to one another

• Opiates, such as morphine, and naturally produced endorphins have similar effects because their shapes are similar and they bind the same receptors in the brain

• The starting molecules of a chemical reaction are called reactants

• The final molecules of a chemical reaction are called products

• All chemical reactions are reversible: Products of the forward reaction become reactants for the reverse reaction

• The two opposite-headed arrows indicate that a reaction is reversible

• Chemical Equilibrium is reached when the forward and reverse reactions occur at the same rate.

At equilibrium the relative concentrations of reactants and products do not change.

Chapter 3: The Molecule That Supports All of Life

Chapter 4-5: Carbon and The Molecules of Life

• Living organisms consist mostly of carbon-based compounds

• Carbon is unparalleled in its ability to form large, complex, and varied molecules

• Proteins, DNA, carbohydrates, and other molecules that distinguish living matter are all composed of carbon compounds

• Organic chemistry is the study of compounds that contain carbon, regardless of origin

• Organic compounds range from simple molecules to colossal ones

• Electron configuration is the key to an atom’s characteristics

• Electron configuration determines the kinds and number of bonds an atom will form with other atoms

• The overall percentages of the major elements of life—C, H, O, N, S, and P—are quite uniform from one organism to another

  §Because of carbon’s ability to form four bonds, these building blocks can be used to make an inexhaustible variety of organic molecules

• The great diversity of organisms on the planet is due to the versatility of carbon

• With four valence electrons, carbon can form four covalent bonds with a variety of atoms

  §This makes large, complex molecules possible

• In molecules with multiple carbons, each carbon bonded to four other atoms has a tetrahedral shape

• However, when two carbon atoms are joined by a double bond, the atoms joined to the carbons are
  in the same plane as the carbons

• Methane- CH4

• Ethane- C2H6

• Ethene(ethylene)- C2H4

• The number of unpaired electrons in the valence shell of an atom is generally equal to its valence, the number of covalent bonds it can form

• Hydrogen Valence=1

• Oxygen Valence= 2

• Nitrogen valence= 3

• Carbon valence= 4

• The electron configuration of carbon gives it covalent compatibility with many different elements

• The valences of carbon and its most frequent partners (hydrogen, oxygen, and nitrogen) are the building code for the architecture of living molecules

• Carbon atoms can partner with atoms other than hydrogen, such as the following:

  Carbon dioxide: CO_{2. O=C=O}

• Carbon chains form the skeletons of most organic molecules and they vary in length and shape

• Hydrocarbons are organic molecules consisting of only carbon and hydrogen

  §Many organic molecules, such as fats, have hydrocarbon components

  §Hydrocarbons can undergo reactions that release a large amount of energy

• §Isomers are compounds with the same molecular formula but different structures and properties

• Enantiomers are important in the pharmaceutical industry

  §Two enantiomers of a drug may have different effects

  §Usually, only one isomer is biologically active

  §Differing effects of enantiomers demonstrate that organisms are sensitive to even subtle variations
  in molecules

• Estradiol and testosterone are both steroids with
  a common carbon skeleton, in the form of four fused rings

  §These sex hormones differ only in the chemical groups attached to the rings of the carbon skeleton

• Distinctive properties of organic molecules depend on the carbon skeleton and on the chemical groups attached to it

  §A number of characteristic groups can replace
  the hydrogens attached to skeletons of organic molecules

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

  §The number and arrangement of functional groups give each molecule its unique properties

  §The seven functional groups that are most important in the chemistry of life are the following: Hydroxyl group, Carbonyl group, Carboxyl group, Amino group, Sulfhydryl group, Phosphate group, Methyl group

• §An important organic phosphate is adenosine triphosphate (ATP)

  §ATP consists of an organic molecule called adenosine attached to a string of three phosphate groups. it stores the potential to react with water. This reaction releases energy that can be used by the cell

• All living things are made up of four classes of large biological molecules: carbohydrates, lipids, proteins, and nucleic acids

• Macromolecules are large molecules and are complex

• A cell has thousands of different macromolecules

  §Macromolecules vary among cells of an organism, vary more within a species, and vary even more between species

• Large biological molecules have unique properties that arise from the orderly arrangement of their atoms

• A polymer is a long molecule consisting of many similar building blocks

  §The repeating units that serve as building blocks are called monomers

  §Carbohydrates, proteins, and nucleic acids are polymers

• Enzymes are specialized macromolecules that speed up chemical reactions such as those that make or break down polymers

• A dehydration reaction occurs when two monomers bond together through the loss of a
  water molecule

• Polymers are disassembled to monomers by hydrolysis, a reaction that is essentially the reverse of the dehydration reaction

• A huge variety of polymers can be built from a small set of monomers

• Carbohydrates include sugars and the polymers of sugars

  §The simplest carbohydrates are monosaccharides, or simple sugars

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

• In aqueous solutions many sugars form rings

  Monosaccharides serve as a major fuel for cells and as raw material for building molecules

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

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

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

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

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

  §The simplest form of starch is amylose

• §Glycogen is a storage polysaccharide in animals

  §Glycogen is stored mainly in liver and muscle cells

• Hydrolysis of glycogen in these cells releases glucose when the demand for sugar increases

• The polysaccharide cellulose is 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 two ring forms for glucose: alpha (α) and beta (β)

• Starch (α configuration) is largely helical

• Cellulose molecules (β configuration) are straight and unbranched

• Some hydroxyl groups on the monomers of cellulose can hydrogen-bond with hydroxyls of parallel cellulose molecules

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

• The cellulose in human food passes through the digestive tract as “insoluble fiber”

  •Some microbes use enzymes to digest cellulose

  •Many herbivores, from cows to termites, have symbiotic relationships with these microbes

• Chitin, another structural polysaccharide, is found in the exoskeleton of arthropods. Chitin also provides structural support for the cell walls of many fungi

• Lipids are the one class of large biological molecules that does not include true polymers. They are hydrophobic.

  §The unifying feature of lipids is that they mix poorly, if at all, with water

  §Lipids consist mostly of hydrocarbon regions

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

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

  •Glycerol is a three-carbon alcohol with a hydroxyl group attached to each carbon

  •A fatty acid consists of a carboxyl group attached to a long carbon skeleton

• Fats separate from water because water molecules hydrogen-bond to each other and exclude the fats

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

  §The fatty acids in a fat can be all the same or of
  two or three different kinds

  §Fatty acids vary in length (number of carbons) and in the number and locations of double bonds

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

• Unsaturated fatty acids have one or more double bonds

• §Fats made from saturated fatty acids are called saturated fats and are solid at room temperature

  §Most animal fats are saturated

  §Fats made from unsaturated fatty acids are called unsaturated fats or oils and are liquid at room temperature

  §Plant fats and fish fats are usually unsaturated

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

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

  §Hydrogenating vegetable oils also creates unsaturated fats with trans double bonds

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

• The major function of fats is energy storage

  §Humans and other mammals store their long-term food reserves in adipose cells

  §Adipose tissue also cushions vital organs and insulates the body

• In a phospholipid, two fatty acids and a phosphate group are attached to glycerol

  §The two fatty acid tails are hydrophobic, but the phosphate group and its attachments form a hydrophilic head

• §When phospholipids are added to water, they
  self-assemble into double-layered sheets
  called bilayers

  §At the surface of a cell, phospholipids are also arranged in a bilayer, with the hydrophobic tails pointing toward the interior

  §The phospholipid bilayer forms a boundary between the cell and its external environment

• Steroids are lipids characterized by a carbon skeleton consisting of four fused rings

• Cholesterol, a type of steroid, is a component in animal cell membranes and a precursor from which other steroids are synthesized

• A high level of cholesterol in the blood may contribute to cardiovascular disease

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

  §Some proteins speed up chemical reactions

  §Other protein functions include defense, storage, transport, cellular communication, movement, and structural support

• Enzymatic Proteins function is selective acceleration f the chemical reactions. (EX; digestive enzymes catalyze the hydrolysis of bonds in food molecules

• Defensive proteins protect against disease. (EX; antibodies inactivate and help destroy viruses and bacteria.)

• Storage proteins store amino acids. (EX: Casein, the 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.)

• Transport proteins job is to transport substances. (EX: Hemoglobin, the iron-containing protein of vertebrate blood, transports oxygen from the lungs to other parts of the body. Other proteins transport molecules across membranes, as shown here.

• Hormonal proteins coordinate an organisms activities. (EX: : Insulin, a hormone secreted by the pancreas, causes other tissues to take

  up glucose, thus regulating blood sugar concentration

• Receptor proteins fuction is response of cell to chemical stimuli.

  (EX: Receptors built into the membrane of a nerve cell detect signaling

  molecules released by other nerve cells)

• Contractile and Motor Proteins control movement. (EX: : Motor proteins are responsible for the undulations of cilia and flagella. Actin and myosin proteins are responsible for the contraction of muscles)

• Structural Proteins function is to support. (EX: Keratin is the protein of hair, horns, feathers, and other skin appendages. Insects and spiders use silk fibers to make their cocoons and webs, respectively.

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

• §Enzymes are proteins that act as catalysts to speed up chemical reactions

  §Enzymes can perform their functions repeatedly, functioning as workhorses that carry out the processes of life

• Proteins are all constructed from the same set of 20 amino acids

• Polypeptides are unbranched polymers built from these amino acids

  §A protein is a biologically functional molecule that consists of one or more polypeptides

• Amino acids are organic molecules with amino and carboxyl groups

  §Amino acids differ in their properties due to differing side chains, called R groups

• Amino acids are linked by covalent bonds called peptide bonds

  §A polypeptide is a polymer of amino acids

  §Polypeptides range in length from a few to more than 1,000 monomers

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

• The specific activities of proteins result from their intricate three-dimensional architecture

  §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 three-dimensional structure

  §A protein’s structure determines how it works

  §The function of a protein usually depends on
  its ability to recognize and bind to some other molecule

• The primary structure of a protein is its unique sequence of amino acids

  §Secondary structure, found in most proteins, consists of coils and folds in the polypeptide chain

  §Tertiary structure is determined by interactions among various side chains (R groups)

  §Quaternary structure results when a protein consists of multiple polypeptide chains

• The primary structure of a protein is its sequence of amino acids

  §Primary structure is like the order of letters in a long word and is determined by inherited genetic information

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

• Typical secondary structures are a coil called an
  αhelix and a folded structure called a βpleated sheet

• Tertiary structure, the overall shape of a polypeptide, results from interactions between R groups, rather than interactions between backbone constituents

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

• Strong covalent bonds called disulfide bridges may reinforce the protein’s structure

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

  §Collagen is a fibrous protein consisting of three polypeptides coiled like a rope

  §Hemoglobin is a globular protein consisting of
  four polypeptides: two α and two β subunits

• 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

  §The abnormal hemoglobin molecules cause the red blood cells to aggregate into chains and to deform into a sickle shape

• 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

• The loss of a protein’s native structure is called denaturation

  §A denatured protein is biologically inactive

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

• Most proteins probably go through several stages on their way to a stable structure

• Diseases such as Alzheimer’s, Parkinson’s, and mad cow disease are associated with misfolded proteins

• Scientists use X-ray crystallography to determine a protein’s structure

• Another method is nuclear magnetic resonance (NMR) spectroscopy, which does not require protein crystallization

• Bioinformatics is another approach to prediction of protein structure from amino acid sequences

• The amino acid sequence of a polypeptide is programmed by a unit of inheritance called a gene

• Genes consist of DNA, a nucleic acid made of monomers called nucleotides

• §There are two types of nucleic acids

  §Deoxyribonucleic acid (DNA)

  §Ribonucleic acid (RNA)

  §DNA provides directions for its own replication

  §DNA directs synthesis of messenger RNA (mRNA) and, through mRNA, controls protein synthesis

  §This process is called gene expression

• Each gene along a DNA molecule directs synthesis of a messenger RNA (mRNA)

  §The mRNA molecule interacts with the cell’s protein-synthesizing machinery to direct production of a polypeptide

• The flow of genetic information can be summarized as DNA → RNA → protein

• Nucleic acids are polymers called polynucleotides

  §Each polynucleotide is made of monomers called nucleotides

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

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

• Nucleoside = nitrogenous base + sugar

  §There are two families of nitrogenous bases

  §Pyrimidines (cytosine, thymine, and uracil)
  have a single six-membered ring

  §Purines (adenine and guanine) have a six-membered ring fused to a five-membered ring

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

  §Nucleotide = nucleoside + phosphate group

• Nucleotides are linked together by a phosphodiester linkage to build a polynucleotide

• A phosphodiester linkage consists of a phosphate group that links the sugars of two nucleotides

  §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

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

• The backbones run in opposite 5′ → 3′ directions from each other, an arrangement referred to as antiparallel

• One DNA molecule includes many genes

  §Only certain bases in DNA pair up and form hydrogen bonds: adenine (A) always with thymine (T), and guanine (G) always with cytosine (C)

  §This is called complementary base pairing and it makes it possible
  to generate two identical copies of each DNA molecule in a cell preparing to divide

• RNA, in contrast to DNA, is single-stranded

  §Complementary pairing can also occur between two RNA molecules or between parts of the
  same molecule

• In RNA, thymine is replaced by uracil (U), so A and U pair

  §While DNA always exists as a double helix, RNA molecules are more variable in form

• Once the structure of DNA and its relationship to amino acid sequence was understood, biologists sought to “decode” genes by learning their base sequences

  §Many genomes have been sequenced, generating large sets of data

• Bioinformatics uses computer software and other computational tools to deal with the data resulting from sequencing many genomes

• Analyzing large sets of genes or even comparing whole genomes of different species is called genomics

• A similar analysis of large sets of proteins including their sequences is called proteomics

• Sequences of genes and their protein products document the hereditary background of an organism

• Linear sequences of DNA molecules are passed from parents to offspring

  §We can extend the concept of “molecular genealogy” to relationships between species

Chapter 6: Fundamental Units of Life

The Fundamental Units of Life

• All organisms are made of cells

• The cell is the simplest collection of matter that can be alive

• All cells are related by their descent from earlier cells

• Cells can differ substantially from one another but share common features

• The resolution of standard light microscopy is too low to study organelles, the membrane-enclosed structures in eukaryotic cells

• Two 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

  •Transmission electron microscopes (TEMs) focus a beam of electrons through a specimen. TEMs are used mainly to study the internal structure of cells

• Cell fractionation takes cells apart and separates the major organelles from one another

  §Centrifuges fractionate cells into their component parts

  §Cell fractionation enables scientists to determine the functions of organelles

  §Biochemistry and cytology help correlate cell function with structure

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

  §Only organisms of the domains Bacteria and Archaea consist of prokaryotic cells

  §Protists, fungi, animals, and plants all consist of eukaryotic cells

• Basic features of all cells:

  §Plasma membrane

  §Semifluid substance called cytosol

  §Chromosomes (carry genes)

  §Ribosomes (make proteins)

• Prokaryotic cells are characterized by having

  §No nucleus

  §DNA in an unbound region called the nucleoid

  §No membrane-bound organelles

• Cytoplasm bound by the plasma membrane

• Eukaryotic cells are characterized by having

  §DNA in a nucleus that is bounded by a double membrane

  §Membrane-bound organelles

  §Cytoplasm in the region between the plasma membrane and nucleus

  §Eukaryotic cells are generally much larger than prokaryotic cell

• The plasma membrane is a selective barrier that allows sufficient passage of oxygen, nutrients, and waste to service the volume of every cell

• Metabolic requirements set upper limits on the size of cells

• The surface area to volume ratio of a cell is critical

• As a cell increases in size, its volume grows proportionately more than its surface area

• A eukaryotic cell has internal membranes that divide the cell into compartments—the organelles

• The basic structure of membranes is a double layer of phospholipids and other lipids

• Plant and animal cells have most of the same organelles

• The nucleus contains most of the DNA in a eukaryotic cell

  §Ribosomes use the information from the DNA to make proteins

• The nucleus contains most of the cell’s genes and is usually the most conspicuous organelle

• The nuclear envelope encloses the nucleus, separating it from the cytoplasm

  §The nuclear envelope is a double membrane; each membrane consists of a lipid bilayer

• Pores, lined with a structure called a pore complex, regulate the entry and exit of molecules from the nucleus

• The nuclear size of the envelope is lined by the nuclear lamina, which is composed of proteins and maintains the shape of the nucleus

  §In the nucleus, DNA is organized into discrete units called chromosomes

• Each chromosome contains one DNA molecule associated with proteins, called chromatin

  §Chromatin condenses to form discrete chromosomes as a cell prepares to divide

• The nucleolus is located within the nucleus and is the site of ribosomal RNA (rRNA) synthesis

• Ribosomes are complexes made of ribosomal RNA and protein

  §Ribosomes carry out protein synthesis in two locations:

  §In the cytosol (free ribosomes)

  §On the outside of the endoplasmic reticulum or the nuclear envelope (bound ribosomes)

• The endomembrane system consists of

  §Nuclear envelope

  §Endoplasmic reticulum

  §Golgi apparatus

  §Lysosomes

  §Vacuoles

  §Plasma membrane

  (These components are either continuous or connected via transfer by vesicles)

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

  §The ER membrane is continuous with the nuclear envelope

• There are two distinct regions of ER:

  §Smooth ER, which lacks ribosomes

  §Rough ER, whose surface is studded with ribosomes

• The smooth ER

  §Synthesizes lipids

  §Metabolizes carbohydrates

  §Detoxifies drugs and poisons

  §Stores calcium ions

• The rough ER

  §Has bound ribosomes, which secrete glycoproteins (proteins covalently bonded to carbohydrates)

  §Distributes transport vesicles, secretory proteins surrounded by membranes

  §Is a membrane factory for the cell

• The Golgi apparatus consists of flattened membranous sacs called cisternae

  §The Golgi apparatus

  §Modifies products of the ER

  §Manufactures certain macromolecules

  §Sorts and packages materials into transport vesicles

• A lysosome is a membranous sac of hydrolytic enzymes that can digest macromolecules

  §Lysosomal enzymes work best in the acidic environment inside the lysosome

  §Hydrolytic enzymes and lysosomal membranes are made by rough ER and then transferred to the Golgi apparatus for further processing

  §Some types of cell can engulf another cell by phagocytosis

  §A lysosome fuses with the food vacuole and digests the molecules

  §Lysosomes also use enzymes to digest and recycle the organelles and macromolecules,
  a process called autophagy

• Vacuoles are large vesicles derived from the ER and Golgi apparatus

  §Vacuoles perform a variety of functions in different kinds of cells

  §Food vacuoles are formed by phagocytosis

  §Contractile vacuoles, found in many freshwater protists, pump excess water out of cells

  §Central vacuoles, found in many mature plant cells, hold organic compounds and water

• The endomembrane system is a complex and dynamic player in the cell’s compartmental organization

• Mitochondria are the sites of cellular respiration, a metabolic process that uses oxygen to
  generate ATP

• Chloroplasts, found in plants and algae, are the sites of photosynthesis

• Peroxisomes are oxidative organelles

• Mitochondria and chloroplasts have similarities with bacteria:

  §Enveloped by a double membrane

  §Contain free ribosomes and circular DNA molecules

  §Grow and reproduce somewhat independently
  in cells

  §These similarities led to the endosymbiont theory (suggests that an early ancestor of eukaryotes engulfed an oxygen-using nonphotosynthetic prokaryotic cell)

  §The engulfed cell formed a relationship with the host cell, becoming an endosymbiont

  §The endosymbionts evolved into mitochondria

  §At least one of these cells may have then taken up a photosynthetic prokaryote, which evolved into a chloroplast

• Mitochondria are found in nearly all eukaryotic cells

  §They have a smooth outer membrane and an inner membrane folded into cristae

• The inner membrane creates two compartments: intermembrane space and mitochondrial matrix

  §Some metabolic steps of cellular respiration are catalyzed in the mitochondrial matrix

  §Cristae present a large surface area for enzymes that synthesize ATP

• Chloroplasts contain the green pigment chlorophyll, as well as enzymes and other molecules that function in photosynthesis

  §Chloroplasts are found in leaves and other green organs of plants and in algae

• Chloroplast structure includes

  §Thylakoids, membranous sacs, stacked to form a granum

  §Stroma, the internal fluid

  §The chloroplast is one of a group of plant organelles, called plastids

• Peroxisomes are specialized metabolic compartments bounded by a single membrane

  §Peroxisomes produce hydrogen peroxide and convert it to water

  §Peroxisomes perform reactions with many different functions

  §How peroxisomes are related to other organelles is still unknown

• The cytoskeleton is a network of fibers extending throughout the cytoplasm

  §It organizes the cell’s structures and activities, anchoring many organelles

  §It is composed of three types of molecular structures

  §Microtubules

  §Microfilaments

  §Intermediate filaments

• The cytoskeleton helps to support the cell and maintain its shape

  §It interacts with motor proteins to produce cell motility

  §Inside the cell, vesicles can travel along tracks provided by the cytoskeleton

• Three main types of fibers make up the cytoskeleton

  §Microtubules are the thickest of the three components of the cytoskeleton

  §Microfilaments, also called actin filaments, are the thinnest components

  §Intermediate filaments are fibers with diameters in a middle range

• Microtubules are hollow rods about 25 nm in diameter and about 200 nm to 25 microns long

  §Microtubules are constructed of dimers of tubulin

  §Functions of microtubules:

  §Shaping the cell

  §Guiding movement of organelles

  §Separating chromosomes during cell division

• In animal cells, microtubules grow out from a centrosome near the nucleus

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

• Microtubules control the beating of flagella and cilia, microtubule-containing extensions that
  project from some cells

  §Many unicellular eukaryotes are propelled through water by cilia or flagella

  §Cilia and flagella differ in their beating patterns

• Microfilaments are solid rods about 7 nm in diameter, built as a twisted double chain of
  actin subunits

  §A network of microfilaments helps support the cell’s shape

  §They form a cortex just inside the plasma membrane to help support the cell’s shape

  §Bundles of microfilaments make up the core of microvilli of intestinal cells

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

• Cells crawl along a surface by extending pseudopodia (cellular extensions) and moving toward them

• Cytoplasmic streaming is a circular flow of cytoplasm within cells, driven by actin-myosin interactions

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

  §Intermediate filaments are more permanent cytoskeleton fixtures than the other two classes

  §They support cell shape and fix organelles
  in place

• Most cells synthesize and secrete materials that are external to the plasma membrane

  §These extracellular materials and structures are involved in a many cellular functions

• The cell wall is an extracellular structure that distinguishes plant cells from animal cells

  §Prokaryotes, fungi, and some unicellular eukaryotes also have cell walls

  §The cell wall protects the plant cell, maintains its shape, and prevents excessive uptake of water

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

• Plant cell walls may have multiple layers:

  §Primary cell wall: Relatively thin and flexible

  §Middle lamella: Thin layer between primary walls of adjacent cells

  §Secondary cell wall (in some cells): Added between the plasma membrane and the primary cell wall

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

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

  §ECM proteins bind to receptor proteins in the plasma membrane called integrins

• The ECM has an influential role in the lives of cells

  •ECM can regulate a cell’s behavior by communicating with a cell through integrins

  •The ECM around a cell can influence the activity of gene in the nucleus

  •Mechanical signaling may occur through cytoskeletal changes that trigger chemical signals in the cell

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

• Plasmodesmata are channels that perforate plant cell walls

  §Through plasmodesmata, water and small solutes (and sometimes proteins and RNA) can pass from cell to cell

• Three types of cell junctions are common in epithelial tissues

  §At Tight junctions, membranes of neighboring cells are pressed together, preventing leakage of extracellular fluid

  §Desmosomes (anchoring junctions) fasten cells together into strong sheets

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

• Cells rely on the integration of structures and organelles in order to function

  §For example, a macrophage’s ability to destroy bacteria involves the whole cell, coordinating components such as the cytoskeleton, lysosomes, and plasma membrane

Chapter 7: Membrane and Structure Function

• The most abundant lipids in most membranes are phospholipids

  •A phospholipid is an amphipathic molecule (both a hydrophilic and hydrophobic region)

  •A phospholipid bilayer as a stable boundary between two aqueous compartments

  •Fluid mosaic model: mosaic of protein molecules drifting in a fluid bilayer of phospholipids

  •Membranes are held together mainly by weak hydrophobic interactions

  •Lipids and proteins move laterally in the plane

  •Membranes stay fluid at lower temperatures if it has unsaturated hydrocarbon tails.

  •Cholesterol helps membranes stay stable by adjusting fluidity based on temperature.

  •Membranes need to be fluid to function, for adaptation

  •Many species adapt their membrane lipids to maintain fluidity in different environments, like fish in cold water and bacteria in hot springs.

  •Some organisms adapt their membrane lipids to changing temperatures to maintain fluidity

  •Winter wheat increases unsaturated phospholipids in autumn and prevent membrane solidifying during cold winter

  •Natural selection favors organisms with membrane lipids that keep their membranes fluid in their environment. 

  •A membrane is a collage of different proteins, embedded in the fluid matrix of the lipid bilayer

  •Two major membrane proteins

  -Integral proteins spanning the membrane with hydrophobic parts inside and hydrophilic parts outside (e.g. Transmembrane proteins)

  -Peripheral proteins loosely bound to the surface of the membrane

• Left Transport proteins: A protein that spans the membrane and may provide a hydrophilic channel across the membrane that is selective for a particular solute

• Right transport protein: A protein that shuttles a substance from one side to the other by changing shape.

• •Cell-cell recognition:binding to molecules on the cell surface, this is crucial for an organisms functioning

  •Membrane carbohydrates, often form glycolipids and glycoproteins and vary widely and serve as markers to distinguish different cells

  •Four human blood types (A, B, AB, O) differ due to variations in the carbohydrates on red blood cell surfaces

• The arrangement of proteins, lipids, and carbohydrates in the plasma membrane is set during the formation of lipid composition

  •A membrane allows some substances to cross more easily than others is Selective Permeability

  •Nonpolar (hydrophobic) molecules can easily cross the lipid bilayer of the membrane

  •A charged atom or molecule with its water shell (hydrophilic) is unlikely to cross the hydrophobic membrane interior

  •Membrane proteins play a crucial role in regulating the transport of these substances

  •A charged atom or molecule can pass through transport proteins

  •Channel proteins have hydrophilic channels that allow certain molecules or ions to pass through the membrane, such as Aquaporins which facilitate water transport

  •Carrier proteins transport molecules across the membrane by holding onto them and changing shape.

  •Diffusion: Movement of particles of any substance so that they spread out into the available space without energy

  •A substance will diffuse from high to low concentration if no other forces act on it.

  •Concentration gradient: Region along which the density of a chemical substance increases or decreases

  •Passive transport: Diffusion of a substance across a biological membrane while using no energy from the cell

  •Osmosis: Diffusion of free water across a selectively permeable membrane

  •Tonicity: Ability of a surrounding solution to cause a cell to gain or lose water

  •Isotonic: no net movement of water across the membrane

  •Organisms that lack cell walls must have other adaptations for osmoregulation (regulation of solute concentrations and water balance)

  •Plants, prokaryotes, fungi, and some protists have cell walls

  •Cell wall helps maintain the cell’s water balance

  •Turgid (very firm) cells are the healthy state for most plant cells

  •In a hypertonic solution, plant cells shrivel -> Plasmolysis -> wilt -> death

  •Facilitated Diffusion: polar molecules and ions diffuse passively through transport proteins in membranes

  •Aquaporins, Ion channels (mostly gated channels:   open or close by electrical or chemical stimulus) are all types of channel proteins

  •Carrier proteins changes in shape that translocate the solute-binding site

  •Some membrane transport proteins use energy to move solutes against their concentration gradients

  •Active Transport allows cells to keep different internal solute concentration from their surroundings. Some transport proteins exert energy to move the substances along

  •ATP hydrolysis provides energy for active transport by change shape and move the solute across the membrane.

• Membrane Potential: Voltage (electrical potential energy) across a membrane

  •The cytoplasmic side of the membrane is negative in charge relative to the extracellular side -> passive transport of cations into the cell and anions out of the cell

  •When electrical forces oppose an ion’s diffusion, the cell uses active transport to move the ion.

  •Electrogenic Pump: Active transport protein that generates voltage across a membrane

  •The sodium-potassium pump appears to be the major electrogenic pump of animal cells.

  •The main electrogenic pump of plants, fungi, and bacteria is a Proton Pump

  •Cells use proton gradients to make ATP during cellular respiration

  •Cotransport: Coupling of the “downhill” diffusion of the solute to the “uphill” transport of another against its own concentration gradient

  •Plants use H⁺/sucrose cotransport to load sucrose produced by photosynthesis, into cells

  •A similar cotransporter in animals transports glucose into intestinal cells together with Na⁺

  •Large molecules cross the membranes by vesicles, not by diffusion or transport proteins

  •Exocytosis: The cell secretion of certain molecules by the fusion of vesicles with the plasma membrane

  •Many secretory cells use exocytosis to export products

  •In endocytosis, the cell takes in molecules by forming new vesicles from the plasma membrane.

  •Most endocytoses look like the reverse of exocytosis

  •Endocytosis and exocytosis contribute to rejuvenating or remodeling membranes

Chapter 8: Metabolism

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

•In a metabolic pathway, a molecule is transformed through enzyme-catalyzed steps into a final product

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

•Anabolic pathways consume energy to build complicated molecules from simpler ones

•Kinetic energy: Energy of motion of an object

•Thermal energy: Kinetic energy from the random movement of atoms or molecules

•Potential energy (not kinetic): Energy that matter has because of its location or structure

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

•Thermodynamics: Study of the energy transformations that occur in a collection of matter

•The First Law of Thermodynamics states that energy in the universe is constant. Energy can be transferred and transformed, but not created or destroyed.

•The Second Law of Thermodynamics: Every energy transfer or transformation increases the entropy (disorder) of the universe

•Organisms convert chemical energy to kinetic energy, increasing the entropy of their surroundings

•If a process increases entropy, it can happen on its own without extra energy; Spontaneous process (energetically favorable)

•Free energy is the energy in a system that can do work when temperature and pressure are uniform. spontaneous process decreases the systems free energy.

•In a spontaneous process, the system must lose free energy during the change from initial state to final state which will be negative. The system in its final state (Lower G) is less likely to change and more stable

•Living cells are not in equilibrium because materials flow in and out, keeping metabolic pathways active.

•In cellular respiration, reactions release free energy in steps, with products becoming reactants in the next step, preventing equilibrium.

• A cell does three main kinds of work: chemical work, transport work, and mechanical work.

•   Chemical work, the pushing of endergonic reactions that would not occur spontaneously

•   Transport work, the pumping of substances across membranes against the direction of  spontaneous movement

• Mechanical work, such as the beating of cilia, the contraction of muscle cells, and the   movement of chromosomes

  •Cells manage energy through energy coupling, using exergonic processes to drive endergonic ones. ATP mediates most of this process and powers cellular work

• Transport and mechanical work in cells are powered by ATP hydrolysis, which changes protein shapes and their binding abilities

• Transport and mechanical work in cells are powered by ATP hydrolysis, which changes protein shapes and their binding abilities

  •An enzyme (macromolecule that acts as a catalyst) speeds up a reaction without being consumed by the reaction

  •Activation energy (E_A): Initial investment of energy for starting a reaction—the energy required to start a reaction by breaking bonds. It acts as a barrier that determines the reaction rate, requiring reactants to absorb enough energy to reach the transition state

• Heat speeds up reactions by helping reactants reach the transition state, but it’s unsuitable for biological systems.

• Instead of heat, organisms carry out catalysis by enzymes (speed up reactions without being consumed)An enzyme cannot change for a reaction

  •The active site is a specific region of an enzyme where the substrate binds and catalysis occurs, shaped to fit the substrate perfectly

  •In enzymatic reactions, the substrate binds to the active site through weak interactions, and is converted to a product, which released and allows the enzyme to repeat the process rapidly and efficiently.

  •Small amounts of enzyme can greatly impact metabolism by repeatedly catalyzing reactions

  •Cofactors: These are nonprotein helpers that can be permanently or temporarily attached to the enzyme for catalytic activican

  •Some enzyme cofactors are inorganic metal ions (Zn, Fe, Cu) or organic cofactors, called coenzymes (vitamins).

  •Enzyme Inhibitors - certain chemicals selectively inhibit the action of specific enzymes. Toxins and poisons are often irreversible enzyme inhibitors

  •Allosteric regulation : activates or inhibit the enzyme’s function

  •In cooperativity, one substrate binding to an enzyme increase activity at other sites

• In feedback inhibition, a metabolic pathway stops when its end product binds to an early enzyme in the pathway