AP Biology Course Review Part 1

AP Biology Course Review Part 1

Section 1: 60 questions - 1 hour 30 minutes (50% of exam score)

Section 2: 6 questions - 1 hour 30 minutes (50% of exam score)

Chemistry of Life

Elements: Substances that cannot be broken down into simpler substances by chemical means

• 96% of the mass of all organisms are made mostly of oxygen (O), carbon (C), hydrogen (H), and nitrogen (N)

  • Calcium, phosphorus, potassium, sulfur, sodium, chlorine, magnesium present in small quantities

  • Trace elements: required by organism in very small quantities (iron, iodine, copper)

Atoms: smallest unit of an element that retains its characteristic properties; building block of the world

• Protons + neutrons are packed together in the core of the atom (nucleus)

  • Protons are positively charged (+), neutrons are uncharged particles

• Electrons are negatively charged particles around the nucleus; considered massless

• Isotopes: Atoms that have the same number of protons but differ in the number of neutrons in the nucleus

Compounds: two or more different types of atoms combined in a fixed ratio

• Ex. hydrogen and oxygen exist in nature as gases and when they combine they make water (chemical reaction; 2H2 + O2 = 2H2O)

• Atoms of a compound are held together by chemical bonds: ionic bonds, covalent bonds, or hydrogen bonds

  • Ionic bonds: formed between 2 atoms when 1+ electrons are transferred from one atom to the other between two oppositely charged ions

    • One atom loses electrons and becomes positively charged and the other atom gains electrons and becomes negatively charged 

    • Charged forms of atoms: ions

  • Covalent bond: formed when electrons are shared between atoms. 

    • If electrons are shared equally between the atoms, the bond is nonpolar covalent

    • If electrons are shared unequally, the bond is polar covalent

Water Properties

• Water has two hydrogen atoms + one oxygen atom and is POLAR

  • Hydrogen atoms have partial positive charge; oxygen has partial negative charge

• Positive ends attract negative ends of other polar compounds, vice-versa= intermolecular attractions are hydrogen bonds (unequal sharing and occurs between water molecules)

  • Weak chemical bonds that form when a hydrogen atom is covalently bonded to one electronegative atom is also attracted to another electronegative atom

Cohesion and Adhesion

• Water exhibits cohesive forces: tendency to stick together

  • Ex. during transpiration, water molecules evaporate from a lead, pulling on neighbor water molecules>draw up the molecules behind them> the resulting chain of water molecules enables water to move up the stem

• The strong cohesion also leads to high surface tension (tension on the surface of water from water molecules tightly packed to minimize contact with air)

• Water molecules stick to other substances/adhesive

• Cohesion + adhesion account for ability of water to rise up the roots, trunks, and branches of trees: capillary action

Heat Capacity

• Heat capacity: ability of a substance to resist temperature changes

• Water has a high heat capacity + high heat of vaporization

  • You have to add lots of heat to get increase in temp 

  • Helps maintain temp in oceans + keep bodies at constant body temp

Expansion on Freezing

• When four water molecules are bound in a solid lattice of ice, the hydrogen bonds cause solid water to expand on freezing

• Liquid water molecules are slightly more dense than in solid water

  • Freezing makes it less dense than liquid water

  • Ice floats on the top of lakes/streams

Acids

• A solution is acidic if it contains a lot of hydrogen ions (H+) 

  • If you dissolve an acid in water, it will release a lot of hydrogen ions

• Bases aka alkaline do not release H+ ions but release a lot of hydroxide ions (OH-)

• Acidity/alkalinity can be measured using a pH scale with 0-6 acidic; 7 neutral; 8-14 basic

• pH scale is not linear>logarithmic: 1 pH change represents a tenfold change in hydrogen ion concentration

Organic Molecules

• Organic compounds: compounds containing carbon atoms and (sometimes) hydrogen atoms

• Inorganic compounds: molecules that do not contain carbon atoms and hydrogen atoms

• Macromolecules<<polymers<< monomers

Carbohydrates

• CHO (carbon, hydrogen, oxygen) in 1:2:1 ratio as Cn H2n On/ (CH2O)n

• Most carbohydrates are categorized as monosaccharides(1), disaccharides (2), or polysaccharides (many)

• Monosaccharides: simplest sugars that serve as an energy source for cells (ex. Glucose use covalent bonds, fructose)

  • glucose/fructose are six-carbon sugars with formula C6H12O6

• Disaccharides: when 2 monosaccharides combine (H from one sugar molecule combines with OH of another sugar molecule to release H2O)

  • Dehydration synthesis/condensation: removal of water when joining

  • Hydrolysis: breaking up disaccharide to form 2 monosaccharides using/adding water

• Polysaccharides: many repeated units of monosaccharides (ex. Starch, cellulose, glycogen)    

  • Animals store glucose in glycogen in liver/muscle cells

  • Plants collect a glucose in plastids

  • Cellulose: made of b-glucose and is part of cell wall in plants/lend structural support

  • Chitin: polymer of b-glucose molecules serves as structural molecule in the walls of fungi

  • Amylose (starch): plant energy storage

  • Peptidoglycan: bacterial cell wall structure

Lipids

• CHO (ex. Triglycerides, phospholipids, steroids)

• To make triglycerides: each carboxyl group (COOH) of the fatty acid must react with one of the three hydroxyl groups (OH) of the glycerol molecule by dehydration synthesis

• Single covalent bond-straight-solid- saturated

• Double covalent bonds-bent-liquid-unsaturated

  • Less hydrogen

• Phospholipids: have 2 fatty acid tails that are hydrophobic/nonpolar and phosphate “head” is hydrophilic= amphipathic molecule

• Cholesterol: four-ringed molecule found in membranes that affects membrane fluidity by preventing it from freezing/melting; making certain hormones; making vitamin D

Protein

• CHON

• Important parts to know: amino group (-NH2); carboxyl group (-COOH), a hydrogen, and an R group

• Amino acids differ only in R groups aka side chain

• Polypeptide: when 2 amino acids join to form a dipeptide 

  • Bond between 2 amino acid=peptide bond

  • Group of amino acids joined= polypeptide and once it twists/folds on itself, a 3D structure protein is formed

• Primary structure: linear sequence of the amino acid coded for by the DNA

• Secondary structure: shape caused by hydrogen bonding between adjacent amino aicds; polypeptides that twist forming either a coil (alpha helix) or zigzag (beta-pleated sheets)

• Tertiary structure: amino acid r groups interact with each other and fold into 3D shape

• Quaternary structure: several different polypeptide chains that interact with each other to creat large protein

Nucleic Acid

• CHONP

• Phosphate group + pentose (deoxyribose in DNA; ribose in RNA) + nitrogenous base unique to each nucleotide (G,C,A,T in DNA; G,C,U,T in RNA)

• Bond together in sugar phosphate backbone with nucleotides in center (joined with hydrogen bond to form double helix)

  • Chargaff's rule: the amount of Guanine=Cytosine and Adenine=Thymine

• DNA: contains hereditary blueprints

• RNA: essential for protein synthesis

  • mRNA: small copy of a protein of DNA that codes for a protein

  • rRNA: 3D RNA chain that makes up the structure of an organelle called a ribosome

  • tRNA: 3D enzymatic RNA molecule that translated the nucleic acid code into amino acid code

Origins of Earth

• Alexander oparin + J.B.S. Haldane proposed that the primitive atmosphere contained methane, ammonia, hydrogen, and water with almost no free oxygen (O2) in the early atmosphere

  • Believed the gases collided producing chemical reactions that led to organic molecules

• Miller and Urey experiment: stimulated the conditions of primitive Earth, struck them with electrical charges to mimic lightning, and organism compounds similar to amino acids appeared

• RNA-world hypothesis: original life forms were make of RNA molecules b/c RNA can take many shapes and is not restricted to double helix; possible that RNA molecules capable of replicating + passing along genomes were first forms

  • Complex organic compounds formed via dehydration synthesis (taking water out to join)

• heterotrophs/consumers: living organism that rely on organic molecules for food

• autotrophs/producers: life-forms that make their own food, most commonly through photosynthesis

Cells

Cells: life’s basic unit of structure and function; smallest unit of living material to carry out all activities necessary for life

• specialization/compartmentalization/surface area-to-volume ratio

• Higher surface area-to volume ratio is more efficient

  • The size of an object increases, the volume grows faster than the surface area

    • As cells become larger, they have smaller surface area/volume

Types of Cells

• Prokaryotic cells: smaller than eukaryotic cells; NO MEMBRANE BOUND ORGANELLES

  • Inside of the cell is filled with cytoplasm + genetic material is one continuous circular DNA molecule found free in the cell in the nucleoid

  • Most have cell wall made of peptidoglycans that surround lipid layer plasma membrane

  • Also have ribosomes and also may have 1+ flagella (projections used for motility/movement)

• Eukaryotic cells: more complex (fungi, protists, plants, animals) 

Organelles

•  Plasma membrane: outer envelope of cell; double-layered structure made of phospholipids and proteins

  • Hydrophobic fatty acid tails face inwards; hydrophilic phosphate heads face outward= phospholipid bilayer

• Semipermeable: only certain substances (small, nonpolar, hydrophobic molecules like O2, N2, and CO2) pass through unaided

  • Anything large needs to pass through the membrane via special tunnels

  • Peripheral proteins: located on inner or outer surface of the membrane

  • Integral proteins: firmly bound to plasma membrane (amphipathic meaning their hydrophilic regions extend out of cell/into cytoplasm; hydrophobic regions interact with tails of membrane phospholipids)

  • brane proteins: integral proteins that extend all  the way through the membrane

• Arrangement of phospholipids and proteins known as fluid-mosaic model: each layer of phospholipids is flexible amd is a mosaic because there are various proteins and carbohydrate chains

• Why should the plasma membrane need so many proteins? Due to the number of activities that take place in/on the membrane

  • Some membranes form junctions between adjacent cells (adhesion proteins), serve as docking sites for arrival at cells like hormones (receptor proteins), some proteins form pumps that use ATP to actively transport solutes across the membrane (transport protein), others form channels that selectively allow the passage of certain ions/molecules (channel proteins), some are exposed on the extracellular surface and play role in cell recognition/adhesion (recognition and adhesion proteins)

• Nucleus: Largest organelle; control center of the cell

• Directs what goes on in cell and cell’s ability to reproduce

• Contains hereditary information (DNA) that is organized into chromosome structures

• structure in the nucleus is where rRNA is made and ribosomes are assembled: nucleolus

• Ribosomes: sites of protein synthesis

  • Job to manufacture all proteins required by the cell or secreted by the cell

• Ribosomes are round structures composed of RNA and proteins

  • “Free floating” ribosomes float in the cytoplasm and in the nucleus (proteins produced in free ribsomes are used within the cell)

  • “Bound: ribosomes are attached to the rough ER (proteins produced by bound used in export of cell)

• Endoplasmic Reticulum (ER): continuous channel that extends into many regions of the cytoplasm

  • The rough ER is attached to the nucleus and is studded with ribosomes

  • The proteins generated in the rough ER are trafficked across the plasma membrane or are used to build golgi bodies, lysosomes, or the ER

  • The smooth ER: lacks ribosomes but instead makes lipids, hormones, and steroids, and breaks down toxic chemicals

• Golgi Bodies: participate in the processing of proteins (and involved in production of lysosomes)

  • Once ribosomes on the rough ER have completed synthesizing proteins, the golgi bodies modify, process, and sort products

  • The packaging and distribution centers to be sent out of the cell; package final products in  little sacs= vesicles, that carry products to the plasma membrane

• Mitochondria: referred to the “powerhouses” of the cell responsible for converting the energy from organic molecules into useful energy for the cell (ATP)

  • The inner mitochondrial membrane forms folds known as cristae that separates the innermost area called matrix from the intermembrane space from the cytoplasm 

    • Most of production of ATP is done in cristae

    • During ETC, H+ ions are pumped in intermembrane space and flow into matrix to create ATP synthase

    • Krebs cycle in matrix

• Lysosomes: carry digestive enzymes that break down old, worn-out organelles, debris, or large ingested particles

  • Contain hydrolytic enzymes that only function at acidic pH, inside lumen of lysosome

• Centrioles: small, paired, cylindrical structures that are found within microtubule organizing centers (MTOCs)

  • When cell is ready to divide, the centrioles produce microtubules that pull chromosomes apart and move them to opposite ends of the cell

• Vacuoles: literally mean “empty cavity” BUT are fluid-filled sacs that store food, water, wastes, salts, or pigments

• Peroxisomes: organelles that detoxify various substances, producing hydrogen peroxide (H2O2) as a byproduct

  • Contain enzymes that break down hydrogen peroxide into oxygen and water (in animal liver/kidney cells)

• Cytoskeleton: network of fibers (microtubules + microfilaments) that determine the shape of the cell

  • Microtubules: made of tubulin, participate in cellular division + movement; integral in centrioles, cilia, flagella

  • Microfilaments: important for movement composed of the protein actin; monomers joined together and broken apart as needed to allow microfilaments to grow/shrink

    • Microfilaments assist during cytokinesis, muscle contraction, formation of pseudopodia extensions during cell movement

• Chloroplast: site of photosynthesis. Uses sunlight to make ATP, uses ATP to make sugars

• PLANT CELL VS ANIMAL CELLS:

Endosymbiotic Theory

• A small prokaryote was engulfed by a large prokaryote but not digested to explain origin of mitochondria and chloroplasts

  • Mitochondria + Chloroplasts have their own DNA

  • Have a double membrane organelles

• Glycolysis: most universal processes of respiration (anaerobic so could have happened when there was no O2 on early earth)

Transport

• If substance is hydrophilic, the bilayer wont let pass without assistance: facilitated transport

  • Depend on proteins that act as tunnels; channels are specialized tunnels (ex. aquaporins)

Passive Transport (HIGH>LOW)

• Diffusion: the substance moves down a concentration gradient (and no outside energy is required) (ex. O2 and CO2)

  • Simple diffusion: when the molecule diffusing is hydrophobic

  • Facilitated diffusion: when the diffusion requires the help of a channel-type protein

Osmosis

• When a water molecule is diffusing from most concentrated to least concentrated

  • Final result: solute concentration are the same on both sides of the membrane

•  Isotonic: the solute (substance being dissolved) concentration is the same inside and outside

• Hypertonic: solution has more total dissolved solutes than the cell

• Hypotonic solution: less total dissolved solutes than cell

• Water Potential: measure of potential energy in water and is the eagerness of water to flow from an area of high water potential to an area of low water potential

  • Affected by pressure potential and solute potential

  • More solute molecules> lower water potential

Active Transport (LOW>HIGH)

• Movement against the natural gradient with the help of ATP

  • Sodium-potassium pump: pumps 3 Na+ and brings in 2 K+ across gradient and depend on ATP to get ions across that would otherwise remain in regions of higher concentrations

Endocytosis

• When particles are too large to enter cell, cell uses portion of cell membrane to engulf substance forming a vacuole/vesicle

  • Pinocytosis: cell ingests liquids

  • Phagocytosis: cell takes in solids

  • Receptor-mediated cytosis: cell surface receptors that work w endocytic pits lined with protein called clathrin

    • When particle binds to receptor, the particle is brought in by folding in of the cell membrane

• Bulk Flow: one-way movement of fluids brought about by pressure

• Dialysis: diffusion of solutes (particles) across a selectively permeable membrane

• Special membranes that have holes of certain size within can be used to sort substances by using diffusion

• Exocytosis: cell ejects waste products or specific secretion products such as hormones by the fusion of a vesicle with the plasma membrane

Cell Junctions

• Cells come into close contact with each other, they develop specialized intercellular junctions that involve plasma membranes + others

  • Allow neighboring cells to form strong connections with each other, prevent passage of materials, or establish rapid communication 

• Desmosomes: hold adjacent animal cells tightly to each other

  • Contain pair of discs associated with plasma membrane of adjacent cells + intercellular protein filaments that cross the small space

• Gap junctions: protein complexes that form channels in membranes + allow communication between cytoplasm of adjacent animal cells for transfer of small molecules/ions

• Tight junctions: tight connections between the membranes of adjacent animal cells

  • So tight that there's no space (ex. Small intestine)

Cell Communication

• Taxis: movement of organism in response to a stimulus and can be positive (toward stimulus) or negative (away from stimulus)

• Signal transduction: process by which an external signal is transmitted to the side of the cell

  • Involves: a signalling molecule binding to a specific receptor

    • Activation of a signal transduction pathway

    • Production of a cellular response

• Ligand-gated ion channels: plasma membrane opens an ion channel upon binding a particular ligand

• Catalytic or enzyme linked receptors: enzymatic active site on the cytoplasmic side of the membrane

  • Enzyme activity initiated by ligand binding at the extracellular receptor

• G protein-linked receptor: does not act as enzyme but will bind different version of a G protein on the intracellular side when a ligand is bound extracellularly

  • Causes activation of secondary messengers within cell

• Tropisms: plants do not have a nervous system but produce proteins found in animal nervous systems such as certain neurotransmitter receptors

  • Phototropism: how plants respond to sunlight

  • Gravitropism: how plants respond to gravity

  • Thigmotropism: how plants respond to touch

  • Photoperiodism: how plants respond to the light/dark cuc;es and the seasonal changes in the lengths of days

Cellular Energetics

• First law of thermodynamics: energy cannot be created or destroyed but transformed

• Second law of thermodynamics: energy transfer leads to less organization and the universe tends towards disorder/entropy

  • p

Types of Reaction

• Exergonic: products have LESS energy than the reactants (energy is given off during the reaction

• Endergonic reactions: reactions that require an input of energy (products have MORE energy than the reactants)

Gibbs Free Energy

• Positive g are endergonic

• Negative g are exergonic

Activation Energy

• Reactants must turn into an intermediate state called the transition state before turning into products

• To reach transition states, certain amount of energy is needed: activation energy

Enzymes

• Enzymes: biological catalysts that speed up reactions

  • Accomplish by lowering the activation energy and helping the transition state form

• Enzymes do NOT change the energy of the starting point or the ending point of the reaction> lower the activation energy

• ENZYMES NOT CONSUMED IN REACTION: SINGLE ENZYME MOLECULE CAN CATALYZE THOUSANDS+ REACTIONS/SEC AND ARE UNAFFECTED BY THE REACTION

  • AFFECTED BY CELLULAR CONDITIONS (TEMP, pH, SALINITY)

Enzyme Specificity

• Each enzyme catalyses only one kind of reaction: enzyme specificity

• In enzymatic reactions the targeted molecules are known as substrates

Enzyme-Substrate Complex

• During a reaction the enzyme’s job is to bring the transition state about by helping the substrate(s) get into position

  • Accomplished through region of enzyme: active site

• The enzyme temporarily binds 1+ more of the substrates to its active site and forms an enzyme-substrate complex

• Once the reaction has occurred + product has formed, enzyme is released from the complex and restored to its original state

Induced Fit

• Enzyme changes its shape slightly to accommodate the shape of the substrates

  • Enzymes only operate under a strict set of biological conditions

    • cofactors/coenzymes can help catalyze reaction

Factors Affecting Reaction Rates

Enzyme Concentration:

• As enzyme concentration increases, reaction rate increases

  • More enzymes = more frequently collide with substrate

• Reaction rate levels off

  • Substrate becomes limiting factor

  • Not all enzyme molecules can find substrate

Substrate Concentration:

• As substrate concentration increases, reaction rate increases

  • More substrate = more frequently collide with enzyme

• Reaction rate levels off

  • All enzymes have active site engaged

  • Enzyme is saturated

  • Maximum rate of reaction

Temperature: 

• rate of reaction increases with increasing temperature

  • Increase in temp= increases chance of collisions among the molecules

  • Too much can damage an enzyme

  • Reaction is conducted at excessively high temperature, the enzyme loses its 3D shape and becomes inactive

  • Denatured: Enzymes damaged by heat and deprived of their ability to catalyze reactions

  • Heat: increase beyond optimum temp: increases energy level of molecules disrupts bonds in enzyme and between enzyme and substrate

    • Denaturation: lose 3D shape

  • Cold: molecules move slower; decrease collisions between enzyme and substrate

pH:

• Enzymes function best at particular pH

  • Most: the optimal ph is at/near 7

• Adds or remove H+/ disrupts bonds and 3D shape

  • Disrupts attractions between charged amino acids

  • Affects 2nd and 3rd degree structure

  • Denatures protein

Salinity

• Changes in salinity

  • Adds or removed cations and anions

  • Disrupts bonds, disrupts 3D shape

    • Disrupts attractions between charged amino acids

    • Affects 2nd and 3rd degree structure

    • Denatures protein

• Enzymes intolerant of extreme salinity

Enzyme Regulation

• Enzymes can be turned off/on by things that bind to them

  • Things can bind at the active site/other sites: allosteric sites

• If the substance has a shape that fits the active site of an enzyme, it can compete with the substrate and block it from getting into the active site: competitive inhibition

  • Can overcome by increasing substrate concentration: saturate solution with substrate so it out-competes inhibitor for active site on enzyme

• If the inhibitor binds to an allosteric site: allosteric inhibitor and is noncompetitive inhibition

  • Noncompetitive inhibition generally distorts the enzyme shape so it cannot function

Sources of ATP

• Bulk comes from cellular respiration(breakdown of glucose into ATP)

• Autotrophs: the sugar is made during photosynthesis

  • heterotrophs: glucose comes from sources of food

Photosynthesis

6CO2 + 6H2O > C6H12O6 + 6O2

• Carbon dioxide + water = glucose + oxygen

• Chloroplasts are the primary sites of photosynthesis

  • Fluid-filled region called stroma

  • Inside stroma are grana

  • disc -like structures: thylakoids that contain chlorophyll, the light-absorbing pigments that drives photosynthesis 

  • 2 stages of photosynthesis: The light reaction (light-dependent reactions); Dark reaction (light-independent reaction)

  • photons of sunlight strike leaf> activate chlorophyll> excite electrons

    • Activated chlorophyll molecule passes excited exelections down series of electron carriers to produce ATP + NADPH

Light Reaction

• Makes ATP or NADPH

Pigments

• Light-absorbing pigments

  • More important ones: chlorophyll a, chlorophyll b, carotenoids clustered in thylakoid membrane into units called antenna complexes

• All pigments in a unit gather light but not able to excite electrons, ONLY reaction center is capable of transforming light energy to chemical energy

  • Antenna pigments gather light AND bounce the energy to reaction center

• 2 reaction centers: photosystem 1(P700), and photosystem II(P680)

• When light energy is used to make ATP, it is photophosphorylation (autotrophs are using light and ADP and phosphate to produce ATP)

• Absorption spectrum: show how well a certain pigment absorbs electromagnetic radiation

  • Light absorbed is plotted as function of radiation wavelength

  • Light in the green range of wavelengths is reflected, and this is why chlorophyll and many plants are green

• Absorption spectrum is the opposite of emission spectrum (gives info on which wavelengths are emitted by a pigment)

Light Reaction/light-dependent reaction

• Occurs in the thylakoids

  • P680 in photosystem II captures light and passes excited electrons down an electron transport chain to produce ATP

  • P700 in photosystem I captures light and passes excited electrons down an ETC to produce NADPH

  • A molecule of water is split by sunlight, releasing electrons, hydrogen, and free O2

• Light-dependent reaction: occurs in grana of chloroplasts, where the thylakoids are found

Dark reaction/light-independent reaction/ Calvin Cycle

• Uses products of the light reaction, ATP and NADPH, to make sugar

• Occurs in the stroma of the chloroplasts

• ATP and NADPH from the light reaction are necessary for carbon fixation

• CO2 is fixed to form glucose (carbohydrates, and other macromolecules)

Cellular Respiration

C6H12O6 + 6O2 > 6CO2 + 6H2O + ATP

• Sugar/glucose + oxygen = carbon dioxide, water, energy in form of ATP

• Cellular respiration + fermentation ae common processes of life

• ATP made in presence of oxygen= aerobic respiration

  • Oxygen isn't present = anaerobic respiration

Aerobic Respiration

1. Glycolysis

2. Formation of acetyl-CoA

3. The Krebs(or citric) cycle

4. Oxidative phosphorylation (or ETC + chemiosmosis)

Stage 1 Glycolysis:

• Strats with splitting of glucose (glycolysis) into 2 3-carbon molecules called pyruvic acid

  • Breakdown of glucose results in net production of 2 molecules of ATP

• Glucose + 2 ATP + 2 NAD+ = 2 pyruvic acid + 4 ATP + 2NADH

• Occurs in the cytoplasm

• net of 2 ATP produces

• 2 pyruvic acids formed

• 2 NADH produced

Stage 2: Formation of Acetyl-CoA

• Pyruvic acid is transported to the mitochondrion

  • Each pyruvic acid is 3-carbon and converted to acetyl coenzyme A (a 2-carbon molecule aka acetyl-CoA) and CO2 is released

• 2 pyruvic acids + 2 Coenzyme A + 2NAD+ = 2 Acetyl-CoA + 2CO2 + 2NADH

Stage 3: The Krebs Cycle/citric acid

• Each of the two acetyl coenzyme A molecules enter the Krebs cycle and all carbons will be converted to CO2

• Happens in the matrix of the mitochondria

• Begins with acetyl-CoA joining with oxaloacetate to make citric acid> exalacetate, 1 ATP, 3 NADH, 1 FADH2

Stage 4: Oxidative Phosphorylation

• ETC: electrons removed from molecule of glucose, then release energy originally stored in their chemical 

  • Electrons + accompanying energy are transferred to readied hydrogen carrier molecules (charged carriers NADH and FADH2)

• Loaded electron carriers: 2 NADH molecules from glycolysis, 2 NADH from the production of acetyl-CoA, 6 NADH from the krebs cycle, 2 FADH2 form the krebs cycle

• Electron carriers NADh and FADH2 shuttle electrons to the electron transport chain, resulting NAD+ and FADH can be recycled to be used as carriers and the Hydrogen atoms are split into hydrogen ions and electrons

Anaerobic Respiration

• Oxygen not available, the TEC strops working and electron carriers have nowhere to drop their electrons

  • The mitochondrial production of acetyl-CoA and the krebs cycle cease too

• Glycolysis continues, broken down to pyruvate to give net 2 ATP (instead of 30)

• Glycolysis also gives 2 NADH and the pyruvate helped the NADH get recycled back into NAD+ and takes it electrons

  • Pyruvic acid > lactic acid or ethyl alcohol (ethanol) and carbon dioxide

Molecular Biology

DNA

Molecular Structure of DNA

• Made of repeated subunits of nucleotides

• Each has a five-carbon sugar, a phosphate, and a nitrogenous base

• Pentose-shaped sugar in DNA: deoxyribose

• Nucleotides can have 4 different nitrogenous bases

  • Adenine: a purine (double-ringed)

  • Guanine: a purine (double-ringed)

  • Cytosine: a pyrimidine (single-ringed)

  • Thymine: a pyrimidine (single-rined)

• Nucleotides linked together by phosphodiester bonds between the sugars and phosphates

  • Sugar-phosphate backbone of DNA

2 DNA strands  

• Each DNA strand wrap around each other to form twisted ladder, double helix

  • Deduced in 1953 by Watson, Crick, and Franklin

• A-T (2) and G-C (3) is known as base pairing

• Two strands are always complementary

  • If one side is ATC, then other is TAG

• DNA strands run in opposite directions

  • 3’ to 5’

  • The 5’ has the phosphate group and the 3’ has an OH or hydroxyl group

  • The 5’ end of one strand is ALWAYS opposite to the 3’ end of the other strand: antiparallel

• DNA strands linked by hydrogen bonds (2 hold together adenine and thymine together and 3 hydrogen bonds hold cytosine and guanine together)

Genome Structure

• Each combination of the nucleotides is a gene (human genome has 20,000 genes)

  • The instructions of all the genes are spread among the nucleotides of DNA and all the DNA for a species is called its genome

  • Each separate chunk of DNA in a genome is called a chromosome

• Prokaryotes have one circular chromosome and eukaryotes have linear chromosomes (DNA more structured)

• DNA is wrapped around proteins called histones, and then histones are bunched together in groups of nucleosome

  • Chromosomes consist of DNA wrapped around proteins called histones

  • When the genetic material is in its loose form in the nucleus it is called euchromatin, with its genes active/available for transcription 

  • When genetic material is fully condensed into coils: heterochromatin and its genes are inactive (DNA METHYLATION AND HISTONE ACETYLATION)

DNA replication

• DNA REPLICATION IS SEMICONSERVATIVE (ONE DNA MOLECULE CONTAINING 1 ORIGINAL STRAND AND A NEWLY SYNTHESIZED COMPLIMENT)

  • BUILDS 5-3 (reads from 3-5)

• Copying of DNA: DNA replication

• DNA molecule is twisted over itself and the first step is to unwind the double helix by breaking hydrogen bonds BY THE HELICASE which exposes DNA strands to form the replication fork

• Each strand serves as a template for the synthesis as another strand

  • DNA replication begins at specific sites: origins of replication

• Topoisomerases cuts and rejoins the helix to prevent tangling

• DNA polymerase: the enzyme that performs the addition of nucleotides long with the naked strand

  • Can only add nucleotides to the 3’ end of an existing strand

  • To start replication at the 5’, RNA primase adds a short strand of RNA nucleotides called the RNA primer (primer is later degraded by enzymes, and the space is filled with DNA)

• Leading strand: is made continuously (nucleotides steadily added one after another by DNA polymerase

• Lagging strand: made discontinuously in pieces known as okazaki fragments

• NUCLEOTIDES ARE BUILT IN 5’ TO 3’ DIRECTION (ADDED TO THE 3’ STRAND TO 5’ OF ORIGINAL)

  • Okazaki fragments eventually linked by DNA ligase to produce continuous strand

• When DNA is replaced, each new molecule has half the original molecule = semi-conservative

  • Helicase: unwinds double helix into 2 strands

  • Polymerase: adds nucleotides to an existing strand

  • Ligase: brings together the okazaki fragments

  • Topoisomerase: cuts and rejoins the helix

  • RNA primase: catalyzes the synthesis of RNA primers

Central Dogma

• DNA’s main role is directing the manufacture of molecules that work in the body

• DNA > (transcription in nucleus) > RNA > (translation in cytoplasm) > protein

RNA

• Messenger RNA (mRNA): temporary RNA version of DNA recipe that gets sent to the ribosome

• Ribosomal RNA (rRNA): produced in the nucleolus, makes up part of the ribosome

• Transfer RNA (tRNA): shuttles amino acids to the ribosomes and is responsible for bringing the appropriate amino acids into place at the appropriate time by reading the message carried by the mRNA

• Interfering RNA (RNAi): small snippets of RNA that are naturally made in body or intentionally created by humans; 

  • Can bind to specific sequences of RNA and mark them for destruction

Transcription

• Making an RNA copy of specific section of DNA code

• 3 steps: initiation, elongation, and termination

  • Unwind and unzip the DNA strands using helicase beginning at special sequences called promoters (docking site)

  • RNA is single-stranded so only one of the 2 DNA strands has to be copied

    • The strand that serves as template is known as the antisense strand/non-coding strand/template strand

    • The other strand that lies dormant is the sense strand/coding strand

• RNA polymerase builds RNA like DNA polymerase, only adding nucleotides to the 3’ side (5’-3’)

• Means that the RNA polymerase must bind to the 3’ end of the template strands

• When transcription begins, RNA polymerase travels along and builds an RNA that is complementary to the template strand of DNA- with replaced nucleotide base

  • Once mRNA finishes adding nucleotides and reaches a termination sequence, it separates from the DNA strand, competing transcription

RNA processing

• Prokaryotes: mRNA is complete

• Eukaryotes: the RNA must be processed before leaving the nucleus

  • The freshly transcribed RNA is called hnRNA (heterogenous nuclear RNA) and contains both coding and noncoding regions

  • Regions that express the code that will turn into proteins: exons

  • The noncoding regions in the mRNA are introns

• Splicing: the introns removed before the mRNA leaves the nucleus and is accomplished by an RNA-protein complex called a spliceosome

• poly(a) tail is added to the 3’ and a 5’ GTP cap is added to the 5’ end

  • Processes produce a final mRNA that is shorter than the transcribes data

Translation

• Turning mRNA to protein

  • Protein made of amino acids

  • The order of the mRNA nucleotides will be read in the ribosome in groups of three

• Three nucleotides are codons

  • Codon corresponds to a particular amino acid

• mRNA attaches to a ribosome to initiate translation and waits for the appropriate amino acids to come to the ribosome

  • tRNA comes and has a molecule that has a unique 3D structure that resembles a four-leaf clover

• One end of the tRNA carries an amino acid

  • other end called ANTICODON has 3 nitrogenous bases that can complementary base pair with the codon in the mRNA

  • tRNAs are between in protein synthesis and becomes charged/enzymatically attaches to an amino acid in the cell’s cytoplasm and shuttles to the ribosome

    • The charging enzyme involved in forming the bond between the amino acid and the tRNA require ATP