Biology - Blueprint for life

Van der Waals forces

van der Waals interactions The binding of temporarily polarised molecules because of the attraction of opposite charges.

Energy

"the capacity to do work" Types of Energy Kinetic - energy that is in motion (e.g movement in muscles) Potential - Stored energy that is released by a change in an object's structure or position. Gibbs free energy (G) The amount of energy available to do work. enthalpy (H) The total amount of energy in a system. entropy (S) The degree of disorder in a system. absolute temperature (T) Temperature measured on the Kelvin scale. G = H - TS The first law of thermodynamics is the law of conservation of energy, which states that the universe contains a constant amount of energy. Therefore, energy is neither created nor destroyed. The second law of thermodynamics states that the transformation of energy is associated with an increase in disorder of the universe. The degree of disorder is called entropy.

The unifying characteristics of life on earth

(1) complexity (2) respond to stimuli (3) can reproduce (4)can evolve

Types of bonds

- Ionic - Covalent - Polar covalent - Non-Polar covalent - Hydrogen

Are they alive?????

- Prions Prions are misfolded proteins with the ability to transmit their misfolded shape onto normal variants of the same protein. They characterise several fatal and transmissible neurodegenerative diseases in humans and many other animals. They aren't alive bc they are a protein - Viruses A small infectious agent that contains a nucleic acid genome packaged inside a protein coat called a capsid. Viruses are not generally considered to be alive because - viruses are completely dependent on another organism to live - viruses cannot reproduce, or make more viruses unless they are in, or on, another organism. - Giruses A giant virus is a very large virus, some of which are larger than typical bacteria. They are giant nucleocytoplasmic large DNA viruses (NCLDVs) that have extremely large genomes compared to other viruses and contain many unique genes not found in other life forms. - Bacteria Bacteria are microscopic, single-celled organisms that thrive in diverse environments. A bacterium is alive. Although it is a single cell, it can generate energy and the molecules needed to sustain itself, and it can reproduce. - Protozoans Protozoa is an informal term for single-celled eukaryotes, either free-living or parasitic, which feed on organic matter such as other microorganisms or organic tissues and debris. - Parasitoids An insect whose larvae live as parasites which eventually kill their hosts

Endergonic vs Exergonic reactions

1. Endergonic reactions: chemical reactions that require an input of energy. Not spontaneous. Products contain more free energy than the reactants. Energetically uphill. 2. Exergonic reactions: chemical reactions that release energy. Proceed spontaneously. Products will have less free energy than the reactants. Energetically downhill. "Spontaneous" in this context means that a reaction releases energy; "non-spontaneous" means that a reaction requires a sustained input of energy. Δ = means change ΔG is the free energy of the products minus the free energy of the reactants thus Exergonic have a negative ΔG and Endergonic has a positive ΔG In a chemical reaction, we can compare the total energy and entropy of the reactants with the total energy and entropy of the products to see if there is energy available to do work. As a result, we get ΔG = ΔH - TΔS Energy in catabolism and anabolism. Catabolic reactions have a negative ΔG and release energy, often in the form of ATP. Anabolic reactions have a positive ΔG and require an input of energy, often in the form of ATP. Energetic coupling Take the positive G from the Exergonic reaction and feed into into and Endergonic reaction. This occurs by having an intermediate between the two reactions.

Essential features of a cell

1. It can store and transmit information 2. It has a plasma membrane 3. It can harness energy from the environment

Minimum requirements of living cells

1. Membrane: cells are comprised of a contained space which separates self from non-self; cells' plasma membranes keep self-contained and prevent the entry of non-self 2. Homeostasis (establish and maintain): the cytoplasm must maintain correct pH, the concentration of ions, Aas, carbs, and other materials in order for the series of biochemical reactions to occur which provide energy and materials for building cells 3. Replication: involves RNA, DNA, polymerases, ribosomes; at a fundamental level, cells are factories that exist to make copies of themselves

Non-polar covalent bond

A covalent bond between atoms that have the same, or nearly the same, electronegativity is a non-polar covalent bond, which means that the atoms share the bonding electron pair almost equally. Non-polar covalent bonds include those in gaseous hydrogen (H2) and oxygen (O2). Molecules held together by non-polar covalent bonds are important in cells because they do not mix well with water.

Experimentation

A disciplined and controlled way of learning about the world and testing hypotheses in an unbiased manner.

Variable

A factor that can change in an experiment

Hydrogen bond

A hydrogen bond is the name given to this interaction between a hydrogen atom with a slight positive charge and an electronegative atom of another molecule. Hydrogen bonds influence the structure of both liquid water and ice . When water freezes, most water molecules become hydrogen bonded to four other water molecules, forming an open crystalline structure we call ice. As the temperature increases and the ice melts, some of the hydrogen bonds are destabilised and break, allowing the water molecules to pack more closely and explaining why liquid water is denser than ice.

Theory

A hypothesis that has been tested with a significant amount of data A general explanation of a natural phenomenon supported by a large body of experiments and observations.

Scientific Method

A logical, systematic approach to the solution of a scientific problem

Polymer

A long molecule consisting of many similar or identical monomers linked together.

Monomer

A molecule that can be bonded to other identical molecules to form a polymer.

Element

A pure substance, such as oxygen, copper, gold, or sodium, that cannot be further broken down by the methods of chemistry. Each element contains only one type of atom, the basic unit of matter. Today, 118 elements are known. Elements are often indicated by a chemical symbol that consists of a one- or two-letter abbreviation of the name of the element.

Redox reaction

A redox reaction is shorthand for an oxidation-reduction reaction and is a chemical reaction in which one molecule loses electrons while another molecule gains electrons. An electron carrier is a molecule that transports electrons during cellular respiration. Oxidation is a loss of electrons Reduction is the gain of electrons Carbohydrates are created (synthesised) from CO2 molecules during photosynthesis. But carbs have more energy than CO2, therefore, to build carbohydrates using CO2 requires an input of energy. This energy comes from sunlight. The synthesis of carbohydrates from CO2 and water is a reduction-oxidation, or redox, reaction. Reduction reactions are reactions in which a molecule acquires electrons and gains energy, whereas oxidation reactions are reactions in which a molecule loses electrons and releases energy. During photosynthesis, CO2 molecules are reduced to form higher-energy carbohydrate molecules. This requires both an input of energy from ATP and the transfer of electrons from an electron donor. In photosynthesis, energy from sunlight is used to produce ATP and electron donor molecules capable of reducing CO2. In photosynthesis carried out by plants and many algae, the ultimate electron donor is water. The oxidation of water results in the production of electrons, protons, and O2. Thus, oxygen is formed in photosynthesis as a by-product of water's role as a source of electrons. The oxidation of water is linked with the reduction of CO2 through a series of redox reactions in which electrons are passed from one compound to another. This series of reactions constitutes the photosynthetic electron transport chain. The process begins with the absorption of sunlight by protein-pigment complexes. The absorbed sunlight provides the energy that drives electrons through the photosynthetic electron transport chain. In turn, the movement of electrons through this transport chain is used to produce ATP and NADPH. And finally, ATP and NADPH are the energy sources needed to synthesize carbohydrates using CO2 in a process called the Calvin cycle.

Compound

A substance consisting of atoms or ions of two or more elements that are chemically bonded together, e.g. carbon dioxide, a substance consisting of carbon and two oxygen atoms

Hypothesis

A tentative explanation for one or more observations that makes predictions that can be tested by experiments or additional observations.

3. It can harness energy from the environment

A third key feature of cells is the ability to harness energy from the environment. For example when eating an apple, the apple contains sugars, which store energy in their chemical bonds. By breaking down sugar, our cells harness this energy and convert it into a form that can be used to do the work of the cell. Energy from the food we eat allows us to grow, move, communicate, and do all the other things that we do. Organisms acquire energy from just two sources—the sun and chemical compounds. The term metabolism describes chemical reactions by which cells convert energy from one form to another and build and break down molecules. These reactions are required to sustain life. Regardless of their source of energy, all organisms use chemical reactions to break down molecules, releasing energy in the process that is stored in a chemical form called adenosine triphosphate, or ATP. This molecule enables cells to carry out all sorts of work, including growth, division, and moving substances into and out of the cell.

Macromolecules

A very large organic molecule composed of many smaller molecules Building macromolecules from simple, repeating units provides a means of generating virtually limitless chemical diversity. Rearranging the building blocks that make up macromolecules provides an important way to make a large number of diverse macromolecules whose functions differ from one to the next. The four major classes of biological macromolecules are - carbohydrates - lipids - proteins - nucleic acids.

Plasma membrane

All cells are enclosed by a selective, semi-permeable barrier called a plasma membrane, (regardless of other cell walls etc) to define them from their external environment. Makeup: amphipathic phospholipids • Glycerol backbone • Phosphate/hydrophilic/polar head • Fatty acid/non-polar/hydrophobic tails) • Amphipathic nature gives the bilayer structure, the hydrophilic heads associate and align toward the water inside (cytoplasm) and outside (extracellular fluid) the cell while the tails point inwards, hiding away from this water toward the inner hydrophobic region of the membrane. • Lipids freely associate with one another because of extensive van der Waals forces between their fatty acid tails Makeup: amphipathic cholesterol (30% of membrane lipid mass) • If the membrane was only lipids, increased heat would cause it to disintegrate, and decreased heat would cause it to solidify too much • Thus, cholesterol is required to promote structure: • At low temperatures, cholesterol increases fluidity as it prevents phospholipids from packing too tightly • In high temperatures, it decreases fluidity as the rigid ring structure interacts with the acid tails and decreases their mobility. • Majority of molecule simply non-polar/hydrophobic hydrocarbon backbone • Hydroxyl group at one end is polar/hydrophilic • Able to wedge between phospholipids; hydrophilic head associates with phosphate head of one phospholipid, and hydrophobic tail associates with the non-polar tail of a neighboring phospholipid, joining them more securely • Cholesterol can accumulate in defined areas of membrane called lipid rafts that become more solid than other areas

Eukaryotes vs Prokaryotes in internal organisation

All cells have a plasma membrane and contain genetic material. In some cells, the genetic material is housed in a membrane-bound space called the nucleus. Cells can be divided into two classes based on the absence or presence of a nucleus Prokaryotes, including bacteria and archaeons, lack a nucleus Eukaryotes, including animals, plants, fungi, and protists, have a nucleus. The presence of a nucleus allows for the processes of transcription and translation to be separated in time and space which allows for more complex ways to regulate gene expression. There are other differences between prokaryotes and eukaryotes. For example - promoter recognition during transcription is different - there are differences in the types of lipid that make up their cell membranes In mammals, as we have seen, cholesterol is present in cell membranes. Cholesterol belongs to a group of chemical compounds known as sterols, which are molecules containing a hydroxyl group attached to a four-ringed structure. In eukaryotes other than mammals, diverse sterols are synthesized and present in cell membranes. Most prokaryotes do not synthesize sterols, but some synthesize compounds called hopanoids. These five-ringed structures are thought to serve a function similar to that of cholesterol in mammalian cell membranes. From an evolutionary perspective, archaeons and eukaryotes are more closely related to each other than either are to bacteria.

The tree of life

All living things can be classified into a place on the Tree of Life. This phylogenetic tree has three major branches, called Archaea, Bacteria, and Eukarya. A phylogenetic tree traces the evolutionary history of organisms and indicates common ancestors. We already see a major difference between archaea and bacteria from this classification: they have a different evolutionary history as they occupy very different places on the Tree of Life. How was this Tree of Life composed? The sequence of 16s ribosomal ribonucleic acid (16s rRNA), a fundamental unit of ribosomes, was compared across organisms. This showed that the underlying genetic code for a component of ribosomes differed greatly between archaea, bacteria, and eukarya. Thus, they form three distinct branches of the Tree of Life.

Chemical bonds

An attraction between two atoms resulting from a sharing of outer-shell electrons or the presence of opposite charges on the atoms. The bonded atoms gain complete outer electron shells.

Structure of an atom

Atoms consist of protons, neutrons, and electrons. Net charge = whether there are more protons or electrons, or they have the same amount The atom contains a nucleus made up of - positively charged particles called protons - electrically neutral particles called neutrons The third type of particle, the negatively charged electron, moves around the nucleus at some distance from it. The atomic number = number of protons Each element has a particular number of protons that no other element has, for example, and an atom with six protons is carbon. Atomic mass = protons + neutrons The atomic mass is sometimes indicated as a superscript to the left of the chemical symbol. Each proton and neutron, by definition, has a mass of 1, whereas an electron has negligible mass. The number of neutrons in atoms of a particular element can vary, changing its mass. Isotopes are atoms of the same element that have different numbers of neutrons. Typically, an atom has the same number of protons and electrons. Some chemical processes cause an atom to either gain or lose electrons. An atom that has lost an electron is positively charged, and one that has gained an electron is negatively charged. Electrically charged atoms are called ions. The charge of an ion is specified as a superscript to the right of the chemical symbol. Thus, H+ indicates a hydrogen ion that has lost an electron and is positively charged.

Carbon

Carbon molecules play such an important role in living organisms that carbon-containing molecules have a special name—they are called organic molecules. The ability of Carbon to be the backbone of life is highlighted by three of its key feature; - The tetrahedral arrangement of carbon's electron orbitals - The ability of a single carbon atom to form up to four covalent bonds - Carbon's ability to link together to form long, chained, branching molecules. Carbon has the ability to combine with many other elements to form a wide variety of molecules, each specialized for the functions it carries out in the cell. Carbon has other properties that contribute to its ability to form a diversity of molecules. - Carbon atoms can link with each other by covalent bonds to form long chains. These chains can be branched, or two carbons at the ends of the chain or within the chain can link to form a ring. Two adjacent carbon atoms can also share two pairs of electrons, forming a double bond, note that each carbon atom has exactly four covalent bonds, but in this case, two are shared between adjacent carbon atoms. One of the special properties of carbon is that, in forming molecular orbitals, a carbon atom behaves as if it had four unpaired electrons. This behavior occurs because one of the electrons in the outermost spherical orbital moves into the empty dumbbell-shaped orbital The ability of carbon to form four covalent bonds, the spatial orientation of these bonds in the form of a tetrahedron, and the ability of each bond to rotate freely all contribute importantly to the structural diversity of carbon-based molecules.

1. It can store and transmit information

Cells require deoxyribonucleic acid, or DNA to act as an accessible, stable and reliable archive of information they can use to reproduce rapidly and accurately. DNA is a double-stranded helix, with each strand made up of varying sequences of four different kinds of molecules connected end to end. It is the arrangement of these molecular subunits that makes DNA special. The information encoded in DNA directs the formation of proteins, the key structural and functional molecules that do the work of the cell including determining it's internal architecture, its shape, its ability to move, and its various chemical reactions. How does the information stored in DNA direct the synthesis of proteins? 1. Transcription. Proteins make a copy of the DNA called ribonucleic acid, or RNA. 2. Translation. Molecular structures read the RNA to determine what building blocks to use to create proteins. This process coverts info from the language of nucleic acids into the language of proteins. This process is called the central dogma of molecular biology. The central dogma describes the basic flow of information in a cell. As proteins are ultimately encoded by DNA, we can define specific stretches or segments of DNA according to the proteins that they encode. This is the simplest definition of a gene: the DNA sequence that corresponds to a specific protein product. DNA is good because - DNA is easily copied or replicated - DNA can be stably and reliably replicated because of the double helix structure. During replication, each strand of the double helix serves as a template for a new strand. Is replication wasn't precise, mistakes could occur which can be lethal to the cell. Errors in DNA can and do occur during the process of replication, and environmental insults can damage DNA as well. Such changes are known as mutations.

Cellular Respiration

Cellular respiration Harvesting energy from carbohydrates and other fuel molecules. The process of cellular respiration converts the chemical potential energy stored in organic molecules to chemical potential energy that is useful to cells (the chemical potential energy stored in ATP's bonds), producing CO2 as a by-product. A major set of catabolic reactions. Fuel molecules such as glucose (carbohydrates), fatty acids (lipids), and proteins and catabolised into smaller units. Energy in cellular respiration: Glucose is oxidized through a series of chemical reactions, releasing energy in the form of ATP and reduced electron carriers. In eukaryotes, glycolysis takes place in the cytoplasm, and pyruvate oxidation, the citric acid cycle, and oxidative phosphorylation all take place in mitochondria. The electron transport chain is made up of proteins and small molecules associated with the inner mitochondrial membrane. In some bacteria, these reactions take place in the cytoplasm, and the electron transport chain is located in the plasma membrane. Aerobic respiration Energy is released/-ve∆G as the bonds of CO2 & H2O contain less potential energy than the fuel molecules. Max free energy released is -686kcal/mol of glucose. This equation skips many intermediate steps. Not all glucose's energy can be released at once (or it would be lost as heat), so it is broken down gradually in a series of reactions. On average: 32 ATP from 1 glucose molecule. Energy to form one mole of ATP from ADP and Pi is at least 7.3 kcal. Thus, cellular respiration harnesses at least 32 × 7.3 = 233.6 kcal of energy in ATP for every mole of glucose that is broken down in the presence of oxygen. Relatively efficient: 34% of the total energy released by aerobic respiration is harnessed in the form of ATP (233.6/686 = 34%). ATP generation 1. Substrate-level phosphorylation A phosphorylated organic molecule directly transfers a phosphate group (Pi) to ADP 2 energetically-coupled reactions: hydrolysis of this organic molecule & addition of Pi to ADP. Pi (produced by PEP hydrolysis) + ADP -> ATP + H2O. PEP hydrolysis drives ATP synthesis. Both carried out by a single hormone. The organic molecule is the enzyme substrate, hence the process name. Responsible for producing 12% of ATP from glucose. Oxidative phosphorylation a. Chemical energy from organic molecules transferred to e- carriers. E- carries transport e- (and thus energy) to the ETC. In turn the ETC transfers e- to a final electron acceptor (H+ and O2), the energy released going toward the production of ATP. Responsible for producing 88% of ATP from glucose. Electron carriers (redox reactions) Two important electron carriers are nicotinamide adenine dinucleotide (NAD) and flavin adenine dinucleotide (FAD). Oxidised forms: NAD+ and FAD Reduced forms: NADH and FADH2 Catabolic oxidation reactions are coupled with the reduction of electron carrier molecules. Such reduction reactions in which electrons are transferred to electron carriers:NAD+ + 2e- + H+ → NADHFAD + 2e- + 2H+ → FADH2 In redox reactions involving organic molecules such as NAD+ or FAD, the gain (or loss) of electrons is often accompanied by the gain (or loss) of protons (H+). In their reduced forms, NADH and FADH2 can donate electrons (reverse of reduction). The oxidation of NADH and FADH2 allows electrons (and energy) to be transferred to the ETC: NADH → NAD+ + 2e- + H+ FADH2 → FAD + 2e- + 2H+ Cycle: NAD+ and FAD can then accept electrons from the breakdown of fuel molecules = shuttle e- from fuel molecules to ETC. Glycolysis Phase 1• Addition of 2 phosphate groups to glucose In eukaryotes, glycolysis takes place in the cytoplasm, and is anaerobic. Series of 10 chemical reactions, in 3 phases. OVERALL: Starts with a glucose molecule, results in its partial oxidation/breaking down into 2 3-carbon molecules of pyruvate, and the synthesis of 2 ATP molecules (by substrate-level phosphorylation) and 2 reduced e- carriers (NADH). Requires input of energy from hydrolysis of 2 ATP molecules : 1 glucose molecule Endergonic Result: phosphorylated glucose is trapped inside the cell, and 2 -ve phosphate groups destabilise the molecue, helping it break in phase 2. Phase 2 Cleavage phase 6-carbon glucose splits into 2 3-carbon molecules Phase 3 Payoff phase Produces 2 pyruvate molecules Yields 4 ATP and 2 e- carrier NADH Net gain of 2 ATP and 2 NADH. After glycolysis some of the energy from the original glucose is held in pyruvate molecules, ATP, and NADH. In anaerobic environments either fermentation (= alcohols) takes place, or anaerobic respiration (= lactic acid); the process becomes truncated, only glycolysis + a few final reactions. The purpose of the extra reactions in fermentation, then, is to regenerate the electron carrier NAD+ from the NADH produced in glycolysis. The extra reactions accomplish this by letting NADH drop its electrons off with an organic molecule (such as pyruvate, the end product of glycolysis). This drop-off allows glycolysis to keep running by ensuring a steady supply of NAD+. Pyruvate oxidation (preparation into acetyl-CoA) First step of respiration that occurs in the mitochondria. Pyruvate is transported into the mitochondrial matrix. Part of the molecule is oxidised and forms CO2 (most ox and thus least energetic carbon form), e- from this donate to NAD+ which is reduced to NADH. Remaining acetyl group (COCH3) is transferred to coenzyme A, forming acetyl-CoA. 1 acetyl-CoA molecule : 1 CO2 : 1 NADH 1glucose:2acetyl-CoA:2CO2:2NADH Citric acid cycle Glucose/fuel molecules become fully oxidised. Pyruvate still contains much chemical potential energy. Oxidation to acetyl-CoA releases some of that, and links glycolysis to the citric acid cycle. Acetyl group of acetyl-CoA is completed oxidised to CO2, and its chemical energy is transferred to reduced e- carriers (NADH & FADH2) & ATP by substrate-level phosphorylation. The cycle turns twice; once each for the 2 pyruvate moleculesResult: e- supplied to the ETC, leading to the production of more ATP. Citrate = "6-carbon molecule" made from acetyl-CoA + oxaloacetate Between 6 & 4-carbon molecule is alpha-ketoglutarate (AKG) Succinyl-CoA = "4-carbon molecule" For organisms that run the cycle forward, the citric acid cycle is used to generate both energy-storing molecules (ATP and reduced electron carriers) and intermediates in the synthesis of other molecules. For organisms that run the cycle in reverse, it is used to generate intermediates in the synthesis of other molecules and also to incorporate carbon into organic molecules. Oxidative phosphorylation The electron transport chain (ETC) E- enter at either complex I (from NADH) or II (from FADH2) NADH is oxidised to NAD+ + H+ and FADH2 to FAD + 2H+, ready to be reduced again by the previous phases E- are transported through all complexes Passed from e- donors to e- acceptors; redox couples Coenzyme Q accepts e- from both I and II Form CoQH2 with 2e- and 2H+ from mitochondrial matrix CoQH2 diffuses to III In III, e- transferred from CoQH2 to cytochrome c, and H+ are released into intermembrane space (other side) When cytochrome c accepts an e- is is reduced, diffuses into intermembrance space, and passes e- to complex IV O2 accepts e- at the chain's end, after complex IV, and is reduced to water: O2 + 4e- + 4H+ → 2H2O • E- transfer = release of energy Some E used to reduce the next e- carrier In complexed I, III, IV, some E used to pump H+ across the inner mitochondrial membrane (from matrix to intermembrance space) Thus, e- transfer is coupled w H+ pumping Result: accumulation of H+ in intermembrane space = proton gradient ~2.5 ATP : NADH that donates electrons to the chain 1.5 molecules ATP : FADH2Proton gradient NADH & FADH2 donate e- to be transported along a series of large protein complexes I to IV (IV is catalyst also) embedded in the inner mitochondrial membrane. Inner mitochondrial membrane is only selectively permeable; H+ cannot diffuse passively but move through membrane-embedded protein complexes, which creates a difference in proton concentration (high concentration in the intermembrane space and a low concentration in the mitochondrial matrix) and charge (more +ve in intermembrane space) across this membrane. Chemical gradient: difference in [H+] Electrical gradient: difference in charge = electrochemical gradientStore of potential energy Tendency for protons to diffuse back to the matrix This movement blocked by membrane This E can be harnessed if a pathway through the membrane is opened, as the movement of H+ will be used to perform work Used to synthesise ATP, thus proton pump powers ATP synthaseATP synthase makes the coupling of proton movement through the enzyme and ATP synthesis possible. Proton gradient potential energy -> mechanical rotational energy (kinetic energy) -> catalysed ATP synthesis Final results of cellular respiraiton GlycolysisNet gain of 2 ATP and 2 NADH.Pyruvate oxidation1 acetyl-CoA molecule : 1 CO2 : 1 NADH1 glucose : 2 acetyl-CoA : 2 CO2 : 2 NADHCitric acid cycle (turns twice for 1 glucose, once for each acetyl-CoA) 4CO2, 2ATP, 6NADH, 2FADH2ETC~2.5 ATP : NADH that donates electrons to the chain1.5 molecules ATP : FADH2 Overall, the complete oxidation of glucose yields about 32 molecules of ATP from glycolysis, pyruvate oxidation, the citric acid cycle, and oxidative phosphorylation.

Organic Molecules

Chemical processes in the cell depend on just a few classes of carbon-based molecules. Proteins provide structural support and act as catalysts that facilitate chemical reactions. Nucleic acids encode and transmit genetic information. Carbohydrates provide a source of energy and make up the cell wall in bacteria, plants, and algae. Lipids make up cell membranes, store energy, and act as signalling molecules. These molecules are all large, consisting of hundreds or thousands of atoms, and many are polymers, complex molecules made up of repeated simpler units connected by covalent bonds. Proteins are polymers of amino acids, Nucleic acids are polymers of nucleotides Carbohydrates such as starch are polymers of simple sugars. Lipids are a bit different, the lipid membranes that define cell boundaries consist of fatty acids bonded to other organic molecules.

Carbohydtrates

Complex carbohydrates are made up of simple sugars. Sugars (AKA Saccharides) belong to a class of molecules called carbohydrates, distinctive molecules composed of C, H, and O atoms, usually in the ratio 1:2:1 = CH20 Carbohydrates provide a principal source of energy for metabolism as well as structure. One sugar molecule is called a monosaccharide (e.g glucose) Two sugar molecules covalently bonded is called a disaccharide (e.g Fructose) Three to ten sugar molecules are called an Oligosaccharide Heaps of sugar molecules bonded together is called a Polysaccharide (E.g Glycogen) Monosaccharides = C6H12O6 Disaccharides = C12H24O12 etc... Polysaccharides can have thousands of molecules bonded together (e.g C180000H360000180000) Long, branched chains of monosaccharides are called complex carbohydrates.

Photosynthesis

Conversion of light energy from the sun into chemical energy. Photosynthesis in the ocean is mainly done in photic zone's (Portion of the marine biome that is shallow enough for sunlight to penetrate and thus enables photosynthesis) On land photosynthesis occurs most readily in environments that are both moist and warm (insert joke here) tropical rain forests for example. However, photosynthetic organisms have evolved adaptations that allow them to tolerate a wide range of environmental conditions

Diffusion

Diffusion During diffusion, substances move from an area of high concentration to an area of low concentration, until the concentration becomes equal throughout a space. This is also true for some substances moving into and out of cells. Because the cell membrane is semipermeable, only small, uncharged substances like carbon dioxide and oxygen can easily diffuse across it. Charged ions or large molecules require different kinds of transport. Simple diffusion Small hydrophobic molecules pass across the cell membrane without assistance Facilitated diffusion Although gases can diffuse easily between the phospholipids of the cell membrane, many polar or charged substances (like chloride) need help from membrane proteins. Membrane proteins can be either channel proteins or carrier proteins.

Active transport

During active transport, substances move against the concentration gradient, from an area of low concentration to an area of high concentration. This process is "active" because it requires the use of energy (usually in the form of ATP). It is the opposite of passive transport. • Primary active transport: uses ATP energy directly to pump materials • Secondary active transport: uses ATP energy indirectly, eg ATP is used to create a concentration gradient of protons & thus an electrical gradient (together called an electrochemical gradient). This gradient stores energy which can then be harnessed to actively transport other molecules.

Electron Shells

Electrons occupy regions of space called orbitals. The maximum number of electrons in any orbital is two. Most atoms have more than two electrons and so have several orbitals positioned at different distances from the nucleus. These orbitals differ in size and shape. Electrons in orbitals close to the nucleus have less energy than do electrons in orbitals farther away, so electrons fill up orbitals close to the nucleus before occupying those farther away. Several orbitals can exist at a given energy level or shell. Each shell can contain only a fixed number of electrons: The first shell can hold up to two electrons, the second shell can hold up to eight (2 + 6) electrons, the third shell can hold up to 18 (2 + 6 + 10)

Valence electron

Electrons on the outermost energy level of an atom. They largely determine the ability of atoms to combine with other atoms

Molecules

Groups of two or more atoms held together by chemical bonds

Cohesion

Hydrogen bonds also give water molecules the property of cohesion, meaning that they tend to stick to one another. A consequence of cohesion is high surface tension, a measure of the difficulty of breaking the surface of a liquid. Cohesion between molecules contributes to water movement in plants. As water evaporates from leaves, water is pulled upward.

Hydrophilic

Hydrophilic compounds are polar; they dissolve readily in water. That is, water is a good solvent, capable of dissolving many substances. E.g When you stir a teaspoon of sugar into water, the sugar seems to disappear as it dissolves. What is happening is that the sugar molecules are dispersing through the water and becoming separated from one another, forming a solution in the watery, or aqueous, environment.

Hydrophobic

Hydrophobic compounds are non-polar. Nonpolar compounds do not have regions of positive and negative charges. As a result, they arrange themselves to minimize their contact with water. For example, oil molecules are hydrophobic, and when oil and water are mixed, the oil molecules organize themselves into droplets that limit the oil-water interface. This hydrophobic effect, in which polar molecules like water exclude nonpolar ones, drives such biological processes as the folding of proteins and the formation of cell membranes.

The internal organisation of cells

In addition to the plasma membrane, many cells contain membrane-bound regions within which specific functions are carried out. Each department has a specific function and internal organization that contribute to the overall "life" of the factory.

Control group

In an experiment, the group that is not exposed to the treatment; contrasts with the experimental group and serves as a comparison for evaluating the effect of the treatment. The group that is not exposed to the variable in an experiment.

pH

In any solution of water, a small proportion of the water molecules exist as protons (H+) and hydroxide ions (OH-). The pH of a solution measures the proton concentration ([H-]), which is important as the pH influences many chemical reactions and biological processes. It is calculated by the following formula: pH = -log [H+] The pH of a solution can range from 0 to 14. Since the pH scale is logarithmic, a difference of one pH unit corresponds to a tenfold difference in hydrogen ion concentration. A solution is neutral (pH = 7) when the concentrations of protons (H+) and hydroxide ions (OH-) are equal. When the concentration of protons is higher than that of hydroxide ions, the pH is lower than 7 and the solution is acidic. When the concentration of protons is lower than that of hydroxide ions, the pH is higher than 7 and the solution is basic. a

Eukaryotes major components

In eukaryotes, DNA is transcribed to RNA inside the nucleus, but the RNA molecules carrying the genetic message travel from inside to outside the nucleus, where they instruct the synthesis of proteins. Eukaryotes have a remarkable internal array of membranes. These membranes define compartments, called organelles, that divide the cell contents into smaller spaces specialized for different functions. The endoplasmic reticulum (ER) is the organelle in which proteins and lipids are synthesized. The Golgi apparatus modifies proteins and lipids produced by the ER and acts as a sorting station as they move to their final destinations. Lysosomes contain enzymes that break down macromolecules such as proteins, nucleic acids, lipids, and complex carbohydrates. Peroxisomes also contain many different enzymes and are involved in important metabolic reactions, including the breakdown of fatty acids and the synthesis of certain types of phospholipid. Mitochondria are specialized organelles that harness energy for the cell. Many cell membranes that define these organelles are associated with a protein scaffold called the cytoskeleton that helps cells to maintain their shape and serves as a network of tracks for the movement of substances within cells. In addition to the organelles described above, plant cells have a cell wall outside the plasma membrane, vacuoles specialized for water uptake, and chloroplasts that convert energy of sunlight into chemical energy. The entire contents of a cell other than the nucleus make up the cytoplasm. The jelly-like internal environment of the cell that surrounds the organelles inside the plasma membrane is referred to as the cytosol.

The Endomembrane system

In eukaryotes, the total surface area of intracellular membranes is about tenfold greater than that of the plasma membrane. This high ratio of internal membrane area to plasma membrane area underscores the significant degree to which a eukaryotic cell is divided into internal compartments. Many of the organelles inside cells are not isolated entities, but instead communicate with one another. The membranes of these organelles are either physically connected by membrane "bridges" or they are transiently connected by vesicles, small membrane-enclosed sacs that transport substances within a cell or from the interior to the exterior of the cell. These vesicles form by budding off an organelle, taking with them a piece of the membrane and internal contents of the organelle from which they derive. They then fuse with another organelle or the plasma membrane, re-forming a continuous membrane and unloading their contents. In total, these interconnected membranes make up the endomembrane system. The endomembrane system includes - the nuclear envelope - endoplasmic reticulum - Golgi apparatus - lysosomes - plasma membrane - vesicles that move between them In plants, the endomembrane system is actually continuous between cells through connecting pores called plasmodesmata Extensive internal membranes are not common in prokaryotic cells. However, photosynthetic bacteria have internal membranes that are specialized for harnessing light energy.

Polar covalent bond

In many bonds, the electrons are not shared equally by the two atoms. The unequal sharing of electrons results from a difference in the ability of the atoms to attract electrons, a property known as electronegativity. Electronegativity tends to increase across a row in the periodic table; as the number of protons across a row increases, electrons are held more tightly to the nucleus. In a molecule of water, oxygen has a slight negative charge, while the two hydrogen atoms have a slight positive charge. When electrons are shared unequally between the two atoms, the resulting interaction is described as a polar covalent bond.

The Calvin cycle

In plants, carbon dioxide enters the interior of a leaf via pores called stomata and diffuses into the stroma of the chloroplast—the site of the Calvin cycle reactions, where sugar is synthesized. These reactions are also called the light-independent reactions because they are not directly driven by light. In the Calvin cycle, carbon atoms are fixed (incorporated into organic molecules) and used to build three-carbon sugars. This process is fueled by, and dependent on, ATP and NADPH from the light reactions. The reactions of the Calvin cycle take place in the stroma (the inner space of chloroplasts). The Calvin cycle consists of 15 chemical reactions that synthesize carbohydrates from CO2. These reactions can be grouped into three main steps: (1) carboxylation, in which CO2 is added to a 5-carbon molecule; (2) reduction, in which energy and electrons are transferred to the compounds formed in step 1; and (3) regeneration of the 5-carbon molecule needed for carboxylation Carbon fixation. A CO2 molecule combines with a five-carbon acceptor molecule, ribulose-1,5-bisphosphate (RuBP). This step makes a six-carbon compound that splits into two molecules of a three-carbon compound, 3-phosphoglyceric acid (3-PGA). This reaction is catalyzed by the enzyme RuBP carboxylase/oxygenase, or rubisco. Reduction. In the second stage, ATP and NADPH are used to convert the 3-PGA molecules into molecules of a three-carbon sugar, glyceraldehyde-3-phosphate (G3P). This stage gets its name because NADPH donates electrons to, or reduces, a three-carbon intermediate to make G3P. . Regeneration. Some G3P molecules go to make glucose, while others must be recycled to regenerate the RuBP acceptor. Regeneration requires ATP and involves a complex network of reactions. In order for one G3P to exit the cycle (and go towards glucose synthesis), CO2 molecules must enter the cycle, providing three new atoms of fixed carbon. When three CO2 molecules enter the cycle, six G3P molecules are made. One exits the cycle and is used to make glucose, while the other five must be recycled to regenerate three molecules of the RuBP acceptor. The Calvin cycle is capable of producing more carbohydrates than the cell needs or, in a multicellular organism, more than the cell is able to export. If carbohydrates accumulated in the cell, they would cause water to enter the cell by osmosis, perhaps damaging the cell. Instead, excess carbohydrates are converted to starch, a storage form of carbohydrates. Because starch molecules are not soluble, they provide a means of carbohydrate storage that does not lead to osmosis. The formation of starch during the day provides photosynthetic cells with a source of carbohydrates that they can use during the night.

Lipids

Instead of being defined by a chemical structure, they share a particular property: Lipids are all hydrophobic. Lipids can group together to function as storage compounds, as they mix poorly with water In living organisms, lipids can be found in cellular membranes Fat is commonly stored in the form of Triacylglycerol (TAG) TAG is comprised of a glycerol head group bonded to three hydrophobic fatty acid tails Two types of fatty acids 1. Saturated fats - have no double bonds and thus are linear in shape. This makes them easier to pack tightly together which means we can store more of them which is bad. 2. Unsaturated fats - have one or more double bonds and thus can be bent and kinks in shape. Harder to pack tightly together because of their kinks which means we can store less which is good. The double bond in unsaturated fatty acids can form in either Cis or Trans configurations Cis double bonds have hydrogen on the same side of the carbon chain (bent or kinked shape) Trans double bonds have hydrogen on opposite sides of the carbon chain (more linear shape) Another type of lipid found in the cellular membrane is Phospholipids - have a negatively charged phosphocholine group bonded to two fatty acid tails - Charged head group is hydrophilic - Fatty acid tail is hydrophobic - Molecules with this combination are called amphipathic - Phospholipids are commonly found in bilayers as part of cellular membranes

ATP (adenosine triphosphate)

Main energy source that cells use for most of their work Majority of energy transfers that happen between molecules are mediated by ATP and thats because it can supply this phosphate group to other molecules increasing the G of the molecule, reducing the delta G of its subsequent reaction which leads to the production of ADP. ADP can then be recycled by processes like photosynthesis

Metabolism

Metabolism is the set of chemical reactions that sustain life. The building and breaking down of sugars such as glucose and the harnessing and release of energy in the process are driven by chemical reactions in the cell. The term metabolism encompasses the entire set of these chemical reactions that convert molecules into other molecules and transfer energy in living organisms. These chemical reactions are occurring all the time in your cells. Many of these reactions are linked, in that the products of one are the reactants of the next, forming long pathways and intersecting networks. Metabolism is divided into two branches: Catabolism is the set of chemical reactions that break down molecules into smaller units and, in the process, produce ATP, and anabolism is the set of chemical reactions that build molecules from smaller units and require an input of energy, usually in the form of ATP For example, carbohydrates can be broken down, or catabolized, into sugars, fats into fatty acids and glycerol, and proteins into amino acids. These initial products can be broken down further to release energy stored in their chemical bonds. The synthesis of macromolecules such as carbohydrates and proteins, by contrast, is anabolic.

Isomers

Molecules that have the same chemical formula but different structures

The evolution of photosynthesis

Not only did photosynthesis provide organisms with a new source of energy, but it also released oxygen into the atmosphere. How did early cells use sunlight to meet their energy requirements? Sunlight is valuable as a source of energy, but it can also cause damage. This is particularly true of ultraviolet wavelengths, which can damage DNA and other macromolecules. Thus, the earliest interactions with sunlight may have been the evolution of UV-absorbing compounds that could shield cells from the sun's damaging rays. Over time, random mutations could have produced chemical variants of these UV-absorbing molecules. One or more of these variant compounds might have been capable of using sunlight to meet the energy needs of the cell—perhaps by transferring electrons to another molecule as a present-day reaction centre does. The earliest reaction centres may have used light energy to drive the movement of electrons from an electron donor outside the cell in the surrounding medium to an electron-acceptor molecule within the cell. In this way, energy from sunlight could have been used to synthesize carbohydrates. The first electron donor could have been a soluble inorganic ion like reduced iron, Fe2+, which is thought to have been abundant in the early ocean. Alternatively, the first forms of light-driven electron transport may have been cyclic and thus not required an electron donor. In either configuration, light-driven electron transport could have been coupled to the net movement of protons across the membrane, allowing for the synthesis of ATP. Similarly, it is unlikely that these first photosynthetic organisms employed chlorophyll as a means of absorbing sunlight for the simple reason that the biosynthetic pathway for chlorophyll is complex, consisting of at least 17 enzymatic steps. Yet some of the intermediate compounds leading to chlorophyll are themselves capable of absorbing light. Perhaps each of these now-intermediate compounds was, at one time, a functional end product used as a pigment by an early photosynthetic organism. The biosynthetic pathway may have gained steps as chemical variants, produced by random mutations, were selected because they were more efficient or able to absorb new portions of the visible spectrum. Selection would have eventually resulted in the chlorophyll pigments that are used by photosynthetic organisms today. The ability to use water as an electron donor in photosynthesis evolved in cyanobacteria. The most ancient forms of photosynthesis have only a single photosystem in their photosynthetic electron transport chains. However, as we have seen, a single photosystem cannot capture enough energy from sunlight both to pull electrons from water and also raise their energy level enough that they can be used to reduce CO2. Thus, photosynthetic organisms with a single photosystem must use more easily oxidized compounds, such as H2S, as electron donors. These organisms can exist only in environments where the electron-donor molecules are abundant. Because these organisms do not use water as an electron donor, they do not produce O2 during photosynthesis. A major event in the history of life was the evolution of photosynthetic electron transport chains that use water as an electron donor. The first organisms to accomplish this feat were the cyanobacteria. These photosynthetic bacteria incorporated two different photosystems into a single photosynthetic electron transport chain, one to pull electrons from water molecules and one to raise the energy level of the electrons so that they can be used to reduce CO2. How did cyanobacteria end up with two photosystems? We cannot say for sure, but one relevant piece of information is that each of the two photosystems present in cyanobacteria is similar in structure to photosystems found in groups of photosynthetic bacteria that contain only a single photosystem. Thus, it is highly unlikely that the photosystems in cyanobacteria evolved independently. One hypothesis is that the genetic material associated with one photosystem was transferred to a bacterium that already had the other photosystem, resulting in a single bacterium with the genetic material to produce both types of photosystems (shown on the left in. Another hypothesis is that the genetic material associated with one photosystem underwent duplication. Over time, one of the two photosystems diverged slightly in sequence and function through mutation and selection, giving rise to two distinct but related photosystems. The ability to use water as an electron donor in photosynthesis had two major impacts on life on Earth. First, it meant that photosynthesis could occur anywhere there was both sunlight and sufficient water for cells to survive. Second, using water as an electron donor results in the release of oxygen. Before the evolution of "oxygenic" photosynthesis, there was little or no free oxygen in Earth's atmosphere. All the oxygen in Earth's atmosphere results from photosynthesis by organisms containing two photosystems. Eukaryotic organisms are believed to have gained photosynthesis by endosymbiosis. Photosynthesis is hypothesized to have gained a foothold among eukaryotic organisms when a free-living cyanobacterium took up residence inside a eukaryotic cell. Over time, the cyanobacterium lost its ability to survive outside its host cell and evolved into the chloroplast. The outer membrane of the chloroplast is thought to have originated from the plasma membrane of the ancestral eukaryotic cell, which surrounded the ancestral cyanobacterium as it became incorporated into the cytoplasm of the eukaryotic cell. The inner chloroplast membrane is thought to correspond to the plasma membrane of the ancestral free-living cyanobacterium. The thylakoid membrane then corresponds to the internal photosynthetic membrane found in cyanobacteria. Finally, the stroma corresponds to the cytoplasm of the ancestral cyanobacterium. The process in which one cell takes up residence inside of another cell is called endosymbiosis. Therefore, the idea that chloroplasts and mitochondria arose in this way is called the endosymbiotic hypothesis. Cellular respiration and photosynthesis are complementary metabolic processes. Cellular respiration breaks down carbohydrates in the presence of oxygen to supply the energy needs of the cell, producing carbon dioxide and water as byproducts, while photosynthesis uses carbon dioxide and water in the presence of sunlight to build carbohydrates, releasing oxygen as a byproduct.

Anoxygenic photosynthesis

Not producing oxygen; anoxygenic photosynthetic bacteria do not gain electrons from water and so do not generate oxygen gas.

Nucleic Acids

Nucleic acids encode genetic information in their nucleotide sequence. Nucleic acids are examples of informational molecules—that is, they are large molecules that carry information in the sequence of nucleotides that make them up. This molecular information is in chemical form. The nucleic acid deoxyribonucleic acid (DNA) is the genetic material in all organisms. It is transmitted from parents to offspring, and it contains the information needed to specify the amino acid sequence of all the proteins synthesised in an organism. The nucleic acid ribonucleic acid (RNA) has multiple functions; it is a key player in protein synthesis and the regulation of gene expression. DNA and RNA are long molecules consisting of nucleotides bonded covalently one to the next. Nucleotides are composed of three components: 1. a 5-carbon sugar 2. a nitrogen-containing compound called a base 3. one or more phosphate groups In DNA there are 4 types of nucleotides 1. Adenine 2. Cytosine 3. Guanine 4. Thymine In RNA they are all the same except Thymine becomes Uracil The bases are built from nitrogen-containing rings and are of two types. - The pyrimidine bases have a single ring and include cytosine (C), thymine (T), and uracil (U). - The purine bases have a double-ring structure and include guanine (G) and adenine (A). Bonding 1. RNA bonding occurs by losing a water in one molecule which creates a covalent bond between two nucleotides 2. DNA bonding - Adenine will always bond with thymine Cytosine will always bond with guanine. These bonds are hydrogen bonds. The sugar in RNA is ribose, and the sugar in DNA is deoxyribose. The sequence of nucleotides determine the information in DNA and RNA molecules. Genetic information in DNA is contained in the sequence, or order, in which successive nucleotides occur along the molecule.

Electronegativity

The ability of atoms to attract electrons.

wildtype

the most common genotype/phenotype observed in a population

Organism classified trophs

Organisms can be classified according to their energy and carbon sources. Organisms have two ways of harvesting energy from their environment: They can obtain energy either from the sun or from chemical compounds Organisms that capture energy from sunlight are called phototrophs. Other organisms derive their energy directly from chemical compounds. These organisms are called chemotrophs, and animals are familiar examples. Organisms can also be classified in terms of where they get their carbon. Some organisms are able to convert carbon dioxide (an inorganic form of carbon) into glucose (an organic form of carbon). These organisms are autotrophs, or "self feeders," because they make their own organic carbon using inorganic carbon as the starting material. Plants again are an example, so plants are both phototrophs and autotrophs, or photoautotrophs. Other organisms do not have the ability to convert carbon dioxide into organic forms of carbon. Instead, they obtain their carbon from organic molecules synthesized by other organisms, called preformed organic molecules. In other words, these organisms eat other organisms or molecules derived from other organisms. Such organisms are heterotrophs, or "other feeders," as they rely on other organisms for their organic forms of carbon. Animals obtain carbon in this way, and so animals are both chemotrophs and heterotrophs, or chemoheterotrophs. Some microorganisms gain energy from sunlight but obtain their carbon from preformed organic molecules; such organisms are called photoheterotrophs. Other microorganisms extract energy from inorganic sources but build their own organic molecules; these organisms are called chemoautotrophs.

Osmosis

Osmosis Osmosis is a passive transport process during which water moves from areas where solutes are less concentrated to areas where they are more concentrated. Osmosis: the movement of water through a semi/selectively-permeable membrane that allows movement of water but not solute, from an area of high water concentration/low solute C to an area of low water concentration/high solute C

Oxygenic photosynthesis

Photosynthesis that oxidizes water to form oxygen; the form of photosynthesis characteristic of plants, protists, and cyanobacteria

Protein sorting

Protein sorting is the process by which proteins end up where they need to be to perform their function. Protein sorting directs proteins to the cytosol, the lumen of organelles, the membranes of the endomembrane system, or even out of the cell entirely. Recall that proteins are produced in two places: free ribosomes in the cytosol and membrane-bound ribosomes on the rough ER. Proteins produced on free ribosomes are sorted after they are translated. These proteins often contain amino acid sequences, called signal sequences, that allow them to be recognized and sorted. There are several types of signal sequences that direct proteins synthesized on free ribosomes to different cellular compartments. Proteins with no signal sequence remain in the cytosol. Proteins destined for mitochondria or chloroplasts often have a signal sequence at their amino ends. Proteins targeted to the nucleus usually have signal sequences located internally. These nuclear signal sequences, called nuclear localization signals, enable proteins to move through pores in the nuclear envelope Proteins produced on the rough ER end up in the lumen of the endomembrane system, secreted out of the cell, or as transmembrane proteins. These proteins are sorted as they are translated. They begin translation on free ribosomes, but a specific signal sequence at their amino terminal end directs the ribosome to the rough ER and into a membrane channel that leads into the ER lumen. If the polypeptide contains no other signal sequence, it continues into the lumen. If it contains a second sequence, called a signal-anchor sequence, it does not continue all the way into the lumen and ends up in the membrane. Proteins destined for the ER lumen or secretion have an amino-terminal signal sequence. As a free ribosome translates the protein, this sequence is recognized by an RNA-protein complex known as a signal-recognition particle (SRP). The SRP binds to both the signal sequence and the free ribosome, and brings about a pause in translation. The SRP then binds with a receptor on the RER so that the ribosome is now associated with the RER. The SRP receptor brings the ribosome to a channel in the membrane of the RER. The SRP then dissociates and translation continues, allowing the growing polypeptide chain to be threaded through the channel. A specific protease cleaves the signal sequence as it emerges in the lumen of the ER. Some proteins are retained in the interior of the ER and others are transported in vesicles to the interior of the Golgi apparatus. Some of these proteins are secreted by exocytosis. Proteins destined for cell membranes contain a signal-anchor sequence in addition to the amino-terminal signal sequence. After the growing polypeptide chain and its ribosome are brought to the ER, it is threaded through the channel in the ER membrane until the signal-anchor sequence is encountered. The signal-anchor sequence is hydrophobic and is therefore able to diffuse laterally in the lipid bilayer. At this point, the ribosome dissociates from the channel while translation continues. When translation is completed, the carboxyl end of the chain remains on the cytosolic side of the ER membrane, the amino end is in the ER lumen, and the region between them resides in the membrane. Transmembrane proteins such as these may stay in the membrane of the ER or end up in other internal membranes or the plasma membrane, where they serve as transporters, pumps, receptors, or enzymes.

chemical reaction

The process by which molecules, called reactants, are transformed into other molecules, called products. During a chemical reaction, atoms keep their identity, but the bonds linking the atoms change. Most chemical reactions in cells are readily reversible: The products can react to form the reactants. For example, carbon dioxide and water react to form carbonic acid, and carbonic acid can dissociate to produce carbon dioxide and water. This reverse reaction also occurs in the blood, allowing carbon dioxide to be removed from the lungs or gills. The reversibility of the reaction is indicated by a double arrow.

Transport proteins in membranes

Proteins Proteins are the second major component of plasma membranes. There are two main categories of membrane proteins: integral and peripheral. Integral membrane proteins are, as their name suggests, integrated into the membrane: they have at least one hydrophobic region that anchors them to the hydrophobic core of the phospholipid bilayer. Some stick only partway into the membrane, while others stretch from one side of the membrane to the other and are exposed on either side. Proteins that extend all the way across the membrane are called transmembrane proteins. The portions of an integral membrane protein found inside the membrane are hydrophobic, while those that are exposed to the cytoplasm or extracellular fluid tend to be hydrophilic. Transmembrane proteins may cross the membrane just once, or may have as many as twelve different membrane-spanning sections. Peripheral membrane proteins are found on the outside and inside surfaces of membranes, attached either to integral proteins or to phospholipids. Unlike integral membrane proteins, peripheral membrane proteins do not stick into the hydrophobic core of the membrane, and they tend to be more loosely attached.

Proteins

Proteins do much of the cell's work. A protein consists of one or more polypeptides (polymers of amino acids) Amino acids - Are organic molecules processing both carboxyl and amino groups - Differ in properties due to differing side chains called R groups - R groups can be Non-polar, Polar, Acidic, Basic or Charged - Are linked by peptide bonds Each amino acid contains a central carbon atom, called the α (alpha) carbon, covalently linked to four groups: an amino group, a carboxyl group, a hydrogen atom (H), and an R group, or side chain, that differs from one amino acid to the next. There are four different levels to protein structure 1. The Primary Structure - The amino acid sequence 2. The Secondary structure - Linear folding of the polypeptide sequence these are held together by hydrogen bonds (coils and folds) e.g the alpha helix 3. The Tertiary structure - Globular 3D folding 4. The Quaternary structure - If a protein consists of more than 1 subunit then these subunits can also specifically associate by the interaction of the surface amino acids to form a multi-subunit protein Enzymes are protein catalysts that specifically recognize substrates due to there 3D structure. The 3D structure of an enzyme is not fixed and its shape can be influenced by the binding of a substrate. (The induced-fit model)

Archaea vs. Bacteria

Similarities Between Them - Archaea and bacteria are both prokaryotes, meaning they do not have a nucleus and lack membrane-bound organelles. - They are tiny, single-cell organisms that cannot be seen by the naked human eye called microbes. - When we look at them through a microscope, we find that archaea and bacteria resemble each other in shape and size. - They exist as rods, cones, plates, and coils. Both archaea and bacteria have flagella, thread-like structures that allow organisms to move by propelling them through their environment. Differences Between Them - As mentioned, the genetic code of rRNA differs enough to place them in quite different branches of the Tree of Life, reflecting differing evolutionary paths. (This still needs to be confirmed by sequencing the 16s rRNA of more organisms.) - Despite this functional similarity, and structural similarity (i.e. they look similar), they have very different genes encoding them and are comprised of different proteins. - Genome sequencing of archaea also reveals genes that resemble eukaryotes more than bacteria. This is a big difference between archaea and bacteria. - Another distinction between these two prokaryotes is the composition of the cell wall. For example, all bacteria contain peptidoglycans (a molecule composed of both protein and sugar rings) in their cell walls. However, archaea do not have this compound in their cell walls. - Cell division in archaea undergoes distinct processes not found in bacteria.

The Golgi apparatus

The Golgi apparatus is often the next stop for vesicles that bud off the ER. These vesicles carry lipids and proteins, either within the vesicle interior or embedded in their membranes. The movement of these vesicles from the ER to the Golgi apparatus and then to the rest of the cell is part of a biosynthetic pathway in which lipids and proteins are sequentially modified and delivered to their final destinations. The Golgi apparatus has three primary roles: (1) It further modifies proteins and lipids produced by the ER; (2) it acts as a sorting station as these proteins and lipids move to their final destinations; and (3) it is the site of synthesis of most of the cell's carbohydrates. Under the microscope, the Golgi apparatus looks like stacks of flattened membrane sacs, called cisternae, surrounded by many small vesicles. These vesicles transport proteins and lipids from the ER to the Golgi apparatus, and then between the various cisternae, and finally from the Golgi apparatus to the plasma membrane or other organelles. Enzymes within the Golgi apparatus chemically modify proteins and lipids as they pass through it. These modifications take place in a sequence of steps, each performed in a different region of the Golgi apparatus, since each region contains a different set of enzymes that catalyzes specific reactions. As a result, there is a general movement of vesicles from the ER through the Golgi apparatus and then to their final destinations. While traffic usually travels from the ER to the Golgi apparatus, a small amount of traffic moves in the reverse direction, from the Golgi apparatus to the ER. This reverse pathway is important to retrieve proteins in the ER or Golgi that were accidentally moved forward and to recycle membrane components.

Lysosomes

The ability of the Golgi apparatus to sort and dispatch proteins to particular destinations is dramatically illustrated by lysosomes. Lysosomes are specialized vesicles derived from the Golgi apparatus that degrade damaged or unneeded macromolecules. They contain a variety of enzymes that break down macromolecules such as proteins, nucleic acids, lipids, and complex carbohydrates. Macromolecules destined for degradation are packaged by the Golgi apparatus into vesicles. The vesicles then fuse with lysosomes, delivering their contents to the lysosome interior. The formation of lysosomes also illustrates the ability of the Golgi apparatus to sort key proteins. The enzymes inside the lysosomes are synthesized in the RER, sorted in the Golgi apparatus, and then packaged into lysosomes. In addition, the Golgi apparatus sorts and delivers specialized proteins that become embedded in lysosomal membranes. These include proton pumps that keep the internal environment at an acidic pH of about 5, the optimum pH for the activity of the enzymes inside. Other proteins in the lysosomal membranes transport the breakdown products of macromolecules, such as amino acids and simple sugars, across the membrane to the cytosol for use by the cell. The function of lysosomes underscores the importance of having separate compartments within the cell bounded by selectively permeable membranes. Lysosomal enzymes cannot function in the normal cellular environment, which has a pH of about 7, and many of a cell's enzymes and proteins would unfold and degrade if the entire cell were at the pH of the inside of a lysosome. By restricting the activity of these enzymes to the lysosome, the cell protects proteins and organelles in the cytosol from degradation.

Observation

The act of viewing the world around us.

Cell

The cell is the smallest unit of life. Every known living organism is either a single cell or multiple cells

Chemical Reaction

The chemical bonds that link atoms in molecules can change in a chemical reaction, a process by which atoms or molecules, called reactants, are transformed into different molecules, called products. During a chemical reaction, atoms keep their identity but change which atoms they are bonded to.

Independent variable

The experimental factor that is manipulated; the variable whose effect is being studied.

Water and heating

The hydrogen bonds of water also influence how water responds to heating. Molecules are in constant motion, and this motion increases as the temperature increases. When water is heated, some of the energy added by heating is used to break hydrogen bonds instead of causing more motion among the molecules, so the temperature increases less than if there were no hydrogen bonding. The abundant hydrogen bonds make water more resistant to temperature changes than other substances, a property that is important for living organisms on a variety of scales. In the cell, water resists temperature variations that would otherwise result from numerous biochemical reactions. On a global scale, the oceans minimise temperature fluctuations, stabilising the temperature on Earth in a range compatible with life.

Nucleus and RNA synthesis

The innermost organelle of the endomembrane system is the nucleus, which stores DNA, the genetic material that encodes the information for all the activities and structures of the cell. The nuclear envelope defines the boundary of the nucleus. It actually consists of two membranes, the inner and outer membranes, and each is a lipid bilayer with associated proteins. These two membranes are continuous with each other at openings called nuclear pores. These pores are large protein complexes that allow molecules to move into and out of the nucleus, and thus are essential for the nucleus to communicate with the rest of the cell. For example, some proteins that are synthesized in the cytosol, such as transcription factors, move through nuclear pores to enter the nucleus, where they control how and when genetic information is expressed. In addition, the transfer of information encoded by DNA depends on the movement of mRNA (messenger RNA) molecules out of the nucleus through these pores. After exiting the nucleus, mRNA binds to free ribosomes in the cytosol or ribosomes associated with the endoplasmic reticulum (ER). Ribosomes are the sites of protein synthesis, in which amino acids are assembled into polypeptides guided by the information stored in mRNA. In this way, the nuclear envelope and its associated protein pores regulate which molecules move into and out of the nucleus.

The endoplasmic reticulum

The outer membrane of the nuclear envelope is physically continuous with the endoplasmic reticulum (ER), an organelle bounded by a single membrane. The ER is a conspicuous feature of many eukaryotic cells, accounting in some cases for as much as half of the total amount of membrane. The ER produces and transports many of the lipids and proteins used inside and outside the cell, including all transmembrane proteins, as well as proteins destined for the Golgi apparatus, lysosomes, or export out of the cell. The ER is also the site of production of most of the lipids that make up the various internal and external cell membranes. Unlike the nucleus, which is a single spherical structure in the cell, the ER consists of a complex network of interconnected tubules and flattened sacs. The interior of the ER is continuous throughout and is called the lumen. The ER has an almost mazelike appearance when sliced and viewed in cross section. Its membrane is extensively convoluted, allowing a large amount of membrane surface area to fit within the cell. When viewed through an electron microscope, ER membranes have two different appearances. Some look rough because they are studded with ribosomes. This portion of the ER is referred to as rough endoplasmic reticulum (RER). The rough ER synthesizes transmembrane proteins, proteins that end up in the interior of organelles, and proteins destined for secretion. As a result, cells that secrete large quantities of protein have extensive rough ER, including cells of the gut that secrete digestive enzymes and cells of the pancreas that produce insulin. All cells have at least some rough ER for the production of transmembrane and organelle proteins. There is a small amount of ER membrane in most cells that appears smooth because it lacks ribosomes. This portion of the ER is therefore called smooth endoplasmic reticulum (SER). Smooth ER is the site of fatty acid and phospholipid biosynthesis. Thus, this type of ER predominates in cells specialized for the production of lipids.

Water

Water molecules have polar covalent bonds, characterized by an uneven distribution of electrons. A molecule like water that has regions of positive and negative charge is called a polar molecule. Molecules, or even different regions of the same molecule, fall into two general classes, depending on how they interact with water: hydrophilic ("water-loving") and hydrophobic ("water-fearing").

Enzymes

The rate of a chemical reaction is defined as the amount of product formed (or reactant consumed) per unit of time. Catalysts are substances that increase the rate of chemical reactions without themselves being consumed. In biological systems, the catalysts are usually proteins called enzymes This intermediate stage between reactants and products is called the transition state. It is highly unstable and therefore has a large amount of free energy. All chemical reactions, even spontaneous ones that release energy, require an input of energy that we can think of as an "energy barrier." The energy input necessary to reach the transition state is called the activation energy (EA) There is an inverse correlation between the rate of a reaction and the height of the energy barrier: the lower the energy barrier, the faster the reaction; the higher the barrier, the slower the reaction. Enzymes reduce the activation energy by stabilizing the transition state and decreasing its free energy. As the activation energy decreases, the speed of the reaction increases. Enzymes participate in a chemical reaction but emerge unchanged by the process. They do this by forming a complex with the reactants and products. Substrate is the reactant in a reaction that involves an enzyme Enzymes are folded into three-dimensional shapes that bring particular amino acids into close proximity to form an active site. An active site is the site where the substrate will bind. It is highly specific for the shape of the substrate and what it does (whether it brings molecules together or breaks them apart) Induced fit rearrangement of the enzyme to clasp over the substrate Enzymes catalyze only one reaction or a very limited number of reactions. The activity of enzymes can be influenced by inhibitors and activators. Inhibitors decrease the activity of enzymes, whereas activators increase the activity of enzymes. There are two classes of inhibitors. Irreversible inhibitors usually form covalent bonds with enzymes and irreversibly inactivate them. Reversible inhibitors form weak bonds with enzymes and therefore easily dissociate from them. Two mechanisms of inhibitor function. (a) Competitive - Some inhibitors bind to the active site of the enzyme and (b) Non-competitive - other inhibitors bind to a site that is different from the active site. Both types of inhibitor reduce the activity of an enzyme and therefore decrease the rate of the reaction. Positive regulation (Activator) An activator will bind to an enzyme and will enable it to open its active site. This activator will bind to another site other than the active site which is called allosteric regulation which creates a change in the shape of the enzyme to allow it to bind to a substrate. Enzyme activators and inhibitors are sometimes important in the normal operation of a cell Many enzymes are not just made up of protein, but also contain metal ions. These ions are one type of cofactor, a substance that associates with an enzyme and plays a key role in its function.

2. It has a plasma membrane

The second essential feature of all cells is a plasma membrane that separates the living material within the cell from the nonliving environment around it. The relationship between cells and their surroundings is mediated by the plasma membrane. All cells require sustained contributions from their surroundings and they also release waste products into the environment. The plasma membrane controls the movement of materials into and out of the cell. Many cells also have internal membranes that divide the cell into discrete compartments, each specialized for a particular function. Such as the nucleus, which houses the cell's DNA. The nuclear membrane selectively controls the movement of molecules into and out of it. As a result, the nucleus occupies a discrete space within the cell, separate from the space outside the nucleus, called the cytoplasm. Cells without a nucleus are called prokaryotes, and cells with a nucleus are eukaryotes. Prokaryotes - emerged about 4 billion years ago - their descendants include bacteria - can live in peaceful coexistence with humans, inhabiting our gut and aiding digestion. - others cause disease—salmonella, tuberculosis, and cholera, etc - most live as single-celled organisms, but some have simple multicellular forms. The success of these cells depends in part on their - small size - their ability to reproduce rapidly - their ability to obtain energy and nutrients from diverse sources Eukaryotes - evolved roughly 2 billion years ago, from prokaryotic ancestors - includes animals, plants, and fungi - exist as single cells like yeasts or as multicellular organisms like humans - In multicellular organisms, cells may specialize to perform different functions The terms "prokaryotes" and "eukaryotes" are useful in drawing attention to a fundamental distinction between these two groups of cells. However, today, biologists recognize three domains of life—Bacteria, Archaea, and Eukarya. Bacteria and Archaea both lack a nucleus and are therefore prokaryotes, whereas Eukarya are eukaryotic. Archaea are single-celled microorganisms.

Functional groups

The simple repeating units of polymers are often based on a non-polar core of carbon atoms. But attached to these carbon atoms are functional groups. Which are groups of one or more atoms that have particular chemical properties of their own, regardless of what they are attached to. These functional groups are more electronegative than the carbon atoms, and functional groups containing these atoms are polar. Because many functional groups are polar, otherwise non-polar molecules containing these groups become polar and so become soluble in the cell's aqueous environment. In other words, they disperse in solution throughout the cell. Moreover, because many functional groups are polar, they are also reactive. Notice in the following sections that the reactions joining simpler molecules into polymers usually take place between functional groups.

Light energy

The sun, like all stars, produces a broad spectrum of electromagnetic radiation ranging from gamma rays to radio waves. Each point along the electromagnetic spectrum has a different energy level and a corresponding wavelength. Visible light is the portion of the electromagnetic spectrum apparent to our eyes, and it includes the range of wavelengths used in photosynthesis. Pigments are molecules that absorb some wavelengths of visible light. Pigments look coloured because they reflect light enriched in the wavelengths that they do not absorb. Chlorophyll is the major photosynthetic pigment; it appears green because it is poor at absorbing green wavelengths. The chlorophyll molecule consists of - a large, light-absorbing "head" containing a magnesium atom at its centre - a long hydrocarbon "tail". The large number of alternating single and double bonds in the head region explains why chlorophyll is so efficient at absorbing visible light. Chlorophyll molecules are bound by their tail region to integral membrane proteins in the thylakoid membrane. These protein-pigment complexes, referred to as photosystems, are the functional and structural units that absorb light energy and use it to drive electron transport. Photosystems contain pigments other than chlorophyll, called accessory pigments. The most notable is the orange-yellow carotenoids, which can absorb light from regions of the visible spectrum that are poorly absorbed by chlorophyll. Thus, the presence of these accessory pigments allows photosynthetic cells to absorb a broader range of visible light than would be possible with just chlorophyll alone. When visible light is absorbed by a chlorophyll molecule, one of its electrons is elevated to a higher energy state. For chlorophyll molecules that have been extracted from chloroplasts in the laboratory, this absorbed light energy is rapidly released, allowing the electron to return to its initial "ground" energy state. Most of the energy (>95%) is converted into heat; a small amount is reemitted as light (fluorescence). By contrast, for chlorophyll molecules within an intact chloroplast, energy can be transferred to an adjacent chlorophyll molecule instead of being lost as heat. When this happens, the energy released as an excited electron returns to its ground state raises the energy level of an electron in an adjacent chlorophyll molecule. This mode of energy transfer is extremely efficient (that is, very little energy is lost as heat), allowing energy initially absorbed from sunlight to be transferred from one chlorophyll molecule to another and then on to another. Most of the chlorophyll molecules in the thylakoid membrane function as an antenna: Energy is transferred between chlorophyll molecules until it is finally transferred to a specially configured pair of chlorophyll molecules known as the reaction centre. The reaction centre is where light energy is converted into chemical energy as a result of the excited electron's transfer to an adjacent molecule. We now know that several hundred antenna chlorophyll molecules transfer energy to each reaction centre. The antenna chlorophylls allow the photosynthetic electron transport chain to operate efficiently. Without the antennae to gather light energy, reaction centres would sit idle much of the time, even in bright sunlight. The reaction centre chlorophylls have a configuration distinct from that of the antenna chlorophylls. As a result, when excited, the reaction centre transfers an electron to an adjacent molecule that acts as an electron acceptor. When the transfer takes place, the reaction centre becomes oxidized and the adjacent electron-acceptor molecule is reduced. The result is the conversion of light energy into a chemical form. This electron transfer initiates a light-driven chain of redox reactions that leads ultimately to the formation of NADPH. Once the reaction centre has lost an electron, it can no longer absorb light or contribute additional electrons. Thus, for the photosynthetic electron transport chain to continue, another electron must be delivered to take the place of the one that has entered the transport chain, these replacement electrons ultimately come from water. Water is an ideal source of electrons for photosynthesis. Water is so abundant within cells that it is always available to serve as an electron donor in photosynthesis. In addition, O2, the by-product of pulling electrons from water, diffuses readily away rather than accumulates. However, from an energy perspective, water is a challenging electron donor: It takes a great deal of energy to pull electrons from water. The amount of energy that a single photosystem can capture from sunlight is not enough both to pull an electron from water and produce an electron donor capable of reducing NADP+. The solution is to use two photosystems arranged in series. The energy supplied by the first photosystem allows electrons to be pulled from the water, and the energy supplied by the second photosystem step allows electrons to be transferred to NADP+. Because the overall energy trajectory has an up-down-up configuration resembling a "Z," the photosynthetic electron transport chain is sometimes referred to as the Z scheme. For the two photosystems to work together to move electrons from water to NADPH, they must have distinct chemical properties. Photosystem II supplies electrons to the beginning of the electron transport chain. When photosystem II loses an electron (that is, when it is itself oxidized), it is able to pull electrons from water. In contrast, photosystem I energizes electrons with a second input of light energy so they can be used to reduce NADP+. The key point here is that photosystem I when oxidized is not a sufficiently strong oxidant to split water, whereas photosystem II is not a strong enough reductant to form NADPH. The major protein complexes of the photosynthetic electron transport chain include the two photosystems as well as the cytochrome-b6 f complex (cyt), through which electrons pass between photosystem II and photosystem I. Small, relatively mobile compounds convey electrons between these protein complexes. Plastoquinone (Pq), a lipid-soluble compound that carries electrons from photosystem II to the cytochrome-b6 f complex. Plastocyanin (Pc), a water-soluble protein, carries electrons from the cytochrome-b6 f complex to photosystem I by diffusing through the thylakoid lumen. Water donates electrons to one end of the photosynthetic electron transport chain, whereas NADP+ accepts electrons at the other end. The enzyme that pulls electrons from water, releasing both H+ and O2, is located on the lumen side of photosystem II. NADPH is formed when electrons are passed from photosystem I to a membrane-associated protein called ferredoxin (Fd). The enzyme ferredoxin-NADP+ reductase then catalyzes the formation of NADPH by transferring two electrons from two molecules of reduced ferredoxin to NADP+ as well as a proton from the surrounding solution: NADP+ + 2e− + H+ → NADPH The accumulation of protons in the thylakoid lumen drives the synthesis of ATP. In chloroplasts, as in mitochondria, ATP is synthesized by ATP synthase, a transmembrane protein powered by a proton gradient. In chloroplasts, the ATP synthase is oriented such that the synthesis of ATP is the result of the movement of protons from the thylakoid lumen to the stroma. How do protons accumulate in the thylakoid lumen? Two features of the photosynthetic electron transport chain are responsible for the buildup of protons in the thylakoid lumen. First, the oxidation of water releases protons and O2 into the lumen. Second, the cytochrome-b6 f complex, the protein complex situated between photosystem II and photosystem I, and plastoquinone together function as a proton pump that is functionally and evolutionarily related to proton pumping in the electron transport chain of cellular respiration. In photosynthesis, the proton pump involves: (1) the transport of two electrons and two protons, by the diffusion of plastoquinone, from the stroma side of photosystem II to the lumen side of the cytochrome-b6 f complex and (2) the transfer of electrons within the cytochrome-b6 f complex to a different molecule of plastoquinone, which results in additional protons being picked up from the stroma and subsequently released into the lumen. Together, these mechanisms are quite powerful. When the photosynthetic electron transport chain is operating at full capacity, the concentration of protons in the lumen can be more than 1000 times greater than their concentration in the stroma (equivalent to a difference of 3 pH units). This accumulation of protons on one side of the thylakoid membrane can then be used to power the synthesis of ATP by oxidative phosphorylation. Cyclic electron transport increases the production of ATP. The Calvin cycle requires two molecules of NADPH and three molecules of ATP for each CO2 incorporated into carbohydrates. However, the transport of four electrons through the photosynthetic electron transport chain, needed to reduce two NADP+ molecules, does not transport enough protons into the lumen to produce the required three ATPs. An additional pathway for electrons is thus needed to increase the production of ATP. In cyclic electron transport electrons from photosystem I are redirected from ferredoxin back into the electron transport chain. These electrons reenter the photosynthetic electron transport chain by plastoquinone. Because these electrons eventually return to photosystem I, this alternative pathway is cyclic in contrast to the linear movement of electrons from water to NADPH. How does cyclic electron transport lead to the production of ATP? As the electrons from ferredoxin are picked up by plastoquinone, additional protons are transported from the stroma to the lumen. As a result, there are more protons in the lumen that can be used to drive the synthesis of ATP.

Dependant variable

The variable that may change in response to manipulations of the independent variable.

Prokaryotes vs. Eukaryotes

What are prokaryotes? Prokaryotes are microscopic organisms belonging to the domains Bacteria and Archaea, which are two out of the three major domains of life. (Eukarya, the third, contains all eukaryotes, including animals, plants, and fungi.) Bacteria and archaea are single-celled, while most eukaryotes are multicellular. Prokaryotes vs. eukaryotes Prokaryotes and eukaryotes are similar in some fundamental ways, reflecting their shared evolutionary ancestry. For instance, both you and the bacteria in your gut decode genes into proteins through transcription and translation. Similarly, you and your prokaryotic inhabitants both pass genetic information on to your offspring in the form of DNA. The most fundamental differences between prokaryotes and eukaryotes relate to how their cells are set up. Specifically: - Eukaryotic cells have a nucleus, a membrane-bound chamber where DNA is stored, while prokaryotic cells don't. This is the feature that formally separates the two groups. - Eukaryotes usually have other membrane-bound organelles in addition to the nucleus, while prokaryotes don't. - Cells, in general, are small, but prokaryotic cells are really small.

Chromosomes

When a cell divides, one of its main jobs is to make sure that each of the two new cells gets a full, perfect copy of genetic material. Mistakes during copying, or unequal division of the genetic material between cells, can lead to cells that are unhealthy or dysfunctional (and may lead to diseases such as cancer). DNA and genomes DNA (deoxyribonucleic acid) is the genetic material of living organisms. In humans, DNA is found in almost all the cells of the body and provides the instructions they need to grow, function, and respond to their environment. When a cell in the body divides, it will pass on a copy of its DNA to each of its daughter cells. DNA is also passed on at the level of organisms, with the DNA in sperm and egg cells combining to form a new organism that has genetic material from both its parents. Physically speaking, DNA is a long string of paired chemical units (nucleotides) that come in four different types, abbreviated A, T, C, and G, and it carries information organized into units called genes. Genes typically provide instructions for making proteins, which give cells and organisms their functional characteristics. In eukaryotes such as plants and animals, the majority of DNA is found in the nucleus and is called nuclear DNA. Mitochondria, organelles that harvest energy for the cell, contain their own mitochondrial DNA, and chloroplasts, organelles that carry out photosynthesis in plant cells, also have chloroplast DNA. The amounts of DNA found in mitochondria and chloroplasts are much smaller than the amount found in the nucleus. In bacteria, most of the DNA is found in a central region of the cell called the nucleoid, which functions similarly to a nucleus but is not surrounded by a membrane. A cell's set of DNA is called its genome. Since all of the cells in an organism (with a few exceptions) contain the same DNA, you can also say that an organism has its own genome, and since the members of a species typically have similar genomes, you can also describe the genome of a species. Chromatin In a cell, DNA does not usually exist by itself, but instead associates with specialized proteins that organize it and give it structure. In eukaryotes, these proteins include the histones, a group of basic (positively charged) proteins that form "bobbins" around which negatively charged DNA can wrap. In addition to organizing DNA and making it more compact, histones play an important role in determining which genes are active. The complex of DNA plus histones and other structural proteins is called chromatin. The DNA wrapped around histones is further organized into higher-order structures that give a chromosome its shape. For most of the life of the cell, chromatin is decondensed, meaning that it exists in long, thin strings that look like squiggles under the microscope. In this state, the DNA can be accessed relatively easily by cellular machinery (such as proteins that read and copy DNA), which is important in allowing the cell to grow and function. Decondensed may seem like an odd term for this state - why not just call it "stringy"? - but makes more sense when you learn that chromatin can also condense. Condensation takes place when the cell is about to divide. When chromatin condenses, you can see that eukaryotic DNA is not just one long string. Instead, it's broken up into separate, linear pieces called chromosomes. Bacteria also have chromosomes, but their chromosomes are typically circular. Chromosomes Each species has its own characteristic number of chromosomes. Humans, for instance, have 46 chromosomes in a typical body cell (somatic cell). Like many species of animals and plants, humans are diploid (2n), meaning that most of their chromosomes come in matched sets known as homologous pairs. The 46 chromosomes of a human cell are organized into 23 pairs, and the two members of each pair are said to be homologues of one another (with the slight exception of the X and Y chromosomes.) Human sperm and eggs, which have only one homologous chromosome from each pair, are said to be haploid (1n). When a sperm and egg fuse, their genetic material combines to form one complete, diploid set of chromosomes. So, for each homologous pair of chromosomes in your genome, one of the homologues comes from your mom and the other from your dad. The two chromosomes in a homologous pair are very similar to one another and have the same size and shape. Most importantly, they carry the same type of genetic information: that is, they have the same genes in the same locations. However, they don't necessarily have the same versions of genes. That's because you may have inherited two different gene versions from your mom and your dad. As a real example, let's consider a gene on chromosome 9 that determines blood type (A, B, AB, or O). It's possible for a person to have two identical copies of this gene, one on each homologous chromosome—for example, you may have a double dose of the gene version for type A. On the other hand, you may have two different gene versions on your two homologous chromosomes, such as one for type A and one for type B (giving AB blood). The sex chromosomes, X and Y, determine a person's biological sex: XX specifies female and XY specifies male. These chromosomes are not true homologues and are an exception to the rule of the same genes in the same places. Aside from small regions of similarity needed during meiosis, or sex cell production, the X and Y chromosomes are different and carry different genes. The 44 non-sex chromosomes in humans are called autosomes. Chromosomes and cell division After DNA replication, each chromosome now consists of two physically attached sister chromatids. After chromosome condensation, the chromosomes condense to form compact structures (still made up of two chromatids). As a cell prepares to divide, it must make a copy of each of its chromosomes. The two copies of a chromosome are called sister chromatids. The sister chromatids are identical to one another and are attached to each other by proteins called cohesins. The attachment between sister chromatids is tightest at the centromere, a region of DNA that is important for their separation during later stages of cell division. As long as the sister chromatids are connected at the centromere, they are still considered to be one chromosome. However, as soon as they are pulled apart during cell division, each is considered a separate chromosome. What happens to a chromosome as a cell prepares to divide. The chromosome consists of a single chromatid and is decondensed (long and string-like). The DNA is copied. The chromosome now consists of two sister chromatids, which are connected by proteins called cohesins. The chromosome condenses. It is still made up of two sister chromatids, but they are now short and compact rather than long and stringy. They are most tightly connected at the centromere region, which is the inward-pinching "waist" of the chromosome. The chromatids are pulled apart. Each is now considered its own chromosome. Why do cells put their chromosomes through this process of replication, condensation, and separation? The short answer is: to make sure that, during cell division, each new cell gets exactly one copy of each chromosome.

Ionic bond

When an atom of very high electronegativity is paired with an atom of very low electronegativity, the difference in electronegativity is so great that the electronegative atom "steals" the electron from its less electronegative partner. In this case, the atom with the extra electron has a negative charge and is a negative ion. The atom that has lost an electron has a positive charge and is a positive ion. The two ions are not covalently bound, but because opposite charges attract they associate with each other in what is called an ionic bond.

Covalent bond

When the outermost orbitals of two atoms come into proximity, two atomic orbitals each containing one electron merge into a single orbital containing a full complement of two electrons. The merged orbital is called a molecular orbital, and each shared pair of electrons constitutes a covalent bond that holds the atoms together. Two adjacent atoms can sometimes share two pairs of electrons, forming a double bond denoted by a double line connecting the two chemical symbols for the atoms. In this case, four orbitals occupied by a single electron merge to form two molecular orbitals. Bonds in which the outermost shells are fully occupied by electrons tend to be the most stable.

Prediction

a prediction is a rigorous, often quantitative, statement, forecasting what would happen under specific conditions;

x-axis y-axis

the horizontal number line in a coordinate plane and the vertical number line in a coordinate plane The "independent" variable goes on the x-axis (the bottom, horizontal one) and the "dependent" variable goes on the y-axis (the left side, vertical one).