BIO452 Exam 1 Study Guide

Information Storage and Transmission in Cells

1. Understand how the information needed to make cells is stored and passed on to new cells

   • Information is primarily stored in DNA and is transferred during cell division and replication.

Central Dogma Framework

2. Outline the steps of the Central Dogma and what major enzymes are involved

   • Steps:

     • DNA → RNA (Transcription): Major enzyme involved is RNA polymerase.

     • RNA → Protein (Translation): Major enzyme involved is the Ribosome.

     • DNA → DNA (Replication): Major enzyme involved is DNA polymerase.

Protein Chemistry

3. Differentiate between the groups of similar amino acids

   • Amino acids are categorized by properties such as polarity, charge, and size (e.g., hydrophobic versus hydrophilic groups).

4. Recognize the four levels of protein structure in 3D models of proteins

   • Levels:

     • Primary: This refers to the linear sequence of amino acids.

     • Secondary: This involves structures like alpha helices and beta sheets.

     • Tertiary: This describes the 3D shape of a single polypeptide chain.

     • Quaternary: This is the assembly of multiple polypeptide chains.

5. Define a protein "domain"

   • A protein "domain" is a distinct functional and structural unit within a protein, often capable of folding independently.

6. Explain why proteins fold into particular structures

   • Protein folding is driven by interactions between amino acids, which can form various covalent and noncovalent bonds (e.g., hydrogen bonds, ionic bonds, hydrophobic interactions).

Chemical Interactions

7. Compare and contrast the covalent and noncovalent bonds that hold biological molecules together

   • Covalent bonds are strong bonds formed by the sharing of electrons.

   • Noncovalent bonds are weaker interactions (e.g., hydrogen bonds, ionic bonds, Van der Waals forces) that facilitate binding and functional specificity.

8. Define affinity, and its relation to binding constants/dissociation constants

   • Affinity measures how tightly a ligand binds to a protein; it is characterized by the dissociation constant ($K<em>d$). A low $K</em>d$ indicates high affinity.

9. Explain the relationship between Gibbs free energy and reaction equilibrium

   • Gibbs free energy ($\Delta G$) is the energy available to do work. Negative $\Delta G$ values indicate spontaneous reactions that favor products at equilibrium.

10. Define cooperative binding, and distinguish cooperative and noncooperative binding curve graphs

    • Cooperative binding occurs when the binding of one molecule influences the binding of subsequent molecules, typically displayed as a sigmoidal curve. Noncooperative binding often shows a hyperbolic curve.

11. Describe how enzymes lower activation energy at the molecular level

    • Enzymes function by stabilizing transition states and lowering the activation energy required for reactions, thereby increasing reaction rates.

Protein Functions and Interactions

12. Understand that all proteins bind to other molecules

    • Protein interactions with ligands, substrates, or other proteins are crucial for their biological function.

13. Recognize the importance of protein phosphorylation in regulation

    • Phosphorylation alters protein conformation and function, often serving as a reversible modification that regulates enzymatic activity and cellular signaling pathways.

14. Contrast biomolecular condensates with proteins in solution

    • Biomolecular condensates are dense, phase-separated structures often involved in cellular organization and function, which differ from dilute protein solutions.

Proteins in Gene Regulation

15. Recognize that transcriptional regulators have shared protein domains which bind specific sequences of DNA

    • Common domains, such as zinc fingers and leucine zippers, facilitate sequence-specific DNA binding by transcriptional regulators.

16. Explain how regulator dimerization enhances DNA specificity and affinity

    • Dimerization can increase both the binding affinity and specificity of regulators by effectively decreasing the number of target sites the dimer can bind.

17. Differentiate between activators, repressors, co-activators, and co-repressors

    • Activators stimulate transcription, repressors inhibit transcription, co-activators assist activators, and co-repressors assist repressors.

Protein Analysis Techniques

18. Understand the principle and use case of western blots, and interpret western blot images

    • Western blotting detects specific proteins. It involves gel electrophoresis followed by transfer to a membrane and probing with antibodies to identify target proteins.

19. Understand the principle and use case of proteomics

    • Proteomics analyzes the quantity and structure of proteins in a system, which is useful for identifying protein interactions and modifications.

20. List the three main methods for protein structure determination

    • The three main methods are X-ray crystallography, NMR spectroscopy, and cryo-electron microscopy (Cryo-EM).

21. Explain how enzyme activity is determined

    • Enzyme activity is assessed through kinetic studies, often measured by substrate conversion rates under defined conditions.

Studying Transmembrane Proteins

22. Explain how to study transmembrane proteins

    • Investigative techniques include solubilization in detergents, reconstitution into lipid bilayers, or using cellular models that express the proteins of interest.

Intracellular Complexity

23. Explain how cryo-electron tomography helps us understand the inside of cells

    • Cryo-electron tomography provides 3D imagery of cellular structures by imaging frozen cells at various angles, revealing their intricate structural complexity.

Cytoskeletal Components

24. Differentiate between actin filaments, microtubules, and intermediate filaments

    • Actin filaments: These are thin filaments involved in cell movement and changes in cell shape.

    • Microtubules: Composed of tubulin, they are involved in intracellular transport and mitosis.

    • Intermediate filaments: These provide structural support to cells, particularly in resistance to mechanical stress.

25. Describe how each filament assembles and disassembles

    • Actin: Assembles dynamically with ATP; typically grows at the plus end.

    • Microtubules: Assembled from GTP-tubulin dimers; undergo dynamic instability through GTP hydrolysis.

    • Intermediate filaments: Assembled from various protein subunits, generally more stable and less dynamic than actin or microtubules.

26. List at least one major process that each filament is involved in

    • Actin: Involved in muscle contraction.

    • Microtubules: Involved in chromosome separation during cell division.

    • Intermediate filaments: Contribute to nuclear integrity.

27. Describe how vesicles fuse with target membranes

    • Vesicle fusion involves SNARE proteins (T-SNAREs on target membranes and V-SNAREs on vesicles) that facilitate membrane merging through conformational changes.

28. Appreciate the complexity of eukaryotic gene regulation

    • Eukaryotic gene regulation is highly multifaceted, integrating signals from various pathways with spatial and temporal controls over transcription.

29. Predict how nucleosome occupancy will affect regulator binding and transcription

    • High nucleosome occupancy may hinder transcription factor access to DNA, while reduced occupancy can facilitate binding and transcriptional activation.

Isolation and Analysis of Proteins

30. Understand the principle and use case of immunohistochemistry

    • Immunohistochemistry is a technique used to visualize the localization of proteins in cells or tissues using specific antibodies and imaging techniques.

31. Understand the principle and use case of affinity purification

    • Affinity purification is a method to isolate specific proteins from complex mixtures based on targeted interactions with binding partners (e.g., antibodies).

32. Explain how protein binding is determined

    • Protein interactions are assessed through techniques such as surface plasmon resonance, electrophoretic mobility shift assays (EMSA), or co-immunoprecipitation.

Intracellular Organization

33. List and describe the major organelles common to all eukaryotic cells

    • Nucleus: Contains and protects the cell's genetic material.

    • Mitochondria: Primarily responsible for energy production through cellular respiration.

    • Endoplasmic reticulum (ER): Involved in protein and lipid synthesis.

    • Golgi apparatus: Modifies, sorts, and packages proteins and lipids for secretion or delivery to other organelles.

    • Lysosomes: Contain enzymes for digestion and waste processing.

Cytoskeletal Dynamics

34. Describe a mechanism to establish cell polarity

    • Intracellular signaling pathways and cytoskeletal organization determine cell orientation and polarity, which is critical for tissue development and function.

Intracellular Transport Basics

35. Describe how proteins end up in the endoplasmic reticulum

    • Proteins are directed to the ER via signal sequences that are recognized by signal recognition particles during translation.

36. Recognize that the signal hypothesis applies to mitochondria as well

    • Mitochondrial precursor proteins possess signal sequences that guide their import into mitochondria post-translationally.

37. Describe how molecules get in and out of the nucleus

    • Molecules cross the nuclear envelope via nuclear pore complexes that selectively permit entry and exit based on size and binding to nuclear transport receptors.

38. Describe how vesicles are transported throughout the cell

    • Vesicle transport utilizes motor proteins, such as kinesin and dynein, which move vesicles along microtubules within the cell's cytoskeleton.

39. Detail the conformational changes in kinesin motor activity

    • Kinesin undergoes conformational shifts during ATP hydrolysis, resulting in coordinated leg movements that propel it along the microtubule tracks.

Intracellular Transport: Vesicles

40. Describe how clathrin-coated vesicles are created

    • Clathrin assembles into a basket-like structure on the cytosolic side of the membrane, initiating invagination and vesicle formation through interaction with adaptor proteins and cargo molecules.