Test 2 Review Flashcards
Define “energy”
The capacity to do work (to cause change)
Compare potential and kinetic energy
Potential Energy: Stored Energy
Kinetic Energy: Energy associated with motion
The energy found in glucose is an example of _ energy
Potential
Explain why cell need energy?
All living systems require an ongoing supply of energy
Photoautotrophs are capable of converting _ carbon into _ carbon, which can then be used by both heterotrophs and autotrophs for growth/development
Inorganic, organic
Humans ultimately depend on autotrophs for the production of ….
Oxygen and Glucose
What is an autotroph?
An organism that produces organic compounds from inorganic molecules
What are heterotrophs?
An organisms that produces organic compounds starting from other organic molecules
What is a phototroph?
An organism able to capture light energy and transform it up to chemical energy
What are chemotrophs?
Organisms that obtain energy by oxidizing chemical bonds in molecules
True or False? Plants make energy from the sun.
False
Define “ thermodynamics”
The study of energy transformations
What is the first law of thermodynamics?
Energy can be transferred and transformed. Energy can not be created or destroyed.
What is the second law of thermodynamics?
Every energy transfer of transformation increases the entropy of the universe. During every energy transfer some energy is unusable.
Which term indicates the amount of energy released or required by a given system?
Delta G
Define free energy
The measure of thermodynamics spontaneity of a system. The amount of energy available to do work.
What does deltaG tell us about a system?
DeltaG tells us whether a process can occur(possibility) and to what extent (directionality)
What does it mean if deltaG is zero ?
This means the system has reached equilibrium.
Can work be done by a system in equilibrium?
No
The oxidation of glucose releases 686 kcal/mol. Is this a spontaneous process?
Yes
A larger EA means a rxn will occur_ compared to a rxn with a smaller EA.
Slower
Which processes (anabolic or catabolic) are associated with a -deltaG?
Catabolic
ATP breakdown is an _process while ATP synthesis is an _
Exergonic, endergonic
Where would opposing charges occur on ATP molecule?
Between adjacent phosphates
What will opposing charges do to the free energy of the ATP molecule?
Increase the free energy
The formation of a bond between phosphate and R will result in the molecule formed being _stable compared to the phosphate group alone.
Less
True or False? The formation of a bond between phosphate and R will result in the molecule formed having a lower amount of free energy compared to the free energy of the phosphate group alone.
False
Describe the activation energy barrier for a reaction. How does EA influence rage of a rxn?
EA is the amount of energy reactant must have in order for a rxn to take place. The amount of energy needed to reach the “transition state”
Rxn rate is determined by EA
Define metabolism
Total collection of chemical reactions that take place in a cell
Differentiate between catabolic and anabolic processes
Anabolism: synthesis pathways , endergonic
Catabolism: break down pathways, exergonic
What type of molecule is ATP?
Nucleotide
What is inorganic phosphate?
Free phosphate ion, not complexed with a largest organic molecule
Explain the role of ATP in a cell
Used to do work
An enzyme will _ chemical reactions and _ activation energy.
Speed up, lower
True of False? The amino acids forming the active site must be adjacent to each other in the primary structure of the enzyme.
False
Sucrose is _ to release it’s constituent monomers, glucose and fructose.
Catabolized
The catabolism of sucrose is ….
Exergonic
True or false? Enzymes speed up a reaction by altering deltaG.
False
Based on the pH optimum, pepsin is a digestive enzyme found in the _, whereas trypsin is localized to the _
Stomach, small intestine
Pepsin and trypsin are both proteolytic enzymes. This means that they….
Catabolize proteins
Pepsin and trypsin went through the _ pathway .
Cotranslational import
True of False? A non competitive inhibitor is a type of an allosteric regulator.
True
What are the six different classes of enzymes ?
Oxidoreductases, Hydrolases, Lyases, Isomerases, Ligases
Type of hydrolase, breaks down nucleic acids by hydrolyzing bonds between nucleotides
Nucleases
Type of hydrolase, breaks down proteins by hydrolyzing bonds between nucleic acids
Proteases
Type of ligase, synthesizes molecules in anabolic reactions by condensing 2 smaller molecules
Synthases
Type of transferase, catalyzes the addition of phosphate groups to protein targets
Phosphorylase
Type of hydrolase, catalyzes the hydrolytic removal of phosphate groups from target
Phosphotase
Important group of kinases that attach phosphate groups to protein targets
Protein Kinases
Type of hydrolase, hydrolyze ATP into ADP +P¡ (Exergonic reaction)
ATPases
Synthesizes ATP from ADP+P¡ (endergonic reaction)
ATP synthases
True or False? The Gram stain exploits differences in the thickness of the extracellular matrix.
True
The coding strand of a gene contains the following codon 5’-TGG-3’. If a point of mutation occurred in which thymine in the codon was converted to cytosine, what would result in corresponding mutant polypeptide sequence?
A] a nonpolar amino acid would be replaced by a basic amino acid
B] a polar uncharged amino acid would by replaced by a basic amino acid
C] a polar uncharged amino acid would be replaced by an acidic amino acid
D]a nonpolar amino acid would be replaced by a polar uncharged amino acid
A]
True or False? Sickle cell anemia results from a change of a non-polar amino acid in the wild-type protein into a negatively charged amino acid in the mutant protein.
False
Which has the greatest surface area to volume ratio?
A) Cell 1, with dimensions of 1um cubed
B) Cell 2, with dimensions if 5 um cubed
C) Cell 3, with dimensions of 0.125 um x 5 um x 200 um
D) Multicellular organism 1, comprised of 125 cells, each with same dimensions as Cell 1
C)
Mitochondria are thought to have evolved from ancestral bacteria. Which characteristics of a free-living bacterium have mitochondria lost over time?
A) circular genome
B) extracellular matrix
C) 70s ribosomes
D) division of binary fission
E) none of the above
B)
Phagocytosis of a bacterium by a white blood cell leads to the bacterium being engulfed inside a phagosome. The WBC will eventually degrade the bacterium. Which of the following events is associated with this overall process?
A) the phagosome will fuse to a peroxisome in order to breakdown the bacterium
B) the membrane of the phagosome is deceived from the cell wall of the bacterium
C) Digestion of the bacterium will occur by enzymes found directly in the cytoplasm of the WBC
D)the hydrolytic enzymes involved with the breakdown of the bacterium were synthesized by the co-translational import pathway
D)
Cytoskeletal elements can be found in the …..
A) cytoplasm
B) nucleus
C) extracellular space
D) all of the above
E) A and B
E
What is enzyme kinetics ?
Study of enzyme catalyzes reaction rate
Who where Leonor Michaelis and Maud Menten and why do we care about them?
1913, German scientist, developed a model to explain enzyme action
What is Km?
Indicator of E-S affinity, inverse relation of E-S affinity
What does Km tell us ?
Km is a substrate concentration. Km permits prediction of whether or not the reaction rate will be affected by substrate availability.
What is a direct plot/ Michaelis-Menten plot?
Plots v against (S). Data in hyperbolic form.
What is a double-reciprocal or Lineweaver-Burke plot?
Double reciprocal plot linearizes Michaelis-Menten data.
Explain the fluid mosaic model of cell membranes
Describe the cell membrane as a tapestry of several types of molecules (phospholipids, cholesterols, and proteins ) that are constantly moving. This movement helps the cell membrane maintain its role as a barrier between the inside and outside of the cell environments
List the functional roles of cell membranes
Boundary/barrier, organization/localization of specific functions, transport, signal detection, communication
Saturated fats tend to have_ melting points at room temperature compared to unsaturated fats
A) higher
B) lower
A) higher
Saturated fats tend to be _ at room temperature while unsaturated fats tend to be _
A) solid, liquid
B) liquid, solid
C) both are solid
D) both are liquid
A) solid, liquid
Cis-fats behave like _ while trans-fats behave like_
A) saturated;unsaturated
B) unsaturated; saturated
B) unsaturated; saturated
The hydrophilic end of a phospholipid is comprised of the _ while the hydrophobic end contains the _
Phosphate + R group ; hydrocarbon tail
Compare and contrast type O to type AB.
Type O is a universal donor, type AB is a universal acceptor.
True or False? A person with type A blood could accept a transfusion from someone who has type AB blood .
False
What type of cholesterol is good?
A) HDL
B) LDL
C) IDL
A) HDL
What is a good level of blood cholesterol ?
A)< 40 mg/dL
B) <200 mg/dL
C)<300 mg/dL
D) <500 mg/dL
B)<200 mg/dL
What are lipoproteins?
They digest and transport lipids in the blood. Surface mono layer of spholipid, cholesterol, and specific proteins. Core consisting of triglycerides and or cholesterol.
What is HDL?
High density lipoprotein (10 nm) transports cholesterol from body cells to liver
What is LDL?
Low density lipoprotein (20 nm) transport cholesterol from liver to body cells
What is antherosclerosis ?
Vascular disease of the arteries, artery wall thickens, narrows lumen of vessel, reduces/blocks blood flow
What combination of lipoproteins increases the risk of developing antherosclerosis?
Promoted by high LDLs and low HDLs
The flow of energy in the biosphere begins primarily with….
A) lightning
B) heat absorption
C) oxidized chemicals
D) phototrophs
E) chemotrophs
D) phototrophs
Which of the following is true for all Exergonic reactions?
A) it is not spontaneous
B) the reactions are rapid
C) the products have more total energy than the reactants
D) the net input of energy from the surroundings is required for the reactions to proceed
E) the reaction proceeds with a net release of free energy
E) the reaction proceeds with a net release of free energy
A chemical reaction that has a positive deltaG is best described as
A) endergonic
B) enthalpic
C) spontaneous
D) entropic
E) exergonic
A) endergonic
In a given system the amount of energy available to do work is called…
Free energy
Energy is important to life forms because
A) all life forms require a continuous supply of energy and energy is required to do work
B) all life forms require a continuous supply of energy
C) all life forms require a continuous supply of energy, energy is required to do work, and energy is required to make specific alterations in the cell
D) energy is required to make specific alterations in the cell
E) energy is required to do work
C) all life forms require a continuous supply of energy, energy is required to do work, and energy is required to make specific alterations in the cell
Which term most precisely describes the cellular process of breaking down large molecules into smaller ones?
A) anabolism
B) metabolism
C) dehydration
D) catabolism
E) catalysis
D) catabolism
What is not true of phototrophs?
A) they capture light energy
B) they can’t function as autotrophs
C) they can be bacteria
D) they store energy as glucose, in the form of starch
E) they provide energy, in the for, of organic carbon, for chemotrophs
B) they can’t function as autotrophs
An enzyme….
A) supplies energy to start a chemical reaction
B) is nonspecific
C) will become part of the products in the reaction catalyzed
D) acts as a biological catalyst
D) acts as a biological catalyst
Which match is not correct regarding the phosphate-transferring enzymes?
A) kinase: catalyzes the transfer of phosphate involving an organic source
B) phosphatase: catalyzes the hydrolytic removal of phosphates
C) phosphorylase: catalyzes the transfer of inorganic phosphate
D) all of the above are correct
D) all of the above are correct
Which of the following best describes enthalpy (H)?
A) the cell’s energy equilibrium
B) the condition of a cell that is not able to react
C) the heat content of a system
D) the system’s entropy
E) the total kinetic energy of a system
C) the heat content of a system
Aerobic refers to what property of chemotrophs?
A) fermentation releases great amounts of gas but only in chemotrophs
B) chemotrophs require oxygen to convert energy into a usable form
C) chemotrophs remove carbon dioxide from the air
D) heat loses occur in the presence of oxygen
E) chemotroph metabolism that doesn’t require oxygen
B) chemotrophs require oxygen to convert energy into a usable form
True or false? Heterotrophs can convert inorganic carbon into organic carbon
False
In accordance with the 2nd law of thermodynamics, whenever the energy is transformed, there is always an increase in the
A) free energy of the system
B) entropy of the universe
C) enthalpy of the universe
D) entropy of the system
E) free energy of the universe
B) entropy of the universe
In a given chemical reaction, if the reactants contain more free energy compared to the products, the reaction will be …
Exergonic
Which of the following is true about anabolic pathways ?
A) they are usually highly spontaneous chemical reactions
B) they do not depend on energy transfer
C) they consume energy to build up polymers from monomers
D) they consume energy to decrease the entropy of the organism and its environment
E) they release energy as they degrade polymers to monomer
C) they consume energy to build up polymers from monomers
Which of the following is true for all exergonic reactions?
A) the products have more total energy than the reactants
B) the reactions are rapid
C) a net input energy form the surroundings is required for the reactions to proceed
D) the reactions proceeds with a net release of free energy
E) they are not spontaneous
D) the reactions proceeds with a net release of free energy
Which of the following statements is true concerning catabolic pathways ?
A) they are endergonic
B) they combine molecules into more energy rich molecules
C) they are non spontaneous
D) they build up complex molecules such as a protein from simpler compounds
E) they supply energy, primarily in the form of ATP, for the cell’s work
E) they supply energy, primarily in the form of ATP, for the cell’s work
The energy found in the bonds of a molecule is an example of … energy
A) electrical
B) concentration gradient
C) kinetic
D) gravitational
E) potential
E) potential
True or false? A system at work can do no work
True
What is the difference between the structure of ATP and the structure of the precursor of the A nucleotide in RNA?
A) the sugar molecule is different
B) the number of phosphates is 3 instead of 2
C) the nitrogen containing base is different
D) the number of phosphates is 3 instead of 1
E) there is no difference
E) there is no difference
The michaelis-menten plot is also known as the …..
Direct plot
Increasing the substrate concentration in an enzymatic reaction could overdone which of the following?
A) saturation of the enzyme activity
B) insufficient cofactors
C) competitive inhibition
D) denaturation of the enzyme
E) allosteric inhibition
C) competitive inhibition
The difference between the free energy content of the reactants and the free energy content of the products is also revered to as the ….
A) change in enthalpy
B) active site
C) free energy change
D) activation energy
C) free energy change
An enzyme is active in the stomach of an animal but quickly loses it’s activity when it leaves the. This example illustrates that enzymes are
A) consumed by the quantities of substrate in the small intestine
B) inactivated by movement
C) sensitive to changer in pH
D) digested in the small intestine
C) sensitive to changer in pH
Which translational pathway would a digestive enzyme go through in order to be localized to the lumen of the GI tract organ in which it was produced ?
A) subscriptional
B) co-translational
C) poly-translational
D) post-translational
E) default pathway
B) co-translational
The equation A-PO4 + B ➡️ A+ B-PO4 would be catalyzed by which of the following classes of enzymes?
A) ligases
B) isomerases
C) transferases
D) oxidreductases
E) hydrolases
C) transferases
Alcohol dehydrogenase catalyzes the oxidation of alcohols into their corresponding aldehydes or ketones. Alcohol dehydrogenase would therefore as which class of enzymes ?
A) transferases
B) oxidoreductases
C) hydrolases
D) isomerases
E) ligases
B) oxidoreductases
Enzymes are important for cells because they ….
A) decrease the rate of reverse rxn in a reversible system
B) increase the exothermic value of a rxn
C) decrease the activation energy of a reaction
D) increase the entropy of the products
E) increase the temperature of the reactants, and therefore speed up the reaction
C) decrease the activation energy of a reaction
The active site of an enzyme is the region that
A) is involved in the catalytic reaction of the enzyme
B) binds in-competitive inhibitors of the enzyme
C) is inhibited by the presence of a coenzyme or a cofactor
D) binds allosteric regulators of the enzyme
A) is involved in the catalytic reaction of the enzyme
Besides turning enzymes on or off, what other means does a cell use to control enzymatic activity ?
A) regulation at the transcriptional or translational level
B) polyadenylation of the enzyme
C) localization of enzymes into specific organelles or membranes
D) all of the above
E) both A and C
E) both A and C
True or False ? Polyadenylation is a post-translational regulatory mechanism used to regulate enzyme activity
False
What does phosphorylation mean?
A) the removal of phosphates from solution by a base
B) the addition of phosphate functional group to a molecule
C) the removal of phosphate group from a molecule
B) the addition of phosphate functional group to a molecule
Enzymes that catalyst the phosphorylation of target molecules are called
A) synthases
B) oxidoreductases
C) kinases
D) ligases
E) phosphatases
C) kinases
True or False? Phosphatases catalyze the removal of phosphate groups from target molecules
True
True or false ? A competitive inhibitor binds to an allosteric site of an enzyme
False
The bindings of a compound to an enzyme is observed to slow down or stop the rate of reaction catalyzed by the enzyme. Increasing the substrate concentration reduces the inhibitory effects of this compound. Which of the following could account for this observation?
A) the compound is a negative allosteric regulator
B) the compound reduces disulfide bonds, causing the enzyme molecules to partially unfold
C) the compound is a competitive inhibitor
D) the compound cases a cofactor to be lost from the enzyme
E) the compound forms a covalent bond with one of the a,into acid residues needed for enzyme activity
C) the compound is a competitive inhibitor
When plotting kinetic data, which of the following plots velocity against [S]?
Michaelis-Menten plot
Trypsin is a protease. This means trypsin catalyzes
A) protein denaturation
B) protein catabolism
C) protein folding
D) protein synthesis
E) protein anabolism
B) protein catabolism
Regarding the Michaelis-Menten equation v=Vmax when
[S] is very large
True or False ? When Vmax has been reached, adding more S can increase the rate of reaction
False
Assuming the N-terminus is located in the cytoplasm what is the identity of the 1st membrane-spanning segment ?
A) N-terminal start transfer
B) internal start transfer
C) internal stop transfer
D) N-terminal stop transfer
E) C-terminal start transfer
B) internal start transfer
Describe the hydropathy analysis techniques for predicting the structure of membrane proteins
It is predicting the orientation of membrane protein based on the analysis of DNA/RNA or amino acid sequence which is indicated by the positive (hydrophobic) or negative (hydrophilic values)
What type of chemical properties/behavior would a membrane protein have compared to a cytoplasmic protein ?
Membrane proteins would have both hydrophobic and hydrophilic regions to facilitate their function as being part of the membrane whereas cytoplasmic proteins are largely hydrophilic due to their being interacting with an aqueous environment
Define Tm for a membrane
Tm is the transition temperature which is the temperature at which membrane is optimally fluid and functional. Dropping below the Tm value will decrease fluidity and conversely it will increase above the Tm value
Describe the fluid properties of the cell membrane and explain how membrane fluidity is influenced by membrane composition
Fluid properties of the cell membrane are influenced by the membrane’s components and composition of those components. In terms of cholesterol, below the Tm, it prevents the adjacent lipids from being tightly packed and thus increases fluidity. Whilst above the Tm, rigid cholesterol molecules interact with adjacent lipids and restrain movement and thus decreasing fluidity
From their affects on Tm, oleate is expected to be a(n) ……fatty acid and stearate is expected to be a(n)….fatty acid
Unsaturated;saturated
How will the length of fatty acid tails influence Tm?
A) longer tails will raise Tm
B) longer tails will lower Tm
A) longer tails will raise Tm
Which type of intermolecular forces hold cholesterol in the membrane?
A) hydrogen bonds
B) Vann der Waals
C) covalent bonds
D)all of the above
E) A and B
E) A and B
Most membranes are several (~4 -8)…… thick
A) micrometers
B) nanometers
C) picometers
D) millimeters
E)meters
B) nanometers
Will molecular oxygen readily diffuse across a lipid bilayer?
Yes
Does osmosis require an input of E?
No
Define homeoviscous adaption
Is compensating for changes in temperature by altering the length and degree of saturation of fatty acids in cell membranes
What sort of changes occur to change membrane fluidity?
Cells can increase membrane fluidity by using shorter fatty acid chains and introducing double bonds
Describe the structure and potential functions of lipid rafts
The structure of lipid rafts is that they are enriched in cholesterol and sphingolipids. They are like platforms and are spatially and temporally transient
Describe the factors that may influence membrane thickness
Membrane thickness may be influenced by
1) length of fatty acid chains
2) degree of saturation of fatty acid chains
3) trans membrane protein content
Describe osmosis
Diffusion of water through a semipermeable membrane form. (High water/low solute) to (low water/high solute ); spontaneous process
What is the driving rate of simple diffusion?
What drives the rate of simple diffusion is the concentration of the gradient. It’s directly proportional
Describe factors that affect the selective permeability of membranes
Size, polarity (nonpolar are favored ), and charge (impermeable to ions )
Define osmolarity
The measure of a solute concentration which is determined by dividing the dissolved solute concentration by the liters of solvent
Explain how salt can be used to preserve food
Salt pulls the water from the cells ( microbial) by osmosis and thus causes it to die as it can’t survive
Explains what is happening inside the paramecium cell regarding osmosis and the role of the contractile vacuole
The vacuole is in taking water by osmosis to increase the size and releases water to decrease in size by active transport
Describe the different types of transport proteins
1) transporters (carriers, permeates) solute binds to transport protein
2) Channels ( porins/pores) solute passage without binding to channel protein
Describe how transport proteins facilitate diffusion and why they are necessary
Transport proteins facilitate diffusion in that they move substances across a membrane. They are necessary to support the function of the cell
How is water getting into the paramecium?
A) osmosis
B) active transport
C) phagocytosis
A) osmosis
How is water getting out of the paramecium?
A) osmosis
B) diffusion
C) active transport
D) exocytosis
E) endocytosis
C) active transport
Facilitated diffusion….. an input of energy
A) requires
B) doesn’t require
B) doesn’t require
True or False ? A channel protein could actively transport a solute across a membrane
False
If a cell has a Vm of -60 mV, the inward movement of which ion would be favored ?
A) chloride
B) sodium
C) neither
B) sodium
True or False ? The CTFR directly transports both Na + and Cl- ions
False
An amoeba has engulfed a paramecium cell. The vesicle formed by the amoeba during the endocytosis or the paramecium is called an …
A) phagosome
B) lysosome
C) hydrolase
D) Golgi body
E) ER vesicle
A) phagosome
The phagosome was derived from the …..
A) Plasma membrane of the amoeba
B) RER of the amoeba
C) plasma membrane of engulfed cell
D) RER of engulfed cell
E) golgi of the amoeba
A) Plasma membrane of the amoeba
