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Questions and Answers
Which of the following is NOT a category of building blocks in cells?
Which of the following is NOT a category of building blocks in cells?
Condensation reactions are energetically favorable and therefore occur spontaneously at a high rate.
Condensation reactions are energetically favorable and therefore occur spontaneously at a high rate.
False
What type of bond is formed between amino acids during a condensation reaction?
What type of bond is formed between amino acids during a condensation reaction?
Peptide bond
In water at pH 7, free amino acids exist in ______ form.
In water at pH 7, free amino acids exist in ______ form.
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Match the types of amino acids with their properties:
Match the types of amino acids with their properties:
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What type of reaction breaks molecules by adding water?
What type of reaction breaks molecules by adding water?
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Hydrophobic interactions play a minor role in protein structure.
Hydrophobic interactions play a minor role in protein structure.
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What are the two ends of a polypeptide chain called?
What are the two ends of a polypeptide chain called?
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The three-dimensional shape of proteins is significantly influenced by ______ bonds.
The three-dimensional shape of proteins is significantly influenced by ______ bonds.
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Which of the following correctly describes the primary structure of a protein?
Which of the following correctly describes the primary structure of a protein?
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The structure of a side chain (R group) is what differentiates one amino acid from another.
The structure of a side chain (R group) is what differentiates one amino acid from another.
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What are the two secondary structures observed in most proteins?
What are the two secondary structures observed in most proteins?
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Macromolecules are formed by generating strong ______ bonds between small organic molecules.
Macromolecules are formed by generating strong ______ bonds between small organic molecules.
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Match the reactions with their descriptions:
Match the reactions with their descriptions:
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What is a common fluorescent dye used in fluorescence microscopy?
What is a common fluorescent dye used in fluorescence microscopy?
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Cells are fixed to glass slides to allow large molecules to pass through their membranes.
Cells are fixed to glass slides to allow large molecules to pass through their membranes.
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What is created when fluorescent dyes are added to DNA sequences?
What is created when fluorescent dyes are added to DNA sequences?
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In _____, antibodies with fluorescent dyes are used to detect specific proteins.
In _____, antibodies with fluorescent dyes are used to detect specific proteins.
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Match the following terms with their descriptions:
Match the following terms with their descriptions:
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Which process involves analyzing two different proteins with different antibodies?
Which process involves analyzing two different proteins with different antibodies?
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Fluorescent proteins can only be created from RNA sequences.
Fluorescent proteins can only be created from RNA sequences.
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What characteristic do fixed cells have that allows for the study of large molecules?
What characteristic do fixed cells have that allows for the study of large molecules?
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What is the role of ubiquitin-conjugating enzyme (E2) in the ubiquitination process?
What is the role of ubiquitin-conjugating enzyme (E2) in the ubiquitination process?
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E1, E2, and E3 enzymes can only target specific proteins using the same combination for all proteins.
E1, E2, and E3 enzymes can only target specific proteins using the same combination for all proteins.
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What is the purpose of cell lysis during cell fractionation?
What is the purpose of cell lysis during cell fractionation?
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Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis (SDS-PAGE) separates proteins based on their _____ .
Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis (SDS-PAGE) separates proteins based on their _____ .
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Match the following techniques with their primary use:
Match the following techniques with their primary use:
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What does Coomassie blue stain do in SDS-PAGE?
What does Coomassie blue stain do in SDS-PAGE?
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Electron microscopes achieve lower magnification compared to light microscopes.
Electron microscopes achieve lower magnification compared to light microscopes.
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What is the first step in immunoprecipitation?
What is the first step in immunoprecipitation?
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In Western blot, the _____ antibody binds specifically to the protein of interest.
In Western blot, the _____ antibody binds specifically to the protein of interest.
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What is the purpose of using beta-mercaptoethanol (BME) in SDS-PAGE?
What is the purpose of using beta-mercaptoethanol (BME) in SDS-PAGE?
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Different cell types can yield the same number of unique proteins.
Different cell types can yield the same number of unique proteins.
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What is the main advantage of fluorescence microscopy over light microscopy?
What is the main advantage of fluorescence microscopy over light microscopy?
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Proteins that are not bound by the antibody in immunoprecipitation are _____ from the sample.
Proteins that are not bound by the antibody in immunoprecipitation are _____ from the sample.
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Match the following components with their functions:
Match the following components with their functions:
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Which structures allow selective passage of molecules and ions into and out of the cell?
Which structures allow selective passage of molecules and ions into and out of the cell?
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All living cells possess a plasma membrane.
All living cells possess a plasma membrane.
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What type of neurotransmitters increase the probability of action potentials in postsynaptic neurons?
What type of neurotransmitters increase the probability of action potentials in postsynaptic neurons?
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The __________ transports sodium ions out of the cell and potassium ions into the cell.
The __________ transports sodium ions out of the cell and potassium ions into the cell.
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Match the following types of fatty acids with their characteristics:
Match the following types of fatty acids with their characteristics:
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What is the primary function of membrane proteins?
What is the primary function of membrane proteins?
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Passive transport requires energy to move solutes across the membrane.
Passive transport requires energy to move solutes across the membrane.
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How does cholesterol affect membrane fluidity?
How does cholesterol affect membrane fluidity?
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Hydrophobic amino acids are often utilized in the formation of __________ proteins.
Hydrophobic amino acids are often utilized in the formation of __________ proteins.
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What is a characteristic of large, polar/charged molecules in relation to their diffusion across the membrane?
What is a characteristic of large, polar/charged molecules in relation to their diffusion across the membrane?
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Proteins without a sorting signal will be targeted to specific organelles.
Proteins without a sorting signal will be targeted to specific organelles.
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What is the role of the nuclear localization signal (NLS)?
What is the role of the nuclear localization signal (NLS)?
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The __________ is a visualization tool used to analyze protein hydrophobicity.
The __________ is a visualization tool used to analyze protein hydrophobicity.
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Match the following types of transport proteins with their functions:
Match the following types of transport proteins with their functions:
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What describes the primary structure of a protein?
What describes the primary structure of a protein?
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Proteins can only exist in one specific structural form.
Proteins can only exist in one specific structural form.
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What type of bonds stabilize the structure of proteins?
What type of bonds stabilize the structure of proteins?
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The _____ structure of a protein involves the combination of multiple polypeptide chains.
The _____ structure of a protein involves the combination of multiple polypeptide chains.
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What characterizes antibodies?
What characterizes antibodies?
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Chaperones can help refold any type of protein, regardless of its folding state.
Chaperones can help refold any type of protein, regardless of its folding state.
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Name two heat shock proteins involved in protein folding.
Name two heat shock proteins involved in protein folding.
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A ________ is defined as any substance that is bound by a protein.
A ________ is defined as any substance that is bound by a protein.
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Match the following types of protein structures with their descriptions:
Match the following types of protein structures with their descriptions:
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What is the role of Hsp60 in protein folding?
What is the role of Hsp60 in protein folding?
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Protein denaturation only occurs due to extreme pH levels.
Protein denaturation only occurs due to extreme pH levels.
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What is the purpose of ubiquitylation in proteins?
What is the purpose of ubiquitylation in proteins?
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Antibodies that are produced from different B cells are termed ________.
Antibodies that are produced from different B cells are termed ________.
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Which of the following is NOT a level of protein structure?
Which of the following is NOT a level of protein structure?
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Study Notes
Cell Biology Final Exam Lecture Slides
- The exam will cover all lectures, excluding content from papers 1-3.
- The exam will consist of 24 multiple choice questions (48 points) and 8 free-response questions (52 points).
- Approximately 25% of the final exam questions will be from previous exams and practice exams.
- Short answer questions will not be multi-part questions.
- The exam will be administered in person on campus.
- Students can use pen or No. 2 pencil, ensuring dark enough ink for scanning.
- Graded exams are not published; students must schedule a one-on-one meeting with the instructor to review their graded final exam.
- Prepare by reviewing the "Final Exam Lecture Slides," the final exam study guide, and previous midterm exams (passive learning). Practice exams, assignments, and discussion activities without notes (active learning) are also helpful.
Macromolecules in Cells
- Building blocks of cells are small organic molecules (subunits).
- Four categories of subunits: sugars, amino acids, fatty acids, and nucleotides.
- Building blocks are used to form macromolecules.
- Macromolecules are formed by generating strong covalent bonds between subunits.
- Condensation reactions combine molecules by removing water. This reaction is energetically unfavourable and thus, the cell must provide energy to overcome this.
- Hydrolysis reactions break molecules by adding water; these reactions are energetically favourable.
- Cells use both condensation and hydrolysis reactions to build macromolecules.
Amino Acids
- Amino acids have an amino group and a carboxyl group attached to an alpha carbon, with a variable R group.
- At pH 7, amino acids exist in an ionized form. The amino group accepts a proton, and the carboxyl group donates a proton.
- R groups vary, creating 20 different amino acids.
- Peptide bonds link amino acids in condensation reactions, forming polypeptide chains, and resulting in the loss of charges on the amino and carboxyl groups at the ends of the polypeptide.
- N-terminus: first amino acid in a polypeptide backbone
- C-terminus: last amino acid in a polypeptide backbone
Protein Structure
- Proteins have different levels of structure
- Primary structure: amino acid sequence
- Secondary structure: alpha-helices and beta sheets
- Tertiary structure: folding of secondary structures due to side-chain interactions
- Quaternary structure: binding of different polypeptide chains
Protein Function
- Protein shape dictates function.
- Protein function depends on interacting with other molecules (ligands) using weak noncovalent bonds.
- Binding sites are cavities of amino acid side chains that bind ligands using noncovalent bonds; these sites often use electrostatic and hydrogen bonds.
- Antibodies are composed of four polypeptide chains (two identical light and two identical heavy chains).
Protein Denaturation
- Protein shape is dependent on weak noncovalent interactions and determines protein activity.
- Denaturation is a change in shape that reduces activity.
- Denaturation can be caused by heat, extreme pH, or chemicals.
Chaperones
- Most proteins cannot refold once completely denatured, so cells use chaperone proteins to refold denatured or improperly folded proteins.
- Chaperones can refold proteins using different strategies.
Protein Degradation
- Cells degrade proteins that cannot fold properly to prevent aggregation.
- Proteins are flagged for degradation using ubiquitin.
- Three steps in ubiquitylation:
- Adding ubiquitin to a ubiquitin-activating enzyme (E1)
- Transferring ubiquitin from E1 to a ubiquitin-conjugating enzyme (E2)
- Adding ubiquitin to the target protein via ubiquitin ligase (E3)
- Degraded proteins are recycled for use in cell.
- The proteasome is a protein complex that degrades proteins that are tagged with multiple ubiquitins.
Cell Fractionation
- Lysing cells using detergent to break plasma membranes; the homogenate will contain cell components.
- Separating cellular components based on density via differential centrifugation .
SDS-PAGE
- Cell fractionation can separate cellular components but scientists also need to be able to analyze specific proteins.
- SDS-PAGE separates proteins in a mixture by size as denatured and reduced proteins are loaded onto polyacrylamide gel with a current applied.
- Large proteins migrate slowly; small proteins migrate quickly.
- Visualize separated proteins by staining with Coomassie blue, which binds to basic amino acids.
Western Blot
- Measures the amount of a specific protein in a sample.
- Uses SDS-PAGE to separate protein, followed by transferring the separated proteins to a membrane.
- Primary antibody recognizes the target protein.
- Secondary antibody binds to primary antibody, enabling signal detection indicating the presence of the target protein.
Immunoprecipitation
- Used to purify proteins and assess protein-protein interactions.
- Proteins are cross-linked using formaldehyde to stabilize protein-protein interactions.
- Antibody conjugated to beads is added.
- Centrifuge to collect the beads, thereby purifying the proteins of interest.
- Reverse cross-linking to detach proteins.
- Analyze via Coomassie blue staining or western blot.
Microscopy
- Light microscopes use light to view cells and their internal structures.
- Fluorescence microscopes use fluorescent labels; this increases the resolution for viewing specific structures.
- Electron microscopes use electrons to view structures at a higher magnification.
Cell Fixation
- Cells are often fixed to glass slides to prevent movement.
Fluorescence Microscopy
- Fluorescent dyes are added to DNA sequence of DNA to produce a fluorescent protein.
- Green fluorescent protein (GFP), a common fluorescent dye, is used for visualization.
- Cells are fixed to glass slides.
- Immunofluorescence: Antibody with fluorescent dye to detect specific protein using fluorescence microscopy.
Plasma Membrane
- All living cells have a plasma membrane that separates the cytosol from the extracellular environment.
- It is composed of fatty acids that are amphipathic.
- The hydrophobic tails of the fatty acids cluster together and the hydrophilic polar heads face the water.
- Membrane fluidity depends on hydrocarbon tails' packing; close packing= less movement, loose packing = more movement.
- Number of double bonds impacts membrane fluidity.
- Animal cells regulate membrane fluidity using cholesterol.
Membrane Proteins
- Proteins embedded in the membrane.
- Hydrophobic amino acids in alpha helix to pass through lipid bilayer.
- Single-pass proteins require one alpha-helix in order to pass.
- Multi-pass proteins require multiple helices to form an aqueous pore.
- Scientists use hydrophobicity plots to determine whether proteins have transmembrane segments.
- Hydrophobicity plot visualization of hydrophobicity in amino acid sequence.
Membrane Transport
- Cells maintain ion concentrations using membrane transport proteins.
- Transporters change shape.
- Channels form pores.
- Passive transport moves with the concentration gradient (high to low).
- Active transport moves against the concentration gradient, requiring energy.
- Electrochemical gradient: combines concentration and electrical potentials to drive ion movement.
Neuronal Signaling
- Three critical steps: reception, transduction, and response.
- Step one: a neuron with a negative resting membrane potential receives a depolarizing stimulus.
- Step two: depolarizing stimulus exceeds threshold potential.
- Step three: sodium channels open, causing a propagation of the signal toward the terminal branches, and neighboring sodium channels open. Neurotransmitters are signal molecules; they are either excitatory or inhibitory. Excitation increases the probability of an action potential while inhibition decreases the probability.
Protein Sorting
- Eukaryotic cells have many organelles that perform different reactions.
- Lipid bilayers on organelles provide selectively permeable barriers.
- Each organelle has a unique set of proteins.
- Protein sorting: mechanisms that direct proteins to their appropriate destination inside or outside the cell.
- Proteins are initially sorted by ribosomes during translation using free ribosomes or membrane-bound ribosomes.
Nuclear Transport
- Nuclear envelope encloses chromosomes and has two lipid bilayered membranes.
- Nuclear pores bypass both membranes to facilitate bidirectional traffic between the cytosol and nucleus.
- Nucleus imports histones, DNA polymerases, RNA polymerases, transcription factors, and RNA processing proteins.
- Nucleus exports ribosomes, mRNAs, rRNAs, tRNAs, and miRNAs.
- Nuclear pores are large.
- Ribosomal subunits can pass through nuclear pores.
- Nuclear pores are selective, meaning they do not allow random cytosolic proteins to enter.
- Nuclear pores contain nucleoporin proteins forming a gel in the pore.
- Small molecules and RNA can diffuse through pores.
- Proteins need a sorting signal (nuclear localization signal or NLS) to get transported.
- Nuclear import proteins bind to the NLS of the cargo protein to move to the nucleus.
- Ran-GTP, Ran-GAP, Ran-GEF: these proteins are involved in directional transport.
- Cargo protein delivered to nucleus; and the nuclear receptor is released and recycled.
Mitochondria and ER Transport
- Proteins pass into organelles by three methods: nuclear pores, transmembrane proteins, or vesicles
- Protein translocators in cell membranes unfold the proteins for transport from cytosol to ER or mitochondria.
- Transport vesicles pinch off of ER and fuse to target membranes.
ER Transport
- Membrane-bound ribosomes carry out translation and insert proteins into the ER lumen.
- Signal sequence directs transport and insertion.
- SRP-ribosome complex binds to the SRP receptor on the ER membrane.
- Signal sequence inserts into protein translocator, protein is released.
- SRP and SRP receptors are recycled.
Endomembrane System
- Nuclear envelope, ER, Golgi apparatus, endosomes, and lysosomes are collectively called the endomembrane system.
- Organelles were created from the invagination of the plasma membrane.
- Transport vesicles bud off the membrane of one organelle and fuse with the membrane of another organelle.
- Protein coats on vesicles help package the cargo but do not select cargo; coats cause membrane curvature.
- COPII-coated vesicles involved in the forwarding pathway to Golgi.
- COPI-coated vesicles involved in retrieval pathway to ER.
- KDEL receptor helps proteins exit Golgi and return to ER.
Endocytosis
- Movement of molecules from the extracellular space into the cytoplasm via the plasma membrane.
- Receptor-mediated: specific molecules bind to receptors; this concentrates molecules from the extracellular fluid.
- Clathrin-coated vesicles move materials.
- LDL receptor and cholesterol are transported in the bloodstream using LDL.
Overview of Cytoskeleton
- Intermediate filaments: ropelike fibers composed of different protein subunits.
- Microtubules: thick, hollow cylinders made of tubulin subunits.
- Actin filaments: thin, flexible fibers made of actin subunits.
Intermediate Filaments
- Intermediate filaments are composed of different protein subunits.
- Subunits are elongated proteins, and two monomers pair up to make dimers.
- One dimer binds to another in an antiparallel orientation, creating a staggered tetramer structure; eight tetramers form a protofilament, and multiple protofilaments create a cytoskeletal filament.
Microtubules
- Microtubules grow from the centrosome (MTOC).
- Centrosomes contain y-tubulin which serves as a nucleation site.
- Microtubules have plus and minus ends and grow and shrink randomly due to dynamic instability.
Actin Filaments
- Actin filaments are composed of protein subunits called actin.
- Actin subunits have plus and minus ends.
- Actin filaments are helical.
- Treadmilling is a simultaneous gain of monomers at the plus end and loss of monomers at the minus end.
- Dynamic instability means filaments alternate between fast growing intervals and rapid shortening
- Actin filament polymerization is dependent on the available actin monomers.
Muscle Contraction
- Steps of muscle contraction:
- Myosin without ATP or ADP bound to actin filament
- ATP binds to myosin, causing myosin to detach from actin
- Myosin hydrolyzes ATP to change position
- Myosin binds to a new site on actin weakly
- ADP and phosphate are released, and myosin regains its original shape
Cell Adhesion
- Cell cohesion is critical for multicellular organisms.
- Tight junctions: epithelia; cells are tightly bound.
- Cell to-cell junctions with little extracellular matrix.
- Anchoring junctions: bone, tendon, blood; extracellular matrix secreted by sparsely distributed cells.
- Cadherins: transmembrane adhesion proteins that mediate cell-cell junctions, and use homophilic binding.
Extracellular Matrix
- ECM made of three major classes: GAGs, fibrous proteins, and glycoproteins.
- GAGs: repetitive disaccharides that occupy large space in the ECM, allowing the ECM to withstand compression
- Fibrous proteins: support ECM structure
- Glycoproteins: attach molecules and help with binding cells to ECM
Cell Signaling
- Reception, Transduction, and Response are the three main steps of cell signaling.
Enzyme-Coupled Receptors
- Enzyme-coupled receptors act as enzymes or associate with enzymes inside the cell when stimulated by a signaling molecule.
- Phosphorylation by protein kinase assembles signaling complex after binding of signal molecule. Several types of enzyme-coupled receptors that also use multiple kinases.
Cell Cycle
- Eukaryotic cells have two phases: interphase and M phase.
- Interphase has three phases: G₁ phase, S phase, and G₂ phase.
- G₁: cell growth; prepares for replication
- S: replication of DNA
- G₂: cell growth; prepares for mitosis
- M: mitosis and cytokinesis
- G₀ phase: quiescent cells no longer divide.
- Cell division can initiate only if resting cells are pulled out of G₀ and into G₁ by extracellular signals (mitogens).
Cell Cycle Control
- Early experiments demonstrate that cytoplasm from M phase cell can induce mitosis.
- Mitosis promoting factor (MPF)
- MPF is a cyclin-dependent kinase (Cdk): non-receptor kinase.
- Cyclins activate Cdks.
- Cyclins, are only expressed at specific times in the cell cycle
- Cdks are expressed and active only when the specific cyclin is present.
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Prepare for your final exam with this quiz focused on exam components and preparation strategies. Discover what percentage of questions come from previous tests and the essential materials needed for the exam. Test your knowledge about the requirements to succeed in your final assessment.
