Membrane Structure and Transport

Membrane Structure

• Membranes comprise phospholipid polymers from fatty acids, glycerol, phosphate, and a terminal amine or alc group
• Amphipathic membranes form layers (mono and bilayers) in water
• Cell membranes compartmentalize metabolic activities
• They act as a medium for energy generation, scaffolding for signaling, and protection

Membrane Transport

• Nernst equation indicates equilibrium between chemical and electrical forces
• GFP is a green fluorescent protein
• Membranes are permeable to small hydrophobic molecules
• They have low permeability to ions and large solutes
• Aquaporins facilitate the creation of a hydrophilic passage for transport
• Molecules are driven by electrical or chemical gradients but it doesn't always mean its going to head towrads it
• Active transport moves against the concentration gradient using pumps and cotransport systems
• Passive transport moves with the concentration gradient using channels and carriers
• Pumps operate by energy coupling: ATPases transport couples with ATP hydrolysis
• Bacteriorhodopsin drives pumps via light energy, inducing a conformational change

Cotransport Systems

• Symport: Couples downward ion movement with upward substrate movement in the same direction (piggyback)
• Antiport: Moves ions and substrates in opposite directions

Stem Cells

• Stem cells are unspecialized cells with potency that reproduce indefinitely and differentiate into various cell types
• Germ layers include ectoderm (lining of organs), endoderm (exoskeleton), and mesoderm (organs)

Stem Cell Potency

• Totipotent stem cells generate all embryonic tissues, including the placenta
• Pluripotent stem cells generate all three germ layers without extra-embryonic tissues
• Multipotent stem cells generate multiple lineages, but not all germ layer types and are haemopoietic
• Unipotent stem cells can only differentiate along one lineage, and are mostly adult stem cells

Stem Cell Derivation and Types

• Stem cells can be derived from blood biopsies, bone marrow, umbilical cord blood, and fetal tissues/organs
• Autologous stem cells are returned to the same person. Allogenic stem cells are from one person to another
• SCN (somatic cell nuclear transplantation) involves replacing an egg's nucleus with a nucleus from a different differentiated cell, allowing it to follow a different lineage and clone
• SCN has a low success rate in cloned embryos, with unknown health repercussions

Stem Cell Cloning

• Reproductive human cloning is banned
• Non-reproductive cloning uses cells derived from the inner cell mass of a blastocyst, these cells are pluripotent and expand indefinitely in culture
• Therapeutic cloning applies patient-specific cell lines via SCNT but is not designed for fetus
• Stem cells are used for research, patient drug testing, and toxicology
• hESC refers to human embryonic stem cells

Stem Cell Risks

• Stem cells pose a risk of teratoma formation if greater than one germ layer expresses in a tissue
• Induced pluripotent stem cells (iPS) require genes Myc, Oct3/4, Sox2, and KLF4 to be switched off

Cellular Energetics

• Energy is captured through respiration and photosynthesis
• Energy is stored as ATP and NADH proton gradient
• Energy is converted into light kinetic or chemical forms
• Anabolism uses energy to build complex molecules
• Catabolism releases energy through molecule breakdown
• Gibbs free energy refers to the portion of a system's energy that can perform work
• Exergonic reactions release energy, while endergonic reactions require energy
• Enzyme activity is regulated through protein modification and gene expression but is often inhibited by end-products in a negative feedback cycle

ATP, Redox, and Chemiosmosis

• ATP stores energy in its outermost phosphate bond, which is released when cleaved off
• ATP forms through transfer of a phosphate group (glycolysis) and through oxidative phosphorylation via ATPsynthase, powered by a proton gradient(chemiosmosis)
• Energy stores redox potential where moving electrons from sugars with weak electronegativity to oxygen with strong electronegativity releases energy
• NADP+ converts to NADPH. FAD converts to FADH2
• NADH is oxidized with the cleaved off H+ creating a proton gradient, chemiosmosis

Glycolysis, Citric Acid Cycle, and Oxidative Phosphorylation

• Glycolysis, citric acid cycle, and oxidative phosphorylation are key metabolic pathways
• Glycolysis occurs in the cytoplasm and its net pay off includes 2X pyruvate + 2 H20, 2 ATP, and 2NADH + 2H+ created from glucose
• The citric acid cycle transpires in the mitochondrion matrix resulting in net pay of 6x NADH
• In aerobic conditions, oxygen recycles NADH and FADH into NAD+ and FAD+
• Oxidative phosphorylation involves oxidizing electron carriers to create a H+ proton gradient via chemiosmosis
• The gradient powers ATP synthase activity to create 26-28 ATP
• Electronegative oxygen is used to make water, creating free energy
• In anaerobic conditions, pyruvate is reversibly converted into lactate or ethanol within the cytosol
• Fermentation yields only 2 ATP per glucose, occurring via glycolysis

Photosynthesis

• Photosynthesis splits into light and dark reactions
• It converts atmospheric CO2 and H2O to carbohydrates
• Solar energy stores as chemical energy in ATP and NADPH for converting CO2 to hexose phosphate
• Light reactions take place in the thylakoids of chloroplasts (stroma surrounds thylakoids)
• Dark reactions comprise the Calvin cycle in the stroma, converting CO2 to carbs using ATP and NADPH
• Chlorophylls contain a tetrapyrrole ring, chl a and chl b, and antenna pigments including carotenoids
• Capturing green wave lengths is more difficult

Photosystems and Light Absorption

• Light absorbs through Photosystems I and II, using the CYT bf complex in the thylakoid membrane (Z scheme)
• Electrons conduct from H2O to NADP+ through redox reaction
• PSI is best suited for P700 (700nm) and PSII is best suited for P680 (680nm)
• Summary of Z scheme: Light absorption converts P680 and P700 into excited molecules, leading to reducing agents
• PSII moves from CYT bf to PSI onto ATP synthase to be created
• For two H2O oxidized to O2, 2 NADP+ are reduced to 2 NADPH
• Cyclic flow increases the proton force and ATP production but does not create NADP+

Photosynthesis Reactions

• The light energy is used to reduce NADP and phosphorylate ADP
• Photosynth 2 comprises dark reactions and carbon fixation completed by RuBisCO
• RuBiSco has 8 large nuclear encoded subunits and 8 small chloroplast encoded subunits
• Carbon dioxide and 5-carbon sugar ribulose form molecules of PGA
• Rubisco catalyzes a competing oxygenation reaction using O2
• Carboxylation occurs threefold more frequently than oxygenation
• Photorespiration uses NADH and ATP to yield glyoxylate, serine, glycine, and CO2
• Photosynthesis yields 3PGA and O2 is given off

Photorespiration and Carbon Fixation

• Photorespiration yields 2PGA and CO2
• Cyanobacteria form carboxysomes concentrating CO2 around rubisco
• Algae form pyrenoids for the same purpose
• Some angiosperms use C4 and CAM to supply rubisco
• C3 is considered the standard pathway, while C4 is adapted to hot climates, and CAM is adapted to dry conditions
• C3 plants are standard wheat
• In C4 plants (such as maize), mesophyll and bundle sheath cells fix CO2 into oxalacetate
• CAM plants (such as pineapple) closes stomata during the day to conserve water, fixing CO2 into malate in vacuoles
• Dark reactions use NADPH and ATP with rubisco to fix CO2 to regenerate RuBP
• C4 and CAM plants bypass CO2 and O2 limitations by pre-fixing carbon as a 4-carbon acid
• C4 and CAM photosynthesis demand high metabolic costs adapted for dry climates

DNA

• DNA holds genetic information, evident from Avery's experiment
• Griffith showed harmless bacteria transforming harmful upon receiving genetic material from dead harmful bacteria
• Avery proved pick up of DNA transforms bacteria
• Hershey and Chase worked out bacteriophages inject into host cells to cause transformation, proving that DNA held genetic information
• Watson and Crick determined DNA structure with T and C as pyrimidines and G and A as purines
• X-ray diffraction indicated three rings fit at a time, enabling the correct helix structure
• DNA replicates semi-conservatively, using heavier isotopes of N to deduce the original DNA location
• DNA replicates in the 3' to 5' direction due to electronegativity
• Dna polymerase always replicates in 3' to 5' end

Cellular Energetics ILOs

• Concept of free energy
• Use of thermodynamics to explain enzyme use in metabolomics
• Role of ATP in energy coupling processes
• Importance of oxidation reduction reactions in energy creation
• Glycolysis, citric acid cycle, and oxidation phosphorylation in energy cycle

Oxidation

• Oxidation = to loose electrons

Energy Conversion and Thermodynamics

• 1st law of thermodynamics: Energy is neither created nor destroyed, only is converted
• 2nd law of thermodynamics: Transfer of energy leads to increase in entropy

ATP and Metabolism

• ATP is the energy reservoir in a cell
• Metabolism is the total of an organism's chemical reactions
• Anabolism uses energy to build complex molecules
• Catabolism releases energy through molecule breakdown
• Delta G = DeltaH + T DeltaS measures Gibbs free energy
• Exergonic reactions release energy
• Endergonic reactions require energy
• Enzymes regulate metabolism by lowering activation energy but also affected by pH, gene expression/protein modification, and end product feedback

ATP Formation

• Substrate-level phosphorylation happens in glycolysis through phosphoglycerate kinase
• Oxidative phosphorylation happens via ATP synthase in the mitochondrial inner membrane
• Chemiosmosis is the movement of ions down electrochemical gradients

Redox Biochemistry

• Relocating electrons from sugar using weak electronegativity to oxygen which is strong, releases energy
• Nad+ converts to NADH
• NADH converts to Nad+
• Chemiosmosis harvest is when energy is stored in a transmembrane proton (H+) gradient, created across the mitochondrial membrane
• This energy turns the ATPsynthase motor and allows forthe production of ATP (H+ goes in ADP to make ATP and the H goes with oxygen to produce water)

Calvin Cycle

• Photosynthesis is split into light and dark reactions
• Carbon dioxide and the 5-carbon sugar ribulose, 1,5-biphosphate form 2 molecules of 3 PGA and is metabolically irreversible
• RuBisCO makes up 50% soluble protein in plants
• It used to catalyze a competing oxygenation reaction

Photosynthetic Reactions

• Carboxylation normally occurs 3x as fast as oxygenation. Photorespiration recycles toxic products, consuming NADH and ATP to yield glyoxylate serine, glycine, and CO2 Alternative photosynthetic reactions are:

DNA Replication

• Replication starts at one site in prokaryotes and at several sites in eukaryotes
• Helicase recognizes DNA, unwinds it, creating replication bubbles. New strands elongate and bubbles fuse
• DNA polymerase adds composite nucleotides to daughter strand for DNA elongation
• Nucleotides can only be added to the free 3' end as it is more electronegative
• DNA polymerase uses triphosphates as sources of nucleotides, leaving pyrophosphate per nucleotide.
• Enzymes extend the chain in one direction(5----->3). Two strands cannot be replicated continuously, creating leading and lagging strand

DNA Synthesis

• Lagging strand: DNA primase attaches RNA primers to the 5' end
• This Creates chunks of 10 nucleotides known as Okazaki fragments and rna provides a 3' end to the 5 allowing replication to occur

Enzymes in DNA Function

• Helicase unwinds DNA helix for replication at replication forks, in both strands
• Single strand binding protein stabilizes single strand DNA to allow it to be used as a template, in both strands
• Topoisomerase corrects the overwinding of strands by breaking, swiveling, and rejoining DNA strands, in both strands

DNA pol Enzymes

• Primase synthesizes a RNA primer at the end of the leading strand
• DNA Pol III synthesizes the leading stread continuously and works a a primer to elongate each Okazaki fragment
• DNA Pol I removes primer from 5' end and replaces it with DNA, adding on the adjacent 3'end, while removing primer from 5' end of each fragment, replacing it with DNA adding it on to the 3' end of each fragment
• DNA Ligase joins the 3' end of DNA to the strand while also joining the fragments

RNA Synthesis and Processing

• Termination of transcription is signaled by polyadenylation signal (AAUAAA)
• All types of RNA are produced by a single polymerase in prokaryotes
• MRNA processing: cap is added to the 5' end and a polyA is added the 3' end serve to keep mRNa from falling apart
• MRNA splicing is the process that removes introns and redions

Translocation

• Translation moves mRNA through a ribosome, codons are read through amino acids one by one
• TRNA recognises the codons on the mRNA chain with their anticodons and is a requirement for accurate transcirption

TRNA Synthesis

• Loading of tRNA is performed by enzyme aminoacyl-tRNA, requires ATP
• Consists of 2 large subunits 50S and small 30s. Ribosoms only join in the presense of mRNA

TRNA Sites

• mRNA binding site ,50' is at the P site
• A site synthesises peptydil/tranfer sites binds chaind
• exit site is a part within the ribosome

Rembering order of sites

• mape
• ape

Elongation

• Process of adding amino acids where ribosomes move tRNA to correct spot

Termination

• stops at UGA, chain removed at P

Protein Folding

• Non polar molecules move to gether
• Chairs are linear until reach th end

Amino Acids

• Polar have amino acid
• Non-polar, proline

Damage control

• Cells dont like mistakes caused by changes in shape

Protein folding levels

1. Primary
2. secondary
3. tertiary
4. quaternary

L12, protein function and enzymology

• emzymes reaction
• structure
• globules
• protein

Protein building

• Catalytics, use substrate and dosacrides
• enzy,es change sha[e
• regulated by proteases

Protein Facts

• can add lipid
• all fold spontanouysly
• help of another molecule to fold it.

Enzyme facts

• catalyse
• all bind
• protein
• globular
• can not