Final Exam Preparation Quiz
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Questions and Answers

Which of the following is NOT a category of building blocks in cells?

  • Sugars
  • Fatty acids
  • Nucleotides
  • Proteins (correct)

Condensation reactions are energetically favorable and therefore occur spontaneously at a high rate.

False (B)

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.

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

Match the types of amino acids with their properties:

<p>Polar = Hydrophilic, interacts with water Nonpolar = Hydrophobic, repels water Ionized = Has a charge at pH 7 Aromatic = Contains an aromatic ring structure</p> Signup and view all the answers

What type of reaction breaks molecules by adding water?

<p>Hydrolysis (B)</p> Signup and view all the answers

Hydrophobic interactions play a minor role in protein structure.

<p>False (B)</p> Signup and view all the answers

What are the two ends of a polypeptide chain called?

<p>N-terminus and C-terminus</p> Signup and view all the answers

The three-dimensional shape of proteins is significantly influenced by ______ bonds.

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

Which of the following correctly describes the primary structure of a protein?

<p>Amino acid sequence (C)</p> Signup and view all the answers

The structure of a side chain (R group) is what differentiates one amino acid from another.

<p>True (A)</p> Signup and view all the answers

What are the two secondary structures observed in most proteins?

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

Macromolecules are formed by generating strong ______ bonds between small organic molecules.

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

Match the reactions with their descriptions:

<p>Condensation = Combines molecules by removing water Hydrolysis = Breaks molecules by adding water Energetically favorable = Reactions that occur spontaneously Energetically unfavorable = Reactions that do not happen spontaneously</p> Signup and view all the answers

What is a common fluorescent dye used in fluorescence microscopy?

<p>Green fluorescent protein (GFP) (D)</p> Signup and view all the answers

Cells are fixed to glass slides to allow large molecules to pass through their membranes.

<p>True (A)</p> Signup and view all the answers

What is created when fluorescent dyes are added to DNA sequences?

<p>Fusion protein</p> Signup and view all the answers

In _____, antibodies with fluorescent dyes are used to detect specific proteins.

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

Match the following terms with their descriptions:

<p>GFP = Common fluorescent dye in microscopy Cells fixed on slides = Locking cells in place Immunofluorescence = Using antibodies to detect proteins Fusion protein = Result of attaching fluorescent dyes to proteins</p> Signup and view all the answers

Which process involves analyzing two different proteins with different antibodies?

<p>Immunofluorescence (A)</p> Signup and view all the answers

Fluorescent proteins can only be created from RNA sequences.

<p>False (B)</p> Signup and view all the answers

What characteristic do fixed cells have that allows for the study of large molecules?

<p>Permeable membranes</p> Signup and view all the answers

What is the role of ubiquitin-conjugating enzyme (E2) in the ubiquitination process?

<p>It transfers ubiquitin from E1 to E3. (D)</p> Signup and view all the answers

E1, E2, and E3 enzymes can only target specific proteins using the same combination for all proteins.

<p>False (B)</p> Signup and view all the answers

What is the purpose of cell lysis during cell fractionation?

<p>To disrupt the plasma membranes and release cellular components.</p> Signup and view all the answers

Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis (SDS-PAGE) separates proteins based on their _____ .

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

Match the following techniques with their primary use:

<p>SDS-PAGE = Separating proteins by size Western Blot = Quantifying specific proteins Immunoprecipitation = Purifying proteins and assessing interactions Fluorescence Microscopy = Visualizing specific structures within cells</p> Signup and view all the answers

What does Coomassie blue stain do in SDS-PAGE?

<p>It stains proteins for visualization. (B)</p> Signup and view all the answers

Electron microscopes achieve lower magnification compared to light microscopes.

<p>False (B)</p> Signup and view all the answers

What is the first step in immunoprecipitation?

<p>Generate cell lysate and cross-link proteins.</p> Signup and view all the answers

In Western blot, the _____ antibody binds specifically to the protein of interest.

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

What is the purpose of using beta-mercaptoethanol (BME) in SDS-PAGE?

<p>To denature proteins and eliminate disulfide bridges. (B)</p> Signup and view all the answers

Different cell types can yield the same number of unique proteins.

<p>False (B)</p> Signup and view all the answers

What is the main advantage of fluorescence microscopy over light microscopy?

<p>It allows for viewing specific structures in greater detail using fluorescent labels.</p> Signup and view all the answers

Proteins that are not bound by the antibody in immunoprecipitation are _____ from the sample.

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

Match the following components with their functions:

<p>E1 = Ubiquitin-activating enzyme E2 = Ubiquitin-conjugating enzyme E3 = Ubiquitin ligase Centrifuge = Separates cellular components</p> Signup and view all the answers

Which structures allow selective passage of molecules and ions into and out of the cell?

<p>Plasma membrane (B)</p> Signup and view all the answers

All living cells possess a plasma membrane.

<p>True (A)</p> Signup and view all the answers

What type of neurotransmitters increase the probability of action potentials in postsynaptic neurons?

<p>Excitatory neurotransmitters</p> Signup and view all the answers

The __________ transports sodium ions out of the cell and potassium ions into the cell.

<p>Na+-K+ pump</p> Signup and view all the answers

Match the following types of fatty acids with their characteristics:

<p>Saturated = No double bonds and typically solid at room temperature Unsaturated = One or more double bonds and typically liquid at room temperature Amphipathic = Has both hydrophilic and hydrophobic regions</p> Signup and view all the answers

What is the primary function of membrane proteins?

<p>Facilitating transport across the membrane (C), Acting as receptors for signals (D)</p> Signup and view all the answers

Passive transport requires energy to move solutes across the membrane.

<p>False (B)</p> Signup and view all the answers

How does cholesterol affect membrane fluidity?

<p>Increases rigidity and decreases fluidity with more cholesterol.</p> Signup and view all the answers

Hydrophobic amino acids are often utilized in the formation of __________ proteins.

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

What is a characteristic of large, polar/charged molecules in relation to their diffusion across the membrane?

<p>They diffuse slowly across the membrane. (B)</p> Signup and view all the answers

Proteins without a sorting signal will be targeted to specific organelles.

<p>False (B)</p> Signup and view all the answers

What is the role of the nuclear localization signal (NLS)?

<p>To signal for the import of proteins into the nucleus.</p> Signup and view all the answers

The __________ is a visualization tool used to analyze protein hydrophobicity.

<p>hydrophobicity plot</p> Signup and view all the answers

Match the following types of transport proteins with their functions:

<p>Transporters = Change shape to transport specific molecules/ions Channels = Form pores for ion transport Active Transport = Requires energy to move against the gradient</p> Signup and view all the answers

What describes the primary structure of a protein?

<p>The sequence of amino acids in a polypeptide chain (A)</p> Signup and view all the answers

Proteins can only exist in one specific structural form.

<p>False (B)</p> Signup and view all the answers

What type of bonds stabilize the structure of proteins?

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

The _____ structure of a protein involves the combination of multiple polypeptide chains.

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

What characterizes antibodies?

<p>They have variable regions that bind to antigens. (B)</p> Signup and view all the answers

Chaperones can help refold any type of protein, regardless of its folding state.

<p>False (B)</p> Signup and view all the answers

Name two heat shock proteins involved in protein folding.

<p>Hsp70 and Hsp60</p> Signup and view all the answers

A ________ is defined as any substance that is bound by a protein.

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

Match the following types of protein structures with their descriptions:

<p>Primary = Amino acid sequence of a polypeptide chain Secondary = Alpha-helices and beta sheets Tertiary = Folded 3D structure of a single protein Quaternary = Multiple polypeptide chains in a complex</p> Signup and view all the answers

What is the role of Hsp60 in protein folding?

<p>It provides an isolation chamber for protein folding. (D)</p> Signup and view all the answers

Protein denaturation only occurs due to extreme pH levels.

<p>False (B)</p> Signup and view all the answers

What is the purpose of ubiquitylation in proteins?

<p>To tag proteins for degradation</p> Signup and view all the answers

Antibodies that are produced from different B cells are termed ________.

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

Which of the following is NOT a level of protein structure?

<p>Composite (D)</p> Signup and view all the answers

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Flashcards

What is the format of the MBS 320 final exam?

The final exam for MBS 320 will have a mix of multiple choice and free-response questions covering all lectures.

What percentage of the final exam is based on previous exams?

Approximately 25% of the final exam questions will be taken from previous exams and practice materials.

How is the MBS 320 final exam administered?

The final exam for MBS 320 is a paper-based exam that must be taken on campus.

What materials should students review for the final exam?

Students should review lecture slides, the final exam study guide, and previous midterm exams to prepare for the final.

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How can students prepare for the final exam actively?

In addition to passive learning, students should actively engage with the material by trying to answer practice questions without notes.

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Macromolecules

Large molecules made up of smaller subunits called monomers.

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Monomers

Small organic molecules that are used to form macromolecules.

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Condensation Reaction

A chemical reaction that joins monomers together to form polymers, releasing a water molecule in the process.

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Hydrolysis Reaction

A chemical reaction that breaks polymers into monomers by adding a water molecule.

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Coupling Reactions

The process of coupling energetically favorable reactions with unfavorable reactions to drive the formation of macromolecules.

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Amino Acids

Organic molecules that contain an amino group, a carboxyl group, and a side chain attached to a central carbon atom.

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Peptide bond

The bond formed between two amino acids through a condensation reaction.

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N-terminus

The first amino acid in a polypeptide chain.

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C-terminus

The last amino acid in a polypeptide chain.

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Side Chain (R group)

The unique chemical group attached to the central carbon atom of an amino acid.

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Polar Amino Acids

Amino acids that have a polar side chain and can form hydrogen bonds with water.

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Nonpolar Amino Acids

Amino acids that have a nonpolar side chain and cannot form hydrogen bonds with water.

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Protein Structure

The three-dimensional shape of a protein.

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Primary Structure

The linear sequence of amino acids in a protein.

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Secondary Structure

The local folding patterns of a polypeptide chain, including alpha helices and beta sheets.

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Fluorescence Microscopy

A type of microscopy that uses fluorescent dyes to visualize specific molecules in cells.

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Fluorescent Protein

A protein that emits light when exposed to specific wavelengths of light, often used as a marker in fluorescence microscopy.

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Immunofluorescence

A specialized type of microscopy that utilizes antibodies labeled with fluorescent dyes to detect specific proteins in cells.

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Fluorescent Dye Labeling

The process of attaching fluorescent dyes to a protein to make it easier to visualize under a fluorescence microscope.

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Green Fluorescent Protein (GFP)

A common fluorescent dye used in microscopy, producing a green fluorescent signal. It can be attached to proteins to make them visible under a microscope.

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Cell Fixation

A technique used in microscopy to fix cells in place on a slide, making them easier to study. The process preserves the cell's structure.

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Fusion Protein

Process of fusing a gene encoding a fluorescent protein to the gene of interest. This allows the protein of interest to be tagged with a fluorescent marker, making it visible under a microscope.

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Dual Labeling with Antibodies

A technique in which two different antibodies, each linked to a different fluorescent dye, are used to visualize two different proteins in the same cell.

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Ubiquitination

A process that involves a series of enzymatic steps leading to the attachment of ubiquitin to a target protein.

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Ubiquitin-activating enzyme (E1)

An enzyme that activates ubiquitin by attaching it to itself.

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Ubiquitin-conjugating enzyme (E2)

An enzyme that receives ubiquitin from E1 and transfers it to E3.

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Ubiquitin ligase (E3)

An enzyme that recognizes specific target proteins and attaches ubiquitin to them.

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Protein Degradation

The process of breaking down proteins into their constituent amino acids.

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Proteasome

A specialized protein structure within cells that breaks down proteins.

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Cell Fractionation

A technique used to separate cellular components from one another.

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Lysis Buffer

A solution used to break open cells and release their contents.

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Cell Lysate or Cell Homogenate

A mixture containing all cellular components after cells have been lysed.

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SDS-PAGE

A technique used to separate proteins in a mixture based on their size.

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Sodium Dodecyl Sulfate (SDS)

A detergent that denatures proteins and coats them with a negative charge.

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Beta-mercaptoethanol (BME)

A reducing agent that eliminates disulfide bridges in proteins.

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Western Blot

A technique used to detect and quantify specific proteins in a sample.

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Immunoprecipitation

A technique used to purify proteins and study protein-protein interactions.

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Tertiary Structure

The overall three-dimensional shape of a single polypeptide chain. It arises from interactions between side chains of amino acids.

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Quaternary Structure

The arrangement of multiple polypeptide chains (subunits) in a protein complex.

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Protein Domain

A distinct functional or structural unit within a protein. They are often associated with specific tasks and can fold independently.

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Protein Subunit

A single polypeptide chain that participates in a protein complex with quaternary structure.

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Ligand

A molecule that binds to a specific site on a protein, often triggering a functional response.

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Binding Site

A specific region on a protein that interacts with a ligand, typically through noncovalent forces.

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Protein Denaturation

A change in protein shape that disrupts its function. It often results from exposure to extreme temperatures, pH, or chemicals.

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Chaperones

Proteins that assist in the proper folding of other proteins. They act as molecular chaperones, preventing misfolding and aggregation.

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Heat Shock Proteins (Hsp)

A class of chaperones that are particularly important in refolding proteins that have been denatured by heat.

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Hsp70

One type of heat shock protein that interacts with hydrophobic amino acids and assists in the proper folding of proteins.

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Hsp60

Another type of heat shock protein that uses a multi-subunit structure to provide a protected environment for proteins to fold.

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What is cell fixation and what is its purpose?

Fixation is a process used to preserve cells for microscopy. Cells are locked in place on a glass slide and treated to make their membranes permeable, allowing large molecules to pass through.

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How does immunofluorescence work to identify and visualize proteins?

Immunofluorescence uses antibodies tagged with fluorescent dyes to detect specific proteins. The antibodies bind to the target protein, allowing visualization under a fluorescence microscope.

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Describe the function of the plasma membrane.

The plasma membrane is a selectively permeable barrier that encloses the cell, separating the cytosol from the extracellular environment.

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What is the importance of internal membranes in eukaryotic cells?

Internal membranes of organelles compartmentalize the cell, allowing for specialized reactions to occur within different regions.

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Describe the structure of fatty acids and how they contribute to the cell membrane.

Fatty acids are amphipathic molecules composed of a hydrophilic head and a hydrophobic tail. They are the building blocks of the cell membrane.

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What is the structure of the lipid bilayer in the cell membrane?

The lipid bilayer is a key component of the cell membrane formed by the arrangement of phospholipids. Their hydrophobic tails cluster together, while their hydrophilic heads interact with water.

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What factors determine the fluidity of the cell membrane?

Membrane fluidity is influenced by factors like the length of fatty acid tails, the degree of saturation (double bonds), and the presence of cholesterol.

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How do membrane proteins interact with the lipid bilayer?

Membrane proteins are often composed of hydrophobic amino acids arranged in alpha helices, allowing them to pass through the hydrophobic lipid bilayer.

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Differentiate between single-pass and multi-pass transmembrane proteins.

Transmembrane proteins can be single-pass, crossing the membrane once, or multi-pass, crossing multiple times to form aqueous pores.

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What is a hydrophobicity plot and how is it used to identify transmembrane segments?

A hydrophobicity plot, also known as a hydropathy plot, visualizes hydrophobic regions within a protein sequence. Peaks in the plot indicate potential transmembrane segments.

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Describe the two main types of membrane transport proteins.

Membrane transport proteins facilitate the movement of molecules and ions across the cell membrane. They can be classified as transporters, which change shape, or channels, which form pores.

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What is passive transport and how does it work?

Passive transport is powered by the concentration gradient, moving molecules from a high concentration to a low concentration without requiring energy.

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What is active transport and how is it different from passive transport?

Active transport moves molecules against their concentration gradient, requiring energy input from sources like ATP.

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What is the function of the Na+/K+ pump?

The Na+/K+ pump is an ATP-driven pump that actively moves sodium ions out of the cell and potassium ions into the cell, maintaining their concentration gradients.

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What is coupled transport and how does it work?

Coupled transport uses the energy from the movement of one molecule down its gradient to transport another molecule against its gradient.

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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.

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