The Chemistry of Biology Flashcards
1
Q
What is electronegativity?
A
The ability to atoms to attract other atoms
2
Q
What is responsible for an atoms electronegativity?
A
- ) The number of protons in its nucleus
2. ) The distance between the nucleus and the valence shells
3
Q
Home come electronegativity decreases as one moves down the columns?
A
As you move down the periodic table the valence electrons get further and further away from the nucleus. One of two factors in determining electronegativity is closeness to Proton. The closer to the proton, the more electronegative.
4
Q
What is the most electronegative atom commonly found in organisms?
A
oxygen
5
Q
What type of bond to C and H form?
A
They have approximately equal electronegativity, so they form a non-polar covalent bond.
6
Q
What happens when electrons are shared non-symetically?
A
a polar covalent bond
7
Q
Where do electrons in polar covalent bonds hang out?
A
The electrons spend the majority of their time near the nucleus of the more electronegative atom.
8
Q
How are partial charges on atoms produced?
A
Polar bond produce them. The more electronegative atom attracts a disproportionate number of electrons to hang out near its nucleus. This makes the less electronegative atom somewhat positive.
9
Q
How are ionic bonds formed?
A
The transfer of electrons
10
Q
Name two common highly electronegative atoms?
A
Oxygen and Nitrogen
11
Q
Are ionic bonds common in biological molecules?
A
No
12
Q
Is structure based on function or vice versa?
A
Function is based on structure
13
Q
Why is water so essential to life?
A
It is an excellent solvent. It can turn many substances into a solution
14
Q
How are water molecules bonded together?
A
The negative oxygen attaches to the positive hydrogen.
15
Q
What makes is possible for almost any charged polar molecule to dissolve in water?
A
Hydrogen bonding.
16
Q
What happens to substances that are uncharged and non-polar when they are dissolved in water?
A
They can’t from bonds with the hydrogen and thus do not dissolve.
17
Q
What does hydrophilic mean?
A
Substances that are capable of forming hydrogen bonds and thus become solutes when water is added.
18
Q
What does hydrophobic mean?
A
Molecules that are uncharged and cannot from hydrogen bonds. For hydrophobic substances water is not a solvent.
19
Q
What is cohesion?
A
Attraction between molecules
20
Q
Why is water cohesive?
A
Because of the hydrogen bonds that form in between molecules.
21
Q
What is adhesion?
A
This attraction between unlike molecules
22
Q
In what situations is water adhesive?
A
When water adheres to a solid surface that has any amount to polarity
23
Q
What are the forces that case a meniscus in a glass tube?
A
- ) The adhesion of the water molecules to the surface of the glass
- ) Water molecules adhere with other water molecules creating a lattice of bonds that resist the upward pressure of adhesion
24
Q
What causes surface tension?
A
Water molecules at the surface have no water molecules above them with which to create a hydrogen bond. As a result they want to cohere with the nearest neighboring surface molecules. This tension created minimized the total surface area as the water is “attracted” to itself.
25
What are the important consequences of surface tension?
Water resists forces that want to increase its surface ears, this resistance means that water functions like an elastic membrane.
26
Why does heating water cause it to become less dense?
Heating water break apart the crystal lattice that has lots of space between its structures.
27
How many hydrogen bonds does each water molecule participate in its solid state?
4
28
What are proteins made of?
Polymers of amino acids
29
How are the amino acids of proteins linked?
The amino acids of a protein are linked by peptide bonds
30
What does the suffix -ose mean?
Sugar
31
How do monosaccharides differ?
Monosaccharides can be classified according to the spatial arrangement of their atoms.
32
Where is Peptidoglycan found?
It support the cell walls of bacteria.
33
What is specific heat?
The amount of energy required to raise the temperature of 1 gram of substance by 1 degree centigrade.
34
What happens to specific heat as molecules increase in polarity?
The higher the polarity, the more energy required to change temperature.
35
Does water have a high specific heat?
Yes! it take a lot more energy to vaporize water than it does most other liquid at room temperature
36
Why does sweating or dousing ourselves with water work to cool us down?
In order for water molecules to evaporate a great deal of heat must be absorbed from one's body.
37
What does endothermic mean?
A process that absorbs or requires heat.
38
What does exothermic mean?
A process that releases heat
39
What are the two forms of energy?
Potential and actual
40
Where is there the most potential energy in an electron?
In the outer shells, further away from the proton
41
What is energy called when it is stored in chemical bonds?
Chemical energy
42
What is the energy of motion called?
Kinetic energy
43
What is thermal energy?
the kinetic energy of molecular motion
44
What is temperature a measure of?
The amount of thermal energy molecules possess. Hot is more. Cold is less
45
What is heat?
The transfer of thermal energy between objects
46
What happens after hydrogen and oxygen become H2O?
Their potential energy drops
47
What happens to the excess energy when H and O become H2O
It is released as heat and light
48
What is the first law of thermodynamics?
Energy is conserved it cannot be created or destroyed
49
What is entropy?
The level of disorder in a system
50
What is the second law of thermodynamics?
Entropy always increases in an isolated system
51
What are the two factors that determine if a reaction will proceed spontaneously? (As in doesn't need energy added to the system)
1. ) When the product is less ordered than the reactants
| 2. ) When the product has lower potential energy than the reactants
52
What is a functional group?
A group of atoms that have a predictable chemical behavior.
53
How many covalent bonds can carbon form?
4
54
What is nucleic acid is made of?
Nucleotides
55
What ar the three components of a nucleotide?
1. ) Phosphate group
2. ) Five carbon sugar
3. ) Nitrogenous base
56
What is the order of the three components of a nucleotide?
The phosphate group is attached to the 5 carbon sugar, which is attached to the nitrogen base.
57
What are the monomers of ribonucleic acid (RNA)?
ribonucleotides
58
What are the monomers of deoxyribonucleic acid (DNA)?
deoxyribonucleotides
59
What the is the difference between DNA and RNA?
The 5-carbon sugar. In ribonucleotides the sugar is ribose. Ribose has an -OH in both functional group. In deoxyrobonucleic acid the sugar is deoxyribose. Deoxyribose is lacking an O in one of its functional groups.
60
What does deoxy mean?
Lacking oxygen.
61
Besides differing the type of sugar they have what are other ways that nucleotides can differ?
They can have different nitrogenous bases.
62
What are the two potential groups that nucleotides' nitrogenous bases can belong to?
Purines and Pyrimidines
63
What are the purines?
Guanine and Adenine
64
What are the pyrimidines?
Cytosine, Uracil, Thymine
65
What is a larger molecule, purines or pyrimidines?
purines
66
Where do the shape of molecules come from?
Carbon atoms furnish molecules with their overall shape
67
What determines the behavior of a compound (the types of chemical reactions in which it participates)?
This is determined by how H, N, O, P or S atoms are bonded to carbon.
68
Do amino functional groups function as acid or bases?
Bases
69
Do carboxyl functional groups function as acids or bases?
Acids
70
What functional groups do amino acid contain?
aminos and carboxyls
71
What steps should I take when I encounter a new molecule?
1. ) Examine the size and shape of the carbon framework
2. ) Examine the types of covalent bonds present based on the electronegativity of the atom. This will tell me two things a.) the polarity of the molecule b.) the amount of energy stored
3. ) Locate functional group and note the properties these groups give the molecules
72
What are four groups that are bonded to the central carbon atom?
1. ) A hydrogen atom
2. ) An amino functional group (NH2 or NH3)
3. ) A carboxyl group (COOH)
4. ) A distinctive R group or side chain
73
What happens to amino acid at a pH of 7?
They act as a base and donate one of their hydrogens. So that the formula of the amino group becomes H2N
74
What happens to molecules that are uncharged?
They cannot form hydrogen bonds. This mean they can't bond with water and are therefore hydorphobic.
75
What is stronger covalent bonds or polar bonds?
covalent bonds.
76
What bonds can sulfhydryl (SH) form?
S-S bonds. These S-S bond link different parts of large proteins
77
What are S-S bond formed by sulfhydryl good for?
They link different part of large proteins
78
What needs to happen before an enzymeattic reaction can take place?
1. ) Enzymes need to collide in a precise orientation
2. ) They need to have enough kinetic energy to overcome the repulsion between electrons that come into contact as a bonds form.
79
List the components of a prokaryotic cell?
Ribosome, plasmid, cell wall, plasma membrane, chromosome and cytoplasm
80
What is the most prominent structure inside a prokaryotic cell?
the chromosome
81
What is the nucleoid?
The nucleoid (meaning nucleus-like) is an irregularly shaped region within the cell of a prokaryote. In contrast to the nucleus of a eukaryotic cell, it is not surrounded by a nuclear membrane.
82
What is a plasmid?
Plasmids contain genes but are independent of the chromosomes. They are small circular DNA strands in the cytoplasm of a bacterium or protozoan, usually.
In many instances the genes carried in the plasmids are often not used in normal circumstances and are instead intended to help the cell adapt to unusual circumstances such as the presence of a poison. Moreover , plasmids are auxiliary genetic elements
83
Where are ribosomes located in prokaryotic cells?
They are throughout the cell interior. It is not usual for a prokaryote to contain 10,000 ribosomes.
84
What do ribosomes do?
They are protein manufacturing centers.
85
what is flagella?
it is how prokaryotes get through water. It is made of 40 proteins.
86
What is cytosol?
The fluid portion between the plasma membrane and the organelles
87
What ar the implications of eukaryotes large size?
This is space for many organelles with allows for compartmentalization of function.
This compartmentalization of function allows for two things:
1.) Incompatible reactions can be separated
2.) Chemical reaction becomes more efficient
88
What makes a molecule hydrophobic?
If it is non-polar
89
What makes molecule hydrophilic?
If it is polar
90
What holds the secondary structure together?
hydrogen bonds such as OH or NH groups or carbonyl group.
91
What are the possible secondary structures?
Alpha helix or beta pleated sheets
92
Are residues and functional groups the same thing?
Yes
93
Why are secondary highly stable?
The large number of hydrogen bonds
94
Where does the shape of secondary structures come from?
Hydrogen bonds
95
Where does the tertiary structure of proteins come from?
It is the interaction between r-groups
96
What are the interactions between r-groups that lead to tertiary protein structure?
1. ) Hydrogen bonds
2. ) Hydrophobic interactions
3. ) Van der Waals interactions
4. ) Covalent bond
5. ) Ionic bonds
97
What are Van der Waals interactions
They are weak electrical interactions. The charge of the interaction is generated by the movement of the electrons
Although the interaction is weak, a large number can increase the stability of the structure.
98
What is a disulfide bond?
A sulfur sulfur. A strong bond between peptides
99
What is a quaternary structure?
is the protein that contains multiple polypeptide chains
100
What is more stable, the folded or unfolded molecule?
The folded molecule
101
How does the medium affect protein shape?
It doesn't affect secondary shape, but it has a significant impact on tertiary shape. When water isn't present hydrogen bonds can't form. Moreover, protein shape is flexible.
102
What happens if proteins are misfolded?
They can becomes infectious. These infectious proteins are called prions
103
What are prions?
Misfolded proteins that can become infectious? This misfolding doesn't result in a change to the amino acid sequence.
104
What causes prions to form?
conformational changes.
105
What are enzymes?
they speed up reaction and they reduce the amount of energy required to begin a reaction.
106
What does polymerization?
units that come together to make a longer chain (this is the biological definition).
107
What elements bond together in when nucleotides link?
The OH of the phosphate group bonds to the OH sugar group. Hydrolysis occurs and a water is lost.
108
What is the a phosphodiester linkage?
the link in nucleic acids between phosphate group and the OH of the sugar/
109
What is the backbones of nucleic acid?
phosphodiester linkages
110
How does polymerization happen?
The potential energy of nucleotide monomers is first raised by a reaction that adds to phosphate groups to
111
What is kinetic energy?
Energy that result from motion
112
Potential energy?
Energy that can be released.
113
What is the relationship of kinetic energy to potential?
Potential energy is always more
114
What is activation energy?
the energy required to catalyze a reaction.
115
What happens when electrons move from high energy orbital to low-energy orbitals?
Some energy is released
116
What is the change in energy after a reaction?
The theoretical change in energy minus the heat loss
117
When are chemical reaction spontaneous?
When the energy required complete is negative
118
How does activation energy initiate a reaction?
By colliding electrons
119
What happens when electrons collide?
The rearrange and form new bonds. The formation of these new bonds is a chemical reaction.
120
What influences the ability of chemical reactions to occur and the ultimate size of the reaction?
1. ) The concentration
| 2. ) The temperature
121
What is energetic coupling?
The release of energy from one reaction that drives another. For something to be energy coupling, it must be an ongoing transfer energy.
Another way of talking about energy coupleing to say that is about transferring one from of energy to another
122
In biology what are the most common oxidizing reactions?
O, N, S, P
123
What makes an reaction exergonic?
When the energy of the released electron is great than can be absorbed by the reduced atom.
124
What is phosphorylation?
The transfer of phosphate group from ATP to the substrate.
125
What are substrates?
Any molecules that can accept a phosphate group. Can be amino acids, lipids, carbohydrates.
126
what happens when ATP is added to a reactant molecule?
The potential energy is increased.
127
Why does ATP have such high potential energy?
The high negative charge in close proximity repulse each other creating a high potential energy.
128
What is another way to talk about ATP?
Stored chemical energy (in the form of the highly negative phosphate groups).
129
What is a substrate?
The things you want to react
130
What is the active site of enzyme?
Where the substrates are brought together.
131
How do I identify a triglyceride?
There are three chains
132
How do I identify a steroid?
It will have four rings
133
Are lipids polymers?
No, lipids are not polymers.
134
How do I identify a triglyceride?
It will have three hydorcarbon chains coming off of the backbone.
135
How do I identify a lipid?
It will have more carbon and hydrogen than anything else.
136
What is a quick way to identify if a reaction is endergonic or exergonic?
Consider oxidation and reduction. If carbon is reduced the reaction is endergonic.
If carbon is oxidized the reaction is exergonic.
If carbon is reduced it is alway endergonic
137
What happens if carbon is reduced in a reaction?
It is always endergonic
138
What happens if carbon is oxidized in a reaction?
It is always exergonic
139
How would you decrease the reaction rate of threonine deaminase?
Add isoleucine
140
To overcome an energy barrier between reactants and products, energy must be provided to get the reaction started. This energy, which is recovered as the reaction proceeds, is called:
Activation energy
141
Why does Reaction Rate (Enzyme Velocity) plateau at a certain point when adding substrates?
The active site is saturated with substrate
142
What does the Golgi apparatus do?
packaging and distribution of proteins
143
What does the Rough ER do?
synthesis of proteins for endomembrane system
144
What does the Smooth ER do?
synthesis of lipids & cellular detoxification
145
What do the Lysomes do?
Recycling of cellular components
146
What are the component of the endomembrane of a plant cell?
```
Golgi apparatus
Central vacuole
Plasma membrane
Nuclear envelope
endoplasmic reticulum
lysomes
```
147
What is the endomembrane?
it is the cell's postal system.
One of its most important roles is to export proteins from the cell
148
What is tugor pressure?
pushes the plasma member against the cells wall.
149
What is the central vacuole?
It is a cellular organelle found in plant cells. It is often the largest organelle in the cell. It is surrounded by a membrane and functions to hold materials and wastes. It also functions to maintain the proper pressure within the plant cells to provide structure and support for the growing plant.
150
Do all plant cells contain mitochondria?
Yes!
151
Are all ribosomes in the cell the same?
yes
152
What is endosymbiosis?
When one symbiotic organism lives inside the other.
153
Are ribosomes the same in all cells?
yes!
154
Name four prices of evidence to support the endosymbiosis theory of the origin of the mitochondria and the chloroplasts?
1. ) Mitochondria and chloroplasts have naked DNA similar to bacteria
2. ) Mitochondria and chloroplasts are approximately the size of prokaryotic cells
3. ) Mitochondria and chloroplasts contain ribosomes very similar to binary fission
155
What a microfilaments composed of?
Actin
156
What is Actin?
Present in all eukaryotic cells, it is what microfilaments are made out of
157
What are microfilaments?
They are flexible and strong. They are the filament so the cytoplasm and the cytoskeleton.
They are important for cytokinesis, cell motility and changes in cell shape.
158
What is myosin?
A large superfamily of motor proteins that move along actin filaments. Well known for its importance in muscle contraction.
159
What is tubulin?
The family of proteins that make microtubules
160
What is dynein?
It is is a motor protein (also called molecular motor or motor molecule) in cells which converts the chemical energy contained in ATP into the mechanical energy of movement.
161
What is the nuclear envelope made of?
two lipid bilayers
162
what is hypotonic?
having a lower osmotic pressure than a particular fluid, typically a body fluid or intracellular fluid.
163
What creates the secondary structure of protein?
Hydrogen bonds
164
How can I measure electronegativity?
Whenever carbon has the most bonds with oxygen.
165
What happens when substrate concentration keeps rising
There is a plateau because the solution is saturated.
166
What happens during Allosteric Inhibition?
A molecule typically having no structural similarity to one of the substrates binds to a portion of the enzyme which is not the active site and inhibits the activity of the enzyme
167
What must a histone have to enter the nucleus?
A Nuclear Localization Signal which allows an importin to bind
168
What are microtubules?
maintaining cell shape and providing a track for motion proteins
169
What is the cytoskeleton made of?
microfilaments, microtubules
170
Is cellular respiration exergonic or endergonic?
It is exergonic. I know this because energy is harvested for other things.
171
How is ATP produced?
By the energetic coupling of the exergonic cellular respiration with the endergonic reaction of creating ATP
172
How can i identify a steroid?
It will have a three six carbon rings sharing sides and a fourth 5 carbon attached.
Always remember that they share sides like carbohydrates.
173
How is energy created in most biomolecular reactions?
Through oxidation. When molecules release their most energetically charged component (electrons) energy is created.
This is called an exergonic reaction.
174
What do lots of C and H indicate?
That is s a lipid
175
What is denaturation?
It is a process in which proteins or nucleic acids lose the quaternary structure, tertiary structure and secondary structure which is present in their native state
176
How can i identify a steroid?
It will have a three six carbon rings sharing sides and a fourth 5 carbon attached.
Always remember that they share sides like carbohydrates.
177
How can I identify a glyceride?
It has a three carbons with a hydroxl group.
178
What kind of reaction connects polypeptides bonds?
condensation reaction.
179
What is denaturation?
It is a process in which proteins or nucleic acids lose the quaternary structure, tertiary structure and secondary structure which is present in their native state
180
Which level of protein structure is made up of different amino acid chains?
quaternary
181
What is the difference between a hydrolysis and condensation reaction?
When a bonding chemical reaction occurs that produces water it is condensation reaction.
When water splits a part bonds (adding two H's and and O to the molecules that have been SPLIT. That is a hydrolysis.
182
What kind of reaction connects polypeptides bonds?
condensation reaction.
183
What is an active site?
Where the substrates fit into the enzyme
184
What is allosteric site?
A site other than the active site where something can bind regular the activity of the enzyme.
185
What is the difference between bound and free ribosomes?
A bound ribosome is bound to the ER making it rough.
Free ribosomes are floating around in the cell.
186
What happens when isoleucine concretion rise?
The pathway that converts threonine to isoleucine is turned off.
187
Are allosteric inhibitors structurally similar to the substrate of the enzyme?
No, they don't.
188
How do proteins get into the nucleus?
Nuclear localization signal
189
What is the difference between bound and free ribosomes?
A bound ribosome is bound to the ER making it rough.
Free ribosomes are floating around in the cell.
190
What influences the capacity to diffuse across membranes?
1. ) Polarity
| 2. ) Size of molecule
191
What is the SNARE model of vesicle fusion?
hhh
192
What packs more closely together, saturated or unsaturated fat?
saturated fat packs more closely together because the lipid tails don't have any kinks.
Where as in unsaturated fat the lipid tails have kinks preventing from being able to pack more closely together.
193
What happens to the composition of the cell membrane when cooled.
Saturated fat converts to unsaturated fat, sot that it will have more space.
194
What is the purpose of cholesterol?
It is a spacer in the membrane. Therefore bacteria from warmer environments will have less of it and those cooler environment swill have more.
195
What is the SNARE model of vesicle fusion?
hhh
196
Why are lipids not a polymers?
Because of how they are defined.
197
Facilitated diffusion
Diffusion w/o energy.
198
Proteins that are destined for export are made where?
There are made in the rough ER.
199
How do I know that glucose is polar?
The lack of symmetry
200
Where are proteins that are membrane bound generally made?
In the rough ER.
201
Facilitated diffusion
Diffusion w/o energy.
