Biology Notes: Enzymes, Membranes, and Macromolecules Overview

Biology Notes

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Enzymes

Enzyme-Substrate Interaction

graph TD;
    Enzyme -->|Active Site| Substrate
    Substrate -->|Binding| Enzyme
    Enzyme --> Product
    Product -->|Release| Enzyme
  • Key Points:
    • Enzymes have specific active sites where substrates bind.
    • The substrate binds to the enzyme’s active site, forming an enzyme-substrate complex, leading to product formation.
    • Enzymes are released unchanged and can be reused.

Denaturation

  • Effect: Alteration in an enzyme's shape, preventing function.
  • Causes:
    • High Temperature: Can cause proteins to unfold.
    • High or Low pH: Alters charge and shape of the enzyme.

Cell Membrane

Phospholipid Bilayer

  • Structure:

    • Hydrophilic (water-attracting) head.
    • Hydrophobic (water-repelling) tail.

  • Fluid Mosaic Model:

    • Describes the cell membrane as a dynamic structure with various proteins embedded within or on the surface.

  • Functions:

    • Barrier: Maintains internal environment by regulating what enters and exits the cell.
    • Cholesterol: Maintains membrane fluidity by preventing fatty acids from packing tightly.

Transport Mechanisms

  • Passive Transport:

    • No energy required.
    • Types:
      • Simple Diffusion: Movement through the bilayer (e.g., gases).
      • Facilitated Diffusion: Movement through proteins (e.g., glucose).

  • Active Transport:

    • Energy required (often ATP).
    • Moves substances against concentration gradient.

  • Membrane Proteins:

    • Peripheral Proteins: On the surface, often involved in signal transduction.
    • Integral Proteins: Embedded within, often transporters or channels.
    • Glycoproteins: Involved in signaling and recognition.

Homeostasis

  • The cell membrane plays a crucial role in maintaining equilibrium, regulating interactions and internal processes.

Summary

Understanding the structure and function of enzymes and cell membranes is crucial for exploring cellular processes. Enzyme activity can be affected by environmental factors, and the cell membrane’s dynamic nature allows it to engage actively with the environment to facilitate transport and communication.

Extended readings:

open.oregonstate.education
3.1 The Cell Membrane – Anatomy & Physiology
www.khanacademy.org
Structure of the plasma membrane (article) | Khan Academy
openstax.org
Ch. 5 Chapter Summary - Biology 2e | OpenStax

Cellular Membranes and Movement

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Dynamic Nature of Phospholipid Bilayer

  • Bilayer Fluidity:

    • The phospholipid bilayer is constantly moving, increasing its permeability.
    • Insights: This movement allows small molecules to pass through more easily and affects how substances are transported across the membrane.

  • Bilayer Rejects Larger Particles:

    • Large particles and charged polar particles are typically not permitted through the bilayer.
    • Additional Info: Molecules like ions and large macromolecules require specific transport proteins to cross.

Passage of Molecules

  • Small Molecules:
    • Can pass through semi-permeable membranes but may require assistance.
    • Proteins: Transport (integral) proteins facilitate this process.
  • Types of Transport:
    • Molecules that cannot pass freely might interact with transport proteins which either provide a channel or actively transport substances using energy (active transport).

Cellular Movement

  • Cell Membrane:

    • Described as semi-permeable, controlling the ingress and egress of substances.

  • Diffusion:

    • Movement of molecules from an area of higher concentration to an area of lower concentration until equilibrium is reached.

  • Types of Solutions:

    • Hypertonic: Contains more dissolved particles compared to another solution.
      • Effect on Cells: Water flows out, causing cells to shrink.
    • Hypotonic: Contains fewer dissolved particles than another solution.
      • Effect on Cells: Water flows in, causing cells to swell or burst.
    • Isotonic: Has an equal number of dissolved particles as another solution.
      • Effect on Cells: Cells maintain normal shape and size.

  • Osmosis:

    • Diffusion of water across a semi-permeable membrane driven by concentration differences.

Diagrams

Osmosis Conditions

graph LR
A(H2O) --> B[Hypotonic Solution] --> C(H2O Flow In)
A(H2O) --> D[Isotonic Solution] --> E(No Net Flow)
A(H2O) --> F[Hypertonic Solution] --> G(H2O Flow Out)
Insights:
  • Plant Cells: Plant cells maintain their rigidity in hypotonic solutions because their cell walls prevent bursting by exerting a counter pressure called turgor pressure.

Containers Representing Different Solution Concentrations

graph TB
    A(Salt Water) -->|Hypotonic| B(Water In)
    C(Water) -->|Isotonic| D(No Net Flow)
    E(Sugar Water) -->|Hypertonic| F(Water Out)

These notes provide a structured overview of the dynamic properties of cellular membranes, the processes involved in cellular transport, and the effects of different osmotic conditions on cells.

Extended readings:

open.oregonstate.education
3.1 The Cell Membrane – Anatomy & Physiology
www.southernbiological.com
Osmosis and Diffusion - Southern Biological
www.labxchange.org
Transport across the Plasma Membrane: Passive ... - LabXchange

Biology Notes: Proteins and Enzymes

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Proteins

Monomers

  • Amino Acid: Humans make 11 out of 20.
    • Building blocks of proteins.
    • Each amino acid has a unique side chain that influences its properties.

Polymer

  • Peptide: Chains of amino acids.
    • Polymeric structure formed when amino acids are linked by peptide bonds.

Elements

  • Composed of Carbon, Hydrogen, Oxygen, and Nitrogen (sometimes Sulfur and Phosphorus).

Structure

  • Amino Group: H-N-H
  • Carboxyl Group: C=O, -OH
  • Side Chain (R Group) : Determines the properties and function differentiating the 20 amino acids.

Functions

  1. Structure: Forms the structure of muscle cells, as in collagen.
  2. Transport: Carries oxygen to cells via hemoglobin.
  3. Immune Defense: Functions as antibodies.
  4. Enzymes: Facilitate biological reactions by lowering activation energy.
  5. Cell Signaling: Present on cell surfaces for cell recognition and signaling.
  6. Hormones: Regulate body processes.

Levels of Protein Structure

  1. Primary: Sequence of amino acids.
    • Determines the basic properties and function of the protein.
  2. Secondary: Hydrogen bonds forming alpha helices and beta-pleated sheets.
  3. Tertiary: 3D folding pattern due to side chain interactions.
    • Polar and Non-polar: Hydrophobic and hydrophilic interactions.
    • Ionic Bonds: Ions attract each other.
  4. Quaternary: Multiple polypeptide chains interact.
    • Essential for proteins like hemoglobin.

Enzymes

  • Function: Speed up chemical reactions by creating an optimal environment.
  • Specificity: Enzyme shape fits substrates perfectly, often described by the "lock and key" model.
  • Active Site: Region on the enzyme where substrate molecules bind.

Characteristics

  • Catalysts: Lower the activation energy required for chemical reactions.
  • Shape Change: Can change shape slightly to better fit the substrate (induced fit).
  • Heat Sensitivity: Most effective at specific temperatures and may denature if too hot.

Structure

  • Amino Acid Sequence: Determines enzyme shape and functionality.
  • Functional Importance: Affected by primary, secondary, tertiary, and quaternary structures.

Understanding these fundamental concepts in proteins and enzymes is essential for grasping higher complexity processes in biology.

Extended readings:

www.ncbi.nlm.nih.gov
Biochemistry, Proteins Enzymes - StatPearls - NCBI Bookshelf
bio.libretexts.org
2.3: Structure & Function- Proteins I - Biology LibreTexts
www.ncbi.nlm.nih.gov
Physiology, Proteins - StatPearls - NCBI Bookshelf

Test 3 Review: Macromolecules

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Carbohydrates

  • Elements: Carbon, Hydrogen, Oxygen (Ratio 1:2:1)

    • Insight: Carbohydrates are composed mainly of carbon, hydrogen, and oxygen, typically in a 1:2:1 ratio. This is crucial for recognizing carbohydrates.

  • Monomer: Monosaccharide (e.g., glucose)

    • Insight: Monosaccharides are the simplest form of carbohydrates and serve as the building blocks for more complex carbohydrates.

  • Polymer: Polysaccharide

    • Insight: Polysaccharides are long chains of monosaccharides. Examples include cellulose, starch, and glycogen.

  • Functions:

    • Energy Source (Short Term):

      • Examples: Glucose, glycogen, starch
      • Insight: Carbohydrates are vital for providing short-term energy through glucose that can be rapidly metabolized.

    • Structure in Cells:

      • Example: Cellulose
      • Insight: Cellulose provides structural support to plant cell walls.

    • Cell Recognition:

      • Insight: Involved in cell-to-cell communication processes, important for immune responses.

Lipids

  • Elements: Carbon, Hydrogen (a bit of Oxygen)

    • Insight: Lipids have a high carbon and hydrogen presence, making them hydrophobic or water-repellent.

  • Monomer: Hydrocarbon chains (Fatty Acids)

    • Insight: Fatty acids are essential components of various types of lipids.

  • Polymer: Fatty Acids

    • Insight: Fatty acids combine in different ways to form various lipid structures.

  • Functions:

    • Long-Term Energy:

      • Example: Triglycerides with long hydrocarbon chains
      • Insight: They store more energy than carbohydrates due to more numerous C-H bonds.

    • Membrane Structure:

      • Example: Lipid bilayers (Phospholipids)
      • Insight: Form the basic structure of cell membranes.

    • Insulation:

      • Example: Triglycerides
      • Insight: Provide thermal insulation and protect organs.

    • Chemical Messengers:

      • Insight: Involve hormones and signaling molecules.

  • Types:

    1. Triglyceride: Three fatty acids + glycerol (Hydrophobic)

      • Insight: Major form of stored energy in animals.

    2. Phospholipids: Hydrophilic head + two hydrophobic fatty acid tails

      • Insight: Crucial for cell membrane formation due to amphipathic nature.

    3. Steroids:

      • Structure: Four fused carbon rings
      • Example: Cholesterol
      • Insight: Serve as precursors for hormones and are involved in signaling.

Understanding these macromolecules is essential for grasping key biological processes and their implications on cellular function and communication.

Extended readings:

opentextbc.ca
2.3 Biological Molecules – Concepts of Biology – 1st Canadian Edition
openstax.org
2.3 Biological Molecules - Concepts of Biology | OpenStax
wou.edu
CH103 - Chapter 8: The Major Macromolecules - Chemistry

Biology Vocabulary Notes

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Activation Energy

  • Definition: The minimum amount of energy needed for atoms to undergo a chemical reaction.
  • Insight: Activation energy is like the initial push needed to start a reaction. Think of it as the energy barrier that reactants must overcome to convert into products.
  • Additional Information: Catalysts, like enzymes, lower the activation energy, speeding up reactions without being consumed.

Competitive Inhibitor

  • Definition: A substance that can bind with an enzyme by a molecule with a similar structure, blocking the active site.
  • Insight: Competitive inhibitors "compete" with the substrate for the active site of the enzyme, preventing the substrate from binding.
  • Additional Information: These inhibitors don't permanently alter the enzyme and can often be overcome by increasing substrate concentration.

Aquaporin

  • Definition: A transport protein that only deals with water.
  • Insight: Aquaporins facilitate the rapid movement of water across cell membranes, essential for maintaining cell turgor and homeostasis.
  • Additional Information: They are crucial in organs like the kidneys for water reabsorption.

Noncompetitive Inhibitor

  • Definition: A molecule that binds to a part of an enzyme that is not the active site, altering enzyme activity.
  • Insight: Noncompetitive inhibitors reduce enzyme activity regardless of substrate concentration because they induce a structural change in the enzyme.
  • Additional Information: These inhibitors can act as a regulatory mechanism for metabolic pathways.

Concentration Gradient

  • Definition: The amount of substance in one area compared to the same substance in a different area.
  • Insight: Concentration gradients are essential for processes like diffusion, osmosis, and cell signaling.
  • Additional Information: Gradients can be used to perform work in biological systems, such as ATP synthesis in mitochondria.

Plasmolysis

  • Definition: When a plant cell shrinks as water moves out from the cell wall.
  • Insight: Plasmolysis occurs in hypertonic environments where water exits the plant cell, leading to wilting.
  • Additional Information: This process is the opposite of turgor pressure where water enters the cell, making it rigid.

Crenation

  • Definition: When an animal cell shrivels up.
  • Insight: Crenation happens when animal cells are placed in a hypertonic solution, causing them to lose water.
  • Additional Information: It's crucial to maintain isotonic environments in medical treatments to avoid cell damage due to crenation or lysis.

Extended readings:

pubmed.ncbi.nlm.nih.gov
The inner mitochondrial membrane has aquaporin-8 water channels ...
pubmed.ncbi.nlm.nih.gov
Aquaporins and glycerol metabolism - PubMed
www.frontiersin.org
Aquaporins in sepsis- an update - Frontiers