The chemical Context of life Flashcards
What determines the compound’s properties?
A compound’s properties depend on its
atoms and how they are bonded together.
What determines the atom’s ability to make bonds?
An atom’s electron ( ) distribution
determines its ability to form bonds
What determines the atoms identity?
The number of protons determines
an atom’s identity.
What is a compound?
A compound is a substance consisting of two or more
different elements combined in a fixed ratio.
What is matter?
Anything that takes up space and has mass
What makes up matter?
Elements make up matter.
What are elements?
An element is a substance
that cannot be broken down to other substances by chemical
reactions.
What are the 4 elements that make up 96% of living matter?
Just four elements—oxygen (O), carbon (C), hydrogen (H),
and nitrogen (N)—make up approximately 96% of living matter.
What are trace elements?
Trace elements are required
by an organism in only minute quantities. Like Iron
How is iodine important for us?
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.
What is an atom?
An atom is
the smallest unit of matter that still retains the properties
of an element.
What are subatomic particles?
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.
What are the main three subatomic particles?
Neutrons, Protons and Electrons
What subatomic particles are electrically charged?
Protons
and electrons are electrically charged. Each proton has one unit
of positive charge, and each electron has one unit of negative
charge.
Where are the protons and neutrons?
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.
Where are the electrons?
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.
What do we use instead of grams for measuring atoms and subatomic particles?
Thus, for atoms and subatomic particles
(and for molecules, too), we use a unit of measurement
called the dalton, in honor of John Dalton,
What are the masses for the 3 subatomic particles?
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.
What is the atomic number of an atom?
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.
How can we tell how many protons are in an element through their symbol, give an example
The abbreviation 2He, for example, tells
us that an atom of the element helium has 2 protons in its
nucleus.
How do we know if an atom is is neutral in electric charge?
Unless otherwise indicated, an atom is neutral in
electrical charge, which means that its protons must be balanced
by an equal number of electrons.
What does the atomic number tell us?
Therefore, the atomic
number tells us the number of protons and also the number
of electrons in an electrically neutral atom.
What is the mass number?
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.
Where is the mass number written
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.
What is the atomic mass of an atom?
the total mass of an atom, called its atomic
mass.
What are isotopes?
These different atomic forms of the same element are called
isotopes of the element.
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.
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.
Are radioactive isotopes used in the medical field?
Radioactive isotopes are often used as diagnostic tools in
medicine.
PET scan stands for and what is it?
positron emission
tomography, and detects locations of intense chemical activity in the body
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.
What is the half-life of the isotopes?
the time it takes for 50% of the parent isotope to decay.
What is energy?
Energy is defined as the capacity to cause change
What is potential energy?
Potential energy is the energy that
matter possesses because of its location or structure.
What is the natural tendency of matter?
Matter has a natural tendency to move toward the lowest
possible state of potential energy
What is an electron’s energy level correlated with?
An electron’s energy level is correlated with its average
distance from the nucleus.
What are electron shells?
Electrons are found in different
electron shells,
Where is the first electron shell?
The first shell is
closest to the nucleus, and electrons in this shell have the lowest
potential energy.
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.
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.
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.
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.
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.
What does inert mean?
inert, meaning chemically
unreactive
What is an orbital of an atom?
The three-dimensional space where
an electron is found 90% of the time is called an orbital.
What is the orbital for the first shell?
The first electron shell has only
one spherical s orbital (called 1s)
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.)
How many electrons can stay in an orbital?
No more than 2 electrons can occupy a single orbital.
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.
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.)
What is a covalent bond?
A covalent bond is the sharing of a pair of valence electrons
by two atoms.
What is a molecule?
Two or more atoms held together by covalent bonds constitute
a molecule
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)
What is a single bond?
A single covalent bond is a chemical bond formed when two atoms share one pair of electrons.
What is a double bond?
A double covalent bond is a chemical bond formed when two atoms share two pairs of electrons.
What is the atom’s valence?
The bonding capacity of the atom is called the atom’s valence
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
What is electronegativity?
The attraction of
a particular atom for the electrons of a covalent bond is called
its electronegativity.
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
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.
The more electronegative an atom is?
The more electronegative an atom is,
the more strongly it pulls shared electrons toward itself.
What are ions?
Ions are atoms or molecules that have gained or lost one or more electrons.
What are positively and negatively charged ions called?
Positive - Cations
Negative - Anions
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.
What are ionic compounds?
Compounds formed by ionic bonds are called ionic
compounds, or salts.
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
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.
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.
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.
How are complicated molecule shapes determined?
These shapes are determined by the positions of the atoms’
orbitals.
Why is molecular shape crucial?
Molecular shape is crucial: It determines how biological molecules recognize and respond to one another with
specificity.
How do opiates relieve pain?
Opiates relieve pain and alter mood by weakly binding to
specific receptor molecules on the surfaces of brain cells.
Endogenous meaning?
made by the body
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.
What do opiates have similar shape to?
Opiates have shapes
similar to endorphins and can bind to endorphin receptors
in the brain.
What are chemical reactions?
The making and breaking of chemical bonds, leading to
changes in the composition of matter, are called chemical
reactions.
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.
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.
Chemical formula for Photo Synthesis
6 CO2 (Carbon Dioxide) + 6 H2O (Water) -> C6H12O6 (Glucose) + 6O2 (Oxygen)
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
What is chemical equilibrium
Chemical equilibrium is a state in which the rates of the forward and reverse chemical reactions are equal.
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.
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.
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
What is cohesion?
Collectively, the hydrogen bonds hold
the substance together, a phenomenon called cohesion.
What is surface tension?
a measure of how difficult it is to stretch
or break the surface of a liquid.
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.
What is adhesion?
Adhesion, the clinging of one substance to another,
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.
What energy does anything that moves have?
Anything that moves has kinetic energy
What is kinetic energy?
Kinetic energy is the energy of motion
What is thermal energy?
The kinetic energy associated with the random movement of atoms is called thermal energy.
is thermal energy and temperature the same thing?
Thermal energy is related to temperature, but is not the same thing/
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.
How does thermal energy move?
Thermal energy passes on from the warmer to the cooler object until they both are at the same temperature
What is heat?
Thermal energy in transfer from one body of matter to another is defined as heat.
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.
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.)
What are joules (J)
Unit of energy
How many calories makes up a joule?
One joule equals 0.239 cal; one calorie equals 4.184 J.
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.
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)
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.
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.
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.
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.
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.
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).
What is the transform from gas to liquid called?
Vaporization (evaporation)
When does evaporation occur?
Some evaporation occurs at any temperature; a glass of water
at room temperature, for example, will eventually evaporate
completely.
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.
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
What is evaporative cooling?
Where the hottest particles of a liquid start to evaporate, cooling the rest of the liquid down
What do other materials do compare to water when they solidify?
While other materials contract
and become denser when they
solidify, water expands.
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.
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.
What is a solution?
A liquid that is a completely homogeneous
mixture of two or more substances is called a solution.
What is a solvent and solute?
The dissolving agent of a solution is the solvent, and the substance
that is dissolved is the solute.
What is an aqueous solution?
An aqueous solution is one
in which the solute is dissolved in water; water is the solvent.
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.
What is a hydration shell
The sphere
of water molecules around each dissolved ion is called a
hydration shell.
Chemical reaction for Hydronium (H3O+) and Hydroxide (OH-)
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.
What is the shape of Cyclohexane and benzene and why is it shown like that?
How do structural isomers differ?
Structural isomers differ in the covalent arrangements of
their atoms.
What happens when ATP reacts with phospate?
Carbonyl group formula
Carboxyl group formula
Amino group formula
Phosphate group
Methyl group
How does abbreviated ring structure work?
Edge on means to look from a side perspective
What is the general composition of an amino acid?
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.
Summarize the flow of genetic information
DNA to RNA to protein
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.
Structure of proteins
