Protein Structure and Organization
50 Questions
0 Views

Choose a study mode

Play Quiz
Study Flashcards
Spaced Repetition
Chat to lesson

Podcast

Play an AI-generated podcast conversation about this lesson

Questions and Answers

What is the term for the portion of each amino acid that gives it its unique properties?

  • R group (correct)
  • Polypeptide backbone
  • Side chain
  • Peptide bond

    • What type of bonds are mainly responsible for the secondary structure of proteins?

  • Disulfide bonds
  • Van der Waals forces
  • Hydrogen bonds (correct)
  • Ionic bonds

    • What is the term for the specific sequence of amino acids in a protein?

  • Tertiary structure
  • Quaternary structure
  • Secondary structure
  • Primary structure (correct)

    • What is the name of the structure formed by two alpha helixes wrapped around each other?

    <p>Coiled coil</p> Signup and view all the answers

    What type of proteins have an elongated shape and are usually found in structural materials?

    <p>Fibrous proteins</p> Signup and view all the answers

    What is the name of the process by which proteins are synthesized and folded simultaneously?

    <p>Co-translational folding</p> Signup and view all the answers

    What type of bonds are responsible for the quaternary structure of proteins?

    <p>Noncovalent bonds</p> Signup and view all the answers

    What is the term for proteins that consist of multiple polypeptide chains?

    <p>Multimer</p> Signup and view all the answers

    What is the name of the proteins that help facilitate the folding of other proteins?

    <p>Chaperones</p> Signup and view all the answers

    What is the term for the abnormal accumulation of proteins that can cause disease?

    <p>Aggregation</p> Signup and view all the answers

    What is the characteristic of amyloid fibrils that contributes to neurodegenerative diseases?

    <p>Their organized array that makes neurons vulnerable</p> Signup and view all the answers

    What is the normal folded conformation of the PrP protein?

    <p>Alpha helices</p> Signup and view all the answers

    What is the result of the abnormal form of PrP converting normal PrP to abnormal?

    <p>Cell death</p> Signup and view all the answers

    What is essential for protein-protein interactions?

    <p>Complementary surfaces</p> Signup and view all the answers

    What is the purpose of allosteric enzymes?

    <p>To regulate enzyme activity</p> Signup and view all the answers

    What is the role of phosphates in post-translational modification?

    <p>To add or remove phosphates can increase or decrease protein activity</p> Signup and view all the answers

    What is the primary purpose of using fluorescent microscopy in protein techniques?

    <p>To visualize protein interactions</p> Signup and view all the answers

    What is the role of the sucrose gradient in cell fractionation?

    <p>To achieve better separation of components with similar sizes</p> Signup and view all the answers

    What is the function of GTP-binding proteins?

    <p>To control phosphorylation and dephosphorylation</p> Signup and view all the answers

    What is the purpose of ubiquitin addition to proteins?

    <p>To regulate protein function</p> Signup and view all the answers

    What is the principle behind ion exchange chromatography?

    <p>Separation of proteins based on charge</p> Signup and view all the answers

    What is the role of coenzymes in enzyme catalysis?

    <p>To participate in catalysis reaction</p> Signup and view all the answers

    What is the purpose of using SDS in electrophoresis?

    <p>To coat proteins with a negative charge</p> Signup and view all the answers

    What is the primary function of the Golgi apparatus?

    <p>Sorting of proteins and lipids</p> Signup and view all the answers

    What is the function of scaffolds in the cell?

    <p>To bind multiple proteins to improve their interaction</p> Signup and view all the answers

    What is the role of biomolecular condensates in cells?

    <p>To segregate macromolecules without membrane-enclosed organelles</p> Signup and view all the answers

    What is the purpose of cell fractionation?

    <p>To isolate specific proteins from within cells</p> Signup and view all the answers

    What is the primary function of the ER?

    <p>Most membrane protein and soluble organelle protein synthesis</p> Signup and view all the answers

    What is the principle behind gel filtration chromatography?

    <p>Separation of proteins based on size</p> Signup and view all the answers

    What is the purpose of FRET in protein techniques?

    <p>To visualize protein interactions</p> Signup and view all the answers

    What is required for proteins to enter the endoplasmic reticulum?

    <p>Hydrophobic stop sequences</p> Signup and view all the answers

    What is the function of PDI (protein disulfide isomerase) in the ER?

    <p>Formation of disulfide bridges correctly</p> Signup and view all the answers

    What happens to proteins that don't fold properly in the ER?

    <p>They are sent to the cytosol for degradation</p> Signup and view all the answers

    What is the function of Calnexin in protein folding?

    <p>To help proteins fold correctly</p> Signup and view all the answers

    What is the Unfolded Protein Response (UPR)?

    <p>A response to unfolded proteins in the ER</p> Signup and view all the answers

    What is the function of COP II coats in vesicle transport?

    <p>To transport proteins forward from ER to Golgi</p> Signup and view all the answers

    What is the function of SAR1 protein in COP II coat formation?

    <p>To catalyze the exchange of GDP to GTP</p> Signup and view all the answers

    What is the function of glucosidases in protein folding?

    <p>To remove sugars from proteins</p> Signup and view all the answers

    What is the function of glycosyltransferases in the ER?

    <p>To add sugars to proteins</p> Signup and view all the answers

    What happens to mutant proteins that are recognized by the quality control pathway?

    <p>They are degraded by the proteasome</p> Signup and view all the answers

    What triggers the release of Sar1 from the vesicle and all other COPII proteins?

    <p>GTP-hydrolysis</p> Signup and view all the answers

    What is the primary function of the Golgi apparatus?

    <p>Protein processing, modification, and sorting</p> Signup and view all the answers

    What is the function of Rab proteins in vesicle transport?

    <p>Recruiting tethering proteins from the cytosol</p> Signup and view all the answers

    What is the purpose of glycosylation in protein modification?

    <p>To prevent protein aggregation and facilitate folding</p> Signup and view all the answers

    What is the difference between constitutive secretion and regulated secretion?

    <p>Constitutive secretion is continuous, while regulated secretion is inducible</p> Signup and view all the answers

    What is the role of SNARE proteins in vesicle fusion?

    <p>To pull membranes together and allow for fusion</p> Signup and view all the answers

    What is the function of the trans Golgi network (TGN)?

    <p>Protein sorting and packaging into vesicles</p> Signup and view all the answers

    How do proteins get retrieved from the Golgi back to the ER?

    <p>Through retrograde movement</p> Signup and view all the answers

    What is the function of mannose 6-phosphate in lysosomal protein sorting?

    <p>To bind to the m6p receptor in the Golgi</p> Signup and view all the answers

    What is the difference between cis and trans faces of the Golgi apparatus?

    <p>Cis face is closest to the ER, while trans face is closest to the plasma membrane</p> Signup and view all the answers

    Study Notes

    Protein Structure

    • Proteins have 4 levels of organization: primary, secondary, tertiary, and quaternary
    • Primary structure: specific sequence of amino acids, with 20 possible amino acids, resulting in 20^n variations
    • Side chain (R group) is the portion of each amino acid that gives it unique properties
    • Polypeptide backbone with peptide bonds and side chains
    • Amino terminus (N-terminus) and carboxyl terminus (C-terminus) are the ends of the protein
    • Sequence is determined by the sequence of the gene encoding the protein (DNA)

    Secondary Structure

    • Folding patterns: alpha helix and beta pleated sheets
    • Alpha helix: hydrogen bond between carbonyl of one amino acid and N-H of another, every 4th amino acid
    • R groups project outwards, can be left-handed or right-handed
    • Beta pleated sheets: hydrogen bonds extend from one part of the chain to another, with amino acids interacting with adjacent lines
    • R groups are exposed, pointing up or down, with arrows pointing from N to C
    • Coiled coil: two alpha helices wrapped around each other, mediated by hydrophobic residues

    Tertiary Structure

    • Native conformation, mediated by hydrophobic interactions (hydrophobic core)
    • Interactions between R-groups: van der Waals forces, hydrogen bonds, ionic bonds, hydrophobic interactions, and disulfide bridges
    • Two types: fibrous and globular
    • Globular proteins are more compact, with polypeptide chains folding into complex shapes
    • Fibrous proteins have an elongated shape, forming long strands or flattened sheets

    Quaternary Structure

    • Linking of multiple proteins to form large complexes with multiple subunits
    • Some proteins stop at tertiary structure, while others form quaternary structures
    • Rely on intermolecular interactions of R groups (disulfide bonds, noncovalent bonds)
    • Homo: same subunits, hetero: two or more different subunits

    Protein Aggregates

    • Can cause disease, such as neurodegenerative diseases
    • Structure goes from monomer to dimer to oligomer to aggregate
    • Not sure what causes aggregates to form, but oxidative stress may be a factor
    • Aggregates tend to form later in life, and can be a symptom of neurodegenerative diseases

    Protein Function

    • Protein-protein interactions can be stable and involved in important cell functions
    • Interacting proteins typically have complementary surfaces
    • Protein functions can be figured out based on the types of proteins it interacts with
    • Protein families: group of proteins that share origin, related function or similar sequence/structure

    Post-Translational Modification

    • Addition or removal of molecules can regulate protein function
    • Addition of phosphates can increase or decrease protein activity
    • Kinase: enzyme that adds phosphate, phosphatase: removes phosphate
    • Signalling cascades: reactions that occur in response to a stimulus, controlled by phosphorylation and dephosphorylation

    Other Protein Techniques

    • Fluorescence microscopy: uses proteins with fluorescent tags or labels
    • FRET (Forster Resonance Energy Transfer): visualizes protein interactions
    • FRAP (Fluorescence Recovery After Photobleaching): studies protein movement
    • Isolating specific proteins from within cells: protein purification, cell fractionation, and column chromatography

    Organelles

    • Anything in the cell with a membrane is an organelle
    • Most organelles overlap between plant and animal cells
    • Cytoplasm: everything except the nucleus, cytosol: everything outside membrane-bound organelles
    • Mitochondria and chloroplasts: ATP production
    • ER: most membrane protein and soluble organelle protein synthesis
    • Golgi apparatus: sorting of proteins and lipids from ER
    • Nucleus: contains genome, DNA and RNA synthesis
    • Endosomes: move material between organelles and uptake extracellular molecules
    • Lysosomes: degradation of unneeded intracellular organelles and extracellular molecules### Protein Synthesis and Secretory Pathway
    • Proteins that enter the secretory pathway must first enter the Endoplasmic Reticulum (ER)
    • Proteins have hydrophobic stop sequences to stay in the membrane
    • Orientation of proteins in the ER membrane is important for their function in the plasma membrane

    Membrane Proteins

    • Membrane proteins have multiple hydrophobic stop sequences to stay in the membrane
    • Proteins can be linked to the membrane with a Glycosylphosphatidylinositol (GPI) anchor, replacing hydrophobic stop sequences
    • GPI anchor is used when the sequence needs to be cleaved to function but still needs to be in the membrane

    Protein Translation

    • Protein translation in the cytosol occurs on "free" ribosomes
    • Proteins that finish synthesis in the cytosol (cytosolic proteins) will never enter the endomembrane system unless needed for an organelle or to leave the cell

    Folding and Modification in the ER

    • ER proteins are folded by chaperones like BiP, GRP94, Calnexin (CNX), and Calreticulin (CRT)
    • PDI (protein disulfide isomerase) helps form disulfide bridges correctly in the ER
    • ER protein modification: enzymes modify proteins, commonly by glycosylation (addition of sugars onto proteins)
    • Glycosylated proteins are known as glycoproteins
    • Glycosylation helps proteins fold and aids interaction with other molecules
    • Nearly all proteins in the ER are modified co-translationally by glycosylation

    Quality Control

    • If proteins don't fold properly, they can interfere with other proteins, aggregate, and activate wrong signals
    • Strict quality control: improperly folded proteins are sent to the cytosol to be degraded by the proteasome
    • Time is allowed for proteins to try to fold properly
    • Glycosylation allows for this quality control: sugars get added to the protein, and then two are trimmed by glucosides

    Unfolded Protein Response (UPR)

    • If large amounts of unfolded/misfolded proteins accumulate in the ER, the UPR is triggered
    • More chaperones and proteases that degrade defective proteins are made
    • Synthesis of new proteins not involved in the UPR is stopped

    Vesicle Transport

    • Budding vesicles have a 'coat' of soluble cytosolic proteins that assemble on the membranes of the donor compartment
    • COP I transports proteins backwards from the Golgi to the ER and within the Golgi
    • COP II transports proteins forward from the ER to the Golgi
    • Clathrin-coated vesicles sort proteins to lysosomes and vacuoles
    • COP II coat is a large complex that includes SAR1, a GTP-bound protein

    Golgi Apparatus

    • Located next to the nucleus, but not connected (ER is connected to the nucleus through the perinuclear compartment)
    • Consists of stacks of membranous cisternae (ribbon-like)
    • Functionally distinct compartments (each ribbon does something different)
    • The Golgi is a "processing plant" that takes proteins from the ER and processes, modifies, and sorts them

    Protein Modification in the Golgi

    • Proteins are processed (like insulin cleavage), modified (like glycans), and sorted in the Golgi
    • Proteins move from the ER to the cis-Golgi, then to the medial Golgi, and finally to the trans Golgi
    • Proteins are sorted to determine which ones need to go back to the ER vs which will move through the Golgi
    • Two hypotheses for maintaining polarized Golgi structure: vesicle transport mechanism and cisternal maturation mechanism

    Golgi Exocytosis

    • Contents of secretory vesicles are released into the extracellular environment
    • Vesicle lumen becomes part of the extracellular space
    • Soluble proteins are released, and membrane proteins get inserted into the plasma membrane
    • Glycosylation sites are on the outside of the cell

    Regulated Secretion

    • Constitutive secretion: synthesis and secretion of proteins continuously in an unregulated manner (most membrane proteins and extracellular matrix proteins)
    • Regulated secretion: proteins to be secreted are densely packaged into large vesicles (secretory granules) that wait for a cellular signal before releasing their contents (hormones, neurotransmitters, digestive enzymes)

    Lysosome Sorting

    • Sorting of proteins to lysosomes uses mannose 6 phosphate (m6p)
    • m6p can bind to an m6p receptor at non-acidic pH
    • In the lysosome, the m6p and m6p receptor dissolve apart

    Studying That Suits You

    Use AI to generate personalized quizzes and flashcards to suit your learning preferences.

    Quiz Team

    Description

    This quiz covers the basics of protein structure, including the four levels of organization and the primary structure of proteins, including polypeptide backbone and side chains.

    More Like This

    Use Quizgecko on...
    Browser
    Open
    Browser
    Browser