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• Study notes based on the provided study guide content.

Experimental Model Systems

• A unicellular simple Eukaryote (yeast) are good model organisms
• Model systems can be manipulated and studied
• Worms, Fruit Flies, Mice, Yeast, are all good model systems
• Model systems are selected based on the desired observation, ranging from unicellular to multicellular organisms
• They are tools used for advancing information in molecular cell biology
• Organelles have a membrane and defined function within the cell
• Animal cells lack a cell wall
• Cells differentiate into various structures like neurons
• Mitochondria feature an outer and inner phospholipid bilayer, containing two bilayers which is not common
• Chloroplasts have an outer phospholipid layer, an inner membrane, and thylakoid discs
• Endosymbiotic theory explains the development of relationships between cells

Biologically Relevant Non-Covalent Interactions:

• Covalent bonds form when atoms share outer-shell electrons
• Non-covalent bonds facilitate most processes inside a cell through interactions with water

Types of Non-Covalent Bonds

• Hydrogren bonds are polarized, electronegativity causes the linkage by sandwiching a hydrogen atom between two electron-attracting atoms in a line
• Electrostatic interactions (ionic bonds) occur between fully charged groups and partially charged groups on polar molecules and diminish as distance increases
• Van der Waals (hydrophobic interactions) are nonpolar, lack charge, and involve insoluble molecules in water
• Water forces hydrophobic groups together to reduce disruption to the water network
• Hydrophilic molecules readily dissolve in water and include ions and polar molecules
• Electrical charge effects allow water molecules to surround ions or polar molecules, aiding in dissolution
• Individually weak non-covalent bonds are collectively strong
• Repulsion of hydrophobic groups from water aids in macromolecule folding
• Disruption occurs through heat, salts, pH, or mechanical force

From Precursor to Macromolecules

• Subunits become macromolecules via covalent bonds (condensation)
• Additional modification and folding occurs through non-covalent interactions

Four Macromolecules and Their Significance

Polysaccharides

• Sugars are a small organic building block
• Sugars form covalent bonds from monomer to polymer (polysaccharide)

Types of Sugars

• 3 carbon sugars (trioses) are good intermediates in energy generation
• 5 carbon sugars (pentoses) are sugar components of nucleotides
• 6 carbon sugars (hexoses) serve as the basic energy source in cells
• Glycogen is most common in humans, while starch is most common in plants
• Monosaccharides have the formula (CH2O)n, contain hydroxyl groups, and contain an aldehyde or ketone group
• Disaccharides form when a carbon with an aldehyde or ketone reacts with a hydroxyl group on a second sugar molecule
  • Maltose = glucose + glucose
  • Lactose = galactose + glucose
  • Sucrose = glucose + fructose
• Oligosaccharides are short chains of linear and branched molecules made from repeating sugar subunits
• Polysaccharides are long chain versions of oligosaccharides

Proteins

• Amino acids are small organic building blocks
• Amino acids form covalent linkages to create dipeptides, tripeptides, and polypeptides (proteins)
• Ionized entities and side groups called R-groups determine their nature

Nucleic Acids

• Nucleotides are small organic building blocks
• Nucleotides form covalent linkages to create dinucleotides, trinucleotides, to polynucleotides (nucleic acid)
• Consist of a nitrogen-containing base, 5-carbon sugar, 1-3 phosphate groups, and organic base (A,T,C,G)
• Bases are nitrogen-containing ring compounds
  • Pyrimidines (1 ring): Uracil, Cytosine, Thymine
  • Purines (2 rings): Adenine, Guanine
• Phosphates make nucleotides negatively charged
• Can exist as a mono, di, or triphosphate in free form
• ATP is adenine triphosphate
• Sugars differ in attachments, hydroxyl = ribose, hydrogen = deoxyribose
  • Hydroxyl (polar) is more reactive, making RNA more fluid than DNA
  • Hydroxyl at carbon number 3 is consumed during condensation
• Nucleic acid polymers form when nucleotides join by phosphodiester bonds between the 5' and 3' carbon atoms of adjacent sugar rings
• Phosphodiester Bond is a covalent bond between a phosphate group and a sugar molecule

Nucleotide Functions:

• Nucleoside di/triphosphates carry chemical energy in easily hydrolyzed phosphoanhydride bonds
• They combine with other groups to form coenzymes
• Used as small intracellular signaling molecules in the cell
• Condensation reaction or dehydration reaction create covalent linkages between two monomers by removing water
• Breaking down a polymer happens through hydrolysis (adding water)
• Cells hydrolyze to release energy and make new polymers

Fats and Membrane Lipids

• Fatty acids are small organic building blocks and are long chains of nonpolar entities
• They are hydrophobic and have a carboxyl end that forms condensation reactions and covalent linkages with glycerol
• Glycerol forms a triacylglycerol from 3 fatty acid chains through 3 condensation reactions. They act as long term storage for energy
• They do not like water so they will aggregate within the cell
• Major constituents of cell membranes including a carboxyl group at one end and a long hydrocarbon tail
• Cells store them as energy reserves through ester linkages to glycerol, which form triacylglycerols (triglycerides)
• Saturated fatty acids have no double bonds
• Unsaturated fatty acids have one or more double bonds in their hydrocarbon tail
• Micelles have polar heads and hydrophobic tails, so water cannot enter the center
• Liposomes are similar to micelles but larger, and have a round area of polar heads inside to allow water in
• Triclyglycerols are from large, spherical fat droplets in the cell cytoplasm
• Phospholipids and Glycolipids form self-sealing lipid bilayers, which are the basis for all cell membranes
• Other Lipids are water-insoluble but soluble in organic solvents
  • Steroids and polyisoprenoids are common lipids (both from isoprene units)

Energenetics

• Condensation is energetically unfavorable
• Hydrolysis or the break down of polymers is energetically favorable
• Molecules are most stable at their relative state of free energy
• Stable conformations are achieved by mostly non-covalent interactions, like micelles and liposomes
  • +G = Endergonic/anabolic reaction (not energetically favorable): Products have higher energy than reactants
  • -G = Exergonic/catabolic reaction: Products have lower energy than reactants
• Coupled reactions occur together • Reactions have a spontaneous direction • ATP coupling
• Endothermic/exothermic reactions can allow other reactions to become favorable
• Activated carrier molecules are byproducts of catabolic reactions that drive anabolic reactions

Steps:

1. Activation step - ATP transfers a phosphate to produce a high energy intermediate
2. Condensation step - The activated intermediate reacts with B-H to form the product A-B, a reaction accompanied by the release of inorganic phosphate.
   • Net Result: A-OH + B-H + ATP -> A-B + ADP (activated diphosphate) + P

• Endothermic is similar to endergonic but only applies to absorption of heat (needs an enzyme and ATP)
• Exergonic needs enzyme, but not ATP
• Endergonic needs enzyme and ATP
• Enzymes lower the activation energy -- They are needed in both catabolic and anabolic reactions -- Enzymes affect only the activation energy
  • Enzymes bind with their substrates in the activation site in order to lower the activation energy
  • Enzymes are not consumed in the reaction, they come in and bind and then leave and start again
  • Not all enzymes are proteins, but most are

Activation Energy

• Energy requirements needed to get the reaction to start
• Phospholipid bilayer core is hydrophobic

Groups of Amino Acids by their Nature

• Always looking for their relative state of free energy
• All 20 amino acids have a backbone, with an amino group and a carboxyl group, but have different R groups or sidechains
  • The R groups can be categorized as:
    • Acidic - Aspartic Acid, Glutamic Acid
    • Basic - Lysine, Arginine, Histidine
    • Uncharged Polar
    • NonPolar (Hydrophobic) - Look for evenly shared electrons in the R group

Special Amino Acids

• Cysteine has an SH in its R group, which can form covalent linkages/disulfide bonds with other Cysteine SH groups
• Proline's amine group is covalently bonded to its R group (Triangle looking R group)
• Glycine doesn't have an R group, only an H.
• • It is often found at the interface of proteins
• The other R groups can interact through NON COVALENT INTERACTIONS.

Proteins

• Primary, secondary, tertiary, and quaternary structures

Primary Structure

• Linear, covalently linked macromolecules of a single polypeptide chain that emerges from condensation reactions and is endothermic
• Secondary structure is formed through hydrogen bonding of the backbone, creating alpha-helical or beta-sheet motifs/shapes
• R groups are NOT involved
• It is local to the molecule
• Backbone interactions are removed; carboxyl and amino ends are the players here through H bonding - Alpha-helical: R groups positioned out and exposed while amino acids interact with neighboring amino acids; intramolecular H bonding - Beta-sheets: R groups positioned out and exposed while amino acids interact with neighboring amino acids; intermolecular H bonding
• Tertiary structure is maintained by interactions between the R groups
• The nature of the R groups is dependent on whether they are positive or negative -- Folding is stabilized by R group interactions (alpha and beta interactions) and 90% noncovalent interactions; R groups are the players here through the four noncovalent interactions within the single polypeptide chain - Cysteine can form covalent disulfide linkages between different groups, using the R group cysteines
• Quaternary structure is intermolecular, interacting between different polypeptide chains of R groups
  • Same type of groups as tertiary but form between DIFFERENT polypeptide chains
  • Noncovalent and/or sulfhydryl; each monomer forms a tertiary structure, then the monomers interact to form this structure
• All proteins reach tertiary structure, but not all reach quaternary
• Structures can go beyond quaternary to form large complexes

Stabilization

• Stabilized by other proteins/nonproteins or disulfide bonds
• Cholesterol stabilizes artificial cells
• Disulfide bonds aid in stabilization
• Quaternary/tertiary structures can be denatured by breaking all noncovalent interactions through salt, heat, mechanical interactions, pH, etc.
  • Disulfide bonds do not break this way (covalent)
• Proteins can theoretically re-nature if they did not need help folding

Other Key Points:

• Peptide chains always grow from the carboxyl end
• A polypeptide chain begins as a linear chain of amino acids
• Phosphorylation is adding a phosphate group (PO4³–) to a molecule, which commonly regulates cellular processes
• The molecule's activity, structure, or function is always altered -- Processes include activating/deactivating enzymes, regulating protein interactions, and controlling cellular processes
• Enzymes called kinases catalyze the transfer of a phosphate group from ATP to the target molecule
• Phosphatases remove phosphate groups, reversing the effects of phosphorylation
• Dephosphorylation removes a phosphate group (PO4³–) from a molecule, reversing phosphorylation and regulating cellular functions
• Enzymes called phosphatases catalyze dephosphorylation to inactivate enzymes, change protein-protein interactions, regulate signaling pathways, and control cellular processes
• Ubiquitylation - A process that attaches ubiquitin to proteins, which regulates many cellular functions.
• Methylation- A chemical process that adds methyl groups to molecules
  • This can be done with DNA, proteins and neurotransmitters
• Chaperones help other proteins fold, then they are removed
• ImmunoglobulinG - Antibodies, V-shaped structures with flexibility
• Hemoglobin - Oxygen carrier molecule in red blood cells, tetramer -- Once its tertiary structured it becomes a globular protein and keeps folding on itself like a ball
  • Proinsulin/insulin- Large version of insulin A version of insulin called proinsulin, which is made larger than its final product, helps with folding but cannot be re-natured
• Shape and surface nature of macromolecules determine their function -- Globular proteins -- Coil-coil proteins like collagen (glycine are prevalent here)
• Protein Domains
  • Protein domains are regions of a protein that form functional modules
    • Proteins can have multiple domains, and these can dictate function
    • Proteins with similar functions may share domains
    • Proteins with similar functions may share a domain which are called Kinases( add phosphates) - Role of enzymes vs ATP direction vs rate of reactions

Nucleic acids: structure and function

• Primary chain, which becomes double helix
• Complementarity results in base pairing (A,T,C,G)
• Specific orientation of the nucleic acid is indicated by the 5' end and which is determined which has a free phosphate group.
• Types of DNA sequences found in eukaryotes and their function
• Each DNA molecule that forms a linear chromosome contains a centromere, two telomeres, and multiple origins of replication

Introns/exons

• Intron: Non-coding segments that are removed during protein synthesis
• Exon: Segments with the information coding for a protein
• Regulatory Sequences
• Regions of a chromosome known as 'Centromeres' are a central point of attachment for a structure known as the 'kinetochore' and help properly allign
• The Kinetochore attaches to the spindle during cellular division
• Telomeres are protective caps - made of DNA and proteins and are found at each and all chromosome ends
• Origin of application - a sequence where replication begins
• mRNA vs functional /non coding
• mRNA - carries information to have proteins translated
• Functional RNA /Non Coding- it not directly coded for.
• Euchromatin will have a transcription that is easily marked. DNA is made more accessible this way.
• Histones are what tighten and condense the packaged DNA.
• DNA Loops- Allows proteins to bind to 2 different sites. Occurs in cytoplasm or nucleus.
• • Condensed/Compacted State of DNA, Histones, methylation and acetylation all relate to significance.
• Making of histones and their significance.
  • Condensed State of DNA and transciption; Relationship
• IN DNA replication - loops can form.
• The Story of DNA Replicaiton
• The Story of Chromatin COmpaction
• The story: We go from amino acis to building the functions -Polypeptide chain begins as a chain which is 2D linear amino acids -Techniques and Tecnical Concepts and Tools The tools and concepts nder the topics of Subcellula Factionation and Metabolic Labellin, Fluorescence tags.