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BCOR 2505 Exam 1 > Comprehensive Exam Study Guide > Flashcards

Comprehensive Exam Study Guide Flashcards

1
Q

What makes a good experimental model?

A

Easy to keep, short life cycle, simple genome, distinct nucleus

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1
Q

Why can we use cells that are not human to study how human cells work?

A

All cells share common fundamental properties, it allows for controlled manipulations, and it makes it easier to study signaling mechanisms

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2
Q

With so many experimental models available, how do scientists choose which model to use?

A

The models we choose are based on the questions we’re asking

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3
Q

Describe Stanley Miller’s experiment.

A

It simulated the conditions of the early prebiotic earth, and it showed us that organic biomolecules can form spontaneously after the earth cools

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4
Q

What is the “RNA World Hypothesis?”

A

The first cell was an enclosed bit of self-replicating RNA in a phospholipid bilayer that formed spontaneously and can form enzymes

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5
Q

Describe the evolution of metabolism

A

The first cells were able to obtain energy directly from their environment, then this became dependent on ATP, then diatomic oxygen accumulated in the atmosphere, leading to oxidative phosphorylation.

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6
Q

What process is believed to have brought about the existence of mitochondria and chloroplasts in eukaryotic cells?

A

Endosymbiosis (one thing living inside the cell of another)

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7
Q

Describe the basics of covalent bonds

A

Can be polar or nonpolar; can be single, double, or triple bonds (depends on valence electrons)

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8
Q

Describe the basics of ionic bonds

A

Form between cations and anions (attraction of opposite charges); salts are ionic compounds

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9
Q

Describe the basics of hydrogen bonds

A

noncovalent bonds between H and O or N, weaker than any other bonds

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10
Q

What does amphipathic mean?

A

One molecule having both hydrophilic and hydrophobic parts

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11
Q

How do the first two laws of thermodynamics apply to cells?

A

1) Conservation of energy: the total energy of a system is constant
2) Entropy increases over time, and a system will go into a state of disorder

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12
Q

What is the difference between catabolic and anabolic reactions?

A

Catabolic reactions break down complex molecules and release energy. Anabolic reactions link simple molecules and require energy to do so.

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13
Q

What are some of the functions of carbs, lipids, nucleic acids, and proteins?

A

Carbs provide energy, lipids are the membranes in a cell, nucleic acids store information, and proteins are enzymes, cytoskeleton, and other structures

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14
Q

Name and describe the reactions used to build and break down macromolecules

A

Hydrolysis: water is added, breaking a macromolecule apart.
Dehydration synthesis: two molecules are joined together, releasing H2O

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15
Q

What type of bond joins carb monomers together?

A

Glycosidic bonds

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16
Q

Name the complex sugars and describe their main roles.

A

Starch and glycogen are complex linear sugars that store energy. Cellulose is a complex twisted sugar that has more of a structural function.

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17
Q

How can you, from the same monomers, make a structure that is very easy to pull apart (starch and glycogen) AND one that is not (cellulose)?

A

Starch is linear and forms alpha 1-4 bonds (which can break by hydrolysis) when the OHs are parallel. Cellulose forms beta 1-4 bonds when the OHs are inverted, and humans don’t have the enzymes necessary to break these bonds.

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18
Q

What are some common features of all phospholipids?

A

All are fatty acids with long hydrocarbon chains, and carboxyl (O=C-O), which is polar

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18
Q

One of the phospholipids we studied was different from the others. What is its name and why is it unique?

A

Sphingomyelin had a phosphate and a choline head group instead of a glycerol

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19
Q

Describe the structure of a triglyceride

A

3 fatty acid chains linked together by a glycerol

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20
Q

If a lipid head group contains glucose instead of a phosphate group, what is it called?

A

Glycolipid

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21
Q

What type of bond holds nucleotides together?

A

Phosphodiester bonds

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22
Q

What is the difference between a nucleic acid, a nucleotide, and a nucleoside?

A

Nucleotide: a base, ribose sugar, and phosphate.
Nucleoside: base and ribose sugar
Nucleic acid: chain of nucleotides

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23
Name the purines and pyrimidines and know which ones are single/double-ringed.
Purines: A and G; pentagon and ring Pyrimidines: C, T, and U; double-bonded ring
24
What are the three common features of all amino acids?
The amino (NH3+), the carboxyl (O=C-O), and the R side chain
25
What are some common functions of proteins?
Transport, transmitting, and the base of an enzyme
26
How is the structure of hydrophobic vs. hydrophilic amino acids different?
Hydrophobic are typically on the inside of a protein and made of CHs. Hydrophilic are typically on the outside of a protein and are made of OH or O=C-NH2.
27
What type of bond holds amino acids together? What part(s) of the amino acid does this bond form between?
Peptide bonds; one carboxyl bonds with the amino of the next acid
28
What are the differences between primary, secondary, tertiary, and quaternary structure?
Primary: polypeptide chains, starting at the N terminus and ending at the C terminus. Secondary: alpha helices and beta sheets; the CO of one peptide bond forms a hydrogen bond with the NH of another peptide bond Tertiary: non-covalent bond interactions; facilitated by chaperones.
29
What type of bond underpins the structure of the alpha helix as well as the beta sheet?
Hydrogen bond
30
What is a prion?
A protein that adopts a beta sheet conformation, which misfolds, leading to insoluble structures that ultimately kill the cell
31
Why are enzymes important?
They're ubiquitous biological catalysts
32
What are two important properties of all catalysts?
1) Not permanently altered in the process 2) Do not alter the chemical equilibrium of the reactants and products
33
How does an enzyme speed up a reaction?
By the laws of thermodynamics; an enzyme decreases the energy of a transition state in a chemical reaction
34
What is the difference between lock-and-key and induced fit models of enzyme function?
Lock-and-key: the substrate fits perfectly into the enzyme's active site. Induced fit: the substrate attaches to the active site and as a result both the substrate and active site change shape slightly
35
What are cofactors?
Enzyme helpers (vitamins).
36
What are the two main subsets of cofactors?
Coenzymes (bind loosely to enzymes) and prosthetic groups (bind covalently to enzymes)
37
Describe allosteric regulation
Allosteric regulation is non-competitive inhibition, where the inhibitor binds to an allosteric site (not the active site), which changes the shape of the enzyme
38
Describe feedback inhibition
The product inhibits an enzyme needed to synthesize that product
39
Feedback inhibition of isoleucine on threonine deaminase is an example of what?
Allosteric inhibition
40
Where on the enzyme do substrates bind?
The active site
41
Where do enzyme inhibitors bind?
Either the active site or an allosteric site, because they can be competitive or non-competitive
42
What are protein kinases and phosphatases?
Kinases are proteins that add a phosphate. Phosphatases are proteins that remove phosphates.
43
What can phosphorylation of an enzyme do?
Usually activates enzyme activity
44
What property of lipids allows them to spontaneously form membranes when exposed to an aqueous environment?
The amphipathic character of the molecules
45
List some of the important roles proteins play in a cell
Prevent mixing of cell contents, create primary zone of interaction, hold a chemical concentration gradient
46
In what ways can and can't lipids move in a membrane?
Lipids can move laterally and rotate, but they're also restricted in their moving a little bit because of the filaments in the cytoskeleton.
47
Describe the structure of a phosphoglyceride, a sphingolipid, sphingomyelin, and a glycolipid.
Phosphoglycerides have a glycerol head, a phosphate, and a choline with two fatty acid chains and a double bond that makes it unsaturated. Sphingolipids have a serine head instead of a glycerol (but still have a phosphate and a choline). Sphingomyelin only has a phosphate and a choline. Glycolipids are glucose and serine.
48
How does cholesterol fit into a membrane?
They fit in the space created by the kink of the cis bond in the hydrophobic tails of the membrane.
49
Why is cholesterol considered a fluidity buffer?
It fills the kink from the cis bond, and makes membranes less fluid at high temperatures, and more fluid at low temperatures
50
What factors can affect membrane fluidity?
Cholesterol and lipid concentrations and compositions, and temperature
51
Describe what lipid rafts are and what scientists think their role is.
They are microdomains of cholesterol, sphingolipids, and glycolipids, and they serve as a base for proteins
52
What membrane components are only found on the outside of the cell?
Sphingomyelin and glycolipids
53
What are the main differences between integral membrane proteins, peripheral membrane proteins, and lipid-linked membrane proteins?
Integral are embedded within the membrane bilayer (nonpolar), peripheral are stuck to the sides of membranes (ionic), and lipid-linked hang from the membrane by the lipid tail.
54
Why is it important that an alpha-helix anchored membrane protein has consecutive hydrophobic amino acids?
The inside of the membrane is hydrophobic, so for them to be integral they must be hydrophobic.
55
Which class of integral membrane proteins can form channels through the cell membrane?
Amphipathic
56
How many transmembrane domains does a G-protein coupled receptor (GPCR) have? Does this structure form a channel?
G-proteins have 7 domains and do not form channels.
57
What are two ways that a peripheral protein can associate with the membrane?
Intramolecular forces or by positively charged amino acids
58
What must a lipid-linked protein contain that allows it to associate with the inside of a phospholipid bilayer?
They must have covalently attached fatty acid tails that make up a lipid
59
Why does it make sense to sometimes limit the mobility of membrane proteins?
Because channels and the cytoskeleton hold the membrane in place, and when mobility is limited there are regions that have separate and specific functions.
60
At rest, is the inside of a cell negatively or positively charged?
Negatively charged (-70mV)
61
At rest, describe the concentration gradient of Na+ and of K+.
The concentration of K+ is greater inside the cell and Na+ is greater outside the cell.
62
What are the three types of membrane transport, and do they need energy?
Diffusion does not, channels depends, and carriers indirectly need energy.
63
Why can't everything diffuse across the membrane?
Because not everything has the characteristics to; they need to be small, and hydrophobic to get through the tails.
64
Do channels require energy? Do pumps?
Some channels do. Pumps do.
65
What are the three different ways that we can control when a channel is open or closed?
Mechanically gated, voltage gated, and ligand gated
66
What component of a voltage-gated channel structure creates selectivity to specific ions?
The p-loop
67
What component of a voltage-gated channel structure responds to a voltage change in the cell?
The transmembrane helix #4 is the voltage sensor and it has wings so that when the membrane is positive, it's closed, and when the membrane is negative, it opens.
68
Can you provide an example of a functioning protein in the form of a tertiary structure? Quaternary structure?
Tertiary: An alpha helix or beta sheet with a polypeptide Quaternary: hemoglobin and the Na+ channel
69
How is a channel different from a carrier?
A channel can be ligand-gated, ion-gated, or also not gated (always open). Carriers are similar, but highly specific, and undergo conformational changes to bind to and transport a molecule from one side of the membrane to the other.
70
How can a carrier move something against its concentration gradient without directly using energy?
They have facilitators, and use the electrochemical gradient.
71
Describe the structure of leak channels and how they work
They are protein channels that allow ions to passively flow across the membrane, but are highly specific (only allow one type of ion to pass through)
72
Describe the structure of voltage gated channels and how they work.
They consist of four homologous subunits arranged around a central pore. They open and close in response to an uneven distribution of ions.
73
Describe the structure of ligand-gated channels and how they work.
They have five subunits arranged around a central pore. They open and close in response to a specific chemical.
74
Describe the structure of mechanically-gated channels and how they work?
They have subunits, pore-forming regions, and specialized domains that interact with the cell membrane and cytoskeleton. They open and close in response to mechanical stimuli (pressure, stretch, or vibration)
75
Describe uniporter facilitators and how they work.
They transport substances across the cell membrane, solely using the chemical potential of the substrates as their driving force, and by binding to their substrate and undergoing a conformational change.
76
Describe symporter facilitators and how they work.
They couple the movement of one molecule down its concentration gradient (releases energy) with the movement of another molecule against its concentration gradient (requires energy). This is secondary active transport.
77
What is the difference between the T domains and the A domains on an ABC pump? Why is it important that the A site faces the intracellular space?
T domains are transmembrane domains, and A domains are ATP-binding domains. A domains must be intracellular so they can bind to ATP.
78
Why does the Na+/K+ pump require energy? Why is it so important that this protein is always functioning?
It creates an ionic gradient for both molecules, and if it wasn't functioning, the voltages of the cell would be imbalanced.
79
Describe the differences between the three general areas of the cytoskeleton within the cytoplasm.
Cortical is the nearest to the plasma membrane and includes microfilaments (actin). Subcortical is in the middle and holds most of the proteins, intermediate filaments, and microtubules. The nuclear cytoskeleton is intermediate filaments.
80
Where in the cell would I most likely find actin? How does this location relate to the main function(s) of actin?
Around the outside, because it maintains the cell shape.
81
Out of G actin and F actin, which is the monomer and which is the polymer?
G actin is the monomer and F actin is the polymer.
82
What favors G actin to polymerize?
Polarity: the barbed + end of G actin is polymerized by the pointed - end of another G actin.
83
What favors G actin to dissociate from the microfilament?
Cofilin
84
What is nucleation?
The formation of trimers
85
Explain the mechanism of treadmilling in actin filaments.
It's a cycle when the barbed end of actin grows faster and binds to ATP, but then the ATP is hydrolyzed to ADP, and the presence of ADP promotes depolymerization.
86
What does profilin do?
Exchanges ADP for ATP
87
What do formin dimers do?
Catalyze the extension of a microfilament
88
What does the Arp 2/3 complex do?
Initiates the formation of branches
89
What do capping proteins and tropomyosin do?
Stabilize filaments
90
What do cross-linking proteins do?
Cross-link filaments into bundles and networks
91
What does cofilin do?
Breaks apart filaments
92
Compare and contrast microvilli and stereocilia
They are both fingerlike extensions formed by actin bundles. Microvilli are for absorption, and stereocilia are for detection.
93
What are Rho proteins and how do they relate to actin?
Rho proteins respond to the environment and activate actin-binding proteins
94
What are the main functions of intermediate filaments?
Strength and flexibility
95
Describe the process of intermediate filament polymerization and how this leads to the final filament structure.
Two polypeptides dimerize in parallel, then tetramers form antiparallel. These tetramers stack to form a protofilament. 8 protofilaments twist to form intermediate filaments.
96
Name three locations/structures where intermediate filaments can be found.
Nucleus, subcortical cytoskeleton, and desmosomes.
97
Contrast hemidesmosomes and desmosomes
Desmosomes are junctions between cells. Hemidesmosomes are junctions between cells and the outside of the cell
98
What are the general functions of microtubules?
Transport within the cells and separation during mitosis
99
How do microtubules grow? What form favors assembly and what form favors disassembly?
By tubulin dimers alpha and beta. Tubulin can hydrolyze GTP to GDP. When GTP is bound, polymerization occurs. When GDP is bound, depolymerization occurs.
100
What does it mean that microtubules are polar? Describe the structure of a microtubule.
They have a positive and a negative end, and they're large and hollow with 13 protofilaments.
101
Can you describe the process of dynamic instability?
When the positive end can grow (rescue) and shrink (catastrophe).
102
How does a centrosome influence microtubule growth and stability?
A centrosome is a specific type of MTOC (microtubule-organizing center). It anchors the negative end and initiates growth
103
What protein is associated with the pericentriolar region and what does this protein do for microtubules?
Gamma tubulin. It's a seed for rapid growth.
104
What are the two microtubule motor proteins?
Dynein moves toward the negative end (centrioles) and kinesin moves towards the positive end (towards the outside of the cell)
105
What are key differences between motile cilium and primary sensory cilium?
Primary cilia sense the environment. Motile cilia move the cell.
106
How can microtubule motors cause cilia movement?
A protein called nexin moves 9 microtubule doublets in a 9+2 arrangement of A (complete) and B (incomplete) tubules
107
Why are drugs that target microtubule dynamics good for cancer-targeting chemotherapy treatments?
Cancer is uncontrolled cell division, and for cell division you need microtubules.
108
What is the difference between astral microtubules, kinetochore microtubules, and interpolar microtubules?
Astral radiate towards the membrane, interpolar radiate towards the center, and kinetochore are atached to the centromeres of chromosomes.
109
How do astral microtubules and motor proteins aid in the separation of chromosomes in mitosis?
They push the spindle poles apart and towards the outside.
110
How do interpolar microtubules and motor proteins aid in the separation of chromosomes in mitosis?
They push the spindle poles apart
111
How do kinetochore microtubules and motor proteins aid in the separation of chromosomes in mitosis?
Kinetochore shortens the chromosomes.

BCOR 2505 Exam 1 (9 decks)

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