Cellular Processes: Membranes and Transport

Atoms, Bonds, Water, and Membranes

• Atoms are the smallest particles retaining an element's properties (e.g., carbon, oxygen).
• Atoms are composed of subatomic particles: protons, neutrons, and electrons.
• Elemental properties are determined by the atomic number (number of protons).
• Most atoms have equal numbers of protons and neutrons, but isotopes have different numbers of neutrons (e.g., carbon-14).
• Chemical bonding occurs when atoms share or exchange electrons to fill or empty shells.
• Stable atomic states involve paired electrons and filled electron shells.
• Atoms with unpaired and partially filled outer shells interact to fill or empty their shells.
• Water is a polar molecule forming hydrogen bonds.
• Water's polarity allows solvation of charged (ionic) and uncharged polar compounds.
• Water's high specific heat and cohesive/adhesive properties are due to hydrogen bonding.
• Membranes are phospholipid polymers composed of fatty acids, glycerol, phosphate, and a terminal group (amine or alcohol).
• Phospholipids exhibit amphipathic properties, spontaneously forming monolayers or bilayers in water.
• Membranes form cell boundaries and support bioenergetics.
• Organelles are membrane-delimited compartments within eukaryotic cells.

Which Bonds Are Important for Life?

• Ionic bonds form when atoms exchange electrons.
• One valence electron from an atom (e.g. Sodium) transfers to the valence shell of another atom (e.g. Chlorine) creating ions with opposite charges.
• Bonds form between oppositely charges ions.
• Covalent bonds form when atoms share electrons.
• These often involve filling or emptying shells.
• Covalent bonds are important for building the structure of many molecules in organisms.
• Weaker interactions, such as hydrogen bonds, are also important for interactions between molecules.
• Van der Waals interactions arise from locally induced dipoles in very close proximity.

Electron Shells

• Electron shells define the arrangement of elements in the periodic table.
• Electron shells determine the reactivity of elements.

Important Bonds for Life

• Covalent bonds, formed through electron sharing, are pivotal in building molecules essential for life.
• Ionic bonds, involving electron transfer, are crucial for forming compounds like salts.
• Hydrogen bonds, weaker than covalent bonds, play a vital role in molecular interactions and are essential for water's properties.
• van der Waals interactions are also important in stabilizing structures and mediating interactions between molecules.

Which Bonds Are Important for Life

• The four most important types of bonds are covalent bonds, ionic bonds, hydrogen bonds, and Van der Waals forces.
• They all involve attraction between atoms and/or molecules.
• Covalent bonds involve the sharing of electrons.
• Ionic bonds involve the transfer of electrons.
• Hydrogen bonds are the electrostatic interactions between a slightly positive hydrogen atom and a slightly negative atom (e.g., oxygen or nitrogen).
• Van der Waals forces are weak attractions between molecules or atoms that are relatively close together due to fluctuating electrical charges.

What Are Membranes?

• Membranes are composed of phospholipids.
• The hydrophilic head of the phospholipid faces the water.
• The hydrophobic tails face away from water.
• Phospholipids self-assemble into layers to form membranes.
• Membranes are selectively permeable.
• They separate environments, compartmentalize reactions, and drive bioenergetics.

Why is Water a Universal Solvent

• Water's polarity allows it to dissolve many substances.
• The polarity of the water molecule allows interactions with charged and uncharged polar compounds.
• Water molecules form hydration shells around these substances, effectively dissolving them.
• Water's high reactivity with other transition metals and atoms also contributes to its role as a solvent.

Why are Membranes Important

• Cellular processes are compartmentalized.
• Cellular components are separated and protected.
• Signal transduction mediated by membranes.
• Cellular energy is generated through processes within membranes and their specific arrangement.

Organelles

• Organelles are membrane-enclosed structures within eukaryotic cells.
• They have specific functions and roles, contributing to cellular processes.
• E.g., mitochondria, chloroplasts, endoplasmic reticulum, and Golgi bodies.

Fluorescence

• Light absorption by a pigment 'excites' electrons.
• Energy is released as light when the electron relaxes to the ground state.

Green Fluorescent Protein

• GFP is an intrinsically fluorescent protein found in the jellyfish Aequoria victoria.
• GFP can be used as a marker in plants and animals.
• The endoplasmic reticulum is very mobile, transferring proteins around the cells.
• SYP121 is a trafficking protein used for transferring GFP.

Chloroplasts and Mitochondria

• Chloroplasts and mitochondria are endosymbiont progenitors suggested by their double membranes.
• Mitochondria and chloroplasts undergo independent division and replication.

Membrane Structure and Function

• Membranes are phospholipid polymers that are amphipathic.
• They spontaneously form mono- or bi-layers in water.
• Membranes serve as physical barriers and structures in cells.
• Organelles are membrane-delimited compartments in eukaryotic cells
• Cells and organelles are highly dynamic.

Membrane Transport

• Membrane transport deals with moving molecules across biological membranes.
• This includes ions, nutrients, and other substances.
• Crucial for maintaining homeostasis and carrying out cellular processes.

Active and Passive Transport

• Active transport moves substances against the electrochemical gradient, requiring energy input.
• Pumps and co-transport systems are examples of active transport.
• Passive transport moves substances down the electrochemical gradient, requiring no energy input.
• Channels and carriers are examples of passive transport.

Pumps

• ATPase pumps couple energy transfer from ATP hydrolysis to transfer of substances across membranes.
• Other pumps are driven by light energy (e.g. bacteriorhodopsin).
• Pumps establish electrochemical gradients.
• These gradients are used to drive active transport of other molecules.

Co-transport Systems

• Co-transporters couple the downhill movement of an ion to the uphill movement of another solute, known as the "piggyback" principle.
• They can be symporters (same direction) or antiporters (opposite direction).

Transport Coupling Summary

• Transport coupling is a common feature of different life forms and organelles, allowing coordinated movement of various molecules.
• Linking primary pumps (such as Na+/K+ ATPase) with co-transport systems is crucial.

Membrane Permeability

• Membranes are selectively permeable.
• Small, hydrophobic molecules and gases can easily pass through.
• Larger, charged molecules and water need specialized channels or proteins to cross.
• Transport proteins create hydrophilic passages in these membranes.
• Facilitated diffusion relies on pre-established electrochemical gradients.

Facilitated Diffusion

• Transport proteins create a hydrophilic pore.
• Small molecules or ions diffuse through this pore into the cell
• Example: aquaporins (water channels).

Driving Forces for Solute Transport

• Chemical gradients (concentration gradient) drive the movement of molecules across membranes.
• Electrical gradients (charge gradient) drive the movement of charged molecules (ions).
• Electrochemical gradient is the combination of both chemical and electrical gradients.
• The electrochemical gradient is a major driving force for the movement of solutes (ions) across membranes.

Energy requirements of Transport

• The electrochemical gradient determines the energy requirement for transport.
• Energy is required when substances move against the concentration gradient (active transport).

Active and Passive Transport (Summary)

• Active transport requires energy (ATP) to move substances against their concentration gradient. Examples include pumps.
• Passive transport moves substances down their concentration gradient; it does not require energy. Examples include channels.

The Electrochemical Gradient

• The electrochemical gradient is the combined effect of the chemical gradient (concentration difference) and the electrical gradient (charge difference) for charged molecules (ions) across a membrane.
• It influences the net driving force for movement across membranes
• The direction and strength of this force vary depending on the charge of the solute.

Test Your Understanding

• Correct answers: A. (The chemical gradient is larger than the electrical gradient leads to an inward force.)

Energy Requirements of Transport

• Electrochemical gradients determine energy needs of transport.
• Active transport requires energy input.

Biological Membranes

• Membranes hold a charge due to differential ion concentration inside and outside of a cell.
• This charge gradient is driven by chemical and electrical forces across a semipermeable membrane.
• The Nernst Equation is useful for calculating the chemical and electrical forces on specific ions across membranes.

Voltage Across Cell Membrane

• Microelectrodes are used to measure the voltage across cells.
• Endomembranes (e.g. mitochondria, lysosomes) can be measured with voltage-sensitive dyes.

Where are Membranes Found?

• Cell membranes and membranes of various organelles surround the cell and its components.
• Examples include the membranes that encapsulate the nucleus, the endoplasmic reticulum, the mitochondria, the chloroplasts, peroxisomes, and vacuoles.

Photosynthesis

• This process converts CO2 into carbohydrates, using sunlight.
• It relies on pigments capturing light energy to perform redox reactions.
• Key components are chlorophyll, PSI, and PSII.

Light Reactions

• Light-dependent reactions occur in thylakoid membranes, producing energy carriers (ATP and NADPH) and releasing oxygen.
• Essential for capturing light energy to generate ATP and NADPH for later reactions.

Chloroplast Structure

• Chloroplasts are organelles with two membranes.
• The internal membrane is stacked to form grana.
• Stroma (liquid) surrounds these structures.

Chlorophyll and Other Pigments

• Chlorophylls are main light-capturing pigments in plants.
• Accessory pigments such as carotenoids help capture light and increase the range of wavelengths of light that can be used by the plant.

Light Absorption in Photosynthesis

• Light absorption is organized by different types of chlorophyll (e.g., Chl. a, Chl. b) and accessory pigments.
• This process is organized into two main photosystems, PSI and PSII.
• The electrons excited by light energy are passed along an electron transport chain, creating a proton gradient.

Z-scheme

• The Z-scheme is an important pathway for light absorption by chlorophyll to create high-energy molecules required for photosynthesis.
• It has different stages, or steps involving PSI and PSII, to harness energy from sunlight.

Chemiosmosis and Energy Conversion

• Energy captured via electron transport is used to pump H+ ions across membranes, creating a proton gradient.
• ATP synthase harnesses the energy stored in this gradient to produce ATP.

Photophosphorylation

• Involves the use of light and photosynthetic pigments to produce ATP.
• Key component: H+-ATP synthase, which captures the energy from the proton gradient to produce ATP.
• ATP and NADPH generate energy for cellular reactions.

Cellular Respiration

• Cellular respiration converts the chemical energy from food to ATP, a cell's energy currency.
• This process occurs in three stages: glycolysis, citric acid cycle, and oxidative phosphorylation.
• It involves the use of electron carriers (e.g. NADH) and the creation of a proton gradient that drives ATP synthesis.

Glycolysis

• Glycolysis is the first stage of cellular respiration, located in the cytosol.
• It involves the breakdown of glucose.
• It produces 2 ATP, 2 NADH, and 2 pyruvate molecules.

Preparing Pyruvate for Citric Acid Cycle

• Preparing pyruvate involves the removal of CO2 and the attachment of Coenzyme A.
• The resulting molecules (acetyl-CoA) enter the citric acid cycle, continuing the process of energy release.

Citric Acid Cycle

• The citric acid cycle, located within the mitochondria, further oxidizes acetyl-CoA.
• This step generates more energy carriers like NADH and FADH2.
• It produces 2 ATP, 6 NADH, and 2 FADH2 molecules.

Electron Transport Chain and ATP Synthase

• The electron transport chain uses energy carriers (NADH and FADH2) from glycolysis and the citric acid cycle.
• A proton gradient is created through electron transfer across the membrane.
• ATP synthase uses this proton gradient to build ATP, the energy currency.

Energy Balance of Fermentation

• Fermentation produces ATP in the absence of oxygen.
• It involves converting pyruvate into either ethanol or lactate, regenerating NAD+ molecules.
• Only produces 2 ATP per molecule of glucose.

Summary of Photosynthesis

• Light-dependent reactions (Photosystems I & II) produce ATP, and NADPH, using light energy.
• Light-independent reactions (Calvin Cycle) use ATP and NADPH to convert CO2 into carbohydrates, forming glucose.

DNA

• DNA carries genetic information, which is comprised of a specific sequence of nucleotides.
• Evidence that DNA carries genetic information includes the work of Griffith, Avery, Hershey, Chase, and Chargaff.
• DNA is formed from nucleotides: a deoxyribose sugar, and a phosphate group, and one of four bases (adenine, guanine, cytosine, or thymine).
• DNA is a double helix with two anti-parallel strands held together by hydrogen bonds between base pairs.

Replication

• DNA replicates semi-conservatively; the two strands separate, and each is used as a template to synthesize a new strand.
• DNA polymerases carry out this process.
• The leading strand is synthesized continuously, while the lagging strand is synthesized discontinuously in segments.
• Okazaki fragments are subsequently joined by DNA ligase.

DNA Repair

• DNA polymerase is crucial for accurately copying DNA.
• It also performs proofreading to correct any errors during replication.
• The cell has multiple enzymes to repair any damaged sections of DNA.
• Examples of this include nucleotide excision repair to remove damaged sections of DNA.

DNA Summary

• DNA contains the genetic information for an organism necessary to construct proteins.
• DNA is structured as a double helix with a specific nucleotide sequence.
• Replication leads to identical copies of DNA.
• DNA damage, and repair mechanisms are crucial for proper cell function in living organisms.

Mitochondrial DNA

• Mitochondrial DNA (mtDNA) is a small amount of DNA that is found in mitochondria.
• It encodes necessary proteins in the respiratory chain (37 genes in total).
• Unlike nuclear DNA, mtDNA is inherited solely from the mother.

RNA

• RNA is a nucleic acid often found as a single strand, and can form secondary structure patterns..
• It plays a critical role in gene expression: DNA-mRNA-protein.
• Different types of RNA exist: tRNA, mRNA, and rRNA.
• mRNA carries the genetic code from DNA to the ribosomes, where it directs protein synthesis.

RNA Processing

• Primary RNA transcripts in eukaryotes are extensively modified (or processed) before leaving the nucleus.
• These modifications include capping the 5' end, adding a poly-A tail to the 3' end and splicing to remove noncoding regions (introns).
• Modifying pre-mRNA to mRNA allows for the protection of the mRNA from degradation.

RNA Splicing

• The RNA splicing process removes noncoding introns from the pre-mRNA molecule.
• Splicing leaves only the coding exons to be translated into proteins.
• The process ensures accuracy and efficiency of gene expression and protein processing.

Translation

• Translation is the process of converting the mRNA sequence into a polypeptide chain.
• It is carried out by ribosomes in the cytoplasm.
• mRNA codons are recognized by tRNA anticodons during translation.
• Amino acids are added one at a time, according to the order specified by mRNA.

tRNA Structure

• tRNA molecules have a specific three-dimensional structure that includes features like anticodons for base matching and an amino acid binding site.
• tRNA molecules transfer the correct amino acids to the ribosomes for assembly into polypeptide chains.
• tRNA has an anticodon to recognize each mRNA codon.

Aminoacyl-tRNA Synthetase

• Aminoacyl-tRNA synthetases are enzymes that attach the correct amino acid to the matching tRNA molecule, creating activated amino acids.

Ribosomes

• Ribosomes are complex molecular machines responsible for protein synthesis, facilitating translation of mRNA.
• The ribosome is composed of rRNA and protein components and has different binding sites for tRNA and mRNA to catalyze polypeptide synthesis.

Translation: Initiation

• Initiation involves the binding of mRNA and the initiator tRNA (carrying methionine) to the small ribosomal subunit, assisted by initiation factors and energy from GTP.

Translation: Elongation

• Elongation proceeds in phases, with amino acids added to the growing polypeptide chain. Each phase involves codon recognition, peptide bond formation, and translocation.
• The ribosome moves along the mRNA in the 5'→3' direction, adding amino acids progressively.

Translation: Termination

• Translation ends when a stop codon in mRNA reaches the A site on the ribosome.
• Release factors bind, causing the polypeptide chain to detach from the ribosome, and the ribosomal subunits to disengage.

Microscopic Analysis of Transcription

• A single ribosome can create multiple copies (polypeptide chains) of a protein in a short time.
• Multiple ribosomes attached to the same mRNA molecule are called polyribosomes, allowing for efficient protein synthesis.

The Genetic Code

• mRNA sequences are translated into amino acid sequences using the genetic code.
• The code is a set of instructions relating 3-nucleotide mRNA codons (triplets) to specific amino acids.
• There are 64 (4x4x4) possible codons; however, 61 specify amino acids. the three remaining are stop codons that signal termination of the protein chain.

Post-translational Modifications

• Proteins produced by ribosomes are usually further modified after translation.
• These modifications (e.g., addition of sugars, lipids, or removal of amino acids) often affect protein function and targeting

Mutations

• Changes in DNA sequences can lead to mutations.
• Mutations can be silent (no change), missense (changes amino acid), or nonsense (introduces premature stop codon.)
• Mutations can alter protein structure and function, potentially leading to diseases.

Protein Structure

• Proteins are complex molecules composed of amino acids linked together by peptide bonds.
• Proteins fold into specific 3-dimensional shapes due to specific interactions between amino acids.
• Understanding protein structure is essential for understanding their function.

Methods of Analyzing Protein Structure

• X-ray crystallography, NMR, and cryo-electron microscopy can be used to investigate the structure of proteins.

Protein Folding

• Proteins fold into regular secondary structures (e.g., a-helices, B-sheets) and irregular tertiary configurations.
• Stabilized by various non-covalent interactions, including H bonds, ionic bonds, and hydrophobic interactions.
• Protein domains, defined by specific folds and functions, are crucial for protein structure and evolution.
• Chaperone proteins assist in the proper folding of some proteins.

Protein Binding

• Proteins bind to other molecules based on the precise, weak interactions between amino acid sidechains and the target molecule.
• These precise interactions between molecules are needed for proper functioning of biological complexes.
• Strength and specificity of bonds is important for proper and successful molecular interactions.

Protein Function Summary

• Enzymes speed up chemical reactions by binding substrates and lowering activation energy.
• Antibodies recognize and bind specific foreign molecules (antigens).
• Globins transport substances such as oxygen.
• Membrane proteins regulate and facilitate transport and signaling across cell membranes.
• Fibrous proteins, such as collagen, provide structural support.