The chemical Context of life Flashcards
(303 cards)
1
Q
What determines the compound’s properties?
A
A compound’s properties depend on its
atoms and how they are bonded together.
2
Q
What determines the atom’s ability to make bonds?
A
An atom’s electron ( ) distribution
determines its ability to form bonds
3
Q
What determines the atoms identity?
A
The number of protons determines
an atom’s identity.
4
Q
What is a compound?
A
A compound is a substance consisting of two or more
different elements combined in a fixed ratio.
5
Q
What is matter?
A
Anything that takes up space and has mass
6
Q
What makes up matter?
A
Elements make up matter.
7
Q
What are elements?
A
An element is a substance
that cannot be broken down to other substances by chemical
reactions.
8
Q
What are the 4 elements that make up 96% of living matter?
A
Just four elements—oxygen (O), carbon (C), hydrogen (H),
and nitrogen (N)—make up approximately 96% of living matter.
9
Q
What are trace elements?
A
Trace elements are required
by an organism in only minute quantities. Like Iron
10
Q
How is iodine important for us?
A
For example, in vertebrates
(animals with backbones), the element iodine (I) is an
essential ingredient of a hormone produced by the thyroid
gland. A daily intake of only 0.15 milligram (mg) of iodine
is adequate for normal activity of the human thyroid. An
iodine deficiency in the diet causes the thyroid gland to grow
to abnormal size, a condition called goiter.
11
Q
What is an atom?
A
An atom is
the smallest unit of matter that still retains the properties
of an element.
12
Q
What are subatomic particles?
A
Although the atom is the smallest unit having the properties
of an element, these tiny bits of matter are composed of even
smaller parts, called subatomic particles.
13
Q
What are the main three subatomic particles?
A
Neutrons, Protons and Electrons
14
Q
What subatomic particles are electrically charged?
A
Protons
and electrons are electrically charged. Each proton has one unit
of positive charge, and each electron has one unit of negative
charge.
15
Q
Where are the protons and neutrons?
A
Protons and neutrons are packed together tightly in a
dense core, or atomic nucleus, at the center of an atom, protons give the nucleus a positive charge.
16
Q
Where are the electrons?
A
The rapidly
moving electrons form a “cloud” of negative charge around
the nucleus, and it is the attraction between opposite charges
that keeps the electrons in the vicinity of the nucleus.
17
Q
What do we use instead of grams for measuring atoms and subatomic particles?
A
Thus, for atoms and subatomic particles
(and for molecules, too), we use a unit of measurement
called the dalton, in honor of John Dalton,
18
Q
What are the masses for the 3 subatomic particles?
A
Neutrons and protons
have masses close to 1 dalton. Because the mass of an electron
is only about 1/2,000 that of a neutron or proton, we
can ignore electrons when computing the total mass of an
atom.
19
Q
What is the atomic number of an atom?
A
This number of protons,
which is unique to that element, is called the atomic
number and is written as a subscript to the left of the symbol
for the element.
20
Q
How can we tell how many protons are in an element through their symbol, give an example
A
The abbreviation 2He, for example, tells
us that an atom of the element helium has 2 protons in its
nucleus.
21
Q
How do we know if an atom is is neutral in electric charge?
A
Unless otherwise indicated, an atom is neutral in
electrical charge, which means that its protons must be balanced
by an equal number of electrons.
22
Q
What does the atomic number tell us?
A
Therefore, the atomic
number tells us the number of protons and also the number
of electrons in an electrically neutral atom.
23
Q
What is the mass number?
A
We can deduce the number of neutrons from a second
quantity, the mass number, which is the total number of
protons and neutrons in the nucleus of an atom.
24
Q
Where is the mass number written
A
The mass
number is written as a superscript (a number, figure, symbol, or indicator that is smaller than the normal line of type and is set slightly above it (superscript) or below it (subscript).) to the left of an element’s symbol. For example, we can use this shorthand to write an atom of helium as 42He.
25
What is the atomic mass of an atom?
the total mass of an atom, called its atomic
mass.
26
What are isotopes?
These different atomic forms of the same element are called
isotopes of the element.
27
What is decay and radioactive isotopes?
Both 12C and 13C are stable isotopes, meaning that their
nuclei do not have a tendency to lose subatomic particles, a
process called decay. The isotope 14C, however, is unstable,
or radioactive. A radioactive isotope is one in which
the nucleus decays spontaneously, giving off particles and
energy.
28
What happens to an atom when radioactive decay occurs?
When the radioactive decay leads to a change in the
number of protons, it transforms the atom to an atom of a
different element. For example, when a carbon-14 (14C) atom
decays, a neutron decays into a proton, transforming the
atom into a nitrogen (14N) atom.
29
Are radioactive isotopes used in the medical field?
Radioactive isotopes are often used as diagnostic tools in
medicine.
30
PET scan stands for and what is it?
positron emission
tomography, and detects locations of intense chemical activity in the body
31
What are parent and daugher isotopes?
A parent isotope is an unstable radioactive isotope. A daughter product isotope results from the decay of a parent.
32
What is the half-life of the isotopes?
the time it takes for 50% of the parent isotope to decay.
33
What is energy?
Energy is defined as the capacity to cause change
34
What is potential energy?
Potential energy is the energy that
matter possesses because of its location or structure.
35
What is the natural tendency of matter?
Matter has a natural tendency to move toward the lowest
possible state of potential energy
36
What is an electron's energy level correlated with?
An electron’s energy level is correlated with its average
distance from the nucleus.
37
What are electron shells?
Electrons are found in different
electron shells,
38
Where is the first electron shell?
The first shell is
closest to the nucleus, and electrons in this shell have the lowest
potential energy.
39
How much energy do electrons have in the second and third shells?
Electrons in the second shell have more
energy, and electrons in the third shell even more energy.
40
How can an electron move between it's shells?
An electron can move from one shell to another, but only by
absorbing or losing an amount of energy equal to the difference
in potential energy between its position in the old shell
and that in the new shell.
41
What determines the chemical behavior of atoms?
The chemical behavior of an atom is determined by the distribution
of electrons in the atom’s electron shells.
42
What is the valence electrons and shell of an atom?
The chemical behavior of an atom depends mostly on the
number of electrons in its outermost shell. We call those outer
electrons valence electrons and the outermost electron
shell the valence shell.
43
What happens to atoms if they have completed valence shells?
An atom with a completed valence shell is unreactive;
that is, it will not interact readily with other atoms.
44
What does inert mean?
inert, meaning chemically
unreactive
45
What is an orbital of an atom?
The three-dimensional space where
an electron is found 90% of the time is called an orbital.
46
What is the orbital for the first shell?
The first electron shell has only
one spherical s orbital (called 1s)
47
What is the orbital for second and third shells?
but the second shell has
four orbitals: one large spherical s orbital (called 2s) and three
dumbbell-shaped p orbitals (called 2p orbitals). (The third
shell and other higher electron shells also have s and p orbitals,
as well as orbitals of more complex shapes.)
48
How many electrons can stay in an orbital?
No more than 2 electrons can occupy a single orbital.
49
How do uncompleted valence atoms react with each other to form molecules or ionic compounds?
Atoms with incomplete
valence shells can interact with certain other atoms in
such a way that each partner atom completes its valence shell:
The atoms either share or transfer valence electrons. These
interactions usually result in atoms staying close together, held
by attractions called chemical bonds.
50
What are the strongest kinds of chemical bonds?
The strongest kinds
of chemical bonds are covalent bonds in molecules and ionic
bonds in dry ionic compounds. (Ionic bonds in aqueous, or
water-based, solutions are weak interactions, as we will see later.)
51
What is a covalent bond?
A covalent bond is the sharing of a pair of valence electrons
by two atoms.
52
What is a molecule?
Two or more atoms held together by covalent bonds constitute
a molecule
53
What is a diagram to show electron sharing and a Lewis Dot Structure?
Electron
sharing can be depicted by an electron distribution diagram
or by a Lewis dot structure, in which element symbols are surrounded
by dots that represent the valence electrons (H : H)
54
What is a single bond?
A single covalent bond is a chemical bond formed when two atoms share one pair of electrons.
55
What is a double bond?
A double covalent bond is a chemical bond formed when two atoms share two pairs of electrons.
56
What is the atom's valence?
The bonding capacity of the atom is called the atom’s valence
57
Difference between pure elements and compound elements?
The molecules H2 and O2
are pure elements rather than
compounds because a compound is a combination of two or
more different elements
58
What is electronegativity?
The attraction of
a particular atom for the electrons of a covalent bond is called
its electronegativity.
59
What is a nonpolar covalent bond?
A covalent bond where the electrons are shared equally between it's atoms as they have the same electronegativity
60
What is a polar covalent bond?
A covalent bond where an atom is bonded to a more electronegative atom, and the electrons of the bond are not shared equally.
61
The more electronegative an atom is?
The more electronegative an atom is,
the more strongly it pulls shared electrons toward itself.
62
What are ions?
Ions are atoms or molecules that have gained or lost one or more electrons.
63
What are positively and negatively charged ions called?
Positive - Cations
Negative - Anions
64
What are ionic bonds?
Because of their opposite charges, cations and anions attract
each other; this attraction is called an ionic bond. They are bonds between atoms where electrons are (mostly) transferred from one atom to another.
65
What are ionic compounds?
Compounds formed by ionic bonds are called ionic
compounds, or salts.
66
What are the strongest chemical bonds in organisms?
In organisms, most of the strongest chemical bonds are covalent
bonds, which link atoms to form a cell’s molecules
67
Explain hydrogen bonds
When a hydrogen atom is covalently bonded to an electronegative
atom, the hydrogen atom has a partial positive charge that
allows it to be attracted to a different electronegative atom with
a partial negative charge nearby. This noncovalent attraction
between a hydrogen and an electronegative atom is called a
hydrogen bond.
68
Are electrons necessarily shared equally in a nonpolar covalent bond?
Even a molecule with nonpolar covalent bonds may have
positively and negatively charged regions. Electrons are not
always evenly distributed; at any instant, they may accumulate
by chance in one part of a molecule
or another.
69
Explain Van der Waals interactions
Electrons are not
always evenly distributed; at any instant, they may accumulate
by chance in one part of a molecule
or another. The results are everchanging
regions of positive and
negative charge that enable all
atoms and molecules to stick
to one another. These van
der Waals interactions are
individually weak and occur only
when atoms and molecules are
very close together.
70
How are complicated molecule shapes determined?
These shapes are determined by the positions of the atoms’
orbitals.
71
Why is molecular shape crucial?
Molecular shape is crucial: It determines how biological molecules recognize and respond to one another with
specificity.
72
How do opiates relieve pain?
Opiates relieve pain and alter mood by weakly binding to
specific receptor molecules on the surfaces of brain cells.
73
Endogenous meaning?
made by the body
74
What are endorphins?
Endorphins are signaling
molecules made by the pituitary gland that bind to the
receptors, relieving pain and producing euphoria (extent happiness) a during
times of stress, such as intense exercise.
75
What do opiates have similar shape to?
Opiates have shapes
similar to endorphins and can bind to endorphin receptors
in the brain.
76
What are chemical reactions?
The making and breaking of chemical bonds, leading to
changes in the composition of matter, are called chemical
reactions.
77
How do we write the equation for a chemical reaction?
When we write the equation for a
chemical reaction, we use an arrow to indicate the conversion
of the starting materials, called the reactants, to the resulting
materials, or products. The coefficients indicate the number
of molecules involved; for example, the coefficient 2 before the
H2 means that the reaction starts with two molecules of hydrogen.
78
Law of conservational energy?
Matter is conserved in a chemical reaction:
Reactions cannot create or destroy atoms but can only rearrange
(redistribute) the electrons among them.
79
Chemical formula for Photo Synthesis
6 CO2 (Carbon Dioxide) + 6 H2O (Water) -> C6H12O6 (Glucose) + 6O2 (Oxygen)
80
Are all chemical reactions reversible, what is the symbol to mark that
All chemical reactions are theoretically reversible and are marked with the symbol above
81
What is chemical equilibrium
Chemical equilibrium is a state in which the rates of the forward and reverse chemical reactions are equal.
82
How are molecules arranged in ice?
In ice, the hydrogen
bonds are stable
and the water
molecules are
farther apart.
Therefore, ice is less
dense than liquid
water, so it floats.
83
How are the hydrogen bonds in liquid water?
When
water is in its liquid form, its hydrogen bonds are very fragile,
each only about 1/20 as strong as a covalent bond. The hydrogen
bonds form, break, and re-form with great frequency.
84
Is a water molecule polar? What is a polar molecule?
A polar molecule is when atoms are bonded through polar covalent bonds, water is a polar molecule
85
What is cohesion?
Collectively, the hydrogen bonds hold
the substance together, a phenomenon called cohesion.
86
What is surface tension?
a measure of how difficult it is to stretch
or break the surface of a liquid.
87
How does water have a high surface tension?
At the air-water interface is an
ordered arrangement of water molecules, hydrogen-bonded to
one another and to the water below, but not to the air above.
This asymmetry gives water an unusually high surface tension,
making it behave as though it were coated with an invisible
film.
88
What is adhesion?
Adhesion, the clinging of one substance to another,
89
How does cohesion help water get through different plants?
Water from the roots reaches the leaves through a network
of water-conducting cells. As water evaporates from a leaf,
hydrogen bonds cause water molecules leaving the veins to
tug on molecules farther down, and the upward pull is transmitted
through the water-conducting cells all the way to the
roots.
90
What energy does anything that moves have?
Anything that moves has kinetic energy
91
What is kinetic energy?
Kinetic energy is the energy of motion
92
What is thermal energy?
The kinetic energy associated with the random movement of atoms is called thermal energy.
93
is thermal energy and temperature the same thing?
Thermal energy is related to temperature, but is not the same thing/
94
Difference between temperature and thermal energy?
Temperature represents the average kinetic energy of the molecules in a body of matter, regardless of volume, where thermal energy of a body of matter reflects the total kinetic energy, and thus depends on the matter's volume.
95
How does thermal energy move?
Thermal energy passes on from the warmer to the cooler object until they both are at the same temperature
96
What is heat?
Thermal energy in transfer from one body of matter to another is defined as heat.
97
What is a calorie (cal)
A calorie is the amount of heat it takes to raise the temperature of 1 g of water by 1 degrees celcius.
98
What is a kilocalorie (Kcal)?
A kilocalorie (Kcal) is worth 1000cal, and is the amount of eat to raise the temperature of 1 kg of water by 1 degrees, (The “Calories” on food packages are actually kilocalories.)
99
What are joules (J)
Unit of energy
100
How many calories makes up a joule?
One joule equals 0.239 cal; one calorie equals 4.184 J.
101
What is the specific heat of a substance?
The specific heat of a substance
is defined as the amount of heat that must be absorbed or lost
for 1 g of that substance to change its temperature by 1°C. In other words to understand the cooling aspect, you need to give off an amount of heat to reduce one gram of the material by 1 degrees celcius.
102
What is the specific heat for water?
We know that it takes 1 calorie to heat up 1 gram of water to 1 degrees celsius. That means the specific heat for water is 1cal/(g x C)
103
Why does water maintain its temperature compared to other liquids?
Because of the high specific heat of water relative to other
materials, water will change its temperature less than other
liquids when it absorbs or loses a given amount of heat.
104
What can specific heat tell us?
Specific heat
can be thought of as a measure of how well a substance resists
changing its temperature when it absorbs or releases heat.
105
What happens to heat when hydrogen bonds form?
Heat must be
absorbed in order to break hydrogen bonds; by the same
token, heat is released when hydrogen bonds form.
106
What is the relevance of water’s high specific heat to life
on Earth?
A large body of water can absorb and store a huge
amount of heat from the sun in the daytime and during
summer while warming up only a few degrees. At night and
during winter, the gradually cooling water can warm the
air. This capability of water serves to moderate air temperatures
in coastal areas.
107
How do organisms benefit from water's high specific heat?
Because water is resistant to heat, organisms (as they are mainly made out of water) can manage their overall temperature as water has a high specific heat meaning that it will take more heat to raise the temperature.
108
How do molecules from a liquid become a gas?
Molecules of any liquid stay close together because they are
attracted to one another. Molecules moving fast enough to
overcome these attractions can depart the liquid and enter
the air as a gas (vapor).
109
What is the transform from gas to liquid called?
Vaporization (evaporation)
110
When does evaporation occur?
Some evaporation occurs at any temperature; a glass of water
at room temperature, for example, will eventually evaporate
completely.
111
What is the heat of vaporization?
The heat of vaporization is the quantity of heat a liquid must
absorb for 1 g of it to be converted from the liquid to the gaseous
state.
112
What is the heat of vaporization for water when it is at 25C
To evaporate 1 g of water at 25°C, about 580 cal of
heat is needed
113
What is evaporative cooling?
Where the hottest particles of a liquid start to evaporate, cooling the rest of the liquid down
114
What do other materials do compare to water when they solidify?
While other materials contract
and become denser when they
solidify, water expands.
115
Does water behave normally like other materials when they solidify?
As the temperature falls from 4°C to
0°C, water begins to freeze because
more and more of its molecules are
moving too slowly to break hydrogen
bonds.
116
What happens to water when it is at 0 degrees?
At 0°C, the molecules
become locked into a crystalline lattice,
each water molecule hydrogenbonded
to four partners (see Figure
3.1). The hydrogen bonds keep the
molecules at “arm’s length,” far
enough apart to make ice about
10% less dense (10% fewer molecules
in the same volume) than liquid
water at 4°C.
117
What is a solution?
A liquid that is a completely homogeneous
mixture of two or more substances is called a solution.
118
What is a solvent and solute?
The dissolving agent of a solution is the solvent, and the substance
that is dissolved is the solute.
119
What is an aqueous solution?
An aqueous solution is one
in which the solute is dissolved in water; water is the solvent.
120
How do water molecules get attracted to positive and negative ions?
Water molecules have regions where they are positive (hydrogen atoms) and negative (oxygen atoms), the hydrogen atoms are attracted to anions and the oxygen atoms are attracted to the cations, which then separates and shields them from one and another.
121
What is a hydration shell
The sphere
of water molecules around each dissolved ion is called a
hydration shell.
122
What does hydrophilic mean?
Any substance that has an affinity for water is said to be
hydrophilic
123
What does hydrophobic mean?
tending to repel or fail to mix with water.
124
What is the molecular mass?
which is the sum of the masses of all
the atoms in a molecule
125
What is a mole (mol)
Just as a dozen always
means 12 objects, a mole (mol) represents an exact number
of objects: 6.02 * 10^23, which is called Avogadro’s number.
126
How many daltons are in 1 g?
Because of the way in which Avogadro’s number and the unit
dalton were originally defined, there are 6.02 * 1023 daltons in
1 g.
127
What is molarity?
The number of moles of solute per liter
of solution
128
What happens if a hydrogen atom in a water hydrogen bond leaves its electron?
When this happens, the hydrogen atom leaves its electron
behind, and what is actually transferred is a hydrogen ion (H+),
a single proton with a charge of 11. The water molecule that lost
a proton is now a hydroxide ion (OH-), which has a charge
of 1-. The proton binds to the other water molecule, making
that molecule a hydronium ion
129
Chemical reaction for Hydronium (H3O+) and Hydroxide (OH-)
130
What are the properties for H+ and OH-
H+ and OH- are very reactive. Changes in their concentrations
can drastically affect a cell’s proteins and other
complex molecules.
131
How do biologists describe if a solution is basic or acidic?
Biologists use something called the pH scale to describe
how acidic or basic (the opposite of acidic) a solution is.
132
What is an acid?
An acid is a
substance that increases the hydrogen ion concentration of a
solution.
133
What is a base?
A substance that reduces the hydrogen ion concentration
of a solution is called a base.
134
What are basic and neutral solutions?
Solutions with a higher concentration of OH- than H+ are
known as basic solutions. A solution in which the H+ and
OH- concentrations are equal is said to be neutral.
135
What is a pH of a solution?
The pH of a solution is defined as the negative
logarithm (base 10) of the H+ concentration: pH = -log [H+]
136
(non-bio but research related) what are logarithms?
Logarithms are another way of thinking about exponents.
Now, suppose someone asked us, "raised to which power equals ?" The answer would be . This is expressed by the logarithmic equation log2(16), read as "log base two of sixteen is four".
137
How to determine if a fluid is basic or acidic using the pH scale?
The pH of a neutral aqueous solution at 25°C is 7, the midpoint
of the pH scale. A pH value less than 7 denotes an acidic
solution; the lower the number, the more acidic the solution. The
pH for basic solutions is above 7.
138
What is the pH of biological fluids?
Most biological fluids, such as
blood and saliva, are within the range of pH 6–8. There are a few
exceptions, however, including the strongly acidic digestive juice
of the human stomach (gastric juice), which has a pH of about 2.
139
What is the pH of blood?
The pH of human blood is very close
to 7.4, which is slightly basic.
140
What do buffers do?
buffers allows biological
fluids to maintain a relatively constant pH despite the addition
of acids or bases. A buffer is a substance that minimizes
changes in the concentrations of H+ and OH- in a solution.
141
How do buffers work?
It
does so by accepting hydrogen ions from the solution when
they are in excess and donating hydrogen ions to the solution
when they have been depleted. Most buffer solutions contain
a weak acid and its corresponding base, which combine
reversibly with hydrogen ions.
142
How does Carbonic acid work as a buffer?
The chemical equilibrium between carbonic acid and bicarbonate
acts as a pH regulator, the reaction shifting left or
right as other processes in the solution add or remove hydrogen
ions. If the H+ concentration in blood begins to fall (that
is, if pH rises), the reaction proceeds to the right and more
carbonic acid dissociates, replenishing hydrogen ions. But
when the H+ concentration in blood begins to rise (when
pH drops), the reaction proceeds to the left, with HCO3
- (the
base) removing the hydrogen ions from the solution and
forming H2CO3. Thus, the carbonic acid–bicarbonate buffering
system consists of an acid and a base in equilibrium with
each other. Most other buffers are also acid-base pairs.
143
What is ocean acidification?
When CO2 dissolves in seawater, it reacts with water to
form carbonic acid, which lowers ocean pH. This process,
known as ocean acidification
144
What determines the properties of a carbon containing molecule?
The properties of a carbon-containing
molecule depend on the arrangement
of its carbon skeleton and on its
chemical groups.
145
What is organic chemistry and organic compounds?
For historical reasons, compounds containing carbon are said
to be organic, and their study is called organic chemistry.
146
Abiotic meaning
Non living
147
How do organisms differ organically?
Different species of organisms, and different individuals
within a species, are distinguished by variations in the types
of organic molecules they make.
148
What is the arrangement of molecules when carbon makes 4 single covalent bonds
When a carbon atom forms four single covalent bonds,
the arrangement of its four hybrid orbitals causes the bonds
to angle toward the corners of an imaginary tetrahedron.
149
What is the arrangement of molecules when 2 carbon atoms are joined by double covalent bonds?
when
two carbon atoms are joined by a double bond, as in ethene
(C2H4), the bonds from both carbons are all in the same
plane, so the atoms joined to those carbons are in the same
plane as well
150
What is the atom's valence?
the number of covalent bonds it can form.
151
is CO2 organic?
Because CO2 is a very simple molecule and lacks hydrogen,
it is often considered inorganic, even though it contains carbon.
152
What is urea?
Urea, CO(NH2)2, is an organic
compound found in urine. Again,
each atom has the required number of
covalent bonds. In this case, one carbon
atom participates in both single and
double bonds.
153
What forms the basis of organic molecules?
Carbon chains form the basis of most organic molecules.
154
What are carbon skeletons and their shape?
Carbon skeletons are the chains of carbon atoms that form the backbone of organic molecules. Carbon skeletons vary in length and may be straight,
branched, or arranged in closed rings
155
What is the shape of Cyclohexane and benzene and why is it shown like that?
156
What are hydrocarbons?
organic molecules consisting of only
carbon and hydrogen
157
What are isomers?
isomers, compounds that have the same numbers of
atoms of the same elements but different structures and hence
different properties.
158
What are the 3 types of isomers?
Structural isomers, cis-trans isomers (geometric isomers), enantiomers
159
How do structural isomers differ?
Structural isomers differ in the covalent arrangements of
their atoms.
160
How do cis-trans isomers differ?
In cis-trans isomers (also known as geometric isomers), carbons
have covalent bonds to the same atoms, but these atoms
differ in their spatial arrangements due to the inflexibility of
double bonds.
161
what are cis isomers and trans isomers?
In cis isomers, the groups are on the same side of the double bond, while in trans isomers, they are on opposite sides.
162
What are enantiomers?
Enantiomers are isomers that are mirror images of
each other and that differ in shape due to the presence of
an asymmetric carbon
163
What is asymmetric carbon?
one that is attached to four different
atoms or groups of atoms.
164
How can you describe enantiomers?
Enantiomers are, in a
way, left-handed and right-handed versions of the molecule.
Just as your right hand won’t fit into a left-handed glove, a
“right-handed” molecule won’t fit into the same space as the
“left-handed” version. Usually, only one isomer is biologically
active because only that form can bind to specific molecules in
an organism.
165
What are functional groups?
In other cases, chemical groups are directly involved in
chemical reactions; such groups are known as functional
groups.
166
What are the 7 most important chemical groups?
The seven chemical groups most important in biological
processes are the hydroxyl, carbonyl, carboxyl, amino, sulfhydryl,
phosphate, and methyl groups
166
What chemical groups are hydrophilic and reactive?
The first six groups can
be chemically reactive; of these six, all except the sulfhydryl
group are also hydrophilic and thus increase the solubility of
organic compounds in water.
166
What is ATP?
A more complicated
organic phosphate, adenosine triphosphate, or ATP
167
What happens to ATP when it loses one phosphate?
Having lost one phosphate,
ATP becomes adenosine diphosphate, or ADP.
168
What happens when ATP reacts with phospate?
169
What are macromolecules?
Large carbohydrates, proteins, and nucleic acids, also known as
macromolecules for their huge size, are chain-like molecules
called polymers
170
What are the structures and functions of the
four important classes of biological molecules?
Carbohydrates are a source of
energy and provide structural
support.
Proteins have a wide
range of functions, such
as catalyzing reactions
and transporting
substances
into and
out of
cells.
Nucleic acids
store genetic
information and
function in gene
expression.
Lipids are a group of
diverse molecules that do
not mix well with water. Key
functions include providing
energy, making up cell
membranes, and acting as
hormones.
171
What is a polymer?
A
polymer is a long molecule consisting of many similar or identical
building blocks linked by covalent bonds
172
What are monomers?
The repeating units that serve as
the building blocks of a polymer are smaller molecules called
monomers
173
What are enzymes?
specialized macromolecules (usually
proteins) that speed up chemical reactions.
174
What is a condensation reaction between polymers and monomers?
The reaction that
connects a monomer to another monomer or a polymer is a
condensation reaction, a reaction in which two molecules are covalently
bonded to each other with the loss of a small molecule.
175
What is a dehydration reaction?
If a
water molecule is lost, it is known as a dehydration reaction.
176
Hydroxyl group formula
--OH
177
Carbonyl group formula
178
Carboxyl group formula
179
Amino group formula
180
Sulfhydryl group formula
--SH
181
Phosphate group
182
Methyl group
183
What is hydrolysis?
Polymers are disassembled to monomers by hydrolysis, a
process that is essentially the reverse of the dehydration reaction
184
What makes up proteins?
Proteins, for example, are
built from 20 kinds of amino acids arranged in chains that are
typically hundreds of amino acids long.
185
What is the molecular logic of life?
The molecular logic
of life is simple but elegant: Small molecules common to all
organisms act as building blocks that are ordered into unique
macromolecules.
186
What are carbohydrates and the simplest of them?
Carbohydrates include sugars and polymers of sugars. The
simplest carbohydrates are the monosaccharides, or simple
sugars; these are the monomers from which more complex
carbohydrates are built.
187
What are Disaccharides?
Disaccharides are double sugars, consisting
of two monosaccharides joined by a covalent bond.
Carbohydrate macromolecules are polymers called polysaccharides,
188
What is the chemical formula for monosaccharides?
CH2O
189
Is glucose a monosaccharide and is it important?
Glucose (C6H12O6), the most
common monosaccharide is of central importance in the chemistry
of life.
190
What determines if a monosaccharide is a ketose or aldose?
Depending on the location of the carbonyl group, a monosaccharide
is either an aldose (aldehyde sugar) or a ketose (ketone
sugar).
191
What are hexoses and give examples of them?
Glucose, fructose, and other sugars that have six carbons
are called hexoses. A sugar that has 6 carbons.
192
What are some other size classifications for monosaccharides?
Trioses (three-carbon sugars) and pentoses
(five-carbon sugars) are also common.
193
What happens when pentoses and hexoses get into water?
Their formation forms a ring, instead of being linear
194
How does abbreviated ring structure work?
Edge on means to look from a side perspective
195
How are monosaccharides used for cellular respiration and in general?
In the process known as cellular respiration, cells extract
energy from glucose molecules by breaking them down in a
series of reactions. Not only are monosaccharides a major fuel for
cellular work, but their carbon skeletons also serve as raw material
for the synthesis of other types of small organic molecules,
such as amino acids and fatty acids.
196
What consists of a disaccharide?
A disaccharide consists of two monosaccharides joined
by a glycosidic linkage
197
What is a glucosidic linkage?
a covalent bond formed between
two monosaccharides by a dehydration reaction
198
What is a lactase?
lactase, the enzyme that breaks down lactose.
199
What is lactose intolerance?
Lactose intolerance is a common condition in humans who
lack lactase,
200
What are polysaccharides?
Polysaccharides are macromolecules, polymers with a few
hundred to a few thousand monosaccharides joined by glycosidic
linkages.
201
How do plants use polysaccharides as storage?
Plants store starch, a polymer
of glucose monomers, as granules within cellular structures
known as plastids. (Plastids include chloroplasts.)
202
How do we extract glucose from starch?
Synthesizing
starch enables the plant to stockpile surplus glucose. Because
glucose is a major cellular fuel, starch represents stored energy.
The sugar can later be withdrawn by the plant from this carbohydrate
“bank” by hydrolysis, which breaks the bonds between
the glucose monomers.
203
What is the simplest form of starch?
The simplest form of
starch, amylose, is unbranched.
204
what polysaccharides do animals store?
Animals store a polysaccharide called glycogen, a polymer
of glucose that is like amylopectin but more extensively
branched
205
Where do vertebrates store their glycogen
Vertebrates store glycogen mainly in
liver and muscle cells.
206
What is the polysaccharides for plants
the polysaccharide called cellulose is
a major component of the tough walls that enclose plant cells
207
What are the different types of glucose?
When glucose becomes a ring its hydroxyl molecule attached to the number 1 carbon is either below or above each other. We call these glucose groups alpha (a) and beta (b). The alpha glucose has the hydroxyl group below the ring and the beta has the hydroxyl group on top of the ring.
208
What is the glucose configuration in cellulose?
the glucose monomers of cellulose are all in the
b configuration, making every glucose monomer “upside down”
with respect to its neighbors
209
What does "insoluble fiber" reffer to and what happens if humans digest cellulose?
If packaging on food shows "insoluble fiber" it is probably referring to the amount of cellulose, most organisms don't produce the enzymes to digest cellulose, as cellulose travels through the body, it abrades the wall of the digestive tract and stimulates the lining to secret mucus.
210
What is chitin?
Another important structural polysaccharide is chitin,
the carbohydrate used by arthropods (insects, spiders, crustaceans,
and related animals) to build their exoskeletons
211
What are exoskeletons for insects?
hard cases that surround the soft parts of an animal
212
What are lipids?
Lipids are the one class of large biological molecules that does
not include true polymers, and they are generally not big
enough to be considered macromolecules.
The compounds called lipids are grouped with each other because they share one important trait: They are hydrophobic: They mix poorly, if at all, with water.
213
What do lipids contain molecular wise?
they may have some polar
bonds associated with oxygen, lipids consist mostly of hydrocarbon
regions with relatively non-polar C—H bonds.
214
What are fats?
Although fats are not polymers, they are large molecules
assembled from smaller molecules by dehydration reactions
215
What does a fat consist of?
A fat
consists of a glycerol molecule joined to three fatty acids
216
What is glycerol?
Glycerol is an alcohol; each of its three carbons
bears a hydroxyl group.
217
What is a fatty acid?
A fatty acid 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 functional
group that gives these molecules the name fatty acid.
218
Why are fatty acids hydrophobic?
The rest of the skeleton consists of a hydrocarbon chain. The
relatively nonpolar C—H bonds in the hydrocarbon chains of
fatty acids are the reason fats are hydrophobic.
219
What is an ester linkage?
This results
in an ester linkage, a bond between a hydroxyl group and
a carboxyl group.
220
What are 2 other names for a fat?
(Other names for a fat
are triacylglycerol and triglyceride)
221
What does it mean to be saturated by hydrogen?
If there are no double bonds between carbon atoms
composing a chain, then as many hydrogen atoms as possible
are bonded to the carbon skeleton. Such a structure is said
to be saturated with hydrogen,
222
What is a saturated fatty acid?
A saturated fatty acid is when their carbon skeleton is saturated with hydrogen molecules.
223
What is an unsaturated fatty acid?
An
unsaturated fatty acid has one or more double bonds, with
one fewer hydrogen atom on each double-bonded carbon.
224
What are the double bonds in unsaturated fatty acids?
An
unsaturated fatty acid has one or more double bonds, with
one fewer hydrogen atom on each double-bonded carbon.
225
What does digestion of saturated fats cause, disease wise?
A diet rich in saturated fats is one of several factors that may
contribute to the cardiovascular disease known as atherosclerosis.
226
What happens in atherosclerosis?
In this condition, deposits called plaques develop within
the walls of blood vessels, causing inward bulges that impede
blood flow and reduce the resilience of the vessels.
227
What are trans fats?
Trans fats are a type of unsaturated fat that has been artificially modified through hydrogenation and now includes trans double bonds.
228
What is the major function of fats?
The major function of fats is energy storage
229
Why are phospholipids essential for cells?
Phospholipids are essential
for cells because they are major constituents of cell membranes
230
What is in a phospholipid?
phospholipid is similar to a fat molecule
but has only two fatty acids attached to glycerol rather than
three.
231
What does the glycerol join to in a phospholipid?
The third hydroxyl group of glycerol is joined to a
phosphate group, which has a negative electrical charge in
the cell.
232
What happens when phospholipids are added to water?
When phospholipids are added to
water, they self-assemble into a double-layered sheet called a
“bilayer” that shields their hydrophobic fatty acid tails from
water
233
What does a steroid consist of?
Steroids are lipids characterized by a carbon skeleton consisting
of four fused rings.
234
What is a crucial steroid for animals?
Cholesterol, a type of steroid, is a crucial molecule
in animals.
235
What are all of the functions of proteins?
Some proteins
speed up chemical reactions, while others play a role in
defense, storage, transport, cellular communication, movement,
or structural support.
236
What are enzymatic proteins?
Enzymatic proteins regulate metabolism
by acting as catalysts
237
What are catalysts?
chemical agents that selectively speed
up chemical reactions without being consumed in the reaction.
238
What is the bond between amino acids called?
The bond
between amino acids is called a peptide bond
239
What is a polymer of amino acids called?
polymer
of amino acids is called a polypeptide
240
What is a protein
A protein is a
biologically functional molecule made up of one or more
polypeptides, each folded and coiled into a specific threedimensional
structure.
241
What is an amino acid?
An amino acid is an
organic molecule with both an amino
group and a carboxyl group.
242
What is the alpha carbon?
At the center of the amino acid
is an asymmetric carbon atom called
the alpha (a) carbon.
243
What is the R group of an amino acid?
The R group, also called the side chain, differs
with each amino acid.
244
What is the general composition of an amino acid?
245
What are the 2 groups of amino acids?
One group consists of amino acids with nonpolar side chains,
which are hydrophobic. Another group consists of amino
acids with polar side chains, which are hydrophilic.
246
What do acidic and base amino acids have to make them at that certain pH?
Acidic
amino acids have side chains that are generally negative in
charge due to the presence of a carboxyl group, which is usually
dissociated (ionized) at cellular pH. Basic amino acids
have amino groups in their side chains that are generally
positive in charge.
247
Defensive proteins function?
Protection against disease
248
Storage proteins function?
Storage of amino acids
249
Transport proteins function?
Transport of substances
250
Hormonal proteins function?
Coordination of an organism‘s activities
251
Receptor proteins function
Response of cell to chemical stimuli
252
Contractile and motor proteins function
Movement
253
Structural proteins
Support
254
How do amino acids join together?
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.
255
What is a polypeptide?
polymer of
many amino acids linked by peptide bonds
255
What is a peptide bond?
The covalent bond that connects two amino acids
256
what does "synthesized" mean?
means to create or build a complex substance from simpler components.
257
What is a polypeptide backbone and the amino acids of it?
The polypeptide backbone is the main structural element of a protein. It is the purple highlighted part of this photo. Extending from this backbone are the different side chains (R groups) of the
amino acids. They are highlighted in yellow and green.
258
What is a protein polypeptide wise?
A functional
protein is not just a polypeptide chain, but one or more polypeptides
precisely twisted, folded, and coiled into a molecule of
unique shape, which can be shown in several different types of
models
259
What are globular and fibrous proteins?
Many proteins
are roughly spherical (globular proteins), while others are
shaped like long fibers (fibrous proteins)
260
What are the 4 levels of structure in proteins?
Primary, Secondary, and tertiary and quaternary structure
261
What is the primary structure of a protein?
The primary structure of a protein is its sequence of amino
acids.
262
What is transthyretin?
transthyretin, a globular
blood protein that transports vitamin A and one of the thyroid
hormones. Transthyretin is made up of four identical polypeptide
chains, each composed of 127 amino acids.
263
What is the a helix of a protein?
One such secondary structure is the c helix, a delicate coil held
together by hydrogen bonding between every fourth amino acid.
264
What is the b pleated sheet of a protein?
The other secondary structure is the d pleated sheet. As shown
above, two or more segments of the polypeptide chain lying side by
side (called d strands) are connected by hydrogen bonds between
parts of the two parallel segments.
265
What is sickle-cell disease?
sickle-cell
disease, an inherited blood disorder, is caused by the substitution
of one amino acid (valine) for the normal one
(glutamic acid) at the position of the sixth amino acid in the
primary structure of hemoglobin
265
What is tertiary structure of proteins?
tertiary structure is the overall shape of
a polypeptide resulting from interactions between the side chains
(R groups) of the various amino acids.
265
What is hemoglobin?
the protein that carries oxygen
in red blood cells.
266
What is denaturation?
If the pH, salt concentration, temperature, or other
aspects of its environment are altered, the weak chemical
bonds and interactions within a protein may be destroyed,
causing the protein to unravel and lose its native shape, a
change called denaturation
267
Name 4 diseases that are related to misfolded polypeptides
Many diseases—such as cystic fibrosis, Alzheimer’s, Parkinson’s,
and mad cow disease—are associated with an accumulation
of misfolded proteins.
268
What is x-ray crystallography?
The
method most commonly used to determine the 3-D structure
of a protein is X-ray crystallography, which depends on the
diffraction of an X-ray beam by the atoms of a crystallized molecule.
269
Why is it hard to determine the structure of a protein?
A growing body of biochemical research
has revealed that a significant number of proteins, or regions
of proteins, do not have a distinct 3-D structure until they
interact with a target protein or other molecule.
270
What determines the primary structure of a protein?
The amino acid
sequence of a polypeptide is programmed by a discrete unit of
inheritance known as a gene.
271
What are nucleic acid?
Nucleic acids are macromolecules that exist as polymers
called polynucleotides.
272
What are the 2 types of nucleic acids?
The two types of nucleic acids, deoxyribonucleic acid
(DNA) and ribonucleic acid (RNA)
273
What is gene expression?
DNA also directs RNA
synthesis and, through RNA, controls protein synthesis; this
entire process is called gene expression
274
What is DNA
DNA is the genetic material that organisms inherit from
their parents. The information that programs all the cell’s activities
is encoded in the structure of the DNA.
275
What does a chromosome contain, what does DNA contain?
Each chromosome contains one long DNA
molecule, usually carrying several hundred or more genes.
276
Summarize the flow of genetic information
DNA to RNA to protein
277
What does a polynucleotide contain?
As indicated by
the name, each polynucleotide consists of monomers called
nucleotides.
278
What does a nucleotide contain?
A nucleotide, in general, is composed of three
parts: a five-carbon sugar (a pentose), a nitrogen-containing
(nitrogenous) base, and one to three phosphate groups
279
What is a nucleoside?
The portion of a nucleotide
without any phosphate groups is called a nucleoside.
280
Why are they called nitrogenous bases?
(They are called nitrogenous bases because the nitrogen
atoms tend to take up H+ from solution, thus acting as
bases.)
281
What are the 2 families of a nitrogenous base?
There are two families of nitrogenous bases: pyrimidines
and purines.
282
What is a pyrimidine?
A 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).
283
What are purines?
Purines are larger, with a six-membered ring fused to a fivemembered
ring. The purines are adenine (A) and guanine (G).
284
Where is gaunine, adenine, cystosine, uracil and thymine found?
Adenine, guanine, and cytosine
are found in both DNA and RNA
thymine is found only in
DNA and uracil only in RNA.
285
What is the sugar for RNA and DNA
In DNA the sugar is deoxyribose; in RNA it is
ribose
286
What is the difference between deoxyribose and ribose?
The only difference between these
two sugars is that deoxyribose lacks an oxygen atom on the
second carbon in the ring, hence the name deoxyribose.
287
How many polynucleotides does DNA have?
A DNA molecule has two polynucleotides, or “strands,” that
wind around an imaginary axis, forming a double helix
288
What is anti-parallel?
The two sugar-phosphate backbones run in
opposite 5 to 3 (number means the carbon atom) directions from each other; this arrangement
is referred to as antiparallel, somewhat like a divided highway.
289
What makes up the strands and the interior of the DNA molecule?
The sugar-phosphate backbones are on the outside of
the helix, and the nitrogenous bases are paired in the interior
of the helix.
290
How are the 2 strands of DNA held together?
The two strands are held together by hydrogen
bonds between the paired bases
291
What bases pair with eachother?
In base pairing, only certain bases in the double helix are
compatible with each other. Adenine (A) in one strand always
pairs with thymine (T) in the other, and guanine (G) always
pairs with cytosine (C).
292
what is tRNA?
transfer RNA (tRNA),
which brings amino acids to the ribosome during the synthesis
of a polypeptide.
293
How many strands does RNA have and is base pairing possible?
RNA only has one strand and base pairing is possible through its own RNA molecule or through stretches of nucleotides to other RNA molecules.
294
What does adenine pair with in RNA?
adenine (A) pairs with uracil (U); thymine
(T) is not present in RNA.
295
What are bioinformatics?
the use of computer
software and other computational tools that can handle
and analyze these large data sets.
296
What is genomics?
Biologists
often look at problems by analyzing large sets of genes or
even comparing whole genomes of different species, an
approach called genomics.
297
What is proteomics
the study of proteomes and their functions.
298
Structure of proteins
