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WorksheetsTest 1, Part 2
Total questions: 117
Worksheet time: 59mins
Relate the nomenclature for proteins and identify the name of a short peptide using three letter abbreviations, written from the N-terminus to the C-terminus. Choose the correctly formatted example.
Ala-Gly-Lys
A-G-K
lys-ala-gly
AlaGlyLys
Relate protein primary, secondary, tertiary and quaternary structure.
Primary is the amino acid sequence; secondary is local α-helices and β-sheets stabilized mainly by hydrogen bonds; tertiary is the overall 3D fold produced by side-chain interactions; quaternary is the association of multiple polypeptide chains.
Primary is the 3D fold; secondary is subunit assembly via disulfide bonds; tertiary is local helices and sheets; quaternary is the linear amino acid sequence.
Primary is side-chain orientation; secondary is ionic interactions between separate subunits; tertiary is hydrogen-bonded helices only; quaternary is a single folded polypeptide.
Primary is determined by hydrogen bonds; secondary is determined entirely by sequence without hydrogen bonds; tertiary is only backbone interactions; quaternary does not involve multiple chains.
Compare and contrast the properties of an α-helix versus a β-sheet (parallel and anti-parallel), including the orientation of the amino acid side chains.
In an α-helix, backbone hydrogen bonds form along the helix axis (i to i+4) with side chains projecting outward; in a β-sheet, strands are extended with side chains alternating above and below the sheet, and antiparallel sheets have more linear hydrogen bonds than parallel sheets.
In an α-helix, side chains point inward toward the axis while hydrogen bonds link different polypeptide chains; in a β-sheet, side chains align in one direction and parallel sheets have the strongest, most linear hydrogen bonds.
An α-helix lacks regular hydrogen bonding and has alternating side chains above and below the axis; a β-sheet’s side chains spiral outward and only antiparallel sheets form hydrogen bonds.
Both α-helices and β-sheets have identical side-chain orientations and hydrogen-bond geometries regardless of parallel or antiparallel arrangement.
What allows the individual atoms to pack so tightly together in the 3D form?
Ionic interactions
Hydrogen bonds
Disulfide bonds
van der Waals interactions
Relate the importance of disulfide bonds in protein structure using the provided notes: Some cysteine residues in proteins form disulfide bonds that are formed enzymatically during protein synthesis; these bonds are very specific and do not control overall protein folding. Rather, a covalent S–S bond locks the protein into a specific structural arrangement. Based on this description, what is the primary structural effect of a disulfide bond on a protein?
It dictates the entire folding pathway of the protein
It locks parts of the protein into a specific structural arrangement
It breaks alpha helices to allow beta sheet formation
It primarily organizes protein–lipid interactions
Relate the importance of disulfide bonds in protein structure using the provided notes and illustration of a protein interior. In a strongly reducing intracellular environment, where are disulfide bonds typically found within proteins?
Exposed on the protein surface
Buried deep within the protein structure
Only at cytosolic membrane interfaces
Restricted to extracellular matrix proteins
Recall the redox relationship between sulfhydryls and disulfides from the notes: “Free sulfhydryls (−SH) are reduced, whereas disulfide bonds (−S–S−) are oxidized.” Which statement correctly reflects this redox pairing?
Both −SH and −S–S− groups are reduced
−SH groups are reduced while −S–S− bonds are oxidized
−SH groups are oxidized while −S–S− bonds are reduced
Both −SH and −S–S− groups are oxidized
Using the notes on formation, how are disulfide bonds established during protein biogenesis?
Spontaneously in the reducing cytosol without catalysts
Enzymatically during protein synthesis
By ATP-dependent peptide bond formation
By non-specific aggregation of cysteine-free segments
From the notes listing characteristics, which property best describes disulfide bonds in proteins?
They are very specific interactions
They are nonspecific and interchangeable
They primarily mediate protein–lipid binding
They only occur in beta sheet regions
Recall super-secondary protein structures using the provided notes: Alpha helices and beta sheets are secondary structures that start to cluster together as the protein moves toward its final form. What term applies to these clusters of secondary structural elements?
Domains
Motifs
Super-secondary structures
Primary structures
According to the notes on super-secondary structure, what primarily drives the clustering of secondary elements into super-secondary arrangements?
Covalent backbone rearrangements
Strong ionic crosslinks exclusively
Weak interactions among elements
Direct lipid insertion into the core
Using the notes on motifs, what are motifs within the context of super-secondary structure?
Unique amino acid sequences only found in enzymes
Common patterns formed by interactions among secondary elements
Large independent folding units equivalent to entire proteins
Sites exclusively responsible for catalytic activity
Relate super-secondary organization to overall protein folding using the notes: Secondary elements and motifs cluster together to form the final folded form of a protein. What higher-level structure do these clustered elements contribute to?
Primary structure
Quaternary structure of multisubunit complexes
Tertiary (final) structure of a single polypeptide
Post-translational sequence editing
Refer to the diagram labeled DNA Binding Protein Motifs. Which motifs are explicitly identified as DNA-binding protein motifs in the figure? Select all that apply.
Zinc fingers
Leucine zipper
Helix–turn–helix
Helix–loop–helix
Beta-sheet hairpin
According to the description of DNA-binding protein motifs, these proteins are typically organized as what structural unit?
Monomers
Dimers
Tetramers
Heptamers
In the description of DNA-binding protein motifs, what two interactions are carried out by different segments within each individual protein? Select all that apply.
Binding to the DNA molecule
Binding to a partner protein
Binding to the lipid bilayer
Binding to a small metabolite
What explanation is given for the high specificity of DNA binding by these proteins?
The geometry of the amino acid sequence matches the geometry of the DNA sequence
Electrostatic repulsion prevents nonspecific binding
Random coil flexibility allows binding anywhere
Covalent cleavage of the DNA backbone ensures target recognition
In the Protein Domains figure, how is a protein domain defined?
A part of a larger whole that itself has defined structure and/or function
The entire protein polypeptide chain regardless of function
A temporary unfolded region created during denaturation
A post-translational modification mark on a residue
In the Protein Domains figure, what does the label N represent?
Nucleotide binding domain
Actuator domain
Phosphorylation domain
Membrane channel domain
In the Protein Domains figure, what does the label A represent?
Actuator domain
Nucleotide binding domain
Phosphorylation domain
Membrane channel domain
In the Protein Domains figure, what does the label P represent?
Phosphorylation domain
Actuator domain
Nucleotide binding domain
Membrane channel domain
In the Protein Domains figure, what does the label M represent?
Membrane channel domain
Nucleotide binding domain
Actuator domain
Phosphorylation domain
According to the Protein Domains description, which functional components can domains form? Select all that apply.
Catalytic site
Interaction site for binding other proteins
Ligand binding site
Ribosomal assembly site
Which statement aligns with the description beneath the Protein Domains figure?
A domain has its own fold and sometimes contributes function, but it is part of the whole protein
A domain is independent of the protein and functions as a separate molecule
A domain is defined only by its amino acid composition and lacks structure
A domain refers to the cellular compartment where a protein is located
Objective: Recognize common protein modifications found in cells and relate the differences between permanent protein modifications and reversible protein modifications. According to the passage, which statement best describes one regulatory purpose of protein modification?
It can turn a protein on or off by altering its function.
It always targets random amino acid positions on a protein.
It permanently destroys protein activity by cleaving the backbone.
It only occurs before proteins are synthesized.
Based on the passage, which of the following are listed as reversible modifications of specific amino acids? Select all that apply.
Phosphorylation
ADP-ribosylation
Acetylation
Hydroxyl addition to proline and lysine
Carboxyl group addition to a side chain
According to the passage, which statement characterizes reversible modification?
It promotes conformational changes in a protein that can be reversed.
It introduces permanent structure–function changes.
It creates new covalent bonds that connect separate proteins.
It irreversibly adds a carboxyl group to a side chain.
Which listed modifications in the passage are described as irreversible? Select all that apply.
Side-chain oxygen atom addition allowing new covalent interactions
Hydroxyl addition to proline and lysine enabling new covalent bonds
Carboxyl group addition to a side chain creating a new site for reactivity and ionic interactions
Phosphorylation of specific amino acids for regulation
The passage states that regulatory modifications such as phosphorylation, acetylation, or ADP-ribosylation of specific amino acids have which effect? Select all that apply.
They induce a conformational change that alters protein activity.
They reversibly regulate protein function.
They create permanent covalent crosslinks between separate proteins.
They randomize protein localization within the cell.
According to the passage, why is it important to localize proteins to specific places in the cell?
To ensure protein function at that place
To make modification sites random
To permanently deactivate proteins
To enable peptide backbone cleavage
Define lipid-anchored proteins and compare and contrast fatty acid lipid anchors and glycerophospholipid anchors of the role of the attached lipid.
Proteins covalently modified with fatty acids (palmitate or myristate), prenyl groups, or whole lipid molecules that target proteins to membrane surfaces and localize their function; fatty acid anchors add a fatty acid, whereas glycerophospholipid anchors add a whole lipid molecule.
Proteins loosely associated with membranes via ionic interactions; fatty acid anchors add carbohydrate chains, whereas glycerophospholipid anchors add prenyl groups.
Proteins destined for secretion that lose all lipid attachments; fatty acid anchors remove fatty acids, whereas glycerophospholipid anchors remove phosphate groups.
Proteins that bind nucleic acids in the cytosol; both anchors direct proteins to the nucleus rather than membranes.
Recognize carbohydrate groups on glycolipids and glycoproteins and recall the orientation of carbohydrate groups relative to the plasma membrane / cell.
Carbohydrate chains added by glycosylation are displayed on the outer surface of the plasma membrane on glycolipids and glycoproteins.
Carbohydrate chains are confined to the inner cytosolic surface of the plasma membrane.
Carbohydrate chains are not present on membranes and exist only free in the cytosol.
Carbohydrate chains randomly flip between inner and outer leaflets without orientation.
Define the structural features of immunoglobulins (antibodies).
A Y-shaped protein composed of two identical heavy chains and two identical light chains linked by disulfide bonds, with variable regions that bind antigen and constant regions that mediate effector functions.
A single polypeptide that forms a helical bundle without disulfide bonds and lacks distinct domains.
A trimeric membrane channel with carbohydrate chains exposed on the outer leaflet of the plasma membrane.
A globular enzyme with an active-site serine and no capacity to bind antigens.
Identify which structural region of immunoglobulins allows for recognition of antigens.
Variable regions on the heavy and light chains
Constant regions on the heavy chains
Carbohydrate moieties attached to the C_H domains
Disulfide bonds linking the chains
Identify what structural feature differentiates the different classes of antibodies.
Differences in the constant region of the heavy chain
Presence or absence of disulfide bonds
Length of the hinge region in the light chain
Number of antigen-binding sites on each arm
Define collagen primary, secondary/tertiary and quaternary structure. Choose the option that correctly identifies collagen’s primary sequence, the conformation of a single collagen chain, and the assembly and stabilization of the triple helix.
Primary: repeating Gly–X–Y sequence (X often Pro, Y often 4‑hydroxyproline); secondary/tertiary: left‑handed helix of a single chain; quaternary: right‑handed triple helix of three chains stabilized by inter‑chain hydrogen bonds between the amide NH of glycine on one chain and the carbonyl of residue X on another.
Primary: random‑coil sequence; secondary/tertiary: right‑handed alpha‑helix; quaternary: dimer stabilized mainly by disulfide bonds.
Primary: alternating polar/nonpolar sequence; secondary/tertiary: beta‑sheet; quaternary: tetramer stabilized primarily by ionic interactions.
Primary: repeating Gly–Pro–Lys sequence; secondary/tertiary: left‑handed sheet; quaternary: triple helix stabilized only by intra‑chain hydrogen bonds.
Define how individual collagen molecules are assembled and held together in a collagen fiber: which amino‑acid modifications enable covalent cross‑linking between collagen triple helices during protein synthesis.
Hydroxylation of lysine and proline residues creates –OH groups for cross‑link formation
Phosphorylation of glycine residues increases negative charge to attract fibrils
Methylation of alanine residues increases hydrophobic packing
Acetylation of serine residues blocks hydrogen bonding
Identify the cofactor required for the enzymatic modification of proline and lysine residues that permits collagen cross‑linking.
Vitamin C (ascorbate)
Vitamin D
Vitamin A
Vitamin K
Which statement best characterizes the collagen cross‑linking reaction during protein synthesis.
It is very specific and carefully regulated
It is random and largely unregulated
It occurs only after secretion and is not enzyme‑mediated
It primarily involves phosphorylation rather than covalent cross‑links
Failure to properly cross‑link individual tropocollagen molecules is most directly due to which biochemical defect described.
Inadequate hydroxylation of lysine and proline residues, often from vitamin C or hydroxylase deficiency
Excess glycosylation of hydroxylysine residues during secretion
Incorrect disulfide bond formation in collagen C‑terminal propeptides
Defective phosphorylation of serine in collagen
During aging, how does the time‑dependent nature of collagen cross‑linking affect tissue mechanical properties.
Increased cross‑links decrease flexibility and pliability, contributing to wrinkles
Reduced cross‑links increase elasticity and smooth the skin
Cross‑linking remains constant and does not affect mechanics
Cross‑linking is replaced by noncovalent interactions that increase stretchiness
Vitamin C deficiency has what consequence for collagen fibrils and connective tissue integrity, as described.
Decreased cross‑links weaken fibrils, leading to loss of connective tissue integrity (e.g., loss of teeth)
Increased cross‑links stiffen fibrils, causing excessive tissue rigidity
No change in cross‑linking but increased glycosylation strengthens fibrils
Enhanced phosphorylation of collagen restores tensile strength
Which disorder listed arises from a genetic mutation where glycine is replaced by another amino acid in collagen.
Osteogenesis imperfecta
Lupus erythematosus
Ehlers‑Danlos syndrome
Scurvy
Which condition is described as an autoimmune disease that attacks healthy collagen.
Lupus erythematosus
Osteogenesis imperfecta
Ehlers‑Danlos syndrome
Vitamin C deficiency
Which agents are noted to attack healthy collagen, contributing to disease.
Specific bacteria and viral virulence factors
Excess dietary sodium
Ultraviolet light alone
Benign commensal fungi only
Which syndrome is described as genetic with deficiency in synthesis of mature collagen types I and III.
Ehlers‑Danlos syndrome
Osteogenesis imperfecta
Rheumatoid arthritis
Marfan syndrome
Compare and contrast the structure of proinsulin versus insulin and relate the physiological significance of this transition. Based on the diagram that shows proinsulin (single peptide with the connecting peptide) and insulin (separate alpha and beta peptides linked by disulfide bonds), select all correct statements.
Proinsulin is a single polypeptide that includes the connecting peptide (C-peptide) and forms the precursor to insulin.
Mature insulin consists of separate alpha (A) and beta (B) peptides that are held together by disulfide bonds after C-peptide is removed.
Conversion of proinsulin to insulin is physiologically important because it yields the correct structural configuration required for secretion and function.
C-peptide remains intact and is essential for insulin’s signaling function.
Relate how the level of insulin C-peptide in the blood can be used as a measure of insulin secretion in diabetic patients. Select all statements that correctly explain why C-peptide serves as a proxy for insulin release.
C-peptide is part of proinsulin and is cleaved stoichiometrically when insulin is produced, so its secretion parallels insulin.
C-peptide is co-released into the blood during insulin maturation, making its concentration reflect endogenous insulin secretion.
C-peptide remains intact and has no signaling function, allowing it to be measured as a relative indicator of insulin release.
C-peptide directly stimulates glucose uptake and therefore its level is the same as insulin’s biological effect.
Interpret why protein flexibility and conformational changes are important for protein function. Select all correct statements.
Flexibility allows proteins to adopt active conformations for binding partners and catalytic activity.
Conformational changes enable allosteric regulation and responsiveness to ligands or environmental cues.
Rigid, fixed structures always maximize protein function; flexibility is generally detrimental.
Dynamic motions permit transitions between inactive and active states that are essential for proper function.
Relate the terms glycocalyx and extracellular membrane, interpret their function, and identify several mammalian cells that have a glycocalyx/extracellular membrane.
The glycocalyx is a carbohydrate-rich coating on the extracellular face of the plasma membrane formed by membrane glycoproteins and glycolipids; it protects cells and mediates adhesion and signaling; examples include intestinal epithelial microvilli, vascular endothelial cells, and red blood cells.
The glycocalyx is an intracellular cytoskeletal network inside the membrane; it primarily generates ATP; examples include mitochondria, skeletal muscle fibers, and neurons.
The extracellular membrane is a second lipid bilayer outside cells that blocks all solute movement; examples include cartilage matrix, bone osteocytes, and pancreatic acinar cells.
The glycocalyx is a nuclear envelope carbohydrate layer that controls gene transcription; examples include hepatocyte nuclei, keratinocyte nuclei, and oligodendrocyte nuclei.
Identify the network that extends outward from the surface of cells and is composed of glycoproteins and proteoglycans.
Glycocalyx
Cytoskeleton
Basal lamina
Nucleolus
Which statement from the quick key correctly describes proteoglycans?
Mostly carbohydrate with some protein included
Mostly protein with some carbohydrate attached
Almost always refers to sphingolipids with attached carbohydrate
Primarily nucleic acid with carbohydrate side chains
According to the quick key, which description best fits glycoproteins?
Mostly protein with some carbohydrate attached
Mostly carbohydrate with some protein included
Primarily lipid with carbohydrate attached
Primarily nucleic acid with protein attached
According to the quick key, glycolipids almost always refer to which class of lipids with attached carbohydrate?
Sphingolipids
Triacylglycerols
Phosphatidylcholines
Sterols
Select the roles explicitly attributed to the glycocalyx.
Protects the outer surface of the cell from mechanical disruption
Allows the cell to attach itself to other surfaces
Serves as a key mechanism for the immune system to identify self versus foreign cells
Replicates nuclear DNA during cell division
Which term is often interchanged with extracellular matrix for most mammalian cells, though the extracellular matrix has more components than just carbohydrate?
Glycocalyx
Cytoplasm
Basement membrane
Ribosome
Which statement best captures how the glycocalyx relates to the cell wall in bacteria versus eukaryotic cells?
The glycocalyx helps serve a similar role to the cell wall
The glycocalyx replaces the nucleus in eukaryotic cells
The glycocalyx is a form of cytoskeletal filament
The glycocalyx is identical to the plasma membrane
Select the mammalian cell types listed as having a glycocalyx.
Mature platelets
Vascular endothelial cells
Sperm cells
Fertilized ovum
Cancer cells
Which function is associated with the glycocalyx of mature platelets?
Allows them to adhere to injury site
Reduces friction of blood flow
Allows them to adhere to ovum
Allows it to adhere to uterine lining
Which function is associated with the glycocalyx of vascular endothelial cells?
Reduces friction of blood flow
Allows them to adhere to injury site
Allows them to adhere to ovum
Allows it to adhere to uterine lining
Which function is associated with the glycocalyx of sperm cells?
Allows them to adhere to ovum
Allows them to adhere to injury site
Reduces friction of blood flow
Allows it to adhere to uterine lining
Which function is associated with the glycocalyx of a fertilized ovum?
Allows it to adhere to uterine lining
Allows them to adhere to ovum
Reduces friction of blood flow
Allows them to adhere to injury site
Which statement describes how cancer cells use their glycocalyx?
They have unique glycocalyx structure, allowing them to be identified against normal cells
Their glycocalyx is absent, preventing immune recognition
Their glycocalyx is identical to that of platelets
Their glycocalyx functions only in mechanical protection
Which feature of the glycocalyx is highlighted as aiding immune identification of self versus foreign cells?
It is unique to every individual
It is composed entirely of nucleic acids
It is restricted to bacteria only
It degrades rapidly in blood
Recognize the glycosaminoglycan group of molecules and recall the six types by name. Which set lists only glycosaminoglycans?
Chondroitin sulfate
Dermatan sulfate
Heparin
Heparan sulfate
Keratan sulfate
Based on the diagram showing locations of proteoglycans, glycoproteins, and glycolipids relative to the cell membrane, which molecule type is located in the cell membrane?
Glycolipids
Proteoglycans
Glycoproteins
Free polysaccharides
Which description best characterizes glycosaminoglycans (GAGs)?
Heteroglycans with linear, regular repeating disaccharide units
Homopolysaccharides with highly branched oligosaccharide chains
Neutral lipids composed of repeating triacyl units
Fibrous proteins formed from peptide repeats
Which item is NOT listed among the six types of GAGs on this page?
Hyaluronic acid (HA)
Chondroitin sulfates (CS)
Keratan sulfate (KS)
Dermatin sulfate (DS)
Cellulose
Which statement accurately reflects the modification of the amino sugar in GAGs and the exception for heparin?
Most GAGs have acetylated amino sugars, whereas heparin has sulfated amino sugars
Most GAGs have sulfated amino sugars, whereas heparin has acetylated amino sugars
All GAGs, including heparin, have acetylated amino sugars
All GAGs, including heparin, have sulfated amino sugars
In most GAGs, the second monosaccharide is an alduronic acid; which GAG is the exception where it is galactose?
Keratan sulfate (KS)
Hyaluronic acid (HA)
Chondroitin sulfates (CS)
Heparan sulfates (HS)
Which GAG lacks sulfate substitution on hydroxyl groups?
Hyaluronic acid (HA)
Chondroitin sulfates (CS)
Dermatin sulfate (DS)
Heparin
Which pair names the alduronic acids noted for GAGs on this page?
Glucuronic acid and iduronic acid
Galacturonic acid and mannuronic acid
Lactic acid and pyruvic acid
Malic acid and citric acid
What functional consequence is attributed to multiple sulfation patterns in GAG sequences?
Specific recognition of other proteins, especially growth factors
Long-term energy storage
Catalysis of peptide bond formation
Facilitated diffusion across membranes
Which list correctly reproduces the six GAG types named on this page?
Hyaluronic acid; chondroitin sulfates; keratan sulfate; dermatin sulfate; heparin; heparan sulfates
Hyaluronic acid; chondroitin sulfates; keratan sulfate; dermatan sulfate; heparin; keratan sulfates
Hyaluronic acid; chondroitin sulfates; keratan sulfates; dermatan sulfate; heparin; heparan sulfate
Hyaluronic acid; chondroitin sulfates; keratan sulfate; dermatan sulfate; heparin; chondroitin sulfates
Identify some functional roles of proteoglycans. Select all that apply.
Key component of the extracellular matrix that interacts directly with collagen, fibronectin, and laminin
Found in synovial fluid, vitreous humor of the eye, arterial walls, bone, and cartilage
Forms a meshwork that limits exposure of the cell surface to various agents
Acts as a lubricant and shock absorber that can expand and compress easily
Highly variable in structure but all contain one or more types of GAGs
Compare and contrast O-linked versus N-linked glycoproteins, including the complexity of the carbohydrate group typical of each type, and some general functions of O-linked versus N-linked glycoproteins. Which statement best summarizes the differences described?
O-linked glycoproteins have highly varied, complex carbohydrate cores that signal protein targeting, while N-linked glycoproteins usually carry 1–3 sugars affecting recognition and structure.
O-linked glycoproteins usually carry 1–3 sugars with effects on recognition and structural properties, whereas N-linked glycoproteins have a common core and more complex, highly varied structures that can signal location and function.
Both O-linked and N-linked glycoproteins typically have 1–3 sugars and mainly influence recognition, with little role in targeting.
N-linked glycoproteins attach to hydroxyl groups and are simpler than O-linked, which attach to amide nitrogens and are more complex.
In N-linked glycoproteins, saccharides are attached via which specific atom and amino acid side chain?
Hydroxyl oxygen of serine
Hydroxyl oxygen of threonine
Hydroxyl oxygen of hydroxylysine
Amide nitrogen of asparagine
Carboxyl oxygen of glutamate
O-linked saccharides are attached to the O atom of which side-chain types according to the description provided? Select all that apply.
Serine
Threonine
Hydroxylysine
Asparagine
Glutamate
Which statement about the relative complexity of O-linked versus N-linked glycoproteins is accurate based on the provided notes?
O-linked glycoproteins tend to be simpler, usually with 1–3 sugars.
N-linked glycoproteins tend to be simpler, usually with 1–3 sugars.
O-linked glycoproteins always have a common core.
N-linked glycoproteins never signal location or function.
Which functional role is specifically attributed to the carbohydrate structure of N-linked glycoproteins in the notes?
Primarily affects recognition and structural properties
Signals location and function
Prevents glycosylation of other proteins
Causes degradation in lysosomes
According to the notes, which patterns of carbohydrate addition per protein are possible?
Exactly one carbohydrate per protein only
A single carbohydrate group per protein, or many single carbohydrates, or many groups added per protein
Only multiple carbohydrate groups per protein
No carbohydrates are ever added to proteins
From the notes: “O-linked saccharides of glycoproteins — Function in many cases is to force protein to adopt an extended conformation.” What is the primary function described for O-linked saccharides of glycoproteins?
To force the protein to adopt an extended conformation
To store metabolic energy for the cell
To catalyze proteolysis of nearby proteins
To fold the protein into a compact globular core
The notes state that extended conformations resemble “bristle brushes” and that this structure extends functional domains up out of the glycocalyx. Which roles are suggested for this bristle brush structure? (Select all that apply.)
A protective role that keeps agents away from the surface
A receptor role that helps agents find receptors above the extracellular matrix
An energy-harvesting role that generates ATP
A role in intracellular protein import through the nuclear pore
According to the section “N-linked oligosaccharides — Many functions known or suspected,” which functions are described for oligosaccharides? (Select all that apply.)
Alter chemical and physical properties of proteins
Stabilize protein conformations and/or protect against proteolysis
Directly produce ATP during cellular respiration
Their cleavage from N-linked glycoproteins in blood can target those proteins for degradation in the liver
The notes say: “Cleavage of monosaccharide units from N-linked glycoproteins in blood targets them for degradation in the liver.” What outcome is described for such cleavage?
The glycoproteins are targeted for degradation in the liver
The glycoproteins are transported to the nucleus for transcriptional regulation
The glycoproteins become activated as membrane receptors
The glycoproteins are recycled to the Golgi apparatus for re-glycosylation
Recall the synthesis of N-linked glycoproteins and define the role of dolichol phosphate in this process. What role does dolichol phosphate play?
It serves as a lipid-linked carrier on the ER membrane that assembles the oligosaccharide precursor for transfer to asparagine
It acts as a cytosolic kinase that phosphorylates sugars before glycosylation
It is a protease that removes signal peptides during protein translocation
It is a nuclear transcription factor that activates glycosylation genes
Relate the role of mannose phosphorylation in N-linked glycoprotein degradation. In the trafficking and sorting of glycoproteins, phosphorylated mannose residues act as a signal; what does this signal do?
Targets glycoproteins to lysosomes via the mannose-6-phosphate receptor for degradation
Enhances glycoprotein secretion from the Golgi to the extracellular space
Stabilizes glycoproteins at the plasma membrane to prevent endocytosis
Directs glycoproteins back to the endoplasmic reticulum for refolding
Identify the three major components of the eukaryotic extracellular matrix.
Fibrous proteins, proteoglycans/glycosaminoglycans, and adhesive glycoproteins
Microtubules, intermediate filaments, and actin microfilaments
Phospholipids, cholesterol, and glycolipids
DNA, RNA, and histones
Relate the general function of elastin, fibrillin, and elastic fibers in the extracellular matrix.
Provide stretch and recoil to tissues such as arteries and lungs
Form rigid tensile cables that resist stretching
Mediate cell–matrix signaling through transmembrane receptors
Serve as soluble carriers for growth factors in the bloodstream
Relate the general function of laminin and fibronectin (soluble and insoluble) in the extracellular matrix.
Mediate cell adhesion and matrix assembly; laminin organizes basement membranes while fibronectin links cells to matrix
Generate contractile force within muscle cells
Transport proteins across the plasma membrane
Break down matrix components during remodeling
Relate the general function of integrins in the extracellular matrix.
Transmembrane receptors that connect cells to the ECM and transmit signals bidirectionally
Secreted enzymes that degrade ECM components
Structural glycoproteins that form elastic fibers
Cytosolic chaperones that fold nascent glycoproteins
Relate the general function of collagen in the extracellular matrix.
Provides tensile strength as the principal fibrous protein of connective tissues
Acts primarily as a signaling receptor at the cell surface
Functions as a soluble adhesive molecule in blood plasma
Stores calcium in lysosomes for release during stress
Compare and contrast the glycocalyx of Gram-positive and Gram-negative bacteria.
Both Gram-positive and Gram-negative bacteria can produce a glycocalyx as a capsule or slime layer composed mainly of polysaccharides.
In Gram-positive bacteria, the glycocalyx lies external to the thick peptidoglycan layer; in Gram-negative bacteria, it lies external to the outer membrane.
Only Gram-negative bacteria form a glycocalyx; Gram-positive bacteria do not.
The glycocalyx in Gram-positive bacteria is always protein-based, whereas in Gram-negative bacteria it is always polysaccharide-based.
Bacterial Glycocalyx – Peptidoglycan. According to the description provided, peptidoglycan is best characterized as what kind of mixture?
DNA and membrane lipids
Glycosaminoglycans and short peptides
Sterols and sphingolipids
Long polypeptides and simple sugars
Bacterial Glycocalyx – Peptidoglycan. Which component is noted as an abundant glycolipid in Gram‑negative bacteria?
Teichoic acid
Lipopolysaccharide (LPS)
Peptidoglycan
Phosphatidylserine
Bacterial Glycocalyx – Peptidoglycan. Based on the paired schematic of Gram‑positive versus Gram‑negative bacterial cell walls, which statement accurately describes the peptidoglycan layer in Gram‑positive bacteria?
A thin peptidoglycan layer lies between inner and outer membranes
Peptidoglycan is absent; the outer layer is lipopolysaccharide
A thick peptidoglycan layer lies external to the plasma membrane
Peptidoglycan is confined within the cytoplasm
Lecture 10 – Myoglobin and Hemoglobin. Heme is described as an iron porphyrin structure. Which description best matches this definition?
A small aliphatic tetrapeptide chelating zinc ions
A large, aromatic tetrapyrrole with an iron atom centered and substituent groups projecting from the core
A carbohydrate ring that coordinates copper and binds oxygen irreversibly
A phospholipid with an iron headgroup embedded in membranes
Lecture 10 – Myoglobin and Hemoglobin. Which statement about the iron atom in heme and reversible oxygen binding is most accurate?
Fe3+ enables reversible O2 binding without geometric constraints
Fe2+ enables reversible O2 binding, and the local geometry of the Fe2+ atom substantially influences this binding
O2 binds irreversibly to heme regardless of iron oxidation state
Reversible O2 binding occurs only when iron is not part of a porphyrin
Lecture 10 – Myoglobin and Hemoglobin. Which description best summarizes the roles and properties of myoglobin (Mb) and hemoglobin (Hb) stated here?
Fibrous proteins that exclude heme and irreversibly bind oxygen
Globular proteins that contain heme and have the property of reversible O2 binding; thus they serve as oxygen‑binding and transport proteins
Membrane enzymes that degrade heme to release oxygen
Cytoskeletal proteins that store oxygen via covalent attachment
Compare and contrast the general structural features of hemoglobin versus myoglobin, in terms of primary, secondary, tertiary and quaternary structure. Which statement best captures the key contrast emphasized in the worksheet?
Hemoglobin and myoglobin are identical at all structural levels.
Hemoglobin differs chiefly in quaternary structure as a tetramer, while myoglobin is a single polypeptide chain.
Myoglobin has four subunits, whereas hemoglobin is a single-chain protein.
They have completely different tertiary structures but the same quaternary arrangement.
Hemoglobin and myoglobin function very differently as oxygen transport and storage proteins. Which description matches their locations and roles as presented?
Hemoglobin is found in skeletal muscle and stays in place; myoglobin circulates in the blood.
Hemoglobin is found exclusively in red blood cells and circulates; myoglobin is found in cardiac and skeletal muscle and serves as an oxygen storage protein in tissues.
Both hemoglobin and myoglobin circulate in the blood and sense oxygen levels.
Neither hemoglobin nor myoglobin stores oxygen in tissues.
Compare the oxygen binding curves for hemoglobin and myoglobin. Which statement reflects the behavior shown for each protein?
Hemoglobin exhibits cooperative, sigmoidal oxygen binding; myoglobin shows noncooperative, hyperbolic binding.
Both hemoglobin and myoglobin display cooperative, sigmoidal oxygen binding.
Myoglobin exhibits cooperative binding due to multiple subunits; hemoglobin binds oxygen noncooperatively.
Neither protein displays a measurable oxygen binding curve.
Adult hemoglobin consists of specific polypeptide chains that assemble via quaternary structure. Which composition is correct?
Two α-globin and two β-globin chains form one hemoglobin tetramer.
One α-globin and one β-globin chain form a dimer.
Four identical β-globin chains form the molecule.
Three α-globin chains and one β-globin chain form the tetramer.
Which statement about cooperativity in oxygen binding matches the worksheet’s description of myoglobin and hemoglobin?
Myoglobin works alone with no cooperativity; the four parts of hemoglobin work together to produce cooperativity.
Both myoglobin and hemoglobin show strong cooperativity because each is a tetramer.
Myoglobin exhibits cooperativity, while hemoglobin does not.
Neither protein demonstrates cooperativity in oxygen binding.
Compare and contrast the sigmoidal oxygen binding curve for hemoglobin versus the hyperbolic oxygen binding curve for myoglobin, in terms of structural changes in the two proteins in response to oxygen binding, and vice versa. Use the figure showing percent O2 saturation versus partial pressure of oxygen (pO2) with separate curves for hemoglobin and myoglobin; venous and arterial pO2 are indicated, and curves for working and resting muscle are shown.
Hemoglobin shows a sigmoidal curve due to cooperative O2 binding among subunits and a T-to-R conformational transition, whereas myoglobin shows a hyperbolic, noncooperative curve.
In hemoglobin, O2 binding draws the heme Fe into the porphyrin plane and propagates conformational changes to other subunits; myoglobin lacks inter-subunit cooperativity.
At venous pO2, hemoglobin has lower saturation than myoglobin, facilitating O2 delivery to working muscle, while myoglobin remains more saturated.
Myoglobin functions primarily as an O2 storage protein with high affinity across pO2 values, whereas hemoglobin is an O2 transport protein that loads in the lungs and unloads in tissues.
Both hemoglobin and myoglobin display identical hyperbolic curves because they have single oxygen-binding sites.
Define allosterism and relate this concept to oxygen binding by hemoglobin.
Allosterism is regulation in which ligand binding at one site alters activity at a distant site; in hemoglobin, O2 binding to one heme increases affinity of other subunits via cooperative conformational changes.
Allosterism refers to irreversible protein denaturation upon ligand binding; in hemoglobin, O2 permanently unfolds one subunit.
Allosterism is the tendency of O2 to bind only in capillaries and never in lungs.
In hemoglobin, O2 binding causes the heme Fe to move into the porphyrin plane, triggering a T-to-R transition that is transmitted to other subunits, exemplifying allosteric interactions.
Relate oxygen loading and unloading by hemoglobin to locations in the circulatory system.
Hemoglobin binds oxygen in the lungs and releases oxygen in tissue capillaries.
Hemoglobin binds oxygen in tissues and releases oxygen in the lungs.
Hemoglobin binds and releases oxygen only in arterial blood.
Hemoglobin maintains identical saturation in arterial and venous blood and does not load or unload oxygen.
Define the term allosteric modulator in the context of hemoglobin and its oxygen binding affinity.
An agent that binds the same site as O2 to increase affinity
An agent that binds a different site and alters hemoglobin structure, changing O2 affinity
A molecule that irreversibly denatures hemoglobin
A factor that only changes O2 concentration without interacting with hemoglobin
In the Bohr effect, what is the impact of increased H+ (lower blood pH) on hemoglobin’s affinity for O2 ?
Affinity increases
Affinity decreases
Affinity does not change
Affinity first increases then decreases
When CO2 binds directly to hemoglobin, how is O2 binding affinity affected?
Affinity increases markedly
Affinity decreases
Affinity is unchanged
Affinity fluctuates with temperature only
How does 2,3-bisphosphoglycerate (2,3-BPG) influence hemoglobin’s O2 binding affinity?
It increases affinity by stabilizing the O2 -bound state
It decreases affinity by stabilizing a conformation less receptive to O2
It has no effect on affinity
It increases affinity only in fetal hemoglobin
Which statement best describes positive cooperativity in hemoglobin?
After one subunit binds O2 , the next subunit is more likely to bind O2 readily
After one subunit binds O2 , the next subunit is less likely to bind O2
Cooperativity means each subunit binds O2 independently
Cooperativity occurs only when hemoglobin dissociates into monomers
What mechanism communicates a conformational change in one hemoglobin subunit to the others?
Long-distance covalent bonding between subunits
Changes in globin gene expression within red cells
Physical contact interactions between subunits that alter weak inter-subunit contacts
Dissociation of hemoglobin into separate monomers
Select the physiological allosteric modulators of hemoglobin listed on the worksheet.
2,3-bisphosphoglycerate (2,3-BPG)
Hemoglobin chain composition
Blood pH
CO2 levels
Identify the structural modification of hemoglobin that gives rise to the sickle cell variant (HbS), and relate how this modification affects hemoglobin structure, oxygen binding ability, and red blood cell morphology.
A single amino acid substitution of glutamate to valine at position 6 of the β chain creates a hydrophobic patch that promotes polymerization of deoxygenated HbS.
The mutation increases Hb’s affinity for 2,3-BPG, thereby raising oxygen release and preventing polymer formation.
Polymerized HbS distorts the red blood cell into a sickle shape and reduces its flexibility, leading to capillary blockage.
Aggregated HbS is an efficient oxygen transporter that improves tissue oxygenation compared with HbA.
Deoxygenated HbS fibers form rope-like structures that cause Hb to fall out of solution inside the red blood cell.
Relate hemoglobin isoform switching in a developing fetus versus an adult.
Fetal blood is dominated by HbF (α2γ2), which transitions after birth to adult HbA (α2β2) as γ-chain expression decreases and β-chain expression increases.
Fetal blood is dominated by HbA (α2β2) throughout gestation and switches to HbF (α2γ2) only in adulthood.
Both fetus and adult primarily express HbS (α2β2 with Val at position 6), with minimal change at birth.
The fetus and adult express identical amounts of HbF and HbA, with no developmental switching.
Compare and contrast the oxygen binding properties of fetal hemoglobin (HbF) versus maternal hemoglobin (HbA), including the structural basis for this difference.
HbF has higher oxygen affinity than HbA because its γ chains bind 2,3-BPG less effectively, facilitating oxygen transfer from mother to fetus.
HbF has lower oxygen affinity than HbA because its γ chains bind 2,3-BPG more strongly, promoting oxygen release by the fetus.
HbF and HbA have identical oxygen affinities because their interactions with 2,3-BPG are the same.
HbF’s higher oxygen affinity is due to stronger heme–oxygen covalent bonding unique to fetal hemoglobin.
