Exam 2 (Chap 6-8, 11) Flashcards
What are enzymes?
Powerful and specific catalysts that increase rates of chemical reactions without being altered at the end of the reaction.
Almost every biochemical reaction is catalyzed by an enzyme.
What is the active site of an enzyme?
A specialized pocket where enzymatic reactions happen.
The active site provides a specific environment for reactions to occur rapidly.
What is a substrate?
The molecule that is bound in the active site and acted upon by the enzyme.
The substrate binds to the enzyme’s active site.
What role do cofactors play in enzymatic reactions?
They participate in catalysis or stabilize protein structure.
Some enzymes require cofactors and coenzymes for their activity.
Define coenzymes.
Organic or metalloorganic molecules that carry functional groups necessary for enzymatic activity.
Coenzymes can be tightly or covalently bound to enzymes.
What is a holoenzyme?
The complete enzyme with its coenzyme or cofactor.
In contrast, an apoenzyme is the enzyme without its cofactor.
What is the enzyme classification based on?
The type of reaction they catalyze.
All enzymes have formal E.C. numbers and names.
What does the suffix ‘ase’ indicate?
It typically indicates an enzyme that converts a substrate (S) to a product (P).
Enzymes are not consumed during the reaction.
What is the transition state (TS)?
The point at which the formation of substrate or product is equally likely to happen, requiring high energy.
ΔG‡ is the free energy associated with this transition state.
What effect do enzymes have on activation energy?
Enzymes lower the activation energy (ΔG‡) of a reaction, allowing it to proceed faster.
They do not change the overall free energy change (ΔG) between reactants and products.
What is a rate-limiting step?
The highest activation energy that determines the overall rate of the reaction.
This step is crucial for the reaction kinetics.
What is the relationship between equilibrium constant (K’) and free energy?
The equilibrium constant is directly related to standard free energy change (ΔG’°).
ΔG’° = -RT * ln(K’).
Fill in the blank: Enzymes alter ______, not equilibria.
RATES
True or False: Enzymes change the free energy of the substrate and product.
False
Enzymes do not alter the free energy (ΔG) between reactants and products.
What is the role of reaction intermediates?
Species with a limited lifetime that are formed during the reaction process.
Examples include ES (enzyme-substrate complex) and EP (enzyme-product complex).
What does a negative ΔG indicate?
A thermodynamically favorable reaction, meaning products have lower free energy than reactants.
This indicates that the reaction can occur spontaneously.
How do enzymes stabilize the transition state?
By lowering the energy barrier to reaching the product state.
This stabilization is key to enhancing reaction rates.
Which of the following aspects of a biochemical reaction is changed by an enzyme?
Free energy (G) of the substrate
Free energy (G) of the product
ΔG’° for the conversion of S -> P
ΔG‡ for the conversion of S -> P
K’eq for the conversion of S -> P
ΔG‡ for the conversion of S -> P
What is the transient complex of the enzyme with the substrate called?
ES
ES stands for enzyme-substrate complex.
What is the transient complex of the enzyme with the product called?
EP
EP stands for enzyme-product complex.
What do enzymes do?
Enzymes are catalysts that speed up chemical reactions without being consumed.
How do enzymes accelerate the conversion of substrate into product?
By lowering the activation energy (ΔG‡).
Do enzymes alter equilibria?
No, enzymes alter rates, not equilibria.
What is the range of enzyme rate enhancements (k_cat/k_uncat)?
5 to 17 orders of rate enhancements.
What is the source of ‘energy’ for enzymes?
Binding energy from non-covalent interactions between enzyme and substrate.
What types of interactions contribute to binding energy?
- H-bonds
- Van der Waals
- Electrostatic interactions
What is the role of weak enzyme-substrate interactions?
They produce binding energy (ΔG_B).
What is enzyme specificity derived from?
Multiple weak interactions between enzyme and substrate.
What does the term ‘induced fit’ refer to?
The change in conformation of enzymes when they interact with substrates.
What are the three additional catalytic mechanisms employed by enzymes?
- Acid-base catalysis
- Covalent catalysis
- Metal ion catalysis
Define acid/base catalysis.
Proton transfer between enzyme and substrate.
What is the difference between specific acid/base catalysis and general acid/base catalysis?
- Specific: acid/base from water (H3O+ or OH-)
- General: acid/base from anything else
What happens during the pre-steady state of enzyme reactions?
ES complex formation occurs, lasting microseconds or less.
What characterizes the steady state in enzyme reactions?
The concentration of ES remains constant.
What does V0 represent in enzyme kinetics?
The initial velocity (or initial rate) of the reaction.
What is the Michaelis constant (K_m)?
K_m = (k-1 + k2) / k1, the ratio of loss vs. gain of the Michaelis complex (ES).
What is Vmax in enzyme kinetics?
Vmax = k2 * [E_t], maximum velocity when the enzyme is saturated as ES.
What occurs when the substrate concentration [S] is much greater than the enzyme concentration [E]?
Steady state for ES complex is achieved.
What happens to substrate entropy during enzyme catalysis?
Substrate entropy is lowered, promoting catalysis.
What is the result of weak bonds formed between substrate and enzyme?
Desolvation of the substrate.
True or False: Enzymes are consumed during the reactions they catalyze.
False.
What is the role of cofactors and prosthetic groups in enzymatic reactions?
They promote catalysis by participating in bond cleavage and formation.
What is the maximum velocity (Vmax) formula in enzyme kinetics?
Vmax = k2 * [Et]
Maximum V0 occurs when enzyme is saturated as ES, and k2 governs the conversion of ES to E + P.
What is the Michaelis constant (Km)?
Km = (k-1 + k2) / k1
It represents the ratio of loss vs. gain of the Michaelis complex, ES.
What does a lower Km indicate about enzyme affinity?
Higher affinity for substrate
Km values are akin to dissociation constants.
Fill in the blank: The Michaelis-Menten equation is V = _____ / (Km + [S]).
Vmax
What is the significance of the steady state in the Michaelis-Menten model?
The enzyme-substrate complex (ES) is in a steady state where its rate of formation equals its rate of breakdown.
True or False: The accumulation of product is negligible in the Michaelis-Menten model.
True
What is the Lineweaver-Burk equation?
1/V = (Km/Vmax)(1/[S]) + 1/Vmax
It is derived by inverting the Michaelis-Menten equation and rearranging terms.
What happens to Vmax in the presence of a competitive inhibitor?
No effect on Vmax
Vmax remains unchanged because increasing [S] can overcome the inhibitor.
What does kcat represent?
Turnover number
It describes the limiting rate of substrate to product at saturating substrate concentration.
What is the effect of uncompetitive inhibition on Km and Vmax?
Lower Vmax and lower apparent Km
Uncompetitive inhibitors bind only to the ES complex.
Fill in the blank: In mixed inhibition, the inhibitor can bind to both _____ and _____ to form ESI or EI.
ES, E
What is the relationship between kcat and Km in determining catalytic efficiency?
Catalytic efficiency = kcat/Km
A higher kcat/Km ratio indicates a higher rate of catalysis.
What does Km tell you about substrate binding affinity?
It indicates the substrate concentration at which the reaction rate is half of Vmax.
What is a key assumption of the Michaelis-Menten model?
The enzyme-substrate complex never dissociates in the steady state.
What is the significance of the double-reciprocal plot?
It linearizes the Michaelis-Menten equation for easier calculation of Vmax and Km.
Which type of enzyme inhibition increases the apparent Km?
Competitive inhibition
The apparent binding affinity of substrate is reduced.
What is the main factor that can limit kcat values?
Diffusion
Some enzymes are limited by how quickly substrate can reach the active site.
What does the term ‘ternary complex’ refer to in multi-substrate reactions?
A complex formed by three or more partners during the reaction.
What is the effect of a high concentration of substrate in uncompetitive inhibition?
Uncompetitive inhibition is most effective at high [S].
What does the term ‘ping-pong mechanism’ refer to?
A type of enzyme mechanism where the substrate is released before a second substrate binds.
Fill in the blank: The apparent Km increases by a factor of _____ in the presence of a competitive inhibitor.
α
What is the effect of inhibitors on Vmax?
Inhibitors lower Vmax because less ES is available.
Vmax is defined as k_cat * [Et], where [Et] is the total enzyme concentration.
What happens to the apparent Km when an inhibitor is present?
The apparent Km increases because more substrate is needed to achieve Vmax/2.
This occurs due to the depletion of ES by the inhibitor.
What does mixed inhibition affect?
Mixed inhibition affects both substrate binding and catalysis.
What is the characteristic change in Km for competitive inhibition?
Km decreases (x-intercept moves left) while Vmax remains the same.
This indicates that the inhibitor competes with the substrate for binding to the enzyme.
What happens to Vmax and Km in uncompetitive inhibition?
Km decreases (x-intercept moves left) and Vmax decreases (y-intercept moves up).
In mixed inhibition, how do Km and Vmax change?
Km increases (x-intercept moves right) and Vmax decreases (y-intercept moves up).
Which type of enzyme inhibition can be overcome by increasing substrate concentration?
Competitive inhibition.
True or False: Uncompetitive inhibition can be overcome by increasing substrate concentration.
False.
Fill in the blank: Inhibitors bind to _____ and free E and remove part of the E from the reaction.
[ES].
What occurs when EI prevents S binding?
Reduces [ES], making it appear that S binds with lower affinity.
Describe the effect of reversible inhibition on reciprocal plots.
Km increases (x-intercept moves right) and Vmax remains the same (y-intercept same).
Which of the following is NOT an assumption of the Michaelis-Menten model of enzyme kinetics?
- Reversion of product back to substrate is negligible
- The accumulation of product is negligible
- Substrate concentration is higher than enzyme concentration
- The enzyme:substrate complex never dissociates
- The enzyme:substrate complex is in a “steady state”
The enzyme:substrate complex never dissociates
Which type of enzyme inhibition can be overcome by increasing the substrate concentration?
- Competitive inhibition
- Uncompetitive inhibition
- Mixed inhibition
- Irreversible inhibition
- All of them
Competitive inhibition
What is enzyme specificity?
Enzyme specificity refers to the ability of an enzyme to select and catalyze a particular substrate.
What is the Michaelis-Menten model?
The Michaelis-Menten model describes the kinetics of enzymatic reactions, relating reaction rate to substrate concentration.
Fill in the blank: The kinetic constant that reflects the maximum rate of an enzymatic reaction is called _______.
kcat
What distinguishes reversible from irreversible enzyme inhibition?
Reversible inhibition can be overcome by increasing substrate concentration, while irreversible inhibition permanently modifies the enzyme.
What is an example of irreversible enzyme inhibition?
The reaction of chymotrypsin with diisopropylfluorophosphate (DIFP) leads to irreversible inhibition of the enzyme.
How does pH affect enzyme activity?
pH alters ionization of R groups, coenzymes, and cofactors, which may affect the enzyme’s three-dimensional structure and active site chemistry.
What is the optimal pH for pepsin?
The optimal pH for pepsin is approximately 1.6.
What are the three key active site residues in chymotrypsin?
- Ser195
- His57
- Asp102
What happens during the first step of the chymotrypsin reaction?
The substrate binds to the chymotrypsin active site, with the aromatic side chain fitting into a hydrophobic pocket.
True or False: Allosteric enzymes have separate binding sites for molecules that can affect catalysis.
True
Fill in the blank: The process where an enzyme’s activity is inhibited when plenty of product is available is called _______.
feedback inhibition
What is a characteristic of allosteric enzymes compared to Michaelis-Menten enzymes?
Allosteric enzymes exhibit sigmoid kinetics instead of hyperbolic kinetics.
What does K0.5 represent in allosteric enzyme kinetics?
K0.5 is analogous to Km but represents the substrate concentration at which the reaction rate is half of Vmax for allosteric enzymes.
What does the term ‘nucleophile’ refer to in the context of chymotrypsin?
A nucleophile is a species that donates an electron pair to form a chemical bond; in chymotrypsin, Ser195 acts as the nucleophile.
What is the significance of the oxyanion hole in chymotrypsin?
The oxyanion hole stabilizes the negative charge on the tetrahedral intermediate during the reaction.
What is the role of His57 in the chymotrypsin reaction?
His57 acts as a proton donor/acceptor, facilitating the nucleophilic attack by Ser195.
What is an example of a positive allosteric modulator?
ATP acts as a positive allosteric modulator in some allosteric enzymes.
What is the relationship between substrate concentration and Km when the enzyme is functioning efficiently?
When substrate concentration is much greater than Km, the enzyme operates near Vmax.
What type of reaction does chymotrypsin catalyze?
Chymotrypsin catalyzes the hydrolytic cleavage of polypeptide bonds.
What is the effect of cellular metabolism on enzyme activity and pH?
A decrease in pH due to cellular metabolism typically decreases enzyme activity.
What is the significance of the catalytic triad in enzymes?
The catalytic triad consists of key residues that work together to facilitate catalysis.
What is the effect of decreased cellular metabolism on enzyme activity?
Would decrease enzyme activity.
At what pH is the enzyme most active?
pH 7
What is the initial rate of an enzyme-catalyzed reaction represented by?
V0
What does Vmax represent in enzyme kinetics?
Maximum V0 at infinite [S]
How is kcat calculated?
Observed Vmax normalized to amount of enzyme present = Vmax/[Et]
What is Km in enzyme kinetics?
[S] at 1/2 Vmax
What does Km equal if k2 is slow relative to S binding?
Same as Kd
What is the formula for catalytic efficiency of an enzyme?
kcat / Km = catalytic efficiency
Kcat= catalytic rate constant or turnover number
Km= Michaelis constant (synonymous with K0.5)
What is the Michaelis-Menten equation?
V0 = Vmax [S] / (Km + [S])
What are the assumptions of the Michaelis-Menten model?
Steady state assumption, formation of ES complex
What does a double reciprocal Lineweaver-Burk plot represent?
1/V0 vs. 1/[S]
What indicates the formation of a ternary complex in Lineweaver-Burk plots?
Intersection of lines
What does NO intersection in Lineweaver-Burk plots imply?
NO ternary complex is formed — ‘ping pong’ mechanism
What happens to the apparent Km when reversible inhibitors are present?
It can go up or down
What happens to the apparent Vmax with reversible inhibitors?
It can go up or down
What are the three components of nucleotides?
- Nitrogenous Base
- Phosphate
- Ribose (a pentose)
Ribose is found in RNA, while deoxyribose is found in DNA.
What distinguishes ribose from deoxyribose?
Ribose has a 2’ OH group; deoxyribose has a 2’ H
This structural difference impacts the stability of RNA and DNA.
What is a nucleoside?
A nucleotide without the phosphate group
Nucleosides are composed of a base and sugar.
What are the two parent compounds of nucleobases?
- Pyrimidine
- Purine
These compounds form the basis of DNA and RNA nucleobases.
What type of bond is formed in nucleobases?
N-β-glycosyl bond formed by removal of water
This bond connects the base to the sugar.
How are nucleobases characterized?
They are weak bases and aromatic molecules
Most bonds in nucleobases have double bond character.
What bases are present in DNA?
- Adenine (A)
- Guanine (G)
- Cytosine (C)
- Thymine (T)
Thymine is unique to DNA; uracil (U) replaces it in RNA.
What is the significance of hydrogen bonding in DNA?
It stabilizes the double helix structure
A-T has 2 hydrogen bonds, while G-C has 3, making G-C pairs stronger.
What is the primary structure of DNA?
Nucleotide sequence
This sequence determines the genetic information encoded in DNA.
What is the secondary structure of DNA?
Right-handed helix
This refers to the physical shape of the DNA molecule.
What are the ends of nucleic acids referred to as?
5’ and 3’ ends
This directionality is important for replication and transcription.
What is the pKa of phosphate groups in nucleic acids?
Approximately 0
This means they always have a negative charge.
Which is less stable RNA or DNA and why?
RNA is less stable due to the ribose 2’ OH group
This makes RNA more prone to hydrolysis.
What are the three structures of DNA discovered to date?
- A-form
- B-form
- Z-form
B-form is most common in vivo; Z-form is linked to gene regulation.
What is a characteristic of Z-DNA?
Found in crystals near promoters
It may play a role in gene regulation and genetic recombination.
What type of DNA structures can palindromes form?
Hairpins and cruciforms
These structures can be recognized by many DNA-binding proteins.
What does Hoogsteen base pairing allow for?
Formation of triple-helical DNA
It involves two pyrimidine strands and one purine strand.
What is a G-tetraplex?
A structure formed by four strands of guanosine bases
It occurs in telomeres at the ends of chromosomes.
What is the significance of torsion angles in DNA structure?
They affect the DNA’s structure and may be important for protein binding
This influences gene regulation.
True or False: RNA is more stable than DNA because it has a 2’ OH.
False
RNA is less stable than DNA due to the presence of the 2’ OH group.
Fill in the blank: Nucleic acids are made up of three main parts: ______, sugar, phosphate.
nucleobase
These components are essential for the structure of nucleic acids.
What are the two orientations that chromosomes can have?
Parallel or anti-parallel
Which form of DNA does it predominantly adopt?
A-form
Is the double helix of DNA left-handed or right-handed?
Right-handed
What do purines pair with in DNA structure?
Pyrimidines
What is more important for the stability of DNA, base pairing or base stacking?
Base pairing
What type of RNA codes for polypeptide chains?
mRNA (messenger RNA)
What is the genetic definition of a gene?
Cistron
What segments do eukaryotic genes include?
Exons and introns
What are untranslated regions (UTRs) important for?
Protein binding sites and regulation of translation
What is the typical stacking pattern of single-stranded RNA?
Right-handed stacking pattern
What are the three major types of RNA?
- mRNA
- tRNA
- rRNA
What is the shape of nearly all tRNA molecules?
L-shaped
What must the anticodon loop of tRNA do?
Base-pair with mRNA codon
What is a codon?
A DNA or RNA sequence of three nucleotides
What do large RNPs provide in the cell?
Catalytic function and binding sites for proteins
What is the function of a ribosome?
Site of protein synthesis in the cell
What does hybridization refer to in nucleic acids?
How strands find each other
What does the melting temperature (T_m) depend on?
GC composition and degree of complementarity between strands
What is the process of ssDNA to dsDNA called?
Annealing
What is a common nonenzymatic reaction of nucleotides that can lead to mutations?
Deamination and depurination
What are nucleotides used for in cellular processes?
- Energy currency
- Signaling
- Coenzymes
What do NTPs store energy as?
ATP/GTP
What does ATP hydrolysis provide energy for?
Biosynthesis
What role does the adenosine part of coenzymes play?
Contributes binding energy
What is the energy yield from ATP hydrolysis?
~30 kJ/mol
What are serine proteases?
Enzymes that cleave peptide bonds.
What is the significance of the approximately 10^12–fold rate acceleration in serine proteases?
It cannot be fully explained by the intrinsic chemical properties of active-site residues.
What hypothesis was proposed regarding reaction rates in serine proteases?
Reaction rates can be determined by the probability of an enzyme reaching its transitional state.
What were the three central questions of the study on serine proteases?
- Molecular changes between reaction states
- Differences between enzymatic and uncatalyzed reactions
- Energetic consequences of these differences.
What methods were used in the study of serine proteases?
- Collection of over 1,000 high X-ray structures
- Quantum mechanical calculations
- Molecular dynamics simulations
- Data from the Protein Data Bank.
What are the three groups of structures categorized in the serine proteases study?
- Apo (no substrate)
- Ground state analog (GSA)-bound
- Transition state analog (TSA)-bound.
How did the enzymatic reaction compare to the uncatalyzed reaction in solution?
The enzymatic reaction travels faster due to shortened distance of the tetrahedral intermediate.
What role does stabilization in the ground state play in serine proteases?
It drives the accelerated rate of folding.
What principle was critical in identifying ground-state destabilization in serine proteases?
Gibbs Free Energy.
What was the main focus of the study on bacterial RNA polymerase?
Understanding the role of the clamp and β-lobe in DNA loading.
How many distinct conformational states of the RNAP gate were revealed in the study?
Four distinct conformational states.
True or False: The β-lobe opens four orders of magnitude slower than the clamp.
False.
What does DNA Hybrid refer to?
A method where double-helical DNA from two species is denatured, cut, and mixed.
What are the components of a nucleotide?
- Nitrogenous base (purine or pyrimidine)
- Pentose sugar
- One or more phosphate groups.
What are the two types of nucleic acid?
- RNA
- DNA.
What is the primary purine found in both RNA and DNA?
- Adenine
- Guanine.
What are the common pyrimidine bases in RNA and DNA?
- RNA: Uracil, Cytosine
- DNA: Thymine, Cytosine.
What structural arrangement does DNA consist of?
Two antiparallel chains in a right-handed double-helical arrangement.
What is the function of messenger RNA (mRNA)?
Transfers genetic information from DNA to ribosomes for protein synthesis.
What is the purpose of the polymerase chain reaction (PCR)?
To amplify segments of DNA if the sequences of the ends of the targeted DNA segment are known.
What are the four components involved in the Sanger method of DNA sequencing?
- Template DNA
- Oligonucleotide
- DNA polymerase
- dNTPs.
Fill in the blank: The lack of 3’OH in ddNTP halts _______.
DNA synthesis.
What happens to native DNA on heating or at extremes of pH?
Undergoes reversible unwinding and separation of strands (melting).
What is the relationship between G≡C richness and melting points of DNA?
DNAs rich in G≡C pairs have higher melting points than those rich in A=T pairs.
What are the four nucleotide pools involved in DNA synthesis?
dATP, dGTP, dCTP, dTTP
What is the role of ddNTP in DNA synthesis?
Lack of 3’OH in ddNTP halts DNA synthesis
How can ssDNA strands be separated?
With electrophoresis
In DNA sequencing, what method is commonly used?
Sanger method
What technology allows modification of DNA in living organisms?
CRISPR
What are the primary structures of polysaccharides?
Composed of one, two, or several different sugars in straight or branched form
What are the most common monosaccharides?
Glucose and fructose
What does ‘mono’ mean in carbohydrates?
One
What does ‘saccharide’ mean?
Sugar
What type of sugars are reducing agents?
Monosaccharides
What is the empirical formula for carbohydrates?
(CH2O)n
What are the three major size classes of carbohydrates?
- Monosaccharides * Oligosaccharides * Polysaccharides
What is the structural difference between D-aldoses and L-aldoses?
D-aldoses have the hydroxyl on the right side, L-aldoses have it on the left
What is an epimer?
Two sugars that differ in configuration at only one carbon
What are the cyclic forms of monosaccharides represented by?
Haworth perspective formulas
What is a hemiacetal linkage?
Formation between the aldehyde group at C-1 and the hydroxyl group at C-5
What differentiates α and β anomers?
α if substituents are on opposite sides, β if on the same side of the ring
What is mutarotation?
Interconversion of α and β anomers in solution
What is the anomeric carbon?
The carbon atom in a sugar that becomes a stereocenter when the sugar forms a ring
What happens during the formation of maltose?
C-1 (anomeric) –OH of one glucose condenses with C-4 –OH of another glucose
What is the result of glycosidic bond formation?
Elimination of H2O and formation of a new bond
What type of bond is resistant to base but hydrolyzed by acid?
Glycosidic bonds
What defines a reducing end in disaccharides?
A monosaccharide unit with its anomeric carbon not involved in a glycosidic bond
What are oligosaccharides?
Short polymers of several monosaccharides joined by glycosidic bonds
What influences the secondary structures of polysaccharides?
Van der Waals interactions, H-bonding, and ionic forces
What is the significance of the anomeric carbon in sugars?
It can assume either of two configurations, α and β
What is a deoxy sugar?
A sugar where H replaces an OH
What is an acidic sugar?
A sugar where COO- replaces a C—OH
What is the process of sugar phosphorylation?
Condensation of phosphoric acid with one of the hydroxyls to trap sugars in the cell
True or False: Most cells have proteins that can transport sugar phosphates.
False
What is intrinsic to the enzyme?
program
The term ‘program’ refers to the underlying mechanisms that enable enzyme function.
Are polysaccharides identical like proteins and nucleic acids?
No, polysaccharides are quite heterogeneous
This heterogeneity is a key characteristic differentiating polysaccharides from proteins and nucleic acids.
What interactions influence the polysaccharide fold?
- van der Waals interactions
- H-bonding
- ionic forces
These interactions are similar to those influencing protein folding.
What can dihedral angles φ and ψ describe in polysaccharides?
The 3D relationship between two adjacent saccharides
This is analogous to the Ramachandran plot used for proteins.
What type of bonds link the residues in polysaccharides?
C-O bonds
Free rotation about these bonds allows flexibility in polysaccharide structures.
What type of conformations are favored in polysaccharides?
Lower energy conformations
This is similar to the behavior observed in proteins.
What secondary structure can polysaccharides form?
A coiled helical structure
This is particularly notable in starch (amylose).
What is amylose primarily composed of?
Many D-glucose units in α1→4 linkage
This structure leads to a tightly coiled helical formation.
What is the significance of the chair conformation of amylose?
It leads to a curved (180°) and tightly coiled helical structure
This structure is responsible for dense granules present in cells.
Define an α(1→4) linkage.
A glycosidic bond where the anomeric carbon (C1) of one glucose unit in α configuration is linked to the C4 carbon of the next glucose unit
This linkage is commonly found in starch and glycogen.
What are the two types of D-glucose polymers found in starch?
- Amylose (MW: ~10^3 to 10^6 Da; linear α1→4)
- Amylopectin (MW: few million Da; linear α1→4, branched at α1→6)
Each of these polymers has one reducing end.
Where do degradative enzymes act on starch?
At nonreducing ends
This allows branches to enable more rapid degradation.
What is the osmolarity effect of storing glucose as polymers?
It decreases osmolarity
High glucose concentration would cause water to enter the cell, leading to swelling and potential lysis.
What is glycogen’s primary function?
Storage of energy in animals
Glycogen is similar to amylopectin but has more branches.
What type of polymer is cellulose?
Glucose beta-linked polymer
Cellulose consists of linear polymers of D-glucose units with β1→4 linkages.
What structure do cellulose polymers adopt?
Extended structures that pack against one another
This is similar to strands in a β-sheet.
What are cellulase enzymes?
Enzymes secreted by bacteria in the stomach of termites
They are responsible for breaking down cellulose.
How does chitin differ from cellulose?
Replacement of OH at C-2 with an acetylated amino group
Chitin consists of N-acetyl glucosamine units.
Why is chitin indigestible for vertebrates?
Lack chitinase enzymes
This makes vertebrates unable to break down chitin.
What does chitin form in insects and lobsters?
Exoskeleton
Chitin is the second most abundant polysaccharide after cellulose.
What is SARS-CoV-2 also known as?
novel coronavirus 2019 (or sometimes just ‘the coronavirus’)
What disease does SARS-CoV-2 cause?
COVID-19
What is the structure of each viral capsid?
Lipid bilayer membrane and proteins
What is the spike protein (S) in SARS-CoV-2 responsible for?
Giving the virus a crown-like shape and is a glycoprotein
What is the function of the nucleocapsid protein (N) in SARS-CoV-2?
Protects the genome
What is the fluid mosaic model?
A model describing the dynamic nature of membranes with lipids and proteins freely diffusing
What is the composition of a lipid bilayer?
Two layers of phospholipids with hydrophilic heads and hydrophobic tails
What are lipid rafts?
Microdomains in the membrane enriched in sphingolipids and cholesterol, thicker and less fluid
How do unsaturated fatty acids differ from saturated fatty acids?
Unsaturated fatty acids contain double bonds, while saturated fatty acids do not
What is the main characteristic of trans fatty acids?
Found in partially hydrogenated oils and are not well metabolized by human lipases
What is the role of glycerophospholipids?
They form the basic structure of cell membranes
What is the function of the Golgi apparatus?
Processes proteins for secretion
What is the significance of the asymmetric distribution of phospholipids?
Regulates signaling and bioenergetics in organelles, cells, and tissues
True or False: Membranes are static structures.
False
What types of membrane proteins are there?
Peripheral, integral, and amphitropic
What is the main characteristic of integral membrane proteins?
Embedded in the membrane and can be removed by detergents
What does the term ‘functional asymmetry’ refer to in membranes?
Different compositions and functions of the extracellular and cytoplasmic faces
Fill in the blank: The lipid bilayer is approximately ______ thick.
~3 nm (~30 Å)
What process allows for the fusion of two membranes?
Membrane fusion
What is the role of flippases in membrane dynamics?
They keep phosphatidylserine away from the outer monolayer to prevent apoptosis
What is the hydropathy plot used for?
To predict membrane-spanning regions of proteins based on hydropathy values
What is the primary function of aquaporins?
Transport water across membranes
What is the difference between liquid-ordered and liquid-disordered phases in membranes?
Liquid-ordered is more structured, while liquid-disordered is more fluid
What are the main cellular processes that involve membrane fusion?
- Exocytosis
- Endocytosis
- Viral infection
- Fertilization
- Cellular division
What do membrane proteins interact with to be retained in the membrane?
Hydrophobic interactions with acyl portions of lipids
What is the function of lysosomes?
Recycling center of the cell
What role do mitochondria play in cells?
ATP synthesis
What is the significance of the asymmetric charge distribution in membrane layers?
It affects the membrane’s functional properties and interactions
What is the role of the endoplasmic reticulum?
- Rough ER: synthesizes proteins
- Smooth ER: synthesizes lipids
What are the characteristics of sterols?
Have mixed polar/hydrophobic character, differ from glycerophospholipids by having fused rings
What happens to lipids during transbilayer diffusion?
They diffuse very slowly between monolayers
What are lipid rafts believed to resemble?
Rafts floating across an ocean
What can alter the physical state of a membrane?
Temperature or lipid composition
What organelle is responsible for packaging proteins?
Golgi
The Golgi apparatus modifies, sorts, and packages proteins for secretion or use within the cell.
What is exocytosis?
Release of cellular material into the environment
Exocytosis is a process where substances are expelled from the cell via vesicles.
What is endocytosis?
Uptake of extracellular material from the environment
Endocytosis involves the engulfing of materials into the cell membrane.
What is the electrochemical gradient?
Combination of concentration gradient (a) and electric gradient (b)
The electrochemical gradient influences the movement of ions across membranes.
What are the types of transport across membranes?
- Simple transport
- Facilitated transport
- Primary active transport
Each type of transport has different mechanisms and energy requirements.
What is a uniport?
One molecule transporter
A uniport facilitates the transport of a single type of molecule across a membrane.
What is a symport?
Two types of molecules transported in the same direction
Symports require energy to transport both molecules simultaneously.
What is an antiport?
Two types of molecules are transported in opposite directions
Antiport transport can be either active or passive, depending on energy use.
What is GLUT1?
Type III glucose transporter, 45 kDa, with 12 helical segments
GLUT1 is a uniport that facilitates the transport of glucose across the cell membrane.
What kinetics does glucose transport follow?
Michaelis-Menten kinetics
This reflects the saturation behavior of glucose transport in cells.
What is the role of carbonic anhydrase in erythrocytes?
Catalyzes formation of bicarbonate from CO2
This reaction helps in the transport of CO2 from tissues to lungs.
What is the function of the chloride-bicarbonate exchanger?
Allows diffusion of HCO3- out of the cell when Cl- enters
This mechanism is crucial for maintaining charge balance in erythrocytes.
What is the selective K+ ion channel responsible for?
Creating action potential in neurons
This channel allows selective diffusion of potassium ions, crucial for nerve signal transmission.
True or False: K+ ions pass through the selective K+ ion channel faster than Na+ ions.
True
K+ ions have a larger radius, allowing them to move through the channel more efficiently.
What stabilizes K+ during its passage through the selective K+ ion channel?
Carbonyl backbone
The carbonyl groups help stabilize K+ ions while preventing Na+ ions from passing.
Fill in the blank: The reaction kinetics for glucose transport is modeled after _______.
Michaelis-Menten kinetics
This model describes the rate of enzymatic reactions.
The Michaelis constant Km is equal to the dissociation constant Kd under what circumstances?
A)kcat is greater than Km
B)The rate constant for the chemical step of enzyme catalysis is very slow relative to association and dissociation of the enzyme:substrate complex
C)The concentration of substrate is much greater than Km
D)The concentration of substrate is equal to the concentration of enzyme
E)None of these answers is correct
The rate constant for the chemical step of enzyme catalysis is very slow relative to association and dissociation of the enzyme:substrate complex
You are studying an enzyme of interest. You perform an enzyme activity assay at a variety of pH conditions, and observe that its maximum kcat and minimum Km are at pH 7. Which of the following is true?
A.It functions efficiently at physiological pH
B.It may have a His in the active site
C.It may have a non-His amino acid in the active site whose pKa is shifted
D.A decrease in pH due to cellular metabolism would decrease, not increase, enzyme activity
E.All of the above
All of the above
A.It functions efficiently at physiological pH
B.Since the enzyme’s maximum kcat and minimum Km occur at pH 7, this suggests that it is optimized for function at or near physiological pH
C.It may have a His in the active site
Histidine has a pKa around 6.0, meaning it can be protonated or deprotonated around neutral pH, making it a common residue involved in catalysis in enzymes that function near pH 7.
D.It may have a non-His amino acid in the active site whose pKa is shifted
There are other residues that can be involved ( ex D, E…)
E.A decrease in pH due to cellular metabolism would decrease, not increase, enzyme activity. the enzyme is most active at pH 7, a decrease in would likely lead to a reduction in enzyme activity.
F.All of the above
