Chapter 2 Flashcards
1
Q
What is the most abundant molecule in cells?
A
Water
2
Q
Hydrophilic
A
Ions and polar molecules are readily soluble in water
3
Q
Hydrophobic
A
Nonpolar molecules cannot interact with water and are poorly soluble
4
Q
What are the inorganic ions that constitute 1% or less of the cell mass? (7)
A
Sodium (Na+) Potassium (K+) Magnesium (Mg2+) Calcium (Ca2+) Phosphate (HPO42−) Chloride (Cl−) Bicarbonate (HCO3−)
5
Q
Carbohydrates
A
include simple sugars and polysaccharides
6
Q
Monosaccharides (simple sugars) are
A
the major nutrients of cells. The basic formula is (CH2O)n.
7
Q
Glucose (C6H12O6) provides the principal
A
source of cellular energy.
8
Q
Monosaccharides are joined together by __reactions resulting in __bonds
A
Dehydration rxn (H2O is removed), glyosidic bonds
9
Q
Oligosaccharides are
A
polymers of a few sugars.
10
Q
Polysaccharides are
A
macromolecules; polymers of hundreds or thousands of sugars.
11
Q
Common polysaccharides:
2
A
Glycogen: stores glucose in animal cells.
Starch: stores glucose in plant cells.
Both are composed entirely of glucose molecules in the α configuration.
12
Q
Glycogen:
A
stores glucose in animal cells.
composed entirely of glucose molecules in the α configuration.
13
Q
Starch:
A
stores glucose in plant cells. composed entirely of glucose molecules in the α configuration.
14
Q
Cellulose is the
A
main structural component of plant cell walls.
15
Q
What is cellulose composed of
A
It is composed entirely of glucose molecules in the β configuration.
The β(1→4) linkages cause cellulose to form long extended chains that pack side by side to form fibers of great mechanical strength
16
Q
Chitin is the
A
animal parallel of cellulose; it forms the exoskeletons of crabs and insects.
17
Q
What roles does Oligosaccharides and polysaccharides also play_
A
play roles in protein folding and act as markers involved in cell recognition and interactions.
18
Q
Lipids have three main roles:
A
Energy storage
Major component of cell membranes
Important in cell signaling as steroid hormones and messenger molecules
19
Q
Fatty acids are long
A
hydrocarbon chains (16 or 18 carbons) with a carboxyl group (COO–) at one end
20
Q
Unsaturated fatty acids have
A
one or more double bonds. Saturated fatty acids have no double bonds
21
Q
T/F
The hydrocarbon chain is hydrophobic
A
T
22
Q
Fatty acids are stored as
A
triacyclglycerols, (triglycerides, or fats):
They are insoluble in water and accumulate as fat droplets in the cytoplasm.
They can be broken down for use in energy-yielding reactions
23
Q
triacyclglycerols, (triglycerides, or fats) are _
A
three fatty acids linked to a glycerol molecule.
They are insoluble in water and accumulate as fat droplets in the cytoplasm.
They can be broken down for use in energy-yielding reactions
24
Q
T/F
Fats are more efficient energy storage than carbohydrates,
A
T
yielding more than twice as much energy per weight of material broken down.
25
What is the principal components of cell membranes
Phospholipids
26
Describe the structure of a phospholipid
Two fatty acids are joined to a polar head group.
27
Glycerol phospholipids:
the fatty acids are bound to glycerol, which is bound to a phosphate group, and often another polar group.
28
Sphingomyelin is the only
nonglycerol phospholipid in cell membranes.
| The polar head group is formed from serine instead of glycerol.
29
All phospholipids have hydrophobic tails and hydrophilic head groups.
They are __
amphipathic molecules: part water-soluble and part water-insoluble.
30
Glycolipids:
two hydrocarbon chains and a carbohydrate polar head group (amphipathic).
31
Cholesterol:
four hydrophobic hydrocarbon rings and a polar hydroxyl (OH) group (amphipathic).
32
Where Cholesterol and Glycolipids found?
Cell membranes
33
The steroid hormones (e.g., estrogens and testosterone) are derivatives of __
they act as chemical messengers.
cholesterol;
34
steroid hormones (e.g., estrogens and testosterone) act as__
chemical messengers
35
Derivatives of phospholipids also serve as
messenger molecules within cells
36
What are Nucleic acids?
| DNA and RNA
principal informational molecules of the cell
37
Messenger RNA (mRNA) carries
information from DNA to the ribosomes
38
Ribosomal RNA and transfer RNA are involved in
protein synthesis
39
Other RNAs are involved in
regulation of gene expression, and processing and transport of RNAs and proteins.
40
DNA and RNA are polymers of
nucleotides, which consist of purine and pyrimidine bases linked to phosphorylated sugars.
41
DNA has two purines __ and two pyrimidines __
Purines:(adenine and guanine)
| pyrimidines (cytosine and thymine)
42
What replaces thymine in RNA?
RNA has uracil in place of thymine.
43
The bases are linked to sugars to form
nucleosides
44
DNA has the sugar __, RNA has __
2′-deoxyribose
| ribose.
45
where are the phosphate grps on nucleotides linked
to the 5' C of the sugars
46
Phosphodiester bonds form between the
5′ phosphate of one nucleotide and the 3′ hydroxyl of another
47
Oligonucleotides are
polymers of a few nucleotides
48
A polynucleotide chain has a sense of direction:
One end terminates in a 5′ phosphate group and the other in a 3′ hydroxyl group.
49
Polynucleotides are always synthesized in the
in the 5′ to 3′ direction.
50
The bases are on the inside, joined by hydrogen bonds between complementary base pairs
Guanine with cytosine
| Adenine with thymine
51
How are Nucleic acids are thus capable of self-replication.
Complementary base pairing allows one strand of DNA (or RNA) to act as a template for synthesis of a complementary strand
52
Functions of proteins include:
- Structural components
- Transport and storage of small molecules (e.g., O2)
- Transmit information between cells (protein hormones)
- Defense against infection (antibodies)
- Enzymes
53
Amino acids are joined by _bonds.
peptide
54
Polypeptides are
chains of amino acids hundreds or thousands of amino acids in length.
55
X-ray crystallography_
Frequently analyzes Protein structure
56
Protein structure has four levels:
Primary, secondary, Tertiary, Quaternary structure
57
Protein structure has four levels:
the sequence of amino acids in the polypeptide chain
58
Secondary structure
regular arrangement of amino acids within localized regions.
Both are held together by hydrogen bonds between the CO and NH groups of peptide bonds.
59
Common types of secondary structure
α helix and β sheet.
60
Tertiary structure:
the polypeptide chain folds due to interactions between side chains of amino acids in different regions of the chain.
61
A critical determinant of tertiary structure
Placement of hydrophobic amino acids in the interior of the protein and hydrophilic amino acids on the surface, where they interact with water.
62
What are domains in proteins
the basic units of tertiary structure
63
Loop regions
connect the elements of secondary structure.
They are on the surface of folded proteins, where polar components of the peptide bonds form hydrogen bonds with water or with the polar side chains of hydrophilic amino acids.
64
Quaternary structure:
interactions between different polypeptide chains in proteins composed of more than one polypeptide.
65
Hemoglobin is composed of __polypeptide chains.
four
66
Enzymes are
catalysts that increase the rate of all chemical reactions in cells
67
Fundamental properties of enzymes:
- Increase rate of chemical reactions without themselves being consumed or permanently altered.
- Increase reaction rates without altering the chemical equilibrium between reactants and products.
68
activation energy
Energy required to reach the transition state
| Enzymes reduce the activation energy.
69
Substrates initially bind by
hydrogen bonds,
| ionic bonds, and hydrophobic interactions.
70
Active sites are clefts or grooves on the surface of an enzyme formed by the
tertiary structure.
71
Substrate binding to the active site is a very
specific interaction
72
lock-and-key model,
the substrate fits precisely into the active site.
73
Induced fit:
conformation of both enzyme and substrate is modified
74
Enzymes also accelerate reactions by altering the conformation
of substrate
75
Chymotrypsin is a serine protease:
these enzymes cleave peptide bonds adjacent to specific types of amino acids.
76
Chymotrypsin digests bonds adjacent to
hydrophobic amino acids
77
trypsin digests bonds next to
basic amino acids.
78
The active sites of serine proteases contain
serine, histidine, and aspartate.
79
features of enzymatic catalysis
- Specificity of enzyme-substrate interactions.
- Positioning of substrate molecules in the active site.
- Involvement of active-site residues in formation and stabilization of the transition state.
80
Active sites may bind other small molecules that participate in catalysis
Prosthetic groups
81
Prosthetic groups
small molecules bound to proteins that have critical functional roles.
82
What is the Prosthetic group in myoglobin and hemoglobin
the prosthetic group is heme, which carries O2.
83
Coenzymes
small organic molecules that work together with enzymes to enhance reaction rates.
Coenzymes are not altered by the reaction.
84
Examples of coenzymes
- Metal ions (e.g., zinc or iron) can be bound to enzymes and play a role in the catalysis
- Nicotinamide adenine dinucleotide (NAD+)
- Vitamins are closely related to coenzymes
85
Nicotinamide adenine dinucleotide (NAD+) is a coenzyme that carries .
electrons in oxidation–reduction reactions
86
How does Nicotinamide adenine dinucleotide (NAD+) carry electrons in oxidation–reduction reactions
NAD+ can accept H+ and two electrons from one substrate, forming NADH. NADH can then donate the electrons to a second substrate, re-forming NAD+.
87
In feedback inhibition
the product of a metabolic pathway inhibits an enzyme involved in its synthesis.
88
Feedback inhibition is a type of
allosteric regulation
89
allosteric regulation:
enzyme activity is controlled by the binding of small molecules to regulatory sites on the enzyme.
- This changes the conformation of the enzyme and alters the active site.
90
a common mechanism of enzyme regulation
Phosphorylation
91
Phosphorylation
- Phosphate groups are added to the side-chain OH groups of serine, threonine, or tyrosine.
- It can either stimulate or inhibit the activities of many enzymes.
92
cell membranes are
phospholipid bilayers with associated proteins.
93
phospholipid bilayers are the
basic structure of all biological membranes
94
T/F
| Plasma membranes of animal cells also contain glycolipids and cholesterol.
T
95
Mammalian plasma membranes have -- major phospholipids.
five
96
Membrane fluidity is determined by
temperature and lipid composition
97
Lipid bilayers are __dimensional fluids in which molecules are free to rotate and move laterally.
2D
98
Unsaturated fatty acids chains have___ that result in kinks.
double bonds
99
How does double bond in unsaturated fatty acids reduces packing and increases membrane fluidity
This reduces packing and increases membrane fluidity
100
How does cholesterol help determine membrane fluidity
- Because of its ring structure, cholesterol helps determine membrane fluidity
- Cholesterol also reduces -interaction between fatty acids, maintaining membrane fluidity at lower temperatures.
101
Interactions between the hydrocarbon rings and fatty acid tails makes the membrane more
rigid.
102
fluid mosaic model of membrane structure is__
Integral membrane proteins inserted into a phospholipid bilayer, with nonpolar regions in the lipid bilayer and polar regions exposed to the aqueous environment.
103
Integral membrane proteins
are embedded directly in the lipid bilayer
104
Peripheral membrane proteins are
associated with the membrane indirectly, generally by interactions with integral membrane proteins.
105
Transmembrane proteins span the lipid bilayer,
with portions exposed on both sides.
106
Membrane-spanning portions are usually
α-helical regions of 20 to 25 nonpolar amino acids.
107
Some membrane-spanning proteins have a
β-barrel, formed by folding of β sheets into a barrel-like structure.
(In some bacteria, chloroplasts, and mitochondria).
108
The selective permeability of membranes allows a cell to control
its internal composition.
Small, nonpolar molecules can diffuse across the lipid bilayer: CO2, O2, H2O.
Ions and larger uncharged molecules, such as glucose, cannot diffuse across.
109
Channel proteins form
open pores across the membrane.
They can be selectively opened and closed in response to extracellular signals.
110
Channel proteins can be selectively opened and closed in response to
extracellular signals.
111
Ion channels allow the passage of
inorganic ions.
112
Carrier proteins selectively bind and transport small molecules, such as
glucose.
113
Carrier proteins bind specific molecules and then undergo
conformational changes that open channels through which the molecule can pass
114
Passive transport: .
molecule movement across the membrane is determined by concentration and electrochemical gradients
115
Active transport:
molecules can be transported against a concentration gradient if coupled to ATP hydrolysis as a source of energy.
116
How many amino acids are commonly incorporated into proteins?
20
117
A disulfide bond is formed between _______ residues.
cysteine
118
Which of the following classes of amino acids is buried within the folded structure of the protein?
Nonpolar
119
The three-dimensional structure of a protein is analyzed most definitively by
X-ray crystallography.
120
Chymotrypsin, trypsin, elastase, and thrombin are all members of the serine protease family because each
uses the same catalytic mechanism involving the same key amino acids.
121
The coenzymes NAD+ and NADP+ are structurally related to the vitamin
niacin.
122
Which of the following is not true of coenzymes?
They are branched amino acids.
123
Coenzymes are chemically related to
vitamins
124
All of the following are ways in which enzyme activity can be regulated except
by binding to an allosteric site.
through feedback inhibition.
by modulation of intracellular sucrose concentrations.
through phosphorylation.
by modulation of intracellular sucrose concentrations.
125
All of the following are ways in which enzymes are regulated by the cell EXCEPT:
a) a gene coding for the enzyme may be turned off
b) by first synthesizing the enzyme in an inactive form
c) by feedback inhibition
d) an inhibitor may block the enzymes active site
e) the substrate binding to the active site
e) the substrate binding to the active site
126
All of the following are correct statements about enzyme regulation EXCEPT:
A. Enzymes can be inhibited by the products they produce.
B. Enzymes can be inactivated by the addition of a functional group.
C. Coenzyme and substrate availability can regulate enzyme reaction rate.
D. The reaction rate slows as equilibrium is approached.
E. The activity of an enzyme is covalently affected by allosteric regulators.
E
127
```
Usually the quickest method of influencing an enzymatic activity is by:
A. allosteric regulation.
B. covalent modification.
C. enzyme induction.
D. activation of a zymogen.
E. enzyme destruction.
```
A
128
All are characteristic of allosteric enzymes EXCEPT:
A. Effectors may show stimulatory or inhibitory activity.
B. They have multiple subunits.
C. They obey Michaelis-Menten kinetics.
D. The regulatory effect is by altering conformation and interaction of subunits.
E. Binding one subunit impacts binding of substrate to other subunits
C
129
About 50% of the mass of most biological membranes consists of lipids and about 50% consists of proteins. Therefore,
Question 20 options:
the membranes contain fewer molecules of lipid than of protein.
the membranes contain equal numbers of lipid and protein molecules.
the membranes contain more molecules of lipid than of protein.
only a few membrane proteins are exposed at the cell surface.
the membranes contain more molecules of lipid than of protein.
130
Introducing a double bond into a fatty acid puts a(n) _______ into the conformation of the molecule.
kink
131
Phospholipids consist of a 3-carbon core to which two fatty acids and a phosphate group are linked. The most common 3-carbon core is
Question 22 options:
dihydroxyacetone.
glyceraldehyde.
glycerol.
serine.
glycerol.
132
Lipids with unsaturated fatty acids
Question 23 options:
decrease fluidity of membranes.
increase the charge associated with the inner face of a membrane.
increase fluidity of membranes.
are present only on the inner side of the plasma membrane
increase fluidity of membranes.
133
In the fluid mosaic model of biological membrane structure, transmembrane proteins are
Question 24 options:
embedded nearly randomly in the lipid bilayer.
almost completely surrounded by membrane lipid.
segregated into large protein clusters or rafts.
weakly held in place on the surface of the lipid bilayer.
embedded nearly randomly in the lipid bilayer.
134
What is the effect of a β barrel on the permeability of a membrane?
Question 25 options:
It decreases permeability.
It increases permeability.
It has no effect.
β barrels are peripheral membrane proteins.
It increases permeability.
135
```
Which class of molecule accelerates transport across biological membranes?
Question 26 options:
```
Carbohydrates
Lipids
Nucleic acids
Proteins
Proteins
136
While small, uncharged molecules can diffuse through the hydrophobic core of a phospholipid bilayer, larger polar molecules such as glucose must enter cells by binding to
Question 27 options:
a nonphospholipid such as cholesterol.
the carbohydrate portion of glycolipids.
peripheral membrane proteins located on the inner side of the membrane.
carrier proteins that facilitate the passage of specific molecules across membranes.
carrier proteins that facilitate the passage of specific molecules across membranes.
137
Passive transport across a membrane refers to
Question 28 options:
transport into the interior of a cell.
transport out of a cell.
transport in the energetically favorable direction.
simple diffusion across membranes, without the help of proteins such as channels or carriers.
transport in the energetically favorable direction.
138
Enzymes affect the transition state of a chemical reaction by
a. binding to the substrate(s).
b. providing a surface on which the reactions converting substrate to product can occur more rapidly.
c. altering the conformation of the substrate(s) to approach that of the transition state.
d. All of the above
All of the above
139
The lock-and-key and induced-fit models are two alternative models that can explain how enzymes and substrates interact. These two models can be distinguished from each other according to changes in the
a. viscosity of the reaction solution as the substrate and enzyme bind.
b. shape as the substrate and enzyme bind.
c. reaction solution temperature as a result of the endothermic cooling that occurs during substrate binding.
d. reaction solution color as the substrate and enzyme bind.
shape as the substrate and enzyme bind.
140
What is the major carbohydrate-storage molecule in plants?
a. Starch
b. Cellulose
c. Glycogen
d. Deoxyribonucleic acid
Starch
141
Different glycosidic linkages give rise to different polysaccharides.
Storage - amylopectin (starch) & glycogen.
* Store carbs for energy; composed entirely of a glucose configuration; PRIMARY LINKAGE = alpha (1-->4)
Occasionally link alpha (1-->4) alpha (1-->6).
Not edible by us - Structural - Cellulose & chitin.
* Plant cell wall; primarily glucose. Beta (1-->4)
142
Fluid Mosaic Model
Proteins are inserted into a lipid bilayer. Phospholipids provide basic structure; membrane proteins carry out specific functions.
Transmembrane or integral membrane proteins = embedded directly into bilayer.
Peripheral membrane proteins = not inserted; associated with membrane INDIRECTLY
143
The growing polypeptide chain coming off the ribosomal complex is fairly unstable. It has a tendency to fold back on itself and can aggregate with adjacent polypeptides, and these processes, if allowed to occur, would yield degraded, improperly folded, or large aggregates of nonfunctional proteins. How does the cell prevent this from occurring?
An entire class of proteins, called chaperones, prevents these potential problems. As polypeptides come off the ribosomes, these chaperones quickly bind to and stabilize the growing chain. This activity prevents improper or premature folding until the entire chain is synthesized and the completed protein can fold appropriately.
144
Can RNA be considered a polysaccharide?
DNA and RNA are polymers of nucleotides linked via a phosphodiester bond. Polysaccharides are polymers of monosaccharides (simple sugars) linked via a glycosidic bond
145
Why is phosphatidylethanolamine considered a neutral phospholipid, while phosphatidylinositol is considered an acidic phospholipid?
PE molecule is electrically neutral lipid, because it has two electrostatic charges, one negative (phosphate group) and one positive (ethanolamine group), on the specific locations in the hydrophilic head
PI has a polar and non-polar region, making the lipid an amphiphile. Phosphatidylinositol has a glycerol backbone, two non-polar fatty acid tails, a phosphate group substituted with an inositol polar head group.
146
Water is a polar molecule and can form hydrogen bonds. How is this property of water an important factor in determining protein structure?
Water molecules can guide folding and facilitate packing of supersecondary structural elements by mediating long-range interactions between polar and charged amino acids, pointing out its important role for folding and stabilization of large and multidomain proteins.
147
Like ribonuclease, insulin is a small protein. However, upon renaturation, insulin is much less efficient in resuming its native conformation. Why is this?
RNase A is a small protein, the mature enzyme only has 124 amino acid residues, with no carbohydrate attached. Unlike other enzymes RNase A contains 19 of the 20 acids, lacking only tryptophan.
Insulin is a protein composed of two chains, an A chain (with 21 amino acids) and a B chain (with 30 amino acids), which are linked together by sulfur atoms
148
Suppose you have completed a series of polyacrylamide gel electrophoresis experiments and found that under both denaturing and non-denaturing conditions, purified hemoglobin migrates as one molecular species. However, the apparent mass of the observed species under denaturing conditions is approximately one-quarter of that observed under non-denaturing conditions. What is the most likely explanation for these results?
If native hemoglobin had a quaternary structure consisting of four polypeptide chains of near identical mass, then the observed experimental outcomes would be exactly the expected outcomes. Hemoglobin is a protein consisting of four very similar polypeptide chains; two α and two β chains. The α and β chains of hemoglobin arose from gene duplication.
149
Suppose you are studying the change in reaction rate for lactate dehydrogenase as the concentration of lactate is increased. You find that initially the reaction rate increases linearly with lactate concentration, but as you continue to increase lactate concentration, there is less and less increase in the reaction rate. Eventually there is almost no increase. Why?
As the concentration of substrate increases, the enzyme becomes saturated with substrate. As soon as the catalytic site is empty, more substrate is available to bind and undergo reaction
As the substrate concentration increases, the enzyme reaction increases until all of the active sites are occupied by the substrate. ... When all active sites are occupied, the enzyme is saturated. At this saturation point, adding more substrate makes no difference to the reaction rate.
150
A rat's liver is respiring actively, and you supply the liver with glucose labeled with carbon-14. Which of the following will rapidly become radioactively labeled: water, carbon dioxide, or NADH?
One must consider here the inputs to, and the outputs from, glycolysis, the citric acid cycle, and the electron transport chain, as well as the chemical structures of the compounds named in the question. Water does not become labeled, as it consists of only hydrogen and oxygen atoms, with no carbons. NADH does not become labeled, since it is formed by the addition of hydrogen, not carbon, to NAD+. The carbon dioxide does become labeled, since the carbons of glucose are all released as carbon dioxide.
151
Cells can both make cholesterol and utilize cholesterol from the diet. High levels of cholesterol depress cholesterol biosynthesis by cells. What is the biochemical term applied to this type of enzyme regulation, and what are the implications of lowered dietary cholesterol for the rate of cellular cholesterol biosynthesis?
feedback inhibition
| increase
152
Suppose that an organic chemist wishes to synthesize an inhibitor of an important enzyme in pyrimidine biosynthesis. What two different kinds of molecules should be considered the most effective inhibitors?
Pyrimidines are heterocyclic bases found as part of DNA and RNA. Biosynthesis of pyrimidines is essential for cell multiplication. One chemical approach to inhibiting an enzyme in pyrimidine biosynthesis would be to synthesize a chemical analog of the enzyme substrate that might bind more tightly to the enzyme's active site or be unable to be reacted on by the enzyme. A second chemical approach would be to synthesize a chemical analog of an allosteric effector of the enzyme. Some enzymes are regulated by metabolic products of the enzyme pathway that bind to a second site on the enzyme that is distant from the active site of the enzyme. A tight binding allosteric effector analog would also inhibit enzyme activity.
153
Transmembrane proteins are water-insoluble. Why?
Membrane proteins (MPs) are insoluble in aqueous media as a result of incompatibility between the hydrophilic property of the solvent molecules and the hydrophobic nature of MP surfaces, normally associated with lipid membranes.
Proteins that extend all the way across the membrane are called transmembrane proteins. The portions of an integral membrane protein found inside the membrane are hydrophobic, while those that are exposed to the cytoplasm or extracellular fluid tend to be hydrophilic
154
The only protein structure known to span a biological membrane, other than α helix, is the β barrel, formed by the folding of β sheets into a barrel-like structure. Why does the presence of β barrel proteins in the outer membrane of chloroplasts and mitochondria make lipid bilayers permeable to small molecules and ions?
beta-barrel It increases permeability.
| the tight packing of amino acid residues bestows a high level of stability to the protein
155
Suppose you are studying the transport of glucose into red blood cells and find that as you increase the concentration of glucose outside of the cells, a concentration is reached at which there is no further increase in the rate of accumulation of glucose in the cells. What is the explanation for this?
As the concentration of substrate increases, the enzyme becomes saturated with substrate. As soon as the catalytic site is empty, more substrate is available to bind and undergo reaction
As the substrate concentration increases, the enzyme reaction increases until all of the active sites are occupied by the substrate. ... When all active sites are occupied, the enzyme is saturated. At this saturation point, adding more substrate makes no difference to the reaction rate.
