Biology Exam Grade 12

Gastrin

(digestive enzyme in stomach) works best at pH 2 and is denatured in small intestine (pH is 10) Protons can interact with enzymes; effect would depends on the enzyme in question Curing meats with high concentrations of salt/sugar, and pickling meat/vegetables in vinegar preserves food by denaturing enzymes Once refolding back into tertiary structure, chaperone proteins help the polypeptide with the folds

The 7 Step Process

1). Acetyl-CoA + Oxaloacetate → Citrate 2). Citrate gets dehydrated and turned into Isocitrate 3). Isocitrate is oxidized into α-ketoglutarate CO2 NADH 4). α-Ketoglutarate → succinyl CoA CO2 NADH 5). A phosphate group is substituted for coenzyme A is formed. This e is used in substrate-level phosphorylation during the conversion of the succinyl group to succinate to form ATP. 6).Through dehydration, Succinate → Fumarate FADH2 7).Through the addition of H2O, Fumarate → Malate 8). Malate gets oxidized into Oxaloacetate NADH Yield of the Krebs Cycle per glucose molecule: 6 NADH 2 FADH2 2 ATP 4 CO2

Antenna complex:

A cluster of light-absorbing pigments embedded in the thylakoid membrane able to capture and transfer energy to special chlorophyll α molecules in the reaction centre.

Photosystem

A combination of proteins and molecules which have chlorophyll, variations of chlorophylls and pigment molecules that are responsive to light, which have e−s that get excited by light which can transfer its energy to P680/P700 which gives its e− to an acceptor molecule which is then passed down through the ETC.

Reaction centre

A complex of proteins and pigments that contain the primary electron acceptor.

Facultative, obligate aerobes/anaerobes:

A facultative anaerobe is an organism that makes ATP by aerobic respiration if oxygen is present, but is capable of switching to fermentation or anaerobic respiration if oxygen is absent. Obligate aerobes cannot make ATP in the absence of oxygen, Obligate anaerobes die in the presence of oxygen.

Deoxyribonucleic Acid (DNA)

A hereditary material in humans and almost all other organisms which contains the genetic info of an organism. + Most DNA is located in the cell nucleus (where it is called nuclear DNA). DNA is a polymer made up of nucleotide subunits. The diameter of DNA is 2 nm. The distance between each bp of DNA is 0.34 nm. 1 complete turn of the double helix is 3.4 nm. DNA rotates clockwise.

Semiconservative replication:

A mechanism of DNA replication in which each of the 2 strands of parent DNA is incorporated into a new double-stranded DNA molecule.

Primary electron acceptor:

A molecule capable of accepting electrons and being reduced during photosynthesis.

Primary e− acceptor:

A molecule capable of accepting e− and becoming reduced during photosynthesis.

Molecular Shape

A molecule's biological function is determined by the types of bonds between its atoms, and by its overall shape and polarity Hybridization- Modification of valence orbitals that changes the orientation of the valence electrons Covalent bonds can be polar or nonpolar However, the molecule's polarity as a whole is dependent on bond polarity as well as its molecular shape Symmetrical molecules produce nonpolar molecules regardless of bonds (as the dipoles would cancel each other out) Asymmetrical molecules produce nonpolar molecules if all bonds are nonpolar, and polar molecules if 1 or more bond is polar (difference in dipole moments)

Absorption spectrum:

A plot of the amount of light energy of various wavelengths that a substance absorbs. Its produced using an instrument called a spectrophotometer, which analyzes a sample of the pigment.

Action spectrum:

A plot of the effectiveness of light at different wavelengths in a driving chemical reaction. Usually determined by using a suspension of chloroplasts or algal cells and measuring the amount of O2 released by photosynthesis at different wavelengths of visible light. If an action spectrum for a physiological phenomenon matches the absorption spectrum of a pigment, it is very likely that the two are linked.

Gene

A region of DNA that codes for the building of a particular polypeptide

Plasmid

A small circular section of DNA found in the cytosol of bacteria; replicates independently of the chromosomal DNA. They often contain genes that code for specific proteins (ex. proteins that provide resistance to antibiotics).

Histone

A special protein that is the core around which the DNA strand wraps.

Chloroplasts

A structure within the cells of plants that is the site of photosynthesis, resulting in the production of oxygen and energy-rich organic compounds.

Cuticle

A waxy, water-resistant surface coat on a leaf that protects against excessive absorption of light and evaporation of water.

Allosteric regulation

Allosteric sites- Receptor sites that bind substances that either inhibit or stimulate an enzyme's activity Activator- Substance that binds to allosteric site and stimulates enzyme Allosteric inhibitor- Substance that binds to allosteric site and inactivates enzyme

Carbon

Almost all chemicals of life are carbon based Organic compound- Any compound that has carbon in it (CO2 along with others are exceptions) Small, relatively light, four single valence electrons oriented toward vertices of a regular tetrahedron Can form up to four stable covalent bonds with other atoms Forms straight, branched chains, and ring structures that act as the backbones of biological molecules

protein structures secondary

Alpha helix- Characterized by tight coil that's stabilized by hydrogen bonds Beta-pleated sheet- Forms between parallel stretches of a polypeptide and are stabilized by hydrogen bonds

Peptide bonds

Amide linkage that holds amino acids together in polypeptides

Essential amino acids

Amino acids that the body can't synthesize from simpler compounds; has to be obtained from diet (tryptophan, methionine, valine, threonine, phenylalanine, leucine, isoleucine, and lysine)

Carotenoids

An accessory pigment molecule. They are called accessory pigments because after light absorption, they transfer this excitation energy to molecules of chlorophyll α. It doesn't absorb red and yellow light waves, therefore reflect as orange.

Heterotroph:

An organism that cannot manufacture its own food by carbon fixation and therefore derives its intake of nutrition from other sources of organic carbon, mainly plant or animal matter.

Photoautotroph:

An organism that carry out photosynthesis, using energy from sunlight, carbon dioxide and water are converted into organic materials to be used in cellular functions

Autotroph:

An organism that produces complex organic compounds from simple substances present in its surroundings, generally using energy from light or inorganic chemical reactions.

Chemoautotroph:

An organisms that obtain energy by the oxidation of e− donors in their environments. These molecules can be organic or inorganic. (doesn't use carbon)

Highest density at 4℃

As water molecules cool below 0℃, crystalline lattice forms H-bonds between V-shaped molecules spread molecules apart, reducing density below that of liquid water As a result, ice floats on liquid water Because of this, fish and other aquatic organisms can survive in the winter (Life exists because of this property)

Conjugate Acids and Bases

Based on Bronsted-Lowry, an acid would be a proton donor, while a base would be a proton acceptor Forward reaction: Acetate is the proton donor (acid) and water is the proton acceptor (base) Reverse reaction: Hydronium ion is the proton donor (conjugate acid) and acetate ion is proton acceptor (conjugate base) Acetate and acetate ion would be a conjugate acid-base pair Same with water and hydronium

Disadvantages of C3 Photosynthesis:

C3 plants have the disadvantage that in hot dry conditions their photosynthetic efficiency suffers because of a process called photorespiration. When the CO2 concentration in the chloroplasts drops below about 50 ppm, the catalyst rubisco that helps to fix carbon begins to fix oxygen instead. This is highly wasteful of the energy that has been collected from the light, and causes the rubisco to operate at perhaps a quarter of its maximal rate, which is already inefficient enough.

Phase I: Carbon Fixation

CO2 combines with a 5-c molecule called RuBP, which form an unstable 6-c molecule. *RuBP (Ribulose-bisphosphate) A 5 carbon compound involved in the Calvin cycle, which is part of the light independent reactions of photosynthesis. Atmospheric CO2 is combined with RuBP to form a 6 carbon compound, with the help of an enzyme called RuBisCo. The importance is that it's part of the cycle that enables plants to 'fix' carbon from the atmosphere and convert into photosynthetic products. Since plants are the main autotrophic group on the planet and are at the bottom of most food chains RuBP is not just important to photosynthesis, but to all heterotrophic life. *How was RuBisCo formed? A single celled organism evolved and created an enzyme called RuBisCo in order to extract carbon, since at the time, there was a lot of CO2 in the atmosphere RuBisCo wasn't rather effective so the cell created a lot of it, in order to balance out the inefficiency. After other reactions including the light dependent reactions, plants increased oxygen levels in the atmosphere, therefore confusing the enzyme. RuBisCo then sliced O2 instead of CO2, creating a toxic byproduct called phosphoglycolate. Plants then had to create other enzymes to break phosphoglycolate into glycine, an amino acid. Immediately, the 6-c molecule splits into two 3-c molecules called 3-phosphoglycerate (PGA). C3 Photosynthesis RuBisCo, an enzyme that is large and slow, catalyzes the reactions above. Carbon fixation is the conversion process of inorganic carbon (carbon dioxide) to organic compounds by living organisms.

Four main classes:

Carbohydrates, lipids, proteins, and nucleic acids

Photosynthesis

Chem. Eq': 6CO2 + 6H2O + light e → C6H12O6 + 6O2 Reactants: Carbon Dioxide, Water Products: Glucose, Oxygen Light E → Chemical E Endothermic (Endergonic) Coenzymes involved: NADP+ # of Stages: 2 Names of Stages: Light-dependent reactions Calvin Cycle (Cyclic) Uses CO2 to create glucose Organelle where process takes place: Chloroplast (double-membrane) ATP is produced by chemiosmosis Has a mobile lipid: Plastoquinone Has a similar cytochrome complex Has an ATP Synthase Has an ETC located in the thylakoid membrane Has proton gradient, between the thylakoid membrane. There is a higher concentration in the thylakoid lumen than the stroma. Direction of H+ flow: stroma → thylakoid lumen

Cellular Respiration

Chem. Eq': C6H12O6 + O2 → H2O + ATP Reactants: Glucose, Oxygen, Water Products: Water, ATP Chemical E → Potential E (ATP) Exothermic (Exergonic) Coenzymes involved: NAD+, FAD # of Stages: 4 Names of Stages: Glycolysis Pyruvate Oxidation Krebs Cycle (Cyclic) ETC Releases CO2 as byproduct Organelle where process takes place: Mitochondria (double-membrane) ATP is produced by chemiosmosis Has a mobile lipid: Ubiquinone Has a similar cytochrome complex Has an ATP Synthase Has an ETC located in the inner mitochondrial membrane Has a proton gradient, between the inner mitochondrial membrane. There is a higher concentration in the inner membrane space than the matrix. Direction of H+ flow: matrix → inner membrane space

Buffers

Chemical systems containing substances that can donate or remove H+ ions in order to maintain a relatively neutral pH Living cells would use this to resist significant pH changes Because of this system, blood pH is around 7.4 pH change of 0.2-0.4 pH can be fatal Proteins can also act as buffers Hemoglobin help maintain constant pH (necessary because some amino acids can be acidic or basic due to their structure)

Structure of Chlorophyll

Chlorophyll ɑ Only chlorophyll that can transfer e of light to Calvin Cycle. Absorbs light in the 400-500 nm range (blue-green) + 650-700 nm range (red). Chlorophyll β Accessory pigment - absorbs photons that chlorophyll ɑ absorbs poorly. Passes on e to chlorophyll ɑ, therefore, allowing the plant to absorb a wide range of light in different wavelengths.

Steroids (or sterols)

Compact hydrophobic molecules with four fused hydrocarbon rings and several functional groups Cholesterol is an important component of steroids; however, too much is bad (creates plaque in blood vessels, which blocks blood vessels) Cells convert it into various compounds, such as vitamin D, bile salts, and sex hormones (testosterone, estrogen, progesteron)

What is deoxyribose?

Deoxyribose, found in DNA, is a modified sugar, lacking 1 oxygen atom (hence the name "deoxy ").

Miscible

Describes two liquids that are soluble in each other Ethanol and ethylene glycol (antifreeze) are miscible in water Subscript (aq), meaning aqueous, is meant to identify molecule/ion that's dissolved in water

Facilitated Diffusion

Diffusion across membrane through transporter proteins Passive- requires no direct energy Often down with changes in shape of transporter to selectively allow molecules across

Phase II: Reduction Reactions

Each 3-phosphoglycerate is phosphorylated by an ATP (6 ATP in total) to form 1,3-bisphosphoglycerate (1,3-BPG). NADPH reduces 1,3-bisphosphoglycerate, making glyceraldehyde-3-phosphate (G3P). (6 NADPH are reduced into 6 NADP+)

Yield of the ETC per glucose molecule:

Each NADH that is oxidized, and therefore for each pair of electrons that down the ETC, 10 H+ ions are pumped into the inner membrane space. 3-4 H+ ions are needed to flow back through the ATP Synthase for the synthesis of ATP. Therefore, at most, 3 ATP are made for every NADH oxidized by the ETC. Since FADH2 delivers its electrons at complex II, fewer protons are pumped across the membrane. Thus, for every FADH2 oxidized, only about two ATP are synthesized. NADH from Glycolysis don't have immediate access to the ETC. To do so, it uses one of the two shuttle systems that transfer high-e electrons from NADH across the inner membrane and into the matrix. Malate-Aspartate Shuttle: The transfer is very efficient The NADH from the cytosol is oxidized to NAD+, and the electrons are transferred across the membrane and used to reduce an NAD+ to NADH within the matrix. For the cells that use the more efficient Malate-Aspartate Shuttle, the ETC and Chemiosmosis produce a total of 34 ATP.

Valence Electrons

Electrons located in the outermost s and p orbitals that determine an atom's chemical behaviour If valence orbital is filled, inert Less electrons in valence orbital, the more reactive

Kinetic energy

Energy possessed by moving objects

Enzyme-substrate complex

Enzyme with substrate attached to active site Since enzymes are proteins, they have optimal temperatures for functioning Around 37℃ for human enzymes Also have optimal pH's Pepsin (found in stomach) has an optimal pH of around 2, while trypsin (found in intestines) has an optimal pH of 8 Both are optimal for where they're found

Sodium-Potassium Pump

Exchanges 3 Na+ ions for 2 K+ ions Creates membrane potential (around-50 to -200 mV) Membrane can function as a battery Greater negative charge inside than outside, along with greater chemical gradient for both Na+ and K+ forms an electrochemical gradient Low Na+ concentration in cytoplasm, high Na+ concentration outside High K+ concentration in cytoplasm, low K+ concentration outside Na+ concentration is greater than that of K+ Process: When facing cytoplasm, protein has high affinity for Na+; 3 Na+ would bind to protein After 3 Na+ bind, protein has high affinity for ATP ATP would phosphorylate protein, making it change conformation Altered conformation- protein faces environment, has a low affinity for Na+, releasing them, and has high affinity for K+ 2 K+ would bind to protein, releasing phosphate group Protein would revert back to original conformation, releasing K+ in cytoplasm

Phospholipid

Fats which make up cell membranes Composed of a glycerol molecule attached to two fatty acids and a highly polar phosphate group Fatty acids are hydrophobic, while phosphate group is hydrophilic Forms a circle when in water (phosphate head out, fatty acid tails in); known as a micelle

Feedback Inhibition

Feedback inhibition- Method of metabolic control where product formed in sequence inhibits enzyme that catalyzes reaction that occurs earlier in the process As reaction occurs, concentration of product increases, meaning that it's more likely to come in contact with enzyme 1 Therefore, it's more likely to inhibit enzyme 1 As a result, the reaction would be less likely to occur ...which results in lower product concentration ...and the cycle repeats

Phase III: RuBP Regeneration

Five glyceraldehyde-3-phosphate are rearranged to regenerate 3 ribulose 1,5- bisphosphate so the Calvin cycle can continue. 3 ATP are used for the reaction above.

Thylakoids:

Flattened sacs inside a chloroplast, bounded by pigmented membranes on which the light reactions of photosynthesis take place.

Yield of the Calvin Cycle:

For every 3 CO2 molecules, 6 G3P are produced but only one of which can be counted as a net gain. In order to produce one G3P molecule (net gain), it requires 9 ATP and 6 NADPH. In order to produce glucose, the Calvin Cycle requires two G3Ps which is basically two rotations. Therefore, for the production of one molecule of glucose, the Calvin Cycle requires a total of 18 ATP and 12 NADPH. Technically, it also releases ADP and NADP+ to send back to the light dependant reactions.

Dipole-dipole forces

Forces between polar molecules Partially positive side of one polar molecule attracts partially negative side of adjacent polar molecule

Photosynthesis:

Formal eq' | 6CO2 + 6H2O + photons → C6H12O6 + 6O2 Carbon Dioxide + Water + photons → Glucose + Oxygen All green plant tissues can photosynthesize, but in most plants, but the majority of photosynthesis usually takes place in the leaves. The cells in a middle layer of leaf tissue called the mesophyll are the primary site of photosynthesis.

Aerobic Respiration:

Formal equation | C6H1206 + 6O2 → 6CO2 + 6H2O + e (ATP + heat) Glucose + Oxygen -> Carbon Dioxide + H2O + e (ATP to heat)

Glycolysis:

Formal equation | Glucose + 2 NAD+ + 2 ADP + 2Pi → 2 pyruvates + 2 ATP + 2 H2O + 2H+ It is a 10-step process that occurs in the cytoplasm of the cell. It req' no oxygen, yet can perform w/ it. (Aerobic/Anaerobic) Simply put, turn a 6-c molecule of glucose into two 3-c molecules of pyruvates. 2 main phases: Investment Phase: 2 ATPs are invested by the cell to provide activation e by phosphorylating glucose. Payoff Phase: 4 ATPs are produced and NAD+ is reduced to NADH by electrons released by the oxidation of glucose. *The electrons from this phase are passed to the Electron Transport Chain (ETC). We end w/ 2 pyruvate molecules, which can be further broken down in the Krebs Cycle. Why does glycolysis req' NAD+? Because cells have only a certain number of NAD+ molecules, which cycle back and forth between oxidized (NAD+) and reduced (NADH). Glycolysis needs NAD+ to accept electrons as part of a specific reaction. If there's no NAD+ around (because it's all stuck in its NADH form), this reaction can't happen and glycolysis will come to a halt. So, all cells need a way to turn NADH back into NAD + to keep glycolysis going. The yield of Glycolysis per glucose molecule 4 ATP (2 net ATP, since 2 ATP were initially invested) 2 NADH

Rosalind Franklin (1953)

Franklin's image of the DNA molecule was key to deciphering its structure, but only Watson, Crick, and Wilkins received the 1962 Nobel Prize in physiology or medicine for their work. Franklin died of ovarian cancer in 1958 in London, four years before Watson, Crick, and Wilkins received the Nobel. Using x-ray crystallography, she was able to figure out a few things; DNA rotates clockwise, has a diameter of 2 nm, 1 turn of DNA is 3.4nm and suggested the possibility of a double helix structure.

Stages of Cellular Respiration Yield of ATP

Glycolysis 2 Pyruvate Oxidation 0 Krebs Cycle 2 Electron Transport Chain 34

High specific heat of vaporization

H-bonds cause liquid water to absorb lost of heat before becoming vapour Evaporative cooling (humans and sweat)

High specific heat capacity

H-bonds require a lot of heat to break, so large amount of heat is required to increase temperature Also large amount of heat has to be lost before temperature decreases As a result, temperature moderation (constant body temperature in organisms can be maintained)

Joseph Priestley

He carried out an experiment that showed that plants produce oxygen. He placed a mouse in a sealed jar. Long story short, it died. He then placed a plant along with another mouse. It lived. This proved that plants provide oxygen. HOWEVER, the experiment did fail in the dark.

Jan Ingenhousz:

He figured out that plants can only produce oxygen when light is present.

Lipids

Hydrophobic molecules composed of C, H, and O Few O-H bonds; more nonpolar C-H bonds than carbohydrates Used to store energy, building membranes/other cell parts, and chemical signalling molecules (hormones) Four families: fats, phospholipids, steroids, and waxes

Friedrich Miescher (1869)

In 1869, Friedrich Miescher isolated "nuclein," DNA w/ associated proteins, from cell nuclei. He was the first to identify DNA as a distinct molecule. Studying under Felix Hoppe-Seyler, Miescher had the task of researching the composition of white blood cells. Using bandages contained pus from his patients, Miescher extracted a substance that was acidic and contained large proportions of phosphorus, which was nuclein. He determined that nuclein was made up of hydrogen, oxygen, nitrogen, and phosphorus and there was a unique ratio of phosphorus to nitrogen. Although Miescher did most of his work in 1869, his paper on nuclein wasn't published until 1871.

Frederick Griffith (1928)

In 1928, Frederick Griffith conducted a series of experiments using Streptococcus pneumoniae bacteria and mice. Griffith wasn't trying to identify the genetic material, but rather, trying to develop a vaccine against pneumonia. In his experiments, Griffith used 2 related strains of bacteria, known as R and S. R strain. When grown in a petri dish, the R bacteria formed colonies, or clumps of related bacteria, that had well-defined edges and a rough appearance (hence the abbreviation "R"). The R bacteria were nonvirulent, meaning that they did not cause sickness when injected into a mouse. S strain. S bacteria formed colonies that were rounded and smooth (hence the abbreviation "S"). The smooth appearance was due to a polysaccharide, or sugar-based, coat produced by the bacteria. This coat protected the S bacteria from the mouse immune system, making them virulent (capable of causing disease). Mice injected w/ live S bacteria developed pneumonia and died. As part of his experiments, Griffith tried injecting mice w/ heat-killed S bacteria (that is, S bacteria that had been heated to high temperatures, causing the cells to die). Unsurprisingly, the heat-killed S bacteria did not cause disease in mice. The experiments took an unexpected turn, however, when harmless R bacteria were combined w/ harmless heat-killed S bacteria and injected into a mouse. Not only did the mouse develop pneumonia and die, but when Griffith took a blood sample from the dead mouse, he found that it contained living S bacteria Although he couldn't identify the exact material involved in inheritance, Griffith understood that some hereditary substance passed from the dead S-strain to the live R-strain. The process in which R-strain acquired the material to transform into the harmful S-strain bacteria is called transformation, as he formulated. He called the substance transforming principle (the term given to the substance that could be transferred from non-living cells to living cells, causing the living cell to show characteristics of the non-living cell)

Erwin Chargaff (1950)

In 1950, Chargaff discovered 2 rules that helped lead to the discovery of the double helix structure of DNA. The 1st rule was that in DNA the number of guanine units is equal to the number of cytosine units, and the number of adenine units is equal to the number of thymine units. This hinted at the bp makeup of DNA. The 2nd rule was that the relative amounts of guanine, cytosine, adenine and thymine bases vary from one species to another. This hinted that DNA rather than protein could be the genetic material.

What is an ester bond?

In DNA, refers to the oxygen-carbon linkage between the triphosphate group and the 5' carbon of the ribose sugar group in a single DNA or RNA nucleotide.

Pyruvate Oxidation

In eukaryotes, it occurs in the mitochondrial matrix It does req' oxygen, which means it's an aerobic process Before the chemical reactions can begin, pyruvate must enter the mitochondrion, crossing its inner membrane and arriving at the matrix. Pyruvate is able to pass through pores in the outer mitochondrial membrane (semi-selective) but for the highly selective inner membrane, does req' a facilitated transport (phosphate glycerol shuttle/malate-aspartate shuttle) to enter. The 3 Step Process: 1). A carboxyl group is snipped off of pyruvate and released as a molecule of carbon dioxide, leaving behind a two-c molecule. (the enzyme responsible for releasing the carbon dioxide is Pyruvate Decarboxylase) 2). The two-c molecule from step 1 is oxidized, and the electrons lost in the oxidation are picked up by NAD+ to form NADH. 3). The oxidized two-c molecule—an acetyl group is attached to Coenzyme A (CoA) to form acetyl CoA. Acetyl CoA is sometimes called a carrier molecule, and its job here is to carry the acetyl group to the citric acid cycle. Yield of Pyruvate Oxidation per glucose molecule: 2 NADH Acetyl CoA serves as fuel for the citric acid cycle in the next stage of cellular respiration. The addition of CoA helps activate the acetyl group, preparing it to undergo the necessary reactions to enter the citric acid cycle.

Light-dependant reactions (Linear)

In plants, the light reactions take place in the thylakoid membranes of chloroplasts. Formal eq' | photons + H2O → ATP + NADPH + O2 photons + water → ATP + NADPH + Oxygen The absorption of a photon by a pigment molecule excites a single e−, moving it from a lower-energy, or ground state, to a higher-energy, or excited state. The difference between the energy level of ground state and the energy level of the excited state must be equivalent to the energy of the photon of light that was absorbed. If the energy aren't equivalent, the photon cannot be absorbed by the pigment.

Chemiosmosis:

In the inner mitochondrial membrane, H+ ions have just one channel available: a membrane-spanning protein known as ATP synthase. Conceptually, ATP synthase is turned by the flow of H+ ions moving down their electrochemical gradient. As ATP synthase turns, it catalyzes the addition of a phosphate to ADP, capturing e from the proton gradient as ATP. (oxidative phosphorylation)

Nucleic Acids

Informational macromolecules used by all organisms to store hereditary information DNA (deoxyribonucleic acid) has no oxygen on 2-carbon of saccharide (deoxyribose), while RNA (ribonucleic acid) does (ribose) DNA's made up of nucleotides with these four organic bases: adenine (A), guanine (G), cytosine (C), and thymine (T) Adenine and guanine are double-ringed purines, while cytosine and thymine are single-ringed pyrimidines RNA has uracil instead of thymine (structurally similar) Specific enzymes link a series of nucleotides to one another, forming a polymer called a strand They facilitate covalent bonding between phosphate group of one nucleotide and hydroxyl group of another nucleotide (forms a phosphodiester bond) Composed of two DNA strands in helical structure Held together by H-bonds between nitrogenous bases on adjacent strands Adenine bonds to thymine (or uracil in RNA) with two hydrogen bonds Guanine bonds to cytosine with three hydrogen bonds The two strands run antiparallel to each other (when one strand goes 5' to 3', the other one goes 3' to 5') Nucleotides are also used as intermediates in cell's energy transformation ATP (adenosine triphosphate) (More on that in Chapter 2) Cyclic adenosine monophosphate (cAMP) is used as a second messenger in various hormone interactions (More on that in Chapter 8)

Endocytosis

Intake of materials by cells from environment Occurs when plasma membrane sinks inward As pocket deepens, plasma membrane pinches off, creating vesicle Three types: Phagocytosis "Cellular eating"; large vesicles are formed that contain solid particles One way cells can obtain nutrients Pinocytosis "Cellular drinking"; small vesicles are formed that usually don't contain solid particles Use for uptake of dissolved materials Receptor mediated endocytosis Receptors on exterior of cells bind materials like cholesterol Area then form vesicles to allow bound materials to be taken up

Isotonic Hypotonic Hypertonic

Isotonic- Solute concentration of environment is equal to that of interior (equal water potential) Hypotonic- Solute concentration of environment is less than that of interior (net movement of water into interior) Hypertonic- Solute concentration of environment is greater than that of interior (net movement of water out of interior)

What is a glycosyl bond?

It is a covalent bond that holds a carbohydrate (sugar) to another group that can or cannot be another sugar. In DNA, glycosyl bonds refer to the nitrogen-carbon linkage between the 9' nitrogen of purine bases or 1' nitrogen of pyrimidine bases and the 1' carbon of the sugar group.

The Krebs Cycle/ Citric Acid Cycle:

It is an 8-step process which occurs in the mitochondrial matrix. *essentially a series of redox, dehydration, hydration, and decarboxylation reactions. It req' oxygen, therefore is an aerobic process HOWEVER doesn't directly consume oxygen. It completes the breakdown of glucose by oxidizing pyruvate to carbon dioxide. The purpose is to produce NADH, the electron carrier, which passes these electrons to the ETC. Acetyl-CoA (2-c molecule) + Oxaloacetate (4-c molecule) goes through the Krebs cycle and turns back into Oxaloacetate (4-c molecule) CoA is bound to a sulfhydryl group (-SH) and diffuses away to eventually combine w/ another acetyl group. This step is irreversible because it is highly exergonic

Light Dependant Reactions (Cyclic):

It occurs in the thylakoid membrane. The e− from PSI is excited by a photon, therefore being grabbed by iron sulfide, PSI's primary e− acceptor. Iron sulfide passes the e− to ferredoxin. Ferredoxin then passes the e− to pastiquinone, which then returns it back to PSI. This process only creates ATP through chemiosmosis. It does not produce oxygen and NADPH. Sometimes, the need of ATP to drive the Calvin Cycle exceeds the limits of what's produced in non-cyclic photophosphorylation. The chloroplast will continue cyclic photophosphorylation until the ATP supply has been replenished.

Why can't 2 purines/pyrimidines bond?

It's bc there is not enough space for 2 purines to fit within the helix and too much space for 2 pyrimidines to get close enough together for h-bonds to form between them.

Macromolecules

Large molecules, usually composed of a large number of repeating subunits

Membrane Synthesis

Lipids and proteins are made in the endoplasmic reticulum Carbohydrates are added Golgi apparatus (or body, whatever floats your boat) further processes components Vesicles are formed and moved from Golgi to plasma membrane Vesicles fuse with plasma membrane Directionality of proteins determined by ER

Waxes

Lipids with long-chain fatty acids linked to alcohols or carbon rings Examples: cutin of epidermal cells of plants (water resistant)

Immiscible

Liquids that form separate layers instead of dissolving Gasoline and oil are immiscible in water; miscible in each other

Role of Stomata:

Lower epidermis It controls gas exchange(O2, CO2)

Proteins

Made up of amino acids, which are made up of an amino group, central carbon, R group (various groups), and carboxyl group Enzymes, or biological catalysts, allow chemical reactions to proceed at speeds that can sustain life Immunoglobulins protect animals from foreign molecules and pathogens

Electronegativity

Measure of an atom's ability to attract shared electron pair when in a covalent bond The higher it is, the more likely electrons are at that atom

Entropy

Measure of randomness/disorder in energy or in collection of objects; symbolized by S Increases in chemical reactions when: Solids turn into liquids/gases Liquids turn into gases Fewer moles of reactant molecules form greater number of moles of product molecules Complex molecules react to form simpler molecules (glucose to CO2 and H2O) Solutes moves from area of high concentration to area of low concentration (diffusion)

Bond energy

Minimum energy required to break one mole of bonds between two species of atoms (higher it is, more stable the bond is) Potential energy diagrams Peaks on the diagrams are transition states (temporary condition in which bonds within reactants are breaking and products' bonds are forming) Activation energy- Energy required to form transition state molecules from reactants

Induced-fit model

Model of enzyme activity that describes an enzyme as a dynamic protein molecule that changes shape to better accommodate the substrate As substrate comes closer to enzyme, partially charged ends of substrate would interact with partially charged parts of enzyme, to the point where the active site would change its conformation to better fit the substrate

Hydrocarbons

Molecules that only have carbon and hydrogen Non polar due to symmetrical arrangement of bonds

Types of Carbohydrates

Monosaccharides Simple sugars; made up of a single chain of carbon atoms Oligosaccharides Two to three simple sugars attached to one another by covalent bonds called glycosidic linkages Polysaccharides Composed of a lot of monosaccharide subunits held together by glycosidic linkages

Fat

Most common energy-storing molecule in living organisms (around 38 kJ per gram) Excess carbohydrates in animals are converted into fat and store them in cells of adipose (fat) tissue Acts as thermal insulation Plants also have fats Most common are triglycerides, lipids containing three fatty acids attached to a single glycerol molecule Glycerol and fatty acids are held together by ester linkages (condensation of a carboxyl group and a hydroxyl group) Fatty acids with no double bonds are called saturated fatty acids; unsaturated fats have one or more double bonds

Diffusion

Movement of particles from area of high concentration to area of low concentration Passive transport- doesn't require input of energy

Cofactors

Nonprotein components that are required for enzymes to work

Bonding capacity

Number of covalent bonds an atom can fork with neighbouring atoms

Electron Transport Chain:

Occurs in the inner mitochondrial membrane. This req' oxygen, which means it's an aerobic process. As electrons travel through the chain, they go from a higher to a lower e level, meaning from a less electron-hungry state to more electron-hungry molecule. This final step uses oxidative phosphorylation to use the NADH and FADH2's H+ ions to form ATP.

Why can't adenine bond w/ cytosine and guanine w/ thymine?

Only w/ adenine & thymine and w/ cytosine & guanine are there opportunities to establish h-bonds between them (2 between A & T; 3 between C & G). The ability to form h-bonds makes the bp more stable structurally.

coenzyme

Organic cofactors

A nucleotide is made of:

Phosphate group Deoxyribose (5-c sugar) Nitrogenous bases

PSI:

Photons hit PSI and the e− from chlorophyll P700 gets excited and passes it's e− to the primary e− acceptor, iron sulfide. It then goes through the ETC to a iron-sulfur containing protein called ferredoxin (Fd). The e−s make their way to an enzyme called NADP reductase which it uses 2 e−s and one H+ ion from the stroma to reduce NADP+ into NADPH.

PSII:

Photons strike PSII and the e−s from chlorophyll P680 becomes excited and is passed on to a primary e− acceptor called pheophytin. The e− is passed on to plastoquinone, which is a mobile e− carrier (PQ). The e− passes through an ETC. As the e− passes through, energy is given off. This energy also is used to power the proton pumps (PQ and Cytochrome Complex) which creates an electrochemical gradient which will power chemiosmosis. A Z protein associated with PSII splits water into oxygen, H+ ions and e−s. The oxygen leaves the chloroplast, the H+ stays inside the lumen to power chemiosmosis and the e−s go back to P680. The e− passes through a Q cycle, which transports a proton from the stroma into the thylakoid space, creating an electrochemical gradient. The e− then passes through more of the transport chain replacing eventually replacing e−s lost in PSI by chlorophyll P700.

Endothermic

Potential energy of products is higher than potential energy of reactants; energy would be absorbed Overall change in energy (heat, enthalpy of reaction) is symbolized by H

Exothermic

Potential energy of products is less than potential energy of reactants; energy would be released Example- Combustion; organic compounds react with oxygen to form carbon dioxide and water (NOTE: Controlled combustion; it's not spontaneous)

protein structures primary

Primary The actual sequence of amino acids in a polypeptide chain Each amino acid in a polypeptide is referred to as a residue

Active Transport

Protein pumps that expend energy to move molecules across membrane

Peripheral Proteins

Proteins loosely attached to membrane Often associated with exposed ends of integral proteins

3 Ways to Create a Gradient:

Proton pump PQ & Cytochrome Complex pump protons from the stroma into the lumen. Splitting of H2O Protons from H2O stay in the lumen. NADP+ takes H+ from the stroma, reducing the level of H+ ions in stroma more.

Coupled Transport

Proton pump- Pumps protons against electrochemical gradient As molecules move down electrochemical gradient, cotransport allows other molecules to enter cell Symport- The two molecules both enter the cell Antiport- One molecule goes in cell, the other comes out

2 Types of Nitrogenous Bases:

Pyrimidines Thymine Cytosine Single-ring molecules (bases) Purines Adenine Guanine Double-ring molecules (bases)

DNA Replication:

RNA Polymerase II binds to the promoter (TATA box). RNA Polymerase II unwinds the DNA helix. RNA Polymerase II builds the 5' to 3' direction using the 3' to 5' template strand. RNA Polymerase II reaches the terminating region of the gene. RNA Polymerase II, DNA strand, and pre-mRNA dissociate from each other. Pre-mRNA strand created contains exons and introns. Pre-mRNA goes through post-transcriptional modifications. 5' cap is added to the pre-mRNA. Poly A Tail is added to the end of the pre-mRNA. Spliceosome complex removes intron segments and joins neighbouring exons together. Translation begins. mRNA is associated with large and small ribosomal subunits. The first A.A. tRNA of the protein chain becomes bound to the AUG codon. Met-tRNA forms a complex with the small subunit. START codon is recognized by Met-tRNA. Large ribosomal unit binds to complete ribosome. Met-tRNA is in the P-site. The second tRNA with the appropriate anticodon and A.A. binds to the codon in the A-site. GTP is to GDP to free electrons. A.A. is separated from tRNA in the P-site and forms a peptide bond. Ribosome moves to the next codon. A-site is vacant. Appropriate tRNA moves into A-site and process repeats. A-site of the ribosome reaches STOP codon. A protein release factor binds to the A-site. Polypeptide chain detaches from the ribosome. Ribosomal subunits separate and detach from the mRNA.

Radioactive tracers

Radioisotopes used to follow chemicals through chemical reactions and trace their path

Substrate

Reactant that an enzyme acts on when it catalyzes a chemical reaction It would bind to the substrate binding site of an enzyme (active site), where polar ends of the protein would strain the bonds of the substrate As a result, less energy would be required to break those bonds

Catabolic reaction

Reaction that break down macromolecules into individual subunits Example: hydrolysis reaction- Water molecule is used to break covalent bond holding subunits together

Anabolic reaction

Reaction that produce large molecules from smaller subunits Example: condensation reaction (or dehydration synthesis)- Hydrogen atom is removed from one of the subunits, and hydroxyl group is removed from other subunit

Functional groups

Reactive clusters of atoms attached to carbon backbone of organic molecules They possess chemical properties that determine molecule's properties More reactive than hydrocarbon parts Hydroxyl group (-OH) and carboxyl group (-COOH) are polar due to electronegative oxygen atom; they make molecules like sugars polar Carboxyl group also makes molecules acidic; amino group (-NH2) (Format after) makes molecules basic Compounds with carboxyl group(s) are organic acids called carboxylic acids Compounds with amino group(s) are organic bases called amines Amino acids have an amino group and carboxyl group

Redox Reactions

Redox reaction- Chemical reaction where electrons are transferred; oxidation and reduction occur Oxidation- Reaction where an atom loses electrons Reduction- Reaction where an atom gains an electron Oxidizing agent- Substance that gains electrons; causes reducing agent to be oxidized Reducing agent- Substance that loses electrons; causes oxidizing agent to be reduced

Functions of the Electron Transport Chain:

Regenerates electron carriers NADH and FADH2 pass their electrons to the electron transport chain, turning back into NAD+ and FAD. This is important because the oxidized forms of these electron carriers are used in glycolysis and the citric acid cycle and must be available to keep these processes running. Makes a proton gradient: The transport chain builds a proton gradient across the inner mitochondrial membrane, w/ a higher concentration of H+ in the intermembrane space and a lower concentration in the matrix. This gradient represents a stored form of e, and, as we'll see, it can be used to make ATP. Complex I: 2 electrons from NADH enter complex I, pairing w/ a hydrogen ion which is pumped to the other side. The electron then moves to Ubiquinone, a small mobile carrier, which is taken to complex II. Complex II: Like NADH, FADH2 deposits its electrons to complex II. FADH2 is a part of complex II, as is the enzyme that reduces it during the Krebs cycle; unlike the other enzymes of the cycle, it's embedded in the inner mitochondrial membrane. The electrons are then passed to ubiquinone (Q), the same mobile carrier that collects electrons from complex I. Once at complex II, each electron is transported one at a time as protons are pumped through complex II. Complex III: Beyond the first two complexes, electrons from NADH and FADH2 travel exactly the same route. As electrons move through complex III, more H+ ions are pumped across the membrane, and the electrons are ultimately delivered to another mobile carrier called cytochrome C (cyt C). ATP Synthase: Cyt C carries the electrons to ATP Synthase, where a final batch of H+ ions is pumped across the membrane. ATP Synthase passes the electrons to oxygen, which splits into two oxygen atoms and accepts protons from the matrix to form water. Four electrons are req'dd to reduce each molecule of oxygen, and two water molecules are formed in the process. *NADH is very good at donating electrons in redox reactions (that is, its electrons are at a high e level), so it can transfer its electrons directly to complex I, turning back into NAD+. *FADH2 is not as good at donating electrons as NADH (that is, its electrons are at a lower e level), so it cannot transfer its electrons to complex I. Instead, it feeds them into the transport chain through complex II, which does not pump protons across the membrane.

Universe favours increase in entropy

Second Law of Thermodynamics: Entropy of the universe increases with any change that occurs; SUniverse>0 Gibbs Free Energy- Energy to do useful work Phosphorylation- Process of attaching a phosphate group to an organic molecule Causes molecules to become more reactive ATP phosphorylating other parts of the cell is how endergonic reactions can be powered

Membrane Carbohydrates

Short chains of carbohydrates attaches to either membrane proteins (glycoproteins) or phospholipids (glycolipids) Allows for: Cell-to-cell recognition Sorting in tissue development Is species specific (For example, blood typing in humans)

Stomata:

Small pores that are found on the surface of leaves in most plants, which let carbon dioxide diffuse into the mesophyll layer and oxygen diffuse out.

Grana

Stacks of thylakoids.

Potential energy

Stored energy. Can be due to object's position in attractive/repulsive force field

Hydrogen bonds

Strongest of the three Strong dipole-dipole forces that only form between electropositive H of one polar molecule and electronegative N, O, or F of neighbouring polar molecule Water molecules hold onto each other with H-bonds

Hydronium ion (H3O+)

Substance that gives rise to acidic properties

Hydroxide ion (OH-)

Substance that gives rise to basic solution properties

Acid

Substance that increase [H3O+] by releasing H+, and has at least one ionizable hydrogen atom

Base

Substance that increase [OH-], either by releasing OH-, or by combining with H+ directly (like ammonia, NH3)

Catalyst

Substance that speeds up a chemical reaction without being consumed in the process Enzymes are protein catalysts They would reduce the activation energy barrier of a reaction, thereby increasing its frequency

Noncompetitive inhibitors

Substances that attach to enzymes binding site other than active site; causes enzyme's shape to change, which would lower substrate affinity

Competitive inhibitors

Substances that compete with substrate for an enzyme's active site Two types: permanent and temporary Permanent competitive inhibitors are BAAAAAD (basically lethal, as they prevent enzymes from catalyzing reactions) Temporary- Binds to active site for a while, then comes off

Substrate Level Phosphorylation Vs Oxidative phosphorlation

Substrate level phosphorylation is direct phosphorylation of ADP w/ a phosphate group by using the e obtained from a coupled reaction. Oxidative phosphorylation is the production of ATP from the oxidized NADH and FADH2.

protein structures tertiary

Supercoiling of a polypeptide that's stabilized by side-chain interactions, such as: hydrogen bonds, hydrophobic and van der Waals interactions, disulfide bridge, ionic bonds Some proteins can just be a tertiary structure

Avery-MacLeod-McCarty experiment (1944)

The Avery-MacLeod-McCarty experiment was an experimental demonstration, reported in 1944 by Oswald Avery, Colin MacLeod, and Maclyn McCarty, that DNA is the substance that causes bacterial transformation, using Frederick Griffith's work as a foundation. They recreated Griffith's experiment but experimented further to find out which part of the S-strain bacterial cell for making R-strain cell virulent. They had narrowed the options to DNA, RNA, and proteins, but their results showed promising conclusions aimed towards DNA. However, Avery was cautious in interpreting his results. He realized that it was still possible that some contaminating substance present in small amounts, not DNA, was the actual transforming principle. Bc of this possibility, the debate over DNA's role continued until 1952, when Alfred Hershey and Martha Chase used a different approach to conclusively identify DNA as the genetic material.

Hershey-Chase experiment (1952)

The Hershey-Chase experiments were a series of experiments conducted in 1952 by Alfred Hershey and Martha Chase that helped to confirm that DNA is the genetic material. In their experiments, Hershey and Chase showed that when bacteriophages, which are composed of DNA and protein, infect bacteria, their DNA enters the host bacterial cell, but most of their protein does not. Although the results were not conclusive, and Hershey and Chase were cautious in their interpretation, previous, contemporaneous, and subsequent discoveries all served to prove that DNA is the hereditary material.

Membrane Structure

The Plasma membrane is the structure that separates the cell from the environment Controls what enters and what leaves the cell Membrane is primarily made up of phospholipid bilayer (two layers of phospholipids, with hydrophobic fatty acid tails away from water, and hydrophilic phosphate group head in contact with water) Proteins are embedded in or attached to the membrane Semi-permeable- Allows non-polar substances to diffuse through, and doesn't tend to allow polar/charged substances to diffuse

Photorespiration:

The catalysis of O2, instead of CO2, by RuBisCo into RuBP, which slows the Calvin cycle, consumes ATP, and results in a release of carbon. "O2 in, CO2 released".

Complementary Base Pairing:

The chemical tendency for adenine to form h-bonds w/ thymine, and cytosine to form h-bonds w/ guanine.

Genome

The complete set of an organism's hereditary info.

Photolysis:

The decomposition or separation of molecules by the action of light.

Why is RuBisCo inefficient?

The enzyme itself is large and slow. (3 molecules of CO2/second) Abundance req' to be somewhat effective. Problem with RuBisCo? As an enzyme (which is a protein), higher temperature can change the shape of it and denature it. (therefore, now has a higher affinity for O2) RuBP + O2 = 1 PGA and 2-c Glycolate RuBisCo has a high affinity to CO2 except when it's hot. It's active site occasionally binds with oxygen instead of carbon dioxide.The product it creates it called phosphoglycolate, which isn't useful to plants. The recovery pathway to convert glycolate is too long and consumes ATP and releases a molecule of carbon dioxide. Instead of fixing a CO2, the oxygenase activity of RuBisCo does the opposite.

3 possible outcomes for the excited e− within a pigment molecule:

The excited e− simply returns to its ground state. Its energy is released as thermal energy or fluorescence. The energy of the e− is transferred to an e− in a neighbouring pigment molecule. The 2nd pigment molecules high-energy e− is excited, and the original e− returns to its ground state. The energizing and transferring of an e−.

Fermentation

The extraction of e from carbohydrates in the absence of oxygen. Alcohol Fermentation: NADH donates its electrons to a derivative of pyruvate, producing ethanol. Steps: 1). A carboxyl group is removed from pyruvate and released in as carbon dioxide, producing a 2-c molecule called acetaldehyde. 2). NADH passes its electrons to acetaldehyde, regenerating NAD+ and forming ethanol. Alcohol fermentation by yeast produces the ethanol found in alcoholic drinks like beer and wine. However, alcohol is toxic to yeasts in large quantities (just as it is to humans), which puts an upper limit on the percentage of alcohol in these drinks. Lactic Acid Fermentation: NADH transfers its electrons directly to pyruvate, generating lactate as a byproduct. Muscle cells also carry out lactic acid fermentation, though only when they have too little oxygen for aerobic respiration to continue—for instance, when you've been exercising very hard. Lactic acid produced in muscle cells is transported through the bloodstream to the liver, where it's converted back to pyruvate and processed normally in the remaining reactions of cellular respiration.

Stroma

The fluid-filled inner space of chloroplasts surrounding thylakoids and grana.

Chlorophyll

The green pigment found in the chloroplasts, which is primarily involved in absorbing light energy for photosynthesis. It traps certain wavelengths of light energy.

The Efficiency of Aerobic Respiration:

The hydrolysis of ATP → ADP +Pi = 31kJ/mol Glucose molecule: 2870 kJ 31 kJ/mol x 38 ATP = 1178 kJ/mol 1178 kJ/mol / 2870 kJ x 100 = 41.0% Therefore, 59% of glucose's e is lost as thermal heat.

What bond connects the sugar-phosphate backbone?

The phosphodiester bond is the linkage between the 3' carbon atom of 1 sugar molecule and the 5' carbon atom of another.

Chemiosmosis:

The protons that accumulated in the thylakoid lumen have created an electrochemical gradient. The H+ ions speed through ATP Synthase and cause ADP + P = ATP. Since light is required for this ATP to be produced, this process of making ATP this way is called Photophosphorylation. ATP and NADPH go on to the Calvin Cycle.

Thylakoid space:

The space inside of the thylakoid.

James Watson and Francis Crick (1953)

They, along w/ Maurice Wilkins, have been credited w/ the discovery of the double helix, the twisted-ladder structure of deoxyribonucleic acid (DNA), by James Watson and Francis Crick marked a milestone in the history of science and gave rise to modern molecular biology, which is largely concerned w/ understanding how genes control the chemical processes w/in cells in 1953. Using Franklin's work to aid in their model, they had conclusively figured out a few things; DNA has a double helix structure, the 2 strands of DNA run antiparallel, and that the nitrogenous bases are h-bonded to each other

Phospholipids

Three components: Phosphate group- Attached via 1 hydroxyl group Becomes hydrophilic head of lipid May be bonded to choline group Glycerol- 3-C alcohol with 3 hydroxyl groups attached Fatty acid tails- Two long hydrocarbon chains with carboxyl group at one end Can either be saturated or unsaturated More saturated chains means higher melting point, and vice-versa (double bond makes unsaturated relatively more unstable)

Gregor Mendel (1965)

Through his work on cross-breeding pea plants, discovered the fundamental laws of inheritance. Essentially, he studied the inheritance of seven different features in peas, including height, flower color, seed color, and seed shape. To do so, he first established pea lines w/ 2 different forms of a feature, such as tall vs. short height. He grew these lines for generations until they were pure-breeding (always produced offspring identical to the parent), then bred them to each other and observed how the traits were inherited. He deduced that genes come in pairs and are inherited as distinct units, one from each parent. Mendel tracked the segregation of parental genes and their appearance in the offspring as dominant or recessive traits. His experiment took eight years, between 1856 and 1863. He only later published his results in 1865. However, it was not until 1900, after the rediscovery of his Laws, that his experimental results were understood.

Why is Cellular Respiration important?

To break the bonds between the 6 carbon atoms of glucose, resulting in 6 carbon dioxide molecules. To move hydrogen atom electrons from glucose to oxygen, forming 6 water molecules. To trap as much of the free e released in the process as possible in the form of ATP. *About 40% of glucose's e is used while 60% is lost as heat.

First Law of Thermodynamics

Total amount of energy in the universe is constant. It can't be created or destroyed; only converted into another form

Problem with the Stomata:

Transpiration (H2O loss) Semi-prevention: Cuticle (waxy, waterproof layer) When it's hot, the stomata closes therefore, oxygen cannot exit and carbon dioxide cannot enter. This will create a higher concentration of oxygen internally, causing a more probable chance for RuBisCo to bind with oxygen to carbon dioxide. In lab conditions, when concentrations of O2 and CO2 are equal, CO2 will bind more frequently because the active site of RuBisCo has a greater attraction for CO2 than O2. In nature, however, the ratio between the gas are NOT equal. In the atmosphere, oxygen is about 21% while carbon dioxide is roughly 0.04%. Under normal conditions, including normal temperature and normal atmospheric pressure, RuBisCo will bind to carbon dioxide 75% of the time. However, 25% of the time, oxygen will bind to it.

Membrane Protein Functions

Transport- Allows passage of material through channel or ATP hydrolyzed gate Enzymatic activity- Enzyme active site exposed to adjacent solution (activated by hormones) Signal transduction- External message (hormone) may bind and induce reactions internally to send message to cell interior Cell-to-cell recognition- Identifies and tags surrounding cells Intercellular joining- Gap/tight junctions holding cell together Attachment to cytoskeleton/extracellular matrix (ECM)- Attachment to microfilaments for cell shape or attachment to ECM

Turgid, flaccid, plasmolysis

Turgid- When plant experiences a high interior water pressure Cell membrane pushes tight against cell wall Flaccid- When plant experiences a normal interior water pressure Cell membrane isn't tight against cell wall Plasmolysis- When plant experiences a low interior water pressure Cell membrane shrinks from cell wall due to low water pressure Since the cell membrane is only permeable to non-polar substances, vital substances for the cell that can't diffuse (such as ions, carbohydrates, proteins) would have two other methods of transport: facilitated diffusion, and active transport

protein structures Quaternary

Two or more polypeptide subunits come together to form a protein Proteins can be denatured, meaning that they can't carry out biological functions hemicals, as well as excess heat, can disrupt hydrogen bonds, ionic bonds, disulfide bridges, and van der Waals interactions As long as primary structure is intact, protein would return to normal shape once denaturing agent is gone Our body does this during fevers As body temperature increases, pathogen proteins would denature However, if it's prolonged, critical enzymes in the brain can be denatured (generally not good)

Integral Proteins

Two types: Transmembrane proteins (span the membrane width) Other integral proteins (penetrate partway through) Regions of integral proteins in contact with hydrophobic tails contain non-polar amino acids

Carbohydrates

Used by organisms as sources of energy, building materials, cell surface markers for communication/identification Contains C, H, and O in a 1:2:1 ratio (empirical formula is CH2O)

Exocytosis

Vesicles produced by Golgi apparatus contain molecules inside When they fuse with plasma membrane, substances inside vesicles are released into environment Cell's form of excreting matter

Orbitals

Volumes of space around the nucleus where electrons are most likely to be found (probability theorem) When two electrons fill up an orbital, they pair up; as a result, it's more stable Higher energy levels contain more electrons with higher energy values

Water

Water is highly polar, due to its polar covalent bonds and asymmetrical structure This polarity allows it to form chemical bonds with other polar molecules and ions (forming intermolecular bonds between other molecules) The bonds are broken when solids melt into liquids, and liquids evaporate into gases Logic can be applied in reverse as well Water's a great dissolving agent because its polarity can provide a partial positive and negative charge to which other polar molecules/ions can attach to When ionic solids dissolve, anions and cations dissociate; as a result, ionic bonds are broken Polar molecules such as sugars alcohols easily dissolve in water Considered the universal solvent

Cohesion

Water molecules form hydrogen bonds with one another High surface tension

Adhesion

Water molecules form hydrogen bonds with other polar molecules Capillary action (water can creep up narrow glass tube and paper)

Osmosis

Water moves from area of low solute concentration (high water potential) to area of high solute concentration (low water potential)

London dispersion forces

Weakest of the three In all atoms and molecules; the only intermolecular forces between noble gas atoms and between nonpolar molecules Weak nature is why nonpolar molecules are usually gaseous Temporary unequal distribution of electrons as they move about the nuclei allow electrons of one neutral atom to attract nucleus of neighbouring atoms

Cholesterol

Wedge between phospholipids to alter fluidity Makes membrane less fluid at higher temperatures Prevents close packing of phospholipids (therefore lower solidification temp)

ATP (Adenosine Triphosphate):

a type of nucleotide consisting of adenine, ribose, and a chain of 3 phosphate groups. (Through hydrolysis, the bonds of the phosphate can be broken which forms ADP or known as Adenosine Diphosphate) Because of their high-e phosphate bonds, they are unstable, which leads to e as hydrolysis breaks them. *technically, the release of e from ATP is from the change of the change of a state of lower e, and not from the bonds itself. ATP yields so much e because: Each of the phosphates has a negative charge. These three charges are crowded together so their mutual repulsion contributes to the instability of this region of the ATP.

O2 and CO2

are non-polar; that's why protein carrier molecules, like hemoglobin, are required to transport these gases

Pure water

has equal numbers of H3O+ and OH- ions: therefore, it's neutral Strong acids and bases- Substances that ionize completely in aqueous solutions

Cellulose

held together by beta 1-4 glycosidic linkages (monosaccharide subunits have alternating orientation) Humans don't have enzymes that can digest these linkages However, it can still help stimulate intestinal cells to secrete mucus, making excretion easier

Jan Baptist van Helmont

his best-known experiment is when he placed a 5-pound willow in an earthen pot containing 200 pounds of dried soil. over a five-year period, he added nothing to the pot but rainwater or distilled water. After five years, he found that the tree weighed 169 pounds (about 77 kg), while the soil had lost only 2 ounces (57 grams). he concluded that "164 pounds of wood, barks, and roots arose out of water only," and he had not even included the weight of the leaves that fell off every autumn. Obviously, he knew nothing of photosynthesis, in which carbon from the air and minerals from the soil are used to generate new plant tissue, but his use of the balance is important; he believed that the mass of materials had to be accounted for in chemical processes.

three types of van der Waals forces

london dispersion forces, dipole dipole forces, hydrogen bonds

Keratin

most common protein in vertebrates; in hair/fingernails

The Calvin Cycle:

occurs in the stroma

Theodor Engelmann:

produced one of the first action spectra in 1882. used a light microscope, aerobic bacteria, light beam and a glass prism. Purpose: To determine which wavelength of light were most effective for photosynthesis. placed a green alga on a microscope glass slide, along with water containing aerobic bacteria. then adjusted the prism to split a beam of light into separate colours. noticed bacteria clustered around the algal strand in the region where O2 was released in great quantities. (specifically around blue & violet and red light). therefore, provided evidence of the influence of different colours of light on photosynthesis.

Osmoregulation

regulation of solute concentrations and water balance by a cell or organism

Weak acids and bases

substances that partially ionize in aqueous solutions Reactions would occur in both ways, until equilibrium is achieved (when opposing reactions occur at equal rates)

Metabolism

sum of all anabolic and catabolic process in a cell/organism Accounts for all molecule breakdowns, and macromolecule synthesis processes

Energy

the ability to do work