Concept Map 1

Solid state = hydrogen bonds form and DO NOT break Strong, ordered crystal lattice structure Expansive upon freezing Liquid state = hydrogen bonds break and reform constantly (Denser state than solidGas state = hydrogen bonds break and DO NOT reform

Dissolve = water seeps inside crystal lattice and surrounds each ion (hydration shell) to break bonds Ionic compounds dissolve in water through Ion-Dipole interactions (ie salt) Polar compounds dissolve inw ater through Hydrogen bonds (ie sugar)Water SURROUNDS Nonpolar compounds because they are Hydrophobic

Allows for water movement against gravity in plants due to hydrogen bonds between water moleculesCauses high surface tension in water - makes it difficult to break water surface

Helps moderate temperature - defined by amount of heat required to raise temperature by 1 degreesWater absorbs heat --> hydrogen bonds break --> water releases heat and bonds reform = water is resistant to changes in temperature

Amount of heat/kinetic energy absorbed is high enough to break hydrogen bonds and NOT reform Evaporation Cooling = stabilizes temperature in water and organism by cooling surface after water evaporates

Primary Structure: Long chain of amino acids Involves MAIN chain of aminosPEPTIDE Bonds are present Secondary Structure: Alpha helicase or Beta pleated sheetsInvolved MAIN chain of aminos HYDROGEN Bonds are present Tertiary Structure: Polypeptide fold into 3D shape Involves R GROUP ALL Bonds are present Disulfide, Ionic, Hydrogen, Hydrophobic, and Van der Waals Quaternary Structure: 2+ Polypeptides form functional protein Involves R GROUPALL bonds are present

Environment alters/heats = Protein cannot retain shape = UNFOLDS back to PRIMARY STRUCTURE Breaks all bonds EXCEPT PEPTIDE BONDSRenature (remove denaturing condition) is successful IF the protein retains original function -- ie cool protein if heat caused denature

Central Carbon bonded to 4 DIFFERENT groups = Enantiomer Isomer (mirror images) ONLY L FORM OF ENANTIOMER PRESENT Link together through dehydration to form Polypeptides Protein functions as Trimer = 3 Polypeptides --> Highest structure = Quaternary Protein function as Dimer = 2 Polypeptides --> Possible structures = Primary, Secondary, Tertiary, Quaternary

Side Chain = R Groups Non Polar (C-H): Hydrophobic and Van der Waals interactions N-H can be both non polar or polar but is GENERALLY MORE NON POLAR Polar (O-H, S-H, C=O): Polar Covalent interactions Acidic: Negatively charged Basic: Positively charged Glycine is NOT an Enantiomer because there are not 4 unique groups around central Carbon

Main Chain = Amino (NH2+), Carboxyl (COOH-), and Hydrogen SAME FOR ALL AMINO ACIDS

Enzymatic Proteins = Accelerates selective chemical reactions Defensive Proteins (ANTIBODIES) = Protection against disease Storage Proteins = Stores amino acid monomers Transport Proteins = Transports substances through cell Hormonal Proteins = Coordinates an organism's activities through secretion of hormones (ie Insulin)Receptor Proteins = Helps with cell response to chemical stimuli Contractile + Motor Proteins = Cell movement (ie Myosin and Actin in muscles) Structural Proteins = Cell support (ie Collagen and Keratin)

Carbohydrates are organic molecules that serve as energy fuel for short-term storage. Carbohydrates are one of the biomolecules that contain monomers and polymers. The monomers of carbohydrates are called monosaccharides while the polymers of carbohydrates are polysaccharides.Carbohydrate skeletons can be drawn in four structures: linear, double bond position, branching, and rings.

Polymers are synthesized through dehydration/condensation. Polymers are broken down via hydrolysis and enzyme catalysts.There are different types of polysaccharides: storage and structure.

Storage polysaccharides

The difference between all the types of polysaccharides is the type of linkages they have and whether or not they are alpha glucose or beta glucose.

What we would think of when we think glucose. Glycogen is a large, formed polysaccharide that is used by the body as fuel. It uses alpha 1-6 glycosidic linkage to branch out the glucose to store energy to use for fuel.

Cellulose is a beta glucose molecule and to make the structure of cellulose found in the cell membrane, it uses beta 1-4 glycosidic linkage. Enzymes cannot be used to break down the linkages, so it is not digestible. Another type of structure polysaccharide is chitin, which is also found in plant cells.

Amylose uses alpha 1-4 glycosidic linkage to form helix chains. Amylose is not soluble in water and doesn't produce a gel when hot water is present.

Amylopectin uses alpha 1-6 glycosidic linkage to form branched helix chains. Amylopectin is soluble in water and does produce a gel when hot water is present.

Monosaccharides are monomers that are simple structures like glucose, fructose, and galactose.

BETWEEN MOLECULES

Hydrogen bonding with F, O, N of adjacent molecule POLAR INTERACTION

Asymmetric electron distribution in molecules Electrons pull towards partial positive side NON POLAR INTERACTIONHappens everywhere

Non Polar parts group together in Polar substance (Water) NON POLAR INTERACTION Seen in Phospholipid tails

Between ions and polar molecules 1 fully charged and 1 partially charged (ie Na+ and Cl- interacting with H2O partial charges) Positive charge interact with negative charge 

Ionic - electrons transferred from one atom to another producing a cation and anion

Covalent - electrons shared between two atoms under the same electron cloud (ΔEN >1.5)

Nonpolar covalent - electrons equally shared between two atoms (ΔEN <0.5)

Polar covalent - electrons unequally shared between two atoms (ΔEN 0.5<x<1.5)

Deoxygenated pentose sugar with a phosphate group and nitrogenous bases (A, T, C, G) Double helix structure easy for stability and replicationHydrogen bonds with nitrogenous bases and phosphodiester linkages

Oxygenated pentose sugar with a phosphate group and nitrogenous bases (A, U, C, G)Alpha bent structure making it easy for replication and systemization of proteinsNo hydrogen bonds with nitrogenous bases and phosphodiester linkages

To not go too much into structure, this is just the basics of Eukaryotic cells. Eukaryotic cells are very complex cells that have different organelles across different cell types.Common Organelles:Nucleus - A complex envelope that contains Deoxyribose Nucleic Acid that contains the instructions for the cell for its function and the template to create amino acids. Mitochondria: Often called the "Powerhouse" of the cell, this is where the synthesis of ATP is done. Rough and Smooth Endoplasmic Reticulum - A network of membranes involved in protein synthesis and folding. Rough ER has ribosomes embedded within it. Smooth ER is involved in Lipid synthesis. Golgi Apparatus - Modifies, sorts, and packages proteins and lipids for transport. Lysosomes: Contain enzymes that break down waste products and cellular debris through the acidic interior of Lysosomes. Ribosomes: Small structures that are responsible for protein synthesis through tRNA and rRNA.Plasma Membrane: The outer boundary of the cell, and it regulates what enters and exits the cell. Chloroplasts: Organelles that capture sunlight for photosynthesis for glucose. These are pretty common organelles but multiple Eukaryotes have cell-exclusive organelles:Flagella for movement through fluidPili for attachmentAxons, Mylean Sheeth, etc. for nerve cells.

Prokaryotic - Basic small cells with a limited number of organellesEukaryotic - Complex larger cells with the presence of membrane-bound organelles Endosymbiotic TheoryProkaryotes were the first cells with Eukaryotes coming after. The proposed theory states that a protoeukaryotic cell absorbs a prokaryotic cell to make Mitochondria, and an autotrophic prokaryotic cell makes Chloroplasts. Evidence for the Endosymbiotic Theory The inner membranes of mitochondria and plastid are similar to the plasma membranes of living bacteriaReplication of mitochondria and plastids is similar to cell division in BacteriaMitochondria and plastids have circular DNA like Bacteria Mitochondria and plastids transcribe their own DNA into proteins. There are Ribosomes in mitochondria - almost having an independent cell structure

Lipids are made from building blocks of sugar:One - Monosaccharides Two - DisaccharidesThree - TrisaccharidesFour or More - Polysaccharides These saccharides link through the Glycolic Cvalend bond - meaning water performs a hydrolysis reaction that breaks this bond. Fructose and Glucose come in contact and allow water to use hydrogen bonds.Types of Polysaccharides Storage PolysaccharidesGlycogen Starch Dextran Structure Polysaccharide Cellulose Chitin Glycerol fatty acids can have multiple chains formed through ester bonds. Tails that contain only a single bonded chain are called saturated fats. Tails that contain double bonds are called unsaturated fatsTrans geometric structures cases have the hydrogens on both sides of the double bondCis geometric structures cases have the hydrogen on the same side of the double bond; this results in a large bend on the hydrocarbon tail.

Lipids are one of the most important molecules for cells to have function:Cellular Membrane: Lipids are fundamental components of cell membranes. Usually phospholipids, these form a structure having hydrophilic facing the outside of the cell and the inside surface of the cell, with the hydrophobic hydrocarbon tails between the membrane. Energy Storage: Lipids serve as a dense source of energy for cells. In animals, fats like triglycerides are stored in cells to provide energy when glucose levels are low Some other functions that are not covered are insulation/protection for macroscopic organisms, Signaling Molecules, and Electron carriers in cellular respiration.

Bacteria are small simple cells that consist of a fundamental Cell Structure.These usually consist of CytoplasmMembraneChromosomes folded within a Nucleoid A small collection of DNA in certain Bacterial cells have a Plasmid. Plasmids can also be exchanged between Bacterial cells. This is how antibiotic-resistant genes are transferred between Bacterial Cells.Cell WallsUniquely Cell walls are made from Peptidoglycan instead of Cellulose & Beta-Glucose in plant cells. Certain Bacteria also contain:Slime layers that are made of PolysaccharidesSome Bacteria have Flagellum to propel through solvents like water. Motile function.Some have fimbriae and pili that attach to surfaces. hey can also use pili to connect to bacteria and transfer DNA - Plasmid Anti-biotic Resistance Some can form endospores which is a hibernation almost where Bacteria can survive in harsh conditions for centuries. Other minor organells:Gas VacuolesRibosomesInclusion BodiesNucleoidsPeriplasmic Space

While the Kingdoms might be similar, there are a few major differences, like their organelles:Both have the presence of cell walls.Both do not have a nucleus Archaea has branched lipids that are uniquely made with ether bonds. Bacteria do not.Bacteria have the presence of peptidoglycan, whereas Archaea does not.

There are four major nutritional modes of Prokaryotes Autotrophic MethodPhotoautotrophs ChemoautotrophsHeterotrophicPhotoheterotrophicChemoheterotrophicRoles of Oxygen in Metabolism Obligate aerobesRequires Oxygen for Cellular Respiration Obligate anaerobesUses fermentation and anaerobic respiration. Poisoned by Oxygen.Facultative anaerobesUses Oxygen when present. Carry out fermentation or anaerobic respiration when Oxygen is not present.

Archea is rumored to be one of the first-ever cells of life. They are extremely basic, yet this simple structure provides the basis for a stable organism and some unique properties.Some Archea live in extreme environments, these are called extremophiles Extreme Halophiles - Can survive in high-solute solutions Extreme Thermophilies - Can survive in extreme temperaturesAcidophiles - Can survive in acidic solutions

Some Archaea are Methanogens, which live in swaps and marshes. These produce Methane a waste product of their metabolism. This provides those environments with a "rotten" smell.

CATABOLIC REACTION (exerting energy) Electron Carriers: NADH and FADH2Glucose = Oxidized, Oxygen = Reduced

Starts with electrons from food (glucose) Occurs with or without oxygen (anaerobic and aerobic) Energy Investment Phase Uses 2 ATPCreates 2 G3PEnergy Payoff Phase Makes 4 ATP Everything is doubled

Start: Glucose Add: Hexokinase Removes Phosphate group from ATPEnd: Glucose 6P + ADP

Start: Fructose 6PAdd: Phosphofructokinase End: Fructose 1-6 Bisphosphate

"I take a NAP @ 2PM"NET: 1 Glucose = 2 NADH, 2 ATP, 2 Pyruvate

Needs Oxygen (Aerobic) Pyruvate from Glycolysis gets oxidized in the Mitochondria if O2 is present Products go through Krebs/Citric Acid Cycle

1 Pyruvate = 1 Acetyl CoA + 1 NADH

Occurs in Mitochondria Goal is to generate ATP

Electrons from NADH travel through Complexes I, Q, III, C, and IV down ELECTRON TRANSPORT CHAIN Complexes I, III, and IV pump out H+ into the intermembrane spaceEnergy from electrons transferring down ETC is used to pump H+ AGAINST concentration gradient Once electrons reach Oxygen, water is formed

H+ traveling AGAINST gradient from ETC supplies energy source to convert ADP to ATP as it travels DOWN to Chemiosmosis ATP Synthase is involved Synthase grabs protons pumped out as electrons travel down ETC - Facilitated Diffusion

Occurs in the Mitochondria

Start: Oxaloacetate Add: Acetyl CoAEnd: Citrate

Start: Isocitrate End: Alpha Ketoglutarate

1 Acetyl CoA + 1 NADH = 1 ATP, 3 NADH, 1 FADH2

Occurs in cytoplasm, without Oxygen (Anaerobic) RECYCLING PROCESSRecycles NADH into NAD+ to generate more Glycolysis

Start: 2 NADH + 2 Pyruvate End: Lactate

Start: 2 NADH + 2 Pyruvate End: Ethanol + Carbon Dioxide

Notes

Electrical signals along nerve cells trigger a release of neurotransmitters that diffuse across the synapse to reach the target cells so that they can become stimulated and get the signal.

Local regulators (or signals or ligands) diffuse through the extracellular fluid to get to the target cell.

Here, we'll look at an example of the amplification effect caused by binding epinephrine to the receptor and causing millions of molecules to be made.

Ion channel receptors often have ligand-gated receptors in which the channel will remain closed until a ligand binds to the receptor. When the ligand binds to the receptor and the channel opens, specific ions can flow through the channel and rapidly change the concentration of that particular ion inside the cell. This change may directly affect the activity of the cell in some way. When the ligand dissociates from this receptor, the channel closes and ions no longer enter the cell.

The steroid hormone, aldosterone, passes through the plasma membrane. Aldosterone binds to an intracellular receptor protein in the cytoplasm, activating it. The hormone-receptor complex enters the nucleus and binds to specific genes. The bound protein acts as a transcription factor, stimulating the transcription of the gene into mRNA. The mRNA is translated into a specific protein.

One steroid hormone can have multiple effects on cells. If can have the same receptor but different intracellular proteins to activate, or it can have different receptors.

DEFINED BY:DNA in nucleusDouble membrane bound organelles EXTERNAL MEMBRANE:Glycolysis FermentationINTERNAL MEMBRANE: Pyruvate Oxidation Citric Acid/Krebs Cycle

Site of plant photosynthesis Contains: Stroma = Internal fluid Thylakoid = Membrane sacs Stacks of Thylakoid = Granum

Cell junction in plants Provides channels for water and nutrients to travel between cells

Made of celluloseMaintains cell shape Contains: Secondary Cell Wall: Between plasma membrane and primary cell wallPrimary Cell Wall: Thin + flexible Middle Lamella: Between primary walls of adjacent cells

Responsible for protein traffic + metabolic functions

Contains:Smooth ER (NO Ribosomes) = Makes Lipids, metabolizes Carbs, detoxify DISEASE = JAUNDICERough ER (Bound Ribosomes) = Folds Proteins, secretes Glycoproteins

Shipping Vesicle Contains: Cis Face = Receiving sideTrans Face = Shipping side

Formed when Phagocytosis occurs

IN PLANTS ONLY Stores Potassium, Water, and Chloride

Pumps excess water out of Freshwater Protists

H+ pump maintains LOW PH INSIDE to keep enzyme functional = Hydrolysis/breaks covalent bondsDISEASE = Build up of toxins

EATCell extends membrane --> Engulf ---> Pinch offDigestion products (amino acids + simple sugars) --> Cytosol as nutrients

RECYCLEHydrolysis enzyme recycles organic materials Digests damaged organelles --> Cytosol for reusage

Regulates transport in + out of nuclear pores

Present OUTSIDE ER Protein inserted in membrane/secreted out of cell

Present in CYTOSOL Makes Proteins

Site of cellular respiration Contains:Intermembrane SpaceCristae: Membrane foldsMitochondrion Matrix = Free ribosomes + DNA Involved in Cell Respiration to make ATP = POWERHOUSE OF CELL DISEASE = Myoclonic Epilepsy

Cell Storage + Organelle Anchorage

ALL EUKARYOTES HAVE THICKEST (Alpha and Beta Dimers) Contains:Dynein = Motor protein to drive bending movement of organellesBasal Body = Ring of 9 triplets to anchor Cilia + Flagellum DIFFER in arrangement of microtubules

THINNEST = made of 2 intertwined actin protein strands Actin Filaments

Myosin head + Actin filament attach and move = actin filament slides = underlying muscle fibers contract

LOCALIZEDMicrofilament + Myosin = Tail squeeze interior fluid = Extending Pseudopodium

LOCALIZEDMyosin contract in PLANTS = Propels Cytoplasm = Distribution of nutrients

MORE PERMANENTMaintains cell shape, anchors nucleus + organelles, forms nuclear lamina Made of KERATIN Proteins

Site of Transcription + DNADISEASE = Progeria

Gives shape to nucleus

Site of rRNA synthesis

Helps transport in and out of nucleus

B Cells = MAKE ANTIBODIES to bind to + destroy antigens Increased Ribosomes and Golgi Apparatus (ship out through ER)

Break down + release toxin (engulf + destroy) Increased Lysosomes

T helper cells activate B cells B + T interact through surface proteins Increased Ribosome, Rough ER, Golgi (for transport)

ECM changes = changes in cell MNEMONIC: "Can Find Party In ECM rave"

Made of protein + sugarAttached to single polysaccharide

Binds to ECM = Transmit signals between inside and outside of cell

Embedded in web of Proteoglycan complexes

Attach ECM to Integrins in Plasma Membrane

Nothing goes through

Leaky junctions Point of direct contact between cells

Everything goes through

Thermodynamics System - matter within a defined region of space Closed SystemOpen System Laws of Thermodynamics First Law of Thermodynamics: Energy can be transferred and transformed, but cannot be created or destroyed. Second Law of Thermodynamics: Every energy transfer or transformation increases the entropy of the universe.

Free Energy is Cellular WorkEntropy = Gibs Free Energy + T(Enthalpy)G = H -TSMeasuring change in each at constant of TFree-Energy Change (ΔG)The change in free energy ΔG during a chemical reaction is different between the free energy of the final state and the free energy of the initial state ΔG = G(final) - G(inital)For a spontaneous process, no energy input is needed - ΔG is negativeFor a nonspontaneous process, energy input is needed ΔG is positive

Most Enzymes have an ideal pH or Temperature that they work at most efficiently, and when these fall outside the parameters the enzyme not might work as well or overall completely denature back to a polypeptide chain.

Competitive Inhibitors bind to the active site of a enzyme prevent substrates from binding to the enzyme and lower overall efficiency of reactions.

Binds to another part of the enzyme but affects the shape so that original substrates cannot bind to the new active site

Membranes have a variety of proteins Peripheral proteins are not fully integrated within the cellsIntegral proteins are integrated fully within the membrane Some Functions of Membranes Proteins Include:TransportEnzymaticSignal TransductionCell-Cell Recognition

Membrane Fluidity Each phospholipid has a specific phase transition temperatureAbove this temperature, lipids are in a liquid crystalline phase and are fluid Below this temperature, lipids are in a gel phase and is more rigid

Selective permeability of Plasma Membrane General rule is the size and charge of the molecule can in and out of the cellTransport proteins allow the passage of hydrophilic substances across the membrane

Movement of substances from low to high concentrations (pushing against the concentration gradient)Maintains a concentration gradient Uses energy (ATP)

Carrier Protein Pump: Carries from protein from inside to outside the cell, uses ATP energy to change shapes within the molecule

A transport protein generates a voltage across a membrane-membrane potential Help stores energy that can be used for cellular work

A protein proton pump uses ATP to pump protons against the concentration gradient Protons want to go back in so they go down the concentration gradient using facilitated diffusion in a Sucrose cotransporterEnergy associated with the proton gradient help protons and sucrose move across the membrane

The Sodium-Potassium Pump: A specific case of Active Transport This pump is present in all animal cellsThis ensures sodium is lower on the inside and more on the outside. This also ensures the potassium is higher on the inside and lower on the outside.

Due to these pumps, a voltage difference is made Outside the membrane is slightly positive (some more Na+ ions)Inside the membrane is slightly negative (some more K+ ions, think of salty banana)

Always Open

Also known as sense stretched, open when membrane is mechanically deformed

Open and close when a neurotransmitter binds to channel

Open and clsoe in response to changes in membrane potential

High permeability Small nonpolar molecules can cross through on their ownSmall uncharged polar molecules like water and glycerol

Large, uncharged molecules such as glucose cannot cross on its onAs well as ions like Na+ and K+

Solvent moving from low solute concentration to higher solute concentration. Desire to create an equilibrium.

Hypotonic: Excess water is in the cell and the cell is lysed and explodes. This is due to high solute concentration within the cell and water rushing inside. Isotonic: Water is both leaving and entering the cell in equilibrium. This is also called normal Hypertonic: High solute concentration outside the cell causes water to rush outside the cell. Cell gets shriveled up, this usually causes cell death.

Facilitated Diffusion is passive transport aided by channel proteins. However, no ATP is required for this type of transport

DNA --> mRNA

Occurs in cytoplasm Transcription and Translation are coupled = happens immediately

Enzyme used to make mRNA during Transcription in Prokaryotes

Occurs in the nucleus

Binds to the promoter FIRST to help RNA Polymerase II bind next

ENZYME: binds to the promoter AFTER Transcription Factors bind = Transcription Initiation ComplexUnwinds DNA and starts RNA synthesis

Section on the promoter for Transcription in Eukaryotes

RNA Polymerase II moves downstream of DNAAdds to the 3' end using dehydration reactions = double helix

Added by Poly A PolymeraseIncreases mRNA stability

ENZYME: cuts introns, joins extrons to form mature mRNAKEEPS 5' CAP AND 3' POLY A TAIL

Removing different introns = different mRNA combinations = different proteins

Aims to control expression at earliest stage - usually at Transcription

Distal Control Elements/ENHANCERS Away from promoter

Lowers transcription to basal/backgroundMeets mediator proteins during bending

Raises transcription above basal levelsMeets mediator proteins during bending

TATA box Where RNA Polymerase II binds during bending to control gene expression

Proximal Control Element Closest to promoter

Regulated expression

Permease Membrane Protein that takes in Lactose

Transacetylase Adds acetyl group

Beta-Galactosidase Breaks Glycosidic linkage of Lactose to form Glucose and Galactose

No lactose = Repressor Protein binds here to turn OFF

GOAL = Break down Lactose --> GlucoseBoth positive AND negative regulation

OPERON OFF - NEGATIVE REGULATIONRepressor protein bind OPERATOR = blocks RNA Polymerase from binding

OPERON ON - POSITIVE REGULATION Repressor protein binds LACTOSE Needs activator

Activated by cAMP (Adenyl Cyclase uses ATP) Binds to Promoter to help RNA Polymerase bind

OPERON OFFGlucose = Adenyl Cyclase INHIBITOR Inhibitor = blocks cAMP product = CAP cannot be activated = RNA Polymerase cannot bind to Promoter

Constitutive (Continuous) expression

Activator attached = Transcription occursActivator unattached = Transcription does not occur

Repressor attached = Transcription does not occurRepressor unattached = Transcription occurs

6CO2 + 6 H2O + Energy --> C6H12O6 + 6O2H2O is oxidized CO2 is reduced GOAL= Make sugar for energy

Occurs in Thylakoid of CytoplasmMakes NADPH Electron Carrier

PRODUCTS = ATP, O2, H+, NADPH Electron CarrierATP goes against gradient in Thylakoid (High H+, Low pH) Down gradient through ATP Synthase into Stroma (Low H+, High pH) = Photophosphorylation Uses PS II (P6800) and PS I (P700)

PRODUCTS = ATPOccurs ONLY when NADPH is in excessONLY uses PS I (P700)ELECTRON TRANSPORT CHAIN

ENZYME = Pep Carboxylase Photorespiration interferes with Carbon Fixation = adaptationsRubisco prefers O2 > CO2 = releases CO2 = blocks photosynthesis = NO ATP/Sugar

DIFFERENT TIME OF DAY Night: CO2 Fixation, Stromata Open Day: Calvin Cycle

DIFFERENT CELLS Mesophyll = CO2 Fixation Bundle Sheath Cell = Calvin Cycle

Site of PhotosynthesisFound in Mesophyll (interior tissue of leaves)

CO2 IN, O2 OUT

Light harvesting pigment

Occurs in Stroma Whole Cycle = 9 ATP, 6 NADPH, produces 1 G3P1 Glucose Molecule = 3 CO2, 18 ATP, 12 NADPH Makes ATP

CO2 + RUBP (use Rubisco - ENZYME) = 6C (unstable) = 3C 6 ATP --> 6 ADP = 6 1-3 Bisphosphoglycerate

5 G3P from Reduction, 3 ATP --> 3 ADP = 3 RuBP for Phase 1

6 NADPH --> 6 NADP+, 6Pi = 6 G3P --> exports 1 (PRODUCT)

Function: Unwinds the double helix by breaking hydrogen bonds between base pairs, creating the replication fork.Interaction: Opens the DNA so other enzymes can access the strands.

Function: Stabilize the unwound DNA strands, preventing them from reannealing or being degraded.Interaction: Coat the strands to keep them separated.

Function: Relieves supercoiling and torsional strain ahead of the replication fork. Basically Untangles the DNA upstream Interaction: Works upstream of helicase to ensure smooth unwinding.

Function: Synthesizes a short RNA primer to provide a starting point for DNA polymerase.Interaction: Adds RNA primers for polymerase to extend.

Function: Adds nucleotides to the 3' end of the growing DNA strand, using the template strand for complementary base pairing.Interaction: Requires RNA primers; synthesizes the leading strand continuously and the lagging strand discontinuously (Okazaki fragments).

Function: Joins Okazaki fragments on the lagging strand by sealing nicks in the sugar-phosphate backbone.Interaction: Follows DNA polymerase to finalize the lagging strand.

Function: Removes incorrect nucleotides during replication to ensure fidelity.Interaction: Built into DNA polymerase as a proofreading mechanism.

Process OverviewHelicase unwinds the DNA, and SSBs stabilize the unwound strands.Topoisomerase relieves tension.Primase lays down primers.DNA polymerase III synthesizes the leading strand continuously and the lagging strand in fragments (Okazaki fragments).DNA polymerase I removes primers and fills with DNALigase seals any remaining nicks to finalize the strand.

Initiation: Helicase unwinds the DNA, primase lays down RNA primers.

Elongation: DNA polymerase synthesizes new strands (leading and lagging).

Termination: DNA ligase seals fragments; proofreading corrects errors.

Definition: Alters a nucleotide but does not change the amino acid sequence due to the redundancy of the genetic code.Consequence: Usually no functional impact on the protein. Hence the word "silent". This happens because the codon wheel has multiple inputs for the same amino acid.

Definition: Changes a codon to a premature stop codon, leading to failed protein synthesis.Consequence: Typically results in nonfunctional proteins or severe loss of function. Also can cause very short proteins

Definition: Alters a codon, resulting in a different amino acid being incorporated into the protein.Consequence: Varies from benign to severe, depending on the location and nature of the amino acid change.Example in RNA TranscriptionCAU -> HisMissense mutation that would change it to CAG -> Gln

Definition: Insertion or deletion of nucleotides (not in multiples of three), shifting the reading frame of the genetic code.Consequence: Alters all downstream codons, usually leading to nonfunctional proteins.

Spontaneous: Errors during DNA replication not caught by proofreading mechanisms.Induced: Exposure to mutagens (e.g., UV radiation, chemicals, or carcinogens) damages DNA. Dont smoke cigarettes! This is one of the most common carcinogens!

Frameshift and Nonsense Mutations are generally the most harmful because they severely disrupt the protein’s structure and function.Missense Mutations can also be dangerous if they affect a critical region of the protein, such as an active site.Ironically, I originally wanted to study more into the consequences of Missense mutations and their effects on PrP gene. Prions are an interesting disease that effects proteins and their structure. This basically causes a protein version of cancer. There is no cure for prion diseases. Commonly this will happen in the brain and the misfolded protein will cause other proteins to fold too

Uracil is also a pyrimidine, but only in RNA.

The experiment was to use bacterial cells and extract DNA from those cells to predict band distribution. The cells were grown in Nitrogen-15 (high density) combined with CsCl and were spun in a centrifuge for 20 minutes for the first round of replication. The bacteria was then transferred and grown in Nitrogen-14 (normal density) with CsCl and were spun in a centrifuge for 20 minutes for the second round of replication. The experiment concluded that DNA replication was semi-conservative.

Introns are non-coding sequence regions that are removed in RNA splicing.Exons are genetic coding regions that are combined into one large region for mRNA after RNA splicing.

Spliceosomes can be used to make cuts in pre-mRNA to extract introns to combine exons.

Sometimes mRNA doesn't need all the exons in the sequence, so introns can be used to extract parts of exons in the sequence to code for different proteins. For example, if there are 7 exons in the chromosomal DNA sequence, but only exons 1, 3, 4, 5, 7 are needed for protein A, then spliceosomes will reduce the mRNA sequence to code for protein A after translation is complete.

A modified guanine with three phosphate groups is attached to the 5' end of pre-mRNA.

About 50 to 250 adenine nucleotides are added to the 3' end

Composed of proteins and RNA. Ribosomes (prokaryotic 70S and eukaryotic 80S) have two subunits: large (50S prokaryotic and 60S eukaryotic) and small (30S prokaryotic and 40S eukaryotic) that's about 52 proteins, if prokaryotic, or about 78 proteins, if eukaryotic, attached to mRNA for translation.