Organic Molecules & Cells

Organic Molecules

• Four major classes:

  • Sugars (polysaccharides)

  • Fats (lipids)

  • Proteins

  • Nucleic acids (genetic material)

• Large complex molecules (macromolecules) are made of smaller subunits.

  • Complex sugars: individual sugars (e.g., cellulose, glycogen, starch)

  • Fats and lipids: fatty acids

  • Proteins: amino acids

  • Nucleic acids (RNA and DNA): nucleotides

Cell Membrane

• Made of phospholipids.

• Also called plasma membranes or phospholipid bilayers.

• Phospholipid structure:

  • Phosphate head: hydrophilic (water-loving), interacts with water.

  • Two fatty acid tails: hydrophobic (water-fearing), hide from water.

• In water, phospholipids spontaneously form a bilayer with tails aggregating away from the water.

• Proteins often embedded in the membrane; regulate the flow of materials in and out of the cell.

Proteins

• Monomeric units: amino acids (20 different types).

• Intricate 3D shapes.

• Diverse functions critical for all cells.

• Functions:

  • Structural: collagen (skin), keratin (skin, hair).

  • Storage: albumin in egg white provides protein for embryo growth; casein in milk provides protein for infant growth.

  • Transport: controls flow of material or across cell membranes; hemoglobin carries oxygen in bloodstream.

  • Hormones: insulin.

  • Information flow: protein interactions cause movement of bacteria.

  • Contractile: actin and myosin in muscles slide to cause contraction or relaxation; cilia and flagella for movement.

  • Defense: antibodies.

  • Enzymes: catalyze chemical reactions.

Amino Acids

• Building blocks of proteins, used by all living cells (bacteria, plants, fungi, viruses).

• 20 different types, needed for growth.

• Humans make some, but others must be ingested.

• Amino acids are brought into the protein by tRNA; the process of making protein is called translation.

• Humans can make 10 amino acids; the other 10 must be eaten.

• Common structure:

  • Central carbon attached to:

    • Amine group (amino term).

    • Carboxylic acid (carboxyl group).

    • R group (varies among the 20 amino acids).

• Amine groups always get added to the carboxyl groups. The bond that we'll get to in a little bit is called a peptide bond.

R Groups

• Different sizes and properties.

• Determine the complex 3D structures of proteins.

• Hydrophobic R groups aggregate in the center of the protein.

• Hydrophilic R groups are on the outer surface, exposed to water.

• Charges: positive and negative charges attract; like charges repel.

• Acidic or basic properties.

• How R groups interact with each other determines the shape of a protein.

Peptide Bonds and Polypeptides

• Chemical bond between amino acids; proteins referred to as polypeptides.

• Carboxyl group binds to the amino group to form the peptide bond.

• Proteins vary in size (50 to 1000+ amino acids; average 100-200).

• Proteins have directionality: amino terminus (amino end) and carboxyl terminus (carboxyl end).

Protein Structure

• Four categories:

  • Primary: sequence of amino acids.

  • Secondary: alpha helix and beta pleated sheet shapes.

  • Tertiary: 3D shape from motifs coming together.

  • Quaternary: multiple proteins coming together.

Primary Structure

• Sequence of amino acids linked by peptide bonds.

• Forms a linear sequence.

• Has directionality: amino terminus and carboxy terminus.

Secondary Structure

• Two common shapes (motifs):

  • Alpha helix: helix-like structure.

  • Beta pleated sheet: folded sheet structure.

Tertiary Structure

• Complex 3D shape with sheets and helices.

• R groups interact to form the shape.

  • Hydrophobic groups inside.

  • Hydrophilic groups outside.

  • Ionic bonds can form between positive and negatively charged groups.

Quaternary Structure

• Multiple proteins (subunits) come together.

• May require cofactors (iron, magnesium), vitamins.

• Example: Hemoglobin requires four proteins and a heme group with iron.

Protein Folding and Denaturation

• Proteins have complex 3D shapes determined by R groups.

• Chaperonins help proteins fold correctly.

• Unfolded protein: scrambled, denatured.

• Properly folded protein: functional.

• Denaturation: unfolding of a protein.

• Causes of denaturation:

  • Heat: disrupts protein structure; example: cooking egg white (albumin).

  • pH: acidic (lots of positive charges) or basic (lots of negative charges) environments disrupt charge interactions; proteins prefer neutral pH; exceptions: proteins can evolve to function in their enviornments such as stomach proteins in acidic environments.

Proteins and Disease

• Example: Hemoglobin carries oxygen; requires heme group and iron.

• Sickle cell anemia: genetic defect in hemoglobin gene; a single amino acid change causes misshapen red blood cells.

Enzymes

• They catalyze chemical reactions (reduce the amount of energy that's required).

• Most enzymes are proteins; some exceptions.

• Catalysis: accelerate chemical reactions.

• Terminology trick: -ase at the end of a word indicates an enzyme (e.g., lipase, peptidase, cellulase, peroxidase).

• Molecules that enzymes act on are called substrates.

Substrate Binding

• Enzymes have intricate 3D shapes with a substrate binding site (active site).

• The binding site grabs and applies force to the substrate (lock and key model).

Enzyme Action

• Enzyme binds to the substrate (e.g., sucrose) at the active site.

• Enzymes are recyclable, and enzyme can bind again, and can theoretically complete an infinitesimal number of chemical reactions if not broken down.

• For example, sucrase breaks sucrose into two simple sugars

• They are recyclable molecules (they are not consumed in the process)

• Allow for chemical reactions to occur faster and at a lower energy.

Enzyme Regulation

• Most enzymes are regulated; they're not constantly performing chemistry; some are inhibited or turned off

• Factors affecting enzyme activity:

  • Temperature (optimal).

  • pH (optimal).

  • Salts in enzyme activity can also be impacted

  • Other substances.

  • Mechanisms:

    • Competitive inhibition: another molecule blocks the active site.

    • Noncompetitive inhibition: a molecule binds away from the active site, alters the shape of the active site.

Enzyme Inhibition

• Competitive: inhibitor blocks the substrate binding site.

• Noncompetitive: inhibitor binds elsewhere, changes the shape of the active site.

Enzyme Inhibitors as Drugs

• Enzymes are often targets for drug development; drugs can target that additional pocket, and they can change how the substrate comes to bind.

• Example: AZT treats viral infections by acting as a substrate analog.

• Reversible or irreversible.

Enzyme Cofactors

• Many enzymes require additional factors such as vitamins or trace elements (minerals) to function properly.

• Vitamins and minerals are commonly required for specific enzymes.

Commercial Enzyme Application

• Present in commercial products, such as detergents and food supplements, and enzyme food supplements.

Proteins and Enzymes - Final Points

• Amino acid sequence and R groups determine 3D shape and function.

• A protein typically has one function (e.g., catalyzes one reaction).

• DNA encodes the amino acid sequence.

• Aromatic groups or bigger groups

  • Lysine just has a single hydrogen

  • There's a couple of amino acids that have sulfur

    • Cysteine has a sulfur

    • Methionine, if I can find it, also has a sulfur

      • They're required for enzyme function

      • Cofacial can require addicional proteins, additional polypeptides, and some require cofactors

Enzyme Terminology

• Apoenzyme: the protein component of an enzyme.

• Catalytic site: the active site of catalysis.

• Cofactors: additional proteins, polypeptides, vitamins, heme, or minerals (iron, magnesium, copper).

• Holoenzyme: enzyme is completely in its final functional state.

Nucleic Acids

• Two major groups: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).

• DNA: genetic material.

• RNA: intermediate between DNA and protein.

• Polymers made of monomers called nucleotides.

Nucleotides Structure

• Three parts:

  • Five-carbon ribose sugar: ribose in RNA; slightly modified ribose (missing oxygen) in DNA.

  • Phosphate group.

  • Nitrogenous base (varies).

Nitrogenous Base

• Two types:
  *Purine bases
  \text{purines have two bases or two two circular structures, I should say, within their base}

• A's and G's are purines.
  *Pyrimidine bases
  \text{pyrimidines have a signal ring}

RNA vs DNA

• Slight sugar difference

• RNA in which you have the u nucleotide instead of t nucleotide in DNA,
  Anytime the DNA is copied into RNA, DNA ultimate kind gets copied into RNA you can find this and the same DNA just get a little slightly different is a Cg and then you have there one nucleotide is really much the same

Pyrimidines and Pyrimidines.

• Pyrimidines are one of the ring in there structures. They use you, you, use all have a in their of a different pyramidians.

• Purines have a have Double ring structure is that and you have what you find in pyramidians. So there is always learn, and you to pure as. Gold. So to you have to just always that in this is going to be this the always pair. With this you, I do get. This out.

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Phosphodiester Bonds

• A specific type of bond between nucleic acids
  *Forms Between adjacent sugars and repeating unit and Bases are gonna protrude away from the sugar phosphates network. Well now and are made you get the bond from it five prime phosphate and three in hydroxyl. Right now just I think you know, we're it's in the and the base are gonna extend away from that sugar phosphate backbone now RNA typically exists in that single stranded form that I just described to you now, that is a single stranded form now a a little bit different. DNA forms a structure. Call the DNA. Double helix. And bases are gonna form kind or between the two extended polymers easier to to see a bigger but.

Base Pairs

• In DNA if we an A' it will always have a P to for season. One strength, it will always be with see in you you you the same thing goes for, you know, same with and you should

Weak Hydrogen Bonds

• Sugars the sugar phosphate backbone. Hey, you have strong Co bonds not easy to break can you have some weak between the bases. you those are high hydrogen bones and. hese are failly. This is to to
  later is the point I'm trying get here is all energy that to make all that that to hold to also

Discovery of the Cell

• Microscopy was the technological breakthrough at the time, which took place during Early seventeen and sixteen hundred.

• Hook was one of the first people to identify the structures that we're gonna call cells.

Cells Aren't Static, Cells are Not Simply

• You can take thin sections of a plant leaf. If you put it under light, can actually see movements. so cells are moving

cell theory

• The cell theory is the idea that all cells must come from preexisting cells. Okay. So. And all living things are composed of cells. So. And the sell came with all
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Cell Discovery Timeline

• Late sixteen hundreds, Early '17 hundreds, people started to describe these cell structures that were developing and moving the original microscopes. Cell theory is the eighteen hundreds, scientific or cellular structures. Alright. So the original microscopes, we're gonna talk a little bit about some advancements in

Compound Light Microscope

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Micrometer Measures and Resolution

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Stains

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Electron Microscope

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Cell Biology

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Prokayotic Cells

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