Biology 186 Midterm PART 1 Flashcards
1
Q
Four most important large molecules
A
Carbohydrates
Lipids
Proteins
Nucleic Acids
2
Q
Three macromolecules
A
Carbohydrates
Proteins
Nucleic Acids (DNA,RNA)
3
Q
Biochemists determined the detailed structure of macromolecules using __
A
Cryomicroscopy
4
Q
Polymer
A
the macromolecules in three of the four classes of life’s organic compounds (carbohydrates, proteins, nucleic acids) are chain like molecules called polymers: A long molecule consisting of many similar or identical building blocks linked by covalent bonds
5
Q
Covalent bonds
A
A covalent bond, also called a molecular bond, is a chemical bond that involves the sharing of electron pairs between atoms. These electron pairs are known as shared pairs or bonding pairs, and the stable balance of attractive and repulsive forces between atoms, when they share electrons, is known as covalent bonding.
6
Q
Monomers
A
The repeating units that serve as building blocks of a polymer are smaller molecules called monomers
7
Q
What are monomers?
A
Small simple molecules that link together to form larger molecules–> Polymers
8
Q
Large polymers=?
A
Macromolecules
9
Q
Dehydration Reaction?
A
SYNTHESIS of a polymer: Dehydration removes a water molecule, forming a new bond (OH, H removed to remove H20)
10
Q
What does hydrolysis do?
A
water molecule breaks bond between monomers to break down polymers
11
Q
Synthesis and breakdown of polymers are facilitated by?
A
Enzymes
12
Q
Enzymes?
A
Specialized macromolecules that speed up chemical reactions
13
Q
Each class of polymer is made up of a _____ type of monomer but the chemical mechanisms which cells make and break down polymers are always ____
A
Different
The same
14
Q
Macromolecules are ___ built from ___
A
Polymers
Monomers
15
Q
Polymers are assembled by ___
A
Dehydration reactions
16
Q
Dehydration reactions?
A
monomer units are attached together with the loss of a molecule of water
17
Q
Polymers are broken down by ___
A
Hydrolysis (Gr. hydro, water, and lysis, break)
18
Q
Hydrolysis?
A
A molecule of water is added to break the bond between the monomers
19
Q
What happens during a dehydration reaction?
A
When a bond forms between 2 monomers, each monomer contributes part of the water molecule that is released during the reaction. One monomer contributes a hydroxyl group (OH) while the other provides a hydrogen (H). This reaction is repeated as monomers are added ton the chain one by one, making a polymer
20
Q
Polymers are disassembled to monomers by ___
A
Hydrolysis
21
Q
Hydrolysis?
A
The bond between the monomers is broken by the addition of a water molecule, with a hydrogen from the water attaching to one monomer and the hydroxyl group attaching to the adjacent monomer.
22
Q
Example of hydrolysis in our bodies?
A
Digestion: Various enzymes attack the polymers, speeding up hydrolysis
23
Q
Each cell has ___ of different macromolecules
A
Thousands
24
Q
Building a huge variety of polymers from such a limited number of monomers is analogous to?
A
Constructing hundreds of thousands of words from only 26 letters in the alphabet
25
Small molecules common yo all organisms are ordered...?
into unique macromolecules
26
Carbohydrates include
both sugars and polymers of sugars
27
Simplest carbohydrates?
Monosaccharides (Simple Sugars)
28
Monosaccharides?
The monomers from which one or more complex carbohydrates are constructed
29
Disaccharides?
Double sugars consisting of two monosaccharides joined by a covalent bond
30
What are carbohydrate molecules?
polymers called polysaccharides composed of many sugar building blocks
31
some polymers are____ arrangements of monomer units, some are ____
Linear
| Branched
32
2 types of polymers?
homopolymers
| heteropolymers
33
Homopolymers?
polymers composed of identical monomers, e.g. starch, which is polymerized glucose
34
Heteropolymers?
polymers composed of different monomers, e.g. DNA
35
Four functions of carbohydrates?
energy storage, energy transport, building material, molecular recognition and communication at the cell surface
36
Energy storage in animals vs plants?
glycogen in human muscle and liver
| starch in plants
37
Energy transport in animals vs plants?
* glucose in blood
| * sucrose in plants
38
Building material in animals vs plants?
* cellulose in plant cell walls
| * chitin in arthropod skeletons and fungal cell walls
39
Formula for monosaccharides?
Some multiple of the unit CH2O
40
Most common monosaccharide?
Glucose (C6H12O6) - has a carbonyl group and multiple hydroxyl groups which shows the trademarks of sugar
41
Depending on the location of the carbonyl group, a sugar is either an ____ or a ____
Aldose (Aldehyde sugar)
| Ketose (Ketone sugar)
42
Glucose is an example of a ___ while Fructose is an example of ___
Aldose
| Ketose
43
Another criteria for clarifying sugars is the ___ of the carbon skeleton, which can range between ____ carbons long
Size
| Three to seven
44
hexose?
Six carbon sugars
45
Triose?
three carbon sugars
46
Pentose?
Five carbon sugar
47
Another source of diversity for monosaccharides is in the ____ of their parts around ____
Spatial arrangement
| Asymmetric Carbons
48
Asymmetric carbon?
A carbon attached to four different atoms or groups
49
How many carbons in a monosaccharide?
3-7
50
2 functional groups in monosaccharides?
hydroxyl and carbonyl
51
aldose?
possesses an aldehyde group, HCOR
52
Ketose?
possesses a ketone group, RCOR
53
isomeric forms?
arrangement of groups on asymmetric carbon atoms, e.g. glucose and galactose
54
straight chain or ring forms?
ring form predominates in aqueous solution at pH 7
55
How do glucose and galactose differ?
only in the placement of parts around one asymmetric carbon
56
When do glucose molecules form rings?
in aqueous solutions
57
Why are monosaccharides useful for the cell?
Cellular respiration, major fuel for cellular work, carbon skeletons serve as raw material for the synthesis of other small organic molecules such as amino acids or fatty acids
58
What happens to monosaccharides when they are not immediately used?
Incorporated as monomers into disaccharides or polysaccharides
59
Disaccharide?
Two monosaccharides joined by a glycosidic linkage
60
Glycosidic linkage?
A covalent bond formed between two monosaccharides by a dehydration reaction (ex: maltose is a disaccharide formed by the linking of two molecules of glucose)
61
____ is a disaccharide from the linking of two glucose molecules
Maltose
62
Sucrose is a disaccharide formed from ____ and ____
Glucose and Fructose
63
The most prevalent disaccharide?
Sucrose (Table sugar)
64
Plants transport carbohydrates from leaves to roots in the form of ___
Sucrose (Table sugar)
65
Lactose?
The sugar present in milk, is another disaccharide (a glucose molecule joined to a galactose molecule)
66
Glycosidic Linkage?
covalent bond formed between two
| monosaccharides by a dehydration reaction
67
isomers?
orientation of the –H and the –OH groups on the #1 carbon in a
ring, e.g. alpha and beta glucose
68
Oligosaccharides?
several monosaccharides attached together (oligo= few)
| often found covalently linked to the noncytoplasmic side of proteins (glycoproteins) and lipids (glycolipids)
69
Polysaccharides?
Macromolecules: Polymers with a few hundred to a few thousand monosaccharides joined by glycosidic linkages.
70
Functions of polysaccharides?
1) Serve as storage material, hydrolyzed as needed to provide sugar for cells
2) Serve as building material for structures that protect the cell or the whole organism
71
Architecture and function of polysaccharides determined by?
It's sugar monomers and by the positions of its glycosidic linkages
72
Plants store ___, a polymer of glucose monomers
Starch: as granules within cellular structures know as plastid, which include chloroplasts
73
What does synthesizing starch allow the plant to do?
Stockpile surplus glucose
74
Starch represents?
Stored energy because glucose is a major cellular fuel
75
How is stored sugar (starch) withdrawn from it's carbohydrate bank?
Hydrolysis (breaks the bonds between the glucose monomers)
76
How are glucose monomers in starch linked?
1-4 linkages (number 1 carbon to number 4 carbon)
77
Simplest form of starch?
Amylose: Unbranched
78
Amylopectin?
A more complex starch
79
How is Amylopectin branched?
a branched polymer with 1-6 linkages at the branch points
80
What polysaccharide do animals store?
Glycogen
81
Glycogen?
A polymer of glucose that is like amylopectin but more extensively branched
82
Where do humans store glycogen?
Liver and muscle cells
83
What happens when demand for sugar increases?
Hydrolysis of glycogen release glucose
84
How long does it take for glycogen storage to be depleted in humans?
One day unless they are replenished by consumption of food
85
Cellulose?
A major component of the tough walls that enclose plant cells
86
Like starch, ___ is a polymer of glucose
Cellulose
87
Alpha and Betta ring forms?
When glucose forms a ring, the hydroxyl group attached to number 1 carbon is positioned either below or above the plane of the ring. These two rings for glucose are called alpha and beta.
88
In starch, all the glucose monomers are in the ___ configuration
Alpha
89
The glucose monomers of cellulose are in the ___ configuration
Beta (makes every glucose monomer upside down with respect to its neighbours
90
Whereas cellulose molecules are ____, starch molecules are___
Straight
| Helical (Spiral)
91
Cellulose is never ____
Branched
92
Some hydroxyl groups on it's ___ monomers are free to hydrogen bond with the hydroxyls of other ____ molecules lying parallel to it
Glucose
| Cellulose
93
In plant cell walls, parallel cellulose molecules held together are grouped into until called _____
Microfibrils
94
Microfibrils?
The cable like microfibrils are a strong building material for plants and an important substance for humans because cellulose is the major constituent of paper and the only component of cotton
95
Enzymes that digest starch by hydrolyzing its ____linkages are unable to hydrolyze the ____ linkages of cellulose because of the distinctly different shapes of the two molecules
Alpha
| Beta
96
Can the human body digest cellulose?
No, it passes through our digestive tract and is eliminated with the feces
97
2 types of storage polysaccharides?
Starch and Glycogen
98
Starch consists of ___ and ___
Amylose and Amylopectin
99
Starch?
main storage polysaccharide of plants and some algae
100
Amylose?
linear polymer of glucose with 1-4 glycosidic linkages
101
Amylose structure?
Unbranched
102
Amylopectin?
like amylose, except it has 1-6 branches
103
Starch is in the shape of a ____
Helix (spiral)
104
Amylopectin structure?
Somewhat branched
105
Glycogen?
main storage polysaccharide of animals; similar to amylopectin, but branch points are more frequent
106
Glycogen structure?
branched
107
What does hydrolyze mean?
Digest
108
Enzymes called ____ digest (hydrolyze) starch and glycogen
Amylases
109
What holds cellulose molecules together (unbranched)?
Hydrogen bonds between parallel cellulose molecules hold them together
110
Starch is stored in ___
Plant cells
111
Glycogen is stored in ____
Muscle cells
112
Structural cellulose fibres are found in ____
Plant cell walls
113
In starch and glycogen, the polymer chains tend to form ____ in unbranched regions because of the angle of the linkages between glucose molecules
Helices (spiral)
114
Chitin?
Important structural polysaccharide, the carbohydrate used by insects, spiders, etc. to build their exoskeletons
115
Exoskeleton?
A hard case that surrounds the soft parts of an animal
116
Chitin is similar to cellulose with ___ linkages
Beta
117
The glucose monomer of chitin has a _________
Nitrogen containing appendage
118
Alpha and beta glucose ring groups differ in the placement of the ____ groups attached to the number 1 carbon
Hydroxyl
119
Cellulose?
principal component of plant cell walls; cellulose is the most abundant polysaccharide in nature
120
Cellulose glucose linkages?
BETA 1-4
121
Structure of cellulose?
the molecule is unbranched, and is straight, not helical
122
How does cellulose become good building material?
its hydroxyl groups can H bond to those on other cellulose molecules lying parallel to it, forming cables called microfibrils; this is good building material.
123
How can cows and termites make sense of cellulose?
cows and termites can make use of cellulose only because they
harbour bacteria in their guts which make cellulases
124
animals that lack ____ cannot derive nutrition from plant cell walls
Cellulose
125
_______ is a homopolymer of a monosaccharide derivative, N-acetylglucosamine
Chitin
126
What is the second most abundant polysaccharide in nature?
Chitin
127
Lipids are the only class of biomolecules that does not include true ____ as they are generally not big enough to be considered macromolecules
Polymers
128
What is lipids most important trait?
Hydrophobic: They mix poorly, if at all, with water
129
Lipids molecular structure?
The hydrophobic behaviour of lipids is based on their molecular structure: Although they may have some polar bonds associated with oxygen, they mostly consist of hydrocarbon regions
130
How are fats assembled?
Although they are not polymers, they are large molecules assembled from smaller molecules by dehydration reactions
131
What is fat made of?
two kinds of smaller molecules: Glycerol and fatty acids
132
Glycerol?
An alcohol, each of its three carbons bears a hydroxyl group
133
Fatty acid structure?
Has a long carbon skeleton, usually 16 or 18 carbon atoms in length; the carbon at one end of the skeleton is part of a carboxyl group, the rest of the skeleton consists of a hydrocarbon chain
134
What is the carboxyl group in a fatty acid?
The functional group that gives these molecules the name fatty ACID
135
Why are fats hydrophobic?
The relatively no polar C-H bonds in the hydrocarbon chains of fatty acids are the reason fats are hydrophobic
136
What happens when fat's are hydrophobic?
Fats separate from water because the water molecules hydrogen bond to one another and excludes the fats
137
How is a fat made?
Three fatty acid molecules are each joined to a glycerol by am ester linkage; a bond formed by a dehydration reaction between a hydroxyl group and a carboxyl group
138
What is the resulting fat in making a fat?
Triacylglycerol
139
What does a triacylglycerol consist of?
Three fatty acids linked to one glycerol molecule
140
What is the major function of fats?
Energy Storage
141
The ____ of fats are similar to gasoline molecules and just as rich in energy
Hydrocarbon chains
142
A gram of fat stores twice as much energy as a gram of _____
Polysaccharide (ex: starch)
143
Where do humans and other mammals stock their long term food reserves?
Adipose Cells
144
Adipose cells?
Store energy and cushions vital organs such as kidneys, and a layer of fat beneath the skin insulates the body
145
Composition of saturated fatty acids?
There are no double bonds between carbon atoms composing a chain, then as many hydrogen atoms as possible are bonded to the carbon skeleton (saturated with hydrogen)
146
Unsaturated fatty acid composition?
One or more double bonds with one fewer hydrogen atom on each double bonded carbon. Nearly all double bonds are CIS double bonds, which causes a kink in the hydrocarbon chain wherever they occur.
147
What allows saturated fat molecules to pack together tightly?
The hydrocarbon chains of their fatty acids (the tails of the fat molecules) lack double bonds, and their flexibility allows the fat molecules to pack together tightly.
148
Why are unsaturated fatty acids liquid at room temperature?
(oils) The kinks where the CIS double bonds are located prevent the molecules from packing together closely enough to solidify at room temperature
149
Difference between saturated and unsaturated fat at room temperature?
Saturated: Solid
Unsaturated: Liquid
150
Where does omega-3 fatty acid get it's name?
They have a double bong at the third carbon-carbon bond from the end of the hydrocarbon chain
151
Why are phospholipids essential for the cell?
They are major constituents of cell membranes; their structure provides an example of how form fits function at a molecular level
152
Structure of a phospholipid?
Similar to a fat molecule but has only two fatty acids attached to glycerol rather than three. The third hydroxyl group of glycerol is joined to a phosphate group, which has a negative electrical charge in the cell. Typically, an additional small charged or polar molecule is also linked to the phosphate group
153
How do the two ends of the phospholipids differ in their behaviour towards water?
The hydrocarbon tails are hydrophobic and are excluded from water, however, the phosphate group and its attachments form a hydrophilic head that has an affinity for water
154
What happens when phospholipids are added to water?
They self assemble into double layered structures called bilayers, shielding their hydrophobic portions from the water
155
How are phospholipids arranged at the surface of the cell?
In a bilayer; the hydrophilic heads of the molecules are on the outside of the bilayer, in contact with the aqueous solutions inside and outside of the cell.The hydrophobic tails point towards the interior of the bilayer, away from the water.
156
The ______ forms a boundary between the cell and its external environment, the existence of cells depends on the ______
Phospholipid Bilayer
| Phospholipids
157
Steroids?
Lipids characterized by a carbon skeleton consisting of four fused rings.
158
How are steroids distinguished?
By the particular chemical group attached to this ensemble of rings
159
What is cholesterol?
A steroid that is a crucial molecule in animals because it is a common component of animal cell membranes and it is also the precursor from which other steroids, such as sex hormones, are synthesized
160
Where is cholesterol synthesized?
The liver (also obtained from diet)
161
What are lipid's general properties?
hydrophobic, often with hydrophilic functional groups attached
162
______ regions soluble in non polar solvents; _____ regions soluble in water
Hydrophobic
| Hydrophilic
163
Examples of lipids?
* fatty acids
* triglycerides: fats and oils
* phospholipids
* steroids and sterols
* waxes
164
Functions of lipids?
```
Energy storage
Fuel
Membrane formation
Communication
Protection
Insulation
```
165
How is ATP produced from fatty acids?
Fatty acids released from fats are oxidized in the mitochondria and ATP is produced as a result
166
Why are lipids important for membrane formations?
phospholipids and glycolipids spontaneously self-assemble into bilayers in aqueous solutions
167
What kind of protection do lipids offer the cell?
adipose tissue cushions the organs
168
How do lipids insulate the cell?
adipose tissue has low thermal conductivity (used by endotherms)
169
General formula for fatty acids?
CH3(CH2)nCOOH
170
What are the two parts of a fatty acid?
1) unbranched, hydrophobic hydrocarbon chain
| 2) hydrophilic carboxyl group
171
What is an amphipathic?
molecules with a hydrophobic region and a hydrophilic region
172
Fatty acids are a type of a_____
amphipathic
173
3 aspects of structural variation in fatty acids?
* length of carbon chain (usually 16 or 18 carbon, e.g. palmitic acid, C16H32O2)
* saturated or unsaturated (double bonds)
* cis or trans configuration at double bonds
174
_____ are fatty acid esters of glycerol (a 3-carbon alcohol)
Glycerides
175
Most animal fats are ___ at room temperature
solid (saturated)
176
Most plant fats are ___ at room temperature
liquid (unsaturated)
177
____- heat is needed to disrupt the solidity of saturated fats while ____ heat is needed to disrupt the liquid unsaturated fats
Higher
| Lower
178
What fats are best for your health?
Monounsaturated oils (canola oil, olive oil)
179
What are the three types of membrane lipids?
* phosphoglycerides (e.g. phosphatidylcholine)
* sphingolipids (e.g. sphingomyelin)
* membrane steroids such as cholesterol
180
Membrane lipids are a_____
Amphipathic (molecules with a hydrophobic region and a hydrophilic region)
181
Membrane lipids spontaneously form ____ when placed in an aqueous solution
Bilayers
182
What formation is favoured when the cross sectional area of the head group is greater than that of the side chains?
Micelle formation
183
Liposome?
sphere in which a phospholipid bilayer encloses an aqueous compartment
184
Characteristics of a steroid?
rigid, planar, amphipathic
185
Example of a steroid?
Cholesterol
186
What are steroids function in the membrane?
Stabilizes it at high temperature by restraining the movement of phospholipids
187
Steroids keep membrane fluids at a _____ temperature
low
188
Nearly every dynamic function of living depends on _____
proteins
189
Most _____ are proteins
Enzymes
190
How do enzymatic proteins regulate metabolism?
By acting as catalysts
191
Catalyst?
Chemical agents that selectively speed up chemical reactions without being consumed by reaction
192
Function and example of enzymatic protein
Selective acceleration of chemical reactions; example: digestive enzymes catalyze the hydrolysis of bonds in food molecules
193
Function and example of defensive proteins?
Protection against disease; example: antibodies inactivate and help destroy viruses and bacteria
194
Storage proteins?
Strorage of amino acids; example: casein is the major source of amino acids for baby mammals
195
Transport proteins?
Transport substances; example: hemoglobin transports oxygen from the lungs to other parts of the body
196
hormonal proteins?
Coordination of an organism's activities; example: insulin
197
Receptor proteins?
response of cell to chemical stimuli; example: receptors built into the membrane of a nerve cell detects signalling molecules released by other nerve cells
198
Contractile and motor proteins?
Movement; example: motor proteins are responsible for the undulations of cilia and flagella. Actin and myosin proteins are responsible for the contraction of muscles
199
Structural proteins?
Support; Keratin is the protein of hair, collagen and elastin provides a fibrous framework in animal collective tissues
200
How are proteins structured?
They are all constructed from the same set of 20 amino acids, linked in unbranched polymers
201
The bond between amino acids is called a _____
peptide bond
202
SO a polymer of amino acids is called a ______
Polypeptide
203
What is the definition of a protein?
A biologically functional molecule made up of one or more polypeptides each folded and coiled into a specific three dimensional structure
204
What is an amino acid?
An organic molecule with both an amino group and a carboxyl group
205
Structure of an amino acid?
At the centre of the amino acid is an asymmetric carbon called the alpha carbon, its four different partners are an amino group, a carboxyl group, a hydrogen atom, and a variable group symbolized by R
206
The R group ____ with each amino acid
Differs
207
What determines the characteristics of an amino acid?
The physical and chemical properties of the side chain, thus also affecting its functional role as a polypeptide
208
How do amino acids usually exist within the pH of a cell?
In ionized form
209
Amino acids with non polar side chains (R group) are _____-
Hydrophobic
210
Which amino acids are hydrophilic?
Those with polar side chains (R group)
211
What are the characteristics of acidic amino acids?
Side chains that are generally negative in charge due to the presence of a carboxyl group, which is usually dissociated (ionized) at cellular pH.
212
Properties of basic amino acids?
Side chains are generally positive in charge
213
Because they are charged, acidic and basic side chains are also ________
Hydrophilic
214
How are amino acids linked together to form polymers?
When two amino acids are positioned so that the carboxyl group of one is adjacent to the amino group of the other, they can become joined by a dehydration reaction, with the removal of a water molecule. The resulting covalent bond is called a peptide bond, when repeated over and over this process yields a polypeptide
215
Polypeptide?
A polymer of many amino acids linked by peptide bonds
216
One end of the polypeptide chain has a free ____ group, while the opposite end has a free carboxyl group
Amino
217
What is the amino end of a polypeptide chain called?
N-terminus
218
C-terminus?
Single carboxyl end to a polypeptide chain
219
What do the activities of proteins result from?
Their intricate three-dimensional architecture (sequence of their amino acids)
220
What is the simplest level of a proteins structure?
The sequence of their amino acids
221
What determines the three dimensional structure of a protein?
The amino acid sequence of each polypeptide
222
2 categories of protein shapes?
Spherical (Globular proteins)
or
Shaped like long fibres (Fibrous proteins)
223
All proteins have three superimposed levels of structure, _____, _____, ______ and _____ which arises when a protein consists of two or more polypeptide chains
Primary
Secondary
Tertiary
Quaternary
224
What is sickle cell disease?
Caused by the substitution of one amino acid for one gleams acids at a particular position in the primary structure of hemoglobin
225
What are the key factors determining protein structure?
A polypeptide chain of a given amino acid sequence can be arranged into a three dimensional shape determined and maintained by the interactions responsible for secondary and tertiary structure
226
Other factors affecting protein structure?
pH, salt concentration, temperature, etc. in the proteins environment
227
Denaturation?
Weak chemical bonds and interactions within a protein are destroyed by changes in environmental conditions which causes the protein to unravel and lose its shape
228
How do most proteins become denatured?
If they are transferred from an aqueous environment to a non polar solvent; chemicals that disrupt the hydrogen bonds, ionic bonds, etc. that maintain a protein's shape; excessive heat which agitates the polypeptide chain enough to overpower the weak interactions that stabilize the structure
229
Primary structure of a protein?
Linked series of amino acids with a unique sequence; determined by inherited genetic information
230
Primary structure summarized?
Linear chain of amino acids`
231
Secondary structure?
regions stabilized bt hydrogen bonds between atoms of the polypeptide backbone
232
Secondary structure composition?
Proteins have segments of they polypeptide chains repeatedly coiled or folded in patterns that contribute to the protein's overall shape. These coils and folds are the secondary structure
233
How are secondary structures formed?
They are the result of hydrogen bonds between the creating constituents of the polypeptide backbone; within the backbone, the oxygen atoms have a partial negative charge, and the hydrogen atoms attached to the nitrogens have a partial positive charge, therefore, hydrogen bonds can form between these atoms. Individually, they are weak, but because they are repeated many times over a relatively long region of the polypeptide chain, they can support a particular shape for that part of the protein
234
Alpha helix?
Secondary structure; a delicate coil held together by hydrogen bonding between every fourth amino acid
235
Beta pleated sheet?
Secondary structure; Two or more strands of the polypeptide chain lying side by side (beta stands) are connected by hydrogen bonds between parts of the two parallel polypeptide backbones
236
Tertiary Structure summarized?
Three dimensional shape stabilized by interactions between side chains (R groups)of the various amino acids
237
Hydrophobic interaction?
Contributes to the tertiary structure; as a polypeptide folds into its functional shape, amino acids with hydrophobic (non polar) side chains usually end up in clusters at the core of the protein, out of contact with water. Thus a hydrophobic interaction is actually caused by the exclusion of non polar substances by water molecules. Once non polar amino acid side chains are close together, van der Waals interactions help hold them together. Meanwhile, hydrogen bonds between the polar side chains and ionic bonds between positively and negatively charged side chains also help stabilize tertiary structure. These are all weak interactions in the aqueous cellular environment, but their cumulative effect helps give protein a unique shape
238
Disulphide bridges?
Covalent bonds that reinforce shape of a protein
239
How do disulphide bridges reinforce proteins shape?
Form where two cysteine monomers, which have sulfhydryl groups (SH) on their side chains are brought close together by the folding of the protein. The sulphur of one cysteine bonds to the sulphur of the second and the disulphide bridge (-S-S-) rivets part of the protein together
240
Quaternary Structure summarized?
Association of multiple polypeptides, forming a functional protein
241
What do quaternary structures result from?
Some proteins consist of two of more polypeptide chains aggregated into one functional macromolecule, and the quaternary structure is the overall protein structure that results from this
242
Examples of quaternary structures?
Hemoglobin, Collagen
243
Chaperonins?
Crucial to the folding process of proteins; do not specify the final structure of a polypeptide but instead they keep the new polypeptide segregated from disruptive chemical conditions in the cytoplasmic environment while it does spontaneously
244
A h____ environment aids the folding process
Hydrophilic
245
If the primary structure of polypeptides determines a protein's shape, what determines primary structure?
The amino acid sequence os a polypeptide is programmed by a discrete unit of inheritance known as a gene
246
Genes consist of ____ which belongs to the class of compounds called nucleic acids
DNA
247
Nucleic acids?
Polymers made of monomers called nucleotides
248
Two types of nucleic acids?
DNA and RNA
249
DNA redirects ____ synthesis and through ____ controls protein synthesis, this process is called gene expression
RNA
| RNA
250
Each chromosome contains one long ___ molecule
DNA (carrying 700 or more genes)
251
____ are required to implement genetic programs
Proteins
252
How does RNA fit into gene expression?
Each gene along a DNA molecule directs synthesis of a type of RNA called messenger (mRNA). The mRNA molecule interacts with the cells protein synthesizing machinery to direct production of a polypeptide, which folds into all or part of a protein
253
Flow of genetic information summarized?
DNA--> RNA--> protein
254
The sites of protein structures are tiny structures called ____
Ribosomes
255
Where are ribosomes in a eukaryotic cell?
In the region between the nucleus and the plasma membrane
256
Where does DNA reside?
the nucleus
257
What does messenger RNA do?
Conveys genetic information into amino acid sequences
258
Nucleic acids are macromolecules that exist as polymers called ______?
Polynucleotides
259
Each polynucleotide consists of monomers called ____?
Nucleotides
260
What are the three parts of a nucleotide?
A nitrogen containing base, a five carbon sugar (pentose), and one or more phosphate groups
261
In a polynucleotide, each monomer has ____ phosphate group(s)
One
262
The portion of a nucleotide without any phosphate groups is called a _____
Nucleoside
263
What are the two families of nitrogenous bases?
Pyrimidine
| Purines
264
Pyrimidine?
Has one six membered ring of carbon and nitrogen atoms. The members of the pyrimidine family are cytosine (C), thymine (T) and uracil (U)
265
Purines?
Larger, with a six membered ring fused t a five membered ring. The purines are adenine (A) and guanine (G)
266
_____, ______, and ______ are found in both DNA and RNA
Adenine, guanine, cytosine
267
___ is found only in DNA
Thymine
268
_____ is found only in RNA
uracil
269
In DNA, the sugar is ____ and in RNA the sugar is ____
Deoxyribose
| Ribose
270
Difference between deoxyribose and ribose?
Deoxyribose lacks an oxygen atom on the second carbon ring
271
What is a nucleoside made of?
Nitrogenous base plus sugar
272
What is a nucleotide made of?
Nitrogenous base plus sugar and a phosphate group added to the 5' sugar
273
the formation of polymers involves a ____ reaction
Dehydration
274
How are polynucleotides built?
Adjacent nucleotides are joined by a phosphodiester linkage, which consists of a phosphate group that links the sugars of two nucleotides. This bonding results in a repeating pattern of sugar phosphate units called the sugar-phosphate backbone
275
How are the two free ends of the polymer distinct from each other?
One end has a phosphate attached to a 5' carbon, and the other end has a hydroxyl group on a 3' carbon
276
What specifies the primary structure of a protein?
The linear order of bases in a gene specifies the amino acid sequence (the primary structure) of a protein, which in turn specifies that proteins three dimensional structure and its function to the cell
277
DNA molecules have two polynucleotides that spiral around an imaginary axis forming a _____ ______
Double Helix
278
What is an antiparallel arrangement?
The two sugar phosphate backbones run in opposite 5'-->3' directions from each other (like a divided highway). The sugar phosphate groups backbones are on the outside of the helix, and the nitrogenous bases are paired in the interior of the helix.
279
What are the two strands of polynucleotides held together by in a double helix?
hydrogen bonds between the paired bases
280
Which bases are compatible with each other in a double helix?
Adenine and Thymine
| Guanine and Cytosine
281
What feature makes it possible for DNA to generate identical copies of each DNA molecule preparing to divide?
If a stretch of one strand has the base sequence of 5'AGGTCC-3' then the base pairing rules tell us that the same stretch of the other trans must have the sequence 3'TCCAGG-5' because the two strands of the double helix are complimentary of each other
282
RNA molecules exist as ___ strands
Single
283
When can base pairing occur with RNA molecules?
Between regions of two RNA molecules or even between two stretches of nucleotides in the same RNA molecule
284
What does base pairing allow an RNA molecule to do?
To take on the particular three dimensional shape necessary for its function
285
What does the shape of a tRNA molecule result from?
Base pairing between nucleotides where complementary stretches of the molecule run antiparallel to each other
286
What are proteins?
Polymers of amino acids
287
most amino acid polymerization in the cell occurs during the process of ______
Translation
288
Functions of proteins?
• catalysis (enzymes)
• defence (antibodies)
• structural support (collagen and elastin in animal connective tissue; keratin in hair, horns, feathers)
• transport (hemoglobin,
membrane transporters)
• storage (ovalbumin in egg white, casein in mammal milk, glutens in wheat seeds, zeins in corn seed)
• communication (hormones, e.g. insulin; cell surface receptors)
• movement (actin, myosin in muscle; tubulin, dynein (motor proteins) in microtubules)
• regulators of gene expression
• antifreeze (e.g. in Antarctic fish)
289
all amino acids possess both an ____ group and a _____ group
Amino
| Carboxyl
290
all amino acids have at least one asymmetric carbon, the ______
carbon (except glycine)
Alpha
291
all amino acids are present in cells as only one optical _____ (L)
Isomer
292
What is an isomer?
An isomer is a molecule with the same molecular formula as another molecule, but with a different chemical structure. That is, isomers contain the same number of atoms of each element, but have different arrangements of their atoms.
293
all amino acids are zwitterions at pH __
7
294
Zwitteron?
A neutral molecule with both positive and negative electrical charges.
295
What is an enantiomer?
One of two stereoisomers that are mirror images of each other that are non-superposable (not identical), much as one's left and right hands are the same except for being reversed along one axis
296
Properties of non polar amino acids?
* hydrophobic
* usually found in the center of the protein
* also found in proteins which are associated with cell membranes
297
Polar uncharged amino acid are ______ and can form H bonds
Hydrophilic
298
In electrically charged amino acids, charge changes when __ changes
pH
299
What happens to electrical charged amino acids when pH becomes lower?
Groups are protonated, because there are a lot of protons around
300
What happens to electrical charged amino acids when pH becomes higher?
groups are unprotonated, because there are few protons around
301
Amino acids are joined together by ______ reactions to give a peptide bond
Dehydration reactions
302
Polypeptide?
Any string of amino acids, functional or not
303
Proteins are complete and folded into an active conformation; a
protein consists of one or more _______ chains
Polypeptide
304
What is a peptide?
A compound consisting of two or more amino acids
305
Oligopeptides?
Have ten or fewer amino acids
306
Polypeptides and proteins are chains of ten or more amino acids, but peptides consisting of more than 50 amino acids are classified as _______
Proteins
307
Primary structure of a protein?
linear order
| of amino acids in the polymer
308
Components of primary structure?
* N-terminus and C-terminus
* built in the N-->C direction during translation of mRNA
* backbone: NCCNCCNCC....
309
Secondary structure of a protein?
regions of regular repetitive structure
310
Components of secondary structure?
* stabilized by H bonds formed between regions of the backbone
* alpha-helix, beta-strand, or β-pleated sheet
311
Tertiary structure of a protein?
the overall bending and folding of a polypeptide chain into its three-dimensional shape
312
Tertiary structure is stabilized mainly by interactions between _______
R groups
313
Components of R groups?
* H bonds
* ionic bonds
* hydrophobic interactions
* disulfide bridges
314
Tertiary structure can be altered by _________ changes
Environmental
315
Quaternary structure?
association of more than one polypeptide chain to form an intact protein
316
Four structures of a protein summarized?
Primary: linear order of amino acids in the polymer
Secondary: local twists and bends of the amino acid chain
Tertiary: folding of the whole chain due to R group interactions
Quaternary: association of two or more polypeptide chains
317
Information needed to build proteins stored in genes, and put to use in the process of ____ _______
Gene expression
318
What influences protein function?
Conformation (shape)
319
How does conformation of protein result from primary structure?
change primary structure (the result of a change in a gene; that is, a mutation)--> change conformation--> change function
320
How does conformation of a protein depend on weak interactions?
denaturation: interactions disrupted (e.g. by heat)--> protein unravels and loses conformation--> function of the protein altered or destroyed
321
protein structure and function may depend on a non-protein helper – a _____
Cofactor Ex: iron and heme group of hemoglobin
322
Characteristics of protein folding?
* some proteins fold up spontaneously
* other proteins always require help in folding
* others may misfold
323
What are chaperones?
Proteins that facilitate protein folding:
• help proteins fold if incompletely folded or partly denatured
• ATP-dependent process
324
What are chaperonins?
* massive macromolecular chaperones that provide an internal cavity in which some proteins fold
* also ATP-dependent
325
Chaperones do not dictate a protein’s final structure; they help shield a protein from unfavourable _______ influences
Environmental
326
How does the primary structure help determine a proteins second, third and fourth structure?
Primary structure determines location of α-helices, β-strands, ionic bonds, SS-bonds
327
even a single____ ____ change in a protein’s primary structure can alter its other levels of structure and in turn alter its functional ability
Amino acid
328
What are nucleic acids?
* used in the storage and transfer of genetic information
| * deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)
329
Structure of amino acids?
* monomers = nucleotides
* pentose (five-carbon sugar)
* nitrogenous base
* phosphate group
330
What is the structure of a nucleoside?
Pentose (five-carbon sugar) and a nitrogenous base
331
Nucleic acid monomers = ______
Nucleotides
332
Nucleic acid polymers = _________ _____
Polynucleotide strands
333
How are polynucleotide strands formed?
By dehydration synthesis
334
What is the backbone of a strand?
Regular alternation of sugars and phosphate groups
335
Strand has a sequence of _____
Bases
336
Strand is ____: 5’ end and 3’ end
Polar
337
What happens when a DNA or RNA polymer is created?
The bond is formed between the 3' -OH group and the 5' phosphate group
338
What pentose sugar is in DNA?
deoxyribose
339
What pentose sugar is in RNA?
Ribose
340
Purine nitrogenous base in DNA?
Adenine
| Guanine
341
Purine nitrogenous base in RNA?
Adenine
| Guanine
342
Pyrimidine nitrogenous base in DNA?
Thymine
| Cytosine
343
Pyrimidine nitrogenous base in RNA?
Uracil
| Cytosine
344
What bases are paired to form DNA?
Adenine and Thymine
| Cytosine and Guanine
345
How is a double helix formed?
• two polynucleotides wrapped around each other
• held together by:
• hydrogen bonds between paired
bases
• van der Waals interactions between stacked bases
• strands are antiparallel
346
In what respect is the polymerization of sugars into polysaccharides similar to the formation of a triacylglycerol molecule from glycerol and fatty acids?
Both processes occur by dehydration reactions.
347
In what respect is the breaking up of a polysaccharide into sugars similar to the breaking up of a polypeptide molecule into amino acids?
Both processes occur by hydrolysis reactions.
348
The molecular weight of glucose is 192 daltons. What is the molecular weight of an oligosaccharide consisting of 10 glucose residues?
To make this oligosaccharide, nine dehydration reactions are required. Each dehydration reaction results in the loss of an H2O equivalent (molecular weight 18). The molecular weight of the oligosaccharide is therefore 10(192) – 9(18) = 1758 daltons.
349
What structural detail explains the fact that starch, glycogen and cellulose consist exclusively of glucose residues, with no galactose residues mixed in?
If you compare the structures of glucose and galactose, you will notice that they differ only with respect to the orientation of the hydroxyl group on the number 4 carbon (C4). The enzymes that synthesize starch, glycogen and cellulose accept only glucose and polymers of glucose as substrates; therefore the enzymes must be able to recognize the C4 difference between glucose and galactose, and reject galactose as a substrate for this reason.
350
What structural fact about cellulose helps explain its suitability as a building material?
Cellulose is a linear molecule, and it can form many hydrogen bonds with other cellulose molecules; therefore bundles of cellulose are very strong.
351
α-glucose and β-glucose have different orientations of their hydroxyl groups at C1. Glucose
and galactose differ in the orientation of their hydroxyl groups at C4. Why, then, are glucose and galactose considered different sugars, with different names, while α-glucose and β-glucose are considered versions of one sugar, glucose?
α-glucose and β-glucose spontaneously interconvert in aqueous solution (see Fig. 5.7); glucose and galactose do not spontaneously interconvert.
352
What is the general formula of a carbohydrate? Name a carbohydrate that does not conform to this general formula.
The general formula is (CH2O)n. Chitin, and its constituent monomer Nacetylglucoseamine, do not conform to this formula.
353
What is the difference between amylopectin and glycogen?
Glycogen has more frequent branching
354
Which has more chemical energy, glycogen or triacylglycerols? Why?
Triacylglycerols have more chemical energy on a weight-for-weight basis than does
glycogen, because triacylglycerols have proportionately more energy rich C-C and C-H
bonds, and few C-O bonds, than does glycogen.
355
Why do salts of fatty acids form micelles in water?
The micelle’s form maximizes contact between water and the charged, hydrophilic carboxyl
groups of the fatty acid, and minimizes the contact between water and the hydrophobic,
hydrocarbon tails of the fatty acid.
356
What makes a phospholipid an amphipathic molecule?
Phospholipids are amphipathic molecules because they have a hydrophobic part (the two
fatty acid chains) and a hydrophilic part (the polar and charged head group).
357
Why is the melting point of the saturated 18-carbon fatty acid, stearic acid, higher than that
of the unsaturated 18-carbon fatty acid, oleic acid?
Double bonds introduce kinks in the fatty acid chain, reducing the efficiency of packing of
unsaturated fatty acids in the solid phase. It will take more thermal motion of the molecules in a saturated fatty acid to break up the regularly-packed molecules. This means that saturated fatty acids will have higher melting points.
358
What is the difference between hydrophobic interactions and van der Waals interactions?
Hydrophobic interactions are the exclusion of hydrophobic molecules and parts of molecules from association with water. Van der Waals interactions are the attractive forces resulting from asymmetric electron distributions on adjacent molecules.
359
Look at the structure of glutamic acid on p. 86. What would its net charge (the sum of its
positive and negative charges) be at pH 2? at pH 7? at pH 11?
at pH 2, +1; at ph 7, -1; at pH 11, -2.
360
What are the aspects of the peptide unit that have significance for the structure of proteins?
First, the peptide unit is rigid and planar, without free rotation around that bond. This limits
the number of conformations the peptide backbone can adopt in space. The pleats in the β - pleated sheet structure are a consequence of this. Second, the presence of the carbonyl and amine groups in the backbone allow it to form hydrogen bonds, which stabilize both the α- helix and β-pleated sheet.
361
The following oligopeptide has distinguishable ends. Why are they distinguishable?
lys-ser-glu-ser-lys
Even though lysine residues are on each end, one end will be the amino terminus, and the other will be the carboxy terminus. We could indicate this by redrawing the oligopeptide as follows:
+H3N-lys-ser-glu-ser-lys-COO–
Incidentally, placing the N terminus on the left and the C terminus on the right when you
write out an amino acid sequence is the accepted convention.
362
What are some of the factors that affect the three-dimensional conformation a protein can
assume?
- Hydrogen bonding between backbone elements in secondary structure.
- The tendency, in the case of soluble proteins, for hydrophobic R groups to be buried in the
protein’s interior, and hydrophilic R groups to be exposed to water at the surface of the
protein.
- The various R group interactions in tertiary structure.
- The various R group interactions in the quaternary structure.
363
If you heat a protein solution to 90° C, would you disrupt the protein’s primary structure?
Its secondary structure? Tertiary structure? Quaternary structure?
You would disrupt secondary, tertiary and quaternary structure, but not primary structure.
364
What is a cofactor?
A cofactor is a non-proteinaceous ion or organic molecule that a protein needs for its
activity. The heme group with its iron atom is an example of a cofactor. Many trace metals
needed by cells, such as nickel and copper, are also cofactors for certain proteins.
365
Which of the following molecules have at least one asymmetric carbon?
a) glycerol, p. 81
b) palmitic acid, p. 81
c) N-acetylglucoseamine, the monomer unit of chitin, p. 80
d) glyceraldehyde, p. 76
e) cholesterol, p. 83
f) glycine, p. 86
g) arginine, p. 86
N-acetylglucoseamine, glyceraldehyde, cholesterol and arginine have at least one
asymmetric carbon.
366
```
How many molecules of water are needed to completely hydrolyze a polymer that is 11 monomers long?
A. 12
B. 11
C. 10
D. 9
E. 8
```
?
367
You now know that the old cliché "oil and water don't mix" is true. Why?
A. Oil exhibits polarity and water does not.
B. Water exhibits polarity and oil does not.
C. Oil is hydrophilic.
D. Water is hydrophobic.
E. Oil is an organic compound and water is not.
?
368
Cellulose differs from starch in that:
A. the monomers of cellulose are held together by covalent bonds, whereas the monomers of
starch are held together by hydrogen bonds.
B. glycogen is formed by plants and cellulose by animals.
C. most animals cannot break down cellulose, whereas starch is easily digested.
D. starch is made of glucose monomers, whereas cellulose is made of fructose monomers.
E. All of the choices are correct.
?
