Unit 1
Neda Parvin
1. Describe the structure of a water molecule
Answer:
A water molecule is consist of two hydrogen and one Oxygen atom. Oxygen shares two of
its outer electrons with hydrogen atoms, so all three atoms in a water molecule gain full
outer hells. But the sharing is not exactly equal. Oxygen has much greater electronegativity
so the shared electrons are way closer to oxygen, making it slightly negative and the
hydrogen atoms slightly positive. Those charge ends are responsible for water’s
phenomenal abilities as a solvent.
2. Describe the importance of the structure of water
Answer: water molecules behave as mini-magnetic molecules with opposite charges
attracting and like charges repelling one another. Bipolarity causes water to have some
degree of structure that extends beyond the individual molecules and cause a community
water effect. The overall property is called hydrogen bonding, i.e. the attraction of the
hydrogen nucleus (a proton) for the electronegative regions of other atoms like oxygen.
This means that water molecules are loosely attracted to one another. The negative charge
on the oxygen attracts the positively charged hydrogen some distance away to produce a
weak bond called a hydrogen bond. Each water molecule can form hydrogen bonds with
up to four neighbors. The structure of water is responsible to its properties such as solvent,
cohesion, adhesion, moderate climate, and transparent. In addition, density of water is
unusual because it is denser than ice (very rare for compounds). Most materials contract as
they solidify, but water expands. Therefore, ice forms on top of water insulating lower
levels. This oddity has important consequences for life. If ice sank, eventually all ponds,
lakes, and even oceans would freeze solid. During the summer, only the upper few inches
of the ocean would thaw. Instead, the surface layer of ice insulates liquid water below,
preventing it from freezing and allowing life to exist under the frozen surface.
3. Function of water
Answer: Water has several function in the body and environment. It acts as a solvent and
is able to dissolve many chemical substances especially other polar molecules such as salt.
Since blood is mainly water, the ability of water to dissolve and transport substances greatly
aids in bringing about necessary chemical reactions in the body. Water moderates climate
(both internal and external climates).Water can absorb a great deal of heat while only rising
in temperature a slight amount. Water also releases heat slowly. This property is referred
to as a high heat of evaporation. As a liquid evaporates the most energetic molecules are
carried away leaving the lower kinetic energy molecules behind which cools the surface of
the liquid that remains - evapourative cooling. Internal example - Body systems are mainly
water, therefore, bodies tend to stay at relatively constant temperatures despite external
conditions. External example - Oceans keep surrounding land masses cool in summer and
warmer in winter. Also, water helps to regulate the body’s internal temperature
(hemostasis). Water molecule help to lubricant and ease movement. For example: food in
esophagus, joint, and eyes. Furthermore, water helps hydrolytic reaction in the body.
Water molecules stick to each other and to other surfaces. This keeps surfaces moist and
lubricated. Diffusion of gases occurs much more efficiently across moist surfaces.
Cohesion (sticking to each other) among water molecules plays a key role in the transport
of water against gravity in plants. Surface tension, is a measure of the force necessary to
stretch or break the surface of a liquid and is related to cohesion. Water has a greater surface
tension than most other liquids because hydrogen bonds among surface water molecules
resist stretching or breaking< the surface. Water behaves as if covered by an invisible film.
Some animals can stand, walk, or runon water without breaking the surface.
4. Describe how hydrogen bonds can form between water molecules
Answer: Although hydrogen bonds are weak, the vast number of these bonds gives water its unique
properties. Each water molecule can form hydrogen bonds with up to four neighbors. This is also
why water is attracted to other surfaces. Remember opposite charges attract.
Hydrogen Bonding
Unit 2
1. Describe the structure of a nucleotide
Answer:
A nucleotide has 3 components to it, a sugar, a phosphate group, and a nitrogenous base.
2. List all the polymers that you know and their monomers
Answer:
Unit molecules join together to form larger molecules called Polymers. Proteins,
carbohydrates, fats, and nucleic acids are all polymers.
Monomer: A monomer is a molecule that forms the basic unit for
polymers.
-Carbohydrates are polymers and Glucose is their monomer.
-Fats (lipids) are polymers and glycerol and fatty acids are their monomer.
-Proteins are polymers and amino acids are their monomer.
-Nucleic acids are polymers and Nucleotides are their monomer.
3. List the functions of a protein
Answer: Functions of Proteins are categorized in two main parts: functional and structural:
1. FUNCTIONAL

Enzymes (catalyze chemical reactions) Reactions that will take 7 hours will take
only a fraction of a second.
1. Maltase - Converts maltose to glucose and glucose
2. Carbonic Anhydrase: In blood, maintains blood pH
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
Transport System - Hemoglobin - Transports O2, CO2, and H+
Infection fighting - Antibodies attack viruses
2. STRUCTURAL

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-Used to build up body systems
Keratin
fingernails
Collagen
Connective
Actin/myosin - muscle fiber for movement
and
hair
tissue
4. What does ATP stand for? Where is it found? Function?
Answer: ATP stands for Adenosine three phosphate. One particularly important
nucleic acid is the modified nucleotide known as ATP. ATP is quite simply an RNA
nucleotide with an adenine base (adenine + ribose = adenosine) with three
phosphate groups attached to it. Note the ~ line in between the phosphate groups
used to indicate high energy bonds. ATP stands for Adenosine Triphosphate. ATP
Provide energy to cellular reaction. ATP is present in all living cells and serves as
an energy source for many metabolic processes; energy is released when ATP is
hydrolyzed into ADP. It is the single most important molecule in all living things
since it serves as the currency for energy in biological systems.)
.
ATP is often called the energy currency of a cell (because cells make and "spend" ATP)
FAT ------ GLYCOGEN ------ GLUCOSE ------ ATP
ATP <---> ADP + P + Energy (7 Kcal per mole)
ATP molecules can be moved all over the body. When energy is needed, the 3rd phosphate group
is broken off. This results in Adenosine Diphosphate (ADP) and the release of heat energy. The
heat energy runs metabolic reactions.
Unit 3
1. List the functions of all the organelles in a cell
-Nucleus
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Largest Organelle.
Surrounded by a double-layered membrane (the nuclear envelope).
Membrane has pores through which larger molecules pass (Nuclear Pores).
Control center for the cell's functions (The brain).
Contains a fluid called the nucleoplasm.
Contains chromatin (DNA strands which forms chromosomes during cell division).
-Nucleolus


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Dark region in the Nucleoplasm.
One or more found in the nucleus.
Site where ribosomal RNA (rRNA) is produced or stored.
Involved in interactions between the nucleus and the cytoplasm.
-Chromatin

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
The hereditary material of the cell.
Condenses to form chromosomes during cell division.
Composed of Protein and DNA
-Chromosomes
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Rod - shaped bodies in the nucleus, particularly during cell division.
Contains the hereditary information (genes).
Condensed chromatin
Each eukaryotic species has a characteristic number of chromosomes.
A typical human cell has 46 chromosomes, but sex cells (eggs and sperm) have only 23
chromosomes.
-Cytoplasm


A colloidal substance, which can change from the gel (solid) to the sol (liquid) state with
the addition of heat or change in metabolic activity.
Contains and supports all the cells organelles.
-Cell Membrane or Plasma Membrane
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Composed of proteins and phospholipids (fats with Phosphorous).
Acts as skin around the cells contents.
Acts as a selectively permeable membrane to allow movement of materials in and out of
the cell.
Located around the outside of the cell.
Single membrane around the vacuoles, lysosomes, E.R., Golgi Apparatus.
Double membrane around the nucleus and mitochondria.
-Smooth Endoplasmic Reticulum
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System of interconnected flattened tubes, sacs, or canals.
Begins at the nuclear envelope and branches throughout the cytoplasm to the cell
membrane.
Moves molecules from one area to another.
Location of lipid manufacture. Cells that produce steroid hormones have abundant smooth
ER.
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Section of both types of ER can break free "blebbing" to produce small membrane bound
sacs of either proteins or lipids called vesicles.
Contains enzymes that synthesize lipids and related products such as steroids.
Also seems to have other enzymes in the smooth ER of the liver that help detoxify drugs
and poisons. These include alcohol and barbiturates.
Frequent exposure leads to the proliferation of smooth ER, increasing tolerance to the target and
other drugs.

Amount of ER in a cell increases or decreases depending on the cell's activity.
-Rough Endoplasmic Reticulum
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Like Smooth ER, but with attached ribosomes.
Abundant in cells that produce large amounts of protein for export from the cell.
-Golgi Body or Golgi Apparatus
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Stack of a half dozen or more flattened sacs.
On one side receives protein-filled vesicles from the E.R.
Sorts the proteins and packages them in vesicles at the other side.
From here the vesicles move to different locations in the cell.
Many transport vesicles from the ER travel to the Golgi apparatus for modification of
their contents.
The Golgi is a center of manufacturing, warehousing, sorting, and shipping.
The Golgi apparatus is especially extensive in cells specialized for secretion.
-Vacuoles

Storage area for water, nutrients, and wastes.
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A small vacuole
Storage site for various kinds of molecules
Can be made by the Golgi Apparatus or from an in-folding of the cell membrane
-Lysosomes
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Special vacuoles formed by the golgi body (double membrane).
Contains powerful hydrolytic enzymes used to digest substances entering the cell or
organelles that are of no further use (autodigestion).
-Ribosomes
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Contain rRNA and protein subunits.
Function as sites for protein synthesis.
Found on E.R. (proteins for export) or in the cytoplasm (proteins for use in the cell).
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Several ribosomes together in a line, all producing the same protein is called a
polyribosome.
Cell types that synthesize large quantities of proteins (e.g., pancreas) have large numbers
of ribosomes and prominent nuclei.
Example of proteins are: keratin, salivary amylase, testosterone, other enzymes.
This endomembrane system plays a key role in the synthesis (and hydrolysis) of
macromolecules in the cell.
-Mitochondria
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Burn glucose to produce adenosine triphosphate (ATP).
Use up oxygen an give off carbon dioxide (this process is called cellular respiration).
Equation for Cellular Respiration:
C6H12O + 6O2 --> 6CO2 + 6H2O + Energy
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Composed of two membranes.
Considered the powerhouse of the cell.
Their inner membranes loop back and forth through the inner fluid, matrix, of the
mitochondria increasing its surface area and producing shelf-like structures called cristae.
This inner membrane is the site of cellular respiration.
-Cytoskeleton
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Provides internal structure to maintain the cell's shape, anchor the organelles, and allow
them to move when appropriate.
Composed of microfilaments and microtubules.
-Cilia
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Short, numerous, hair-like projections that are used for locomotion by many unicellular
organisms.
Membrane-bound collections of microtubules
-Flagella
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Like cilia but can be much longer.
Also for locomotion of organisms and gametes (sperm).
2. Describe the inter relationship between the ER, Golgi and vesicles
Answer: Sections of both types of E.R. can break free (blebbing) to produce small
membrane bound sacs of either proteins or lipids bound instructors called
vesicles. The vesicles move through the cytoplasm and join into another
membranous structure called the Golgi apparatus. At first glance the
Golgi apparatus is similar looking to smooth E.R. The Golgi apparatus
prepares the contents of the vesicles for their storage or secretion from the cell. Either way,
new vesicles bleb off. Those destined for secretion move to the cell membrane and
exocytosis occurs. Those destined for future use in the cell become known as Lysosomes
and contain digestive hydrolytic enzymes used for hydrolysis of molecules in a cell.
Lysosomes digest food particles that have been taken in.)
Protein synthesis occurs in the rough ER within the ribosomes (ie protein builders). The
rough ER then transports the newly synthesized proteins to the Golgi apparatus. The Golgi
apparatus is responsible for the flow of molecules in a cell, like the protein sent over from
the ER. In this stage, carbohydrates are added to the protein to create glycoprotein. The
glycoprotein is pinched off and sent to the vesicles (small membrane enclosed sac that
stores and transports various substances).
3. Explain the inter relationship of vacuoles, cell membrane and lysosomes
Answer: Vacuoles are formed by the fusion of multiple membrane vesicles and are effectively just
larger forms of these. The organelle has no basic shape or size; its structure varies according to the
needs of the cell. Vacuoles are storage area for water, nutrients, and wastes. Vesicles are small
vacuoles which are storage site for various kinds of molecules deliver enzymes such as hydrolases
to the lysosome so that it can function properly, as well, endocytic vesicles bring particles into the
cell and then fuse with the lysosome so that these particles can be digested by the hydrolases.
Lysosomes are special vacuoles contain powerful hydrolytic enzymes used to digest substances in
the cell (auto-digestion).
In short, nutrient vacuole fuses to the lysosome, and its contents digest. During exocytosis a
vacuole containing material to be excreted from the cell.
…………….
Unit 4
1. Describe active transport, some examples of molecules that move by active transport.
Answer: Solutes move from an area of [low solute] to and area of [high solute] across a membrane
with the aid of a protein carrier molecule and ATP. Example of solute: Ions such as Na+. Since
the movement is against the concentration gradient, energy is required.
o
o
Example: Sugar (glucose) is removed from the urine, by active transport, into the
blood. Since there is already a lot of glucose in the blood, it is traveling against the
concentration gradient.
Example: Na+/K+ Pump. Found in nerve and muscle cells. Same carrier, but
changes shape to fit Na+ and K+.
2. Define facilitated transport, diffusion, osmosis
Answer: A: FACILITATED TRANSPORT: (passive transport)
o
o
Solutes move across a membrane from an area of [high solute] to and area of [low
solute] with the help of a carrier molecule (protein). No energy in the form of ATP
is required.
Example of Solute: Glucose
Molecules need by the cell such as glucose, enter through facilitated transport from the blood.
B: OSMOSIS: A special type of diffusion in which water moves from an area of high water
concentration to an area of low concentration across a membrane. No carrier or energy in the form
of ATP are required. Pressure caused by the concentration gradient between two different solutions
is called Osmotic Pressure. Hydrostatic pressure offsets osmotic pressure. (Gravity)
o
o
The solute cannot spread out because it is too big to pass through the membrane.
Therefore, water moves across the membrane from [high water] to [low water].
Water moves through the protein-lined pores of the cell membrane.
C: DIFFUSION: Movement of a solute from an area of high concentration to an area of low
concentration until evenly distributed. No membrane, carrier, or ATP required.
o
o
Example: A foul odour in the corner of a room will spread out until it is evenly
distributed
Example: Cream in coffee will diffuse until concentration are balanced
o
Diffusion refers to the process by which molecules intermingle as a result of their
kinetic energy of random motion. Consider two containers of gas A and B separated
by a partition. The molecules of both gases are in constant motion and make
numerous collisions with the partition.
o
If the partition is removed as in the illustration, the bases will mix because of the
random velocities of their molecules. In time a uniform mixture of A and B
molecules will be produced in the container
3. List all the factors that affect the rate of diffusion
Answer: Factors Affecting diffusion are:
-Surface Area vs. Volume
Nutrients (oxygen and glucose) enter a cell while wastes (carbon dioxide and urea) exit a cell
across the cell membrane.
-The amount of cell membrane = surface area

Inside the cell, organelles use up nutrients and produce wastes. The larger the cell, the more
nutrients needed and the more wastes produced.
-The size of the cell (# of organelles) = Volume
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Small cells have a high SA: Volume ration. They can supply the organelles with plenty of
nutrients and remove wastes.
Large cells have a low SA: Volume ratio because volume increases faster than surface area.
If a cell gets too big, wastes will build up and nutrients will run out.
Therefore, cells are limited in size. Active cells must be smaller than less active cells.
Active cells need more nutrients and produce more wastes.
Cells reproduce by mitosis to become smaller
Some cells get larger than they should be by producing folds.
These folds allow the cell to gain more surface area without a large increase in volume.
Factors That Will Increase Diffusion
4. Describe hypertonic, hypotonic and isotonic
Answer: Hypertonic, Hypotonic and Isotonic Solutions
Hypertonic Solutions: Solution with the greatest amount of solute compared to another solution.
Hypotonic Solutions: Solution with the least amount of solute compared to another.
Isotonic Solutions: Two solutions with equal concentrations of solute to solvent.
Water will always move from a hypotonic solution to a hypertonic solution. There is no net
movement
of
water
between
isotonic
solutions.
Unit 5
1. Explain DNA replication
Answer: Steps in DNA Replication
1. The DNA molecule becomes untwisted by enzymes breaking the bonds. The two strands that
make up DNA become unzipped and each side acts as a template. The weak hydrogen bonds
between the nitrogenous base pairs are broken by the enzyme helicase.
2. New complementary nucleotides, always present in the nucleus, move into place and pair with
complementary bases on the exposed strands. The enzyme DNA polymerase assists with the
complementary
base
pairing.
T
joins
to
A
C joins to G.
3. The adjacent nucleotides, through their sugar-phosphate components become joined together
along the newly forming chain. The enzyme Ligase glues the alternating sugar phosphate
backbone
together.
4. When the process is finished, 2 complete DNA molecules are present, identical to each other
and
to
the
original
molecule.
5. Both new DNA strands will now wind back up into their helical shape.
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DNA replication is called semiconservative because each new double helix is
composed of an old (parental) strand and a new (daughter) strand.
Enzymes assist the unwinding process, join together the nucleotides, and assist the
rewinding process and many others.
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Unit 6
1. Describe the relationship of DNA to mRNA to tRNA
Answer:
Messenger RNA (mRNA) is translated into protein by the joint action of transfer RNA
(tRNA) and the ribosome, which is composed of numerous proteins and two major
ribosomal RNA (rRNA) molecules. Messenger RNA (mRNA) carries the genetic
information copied from DNA in the form of a series of three-base code “words,” each of
which specifies a particular amino acid.
DNA is the master copy (or template) containing instructions for the production of proteins
(structural and functional). Proteins are put together in the cytoplasm, but DNA never
leaves the nucleus. A copy of the DNA must be made. This copy is called messenger RNA
(mRNA). Think of it this way, there has to be some mechanism to get the message from
DNA that is confined in the nucleus to the site of protein synthesis in the cytoplasm and
this is done with the aid of a messenger molecule called messenger RNA or mRNA. Only
the genes for the specific required proteins are copied into mRNA. The process of making
the mRNA from a DNA template is called transcription. The newly synthesized mRNA
molecule then travels into the cytoplasm where it is translated into proteins.
DNA ---------------------> mRNA --------------------> Protein
Transcription
Translation
…………….
2. What is the purpose of transcription/translation
Answer: The process of making the mRNA from a DNA template is called transcription,
so the purpose of transcription is making mRNA from a DNA. The newly synthesized
mRNA molecule then travels into the cytoplasm where it is translated into proteins;
therefore, the purpose of translation is making proteins from mRNA. In short, the purpose
of transcription is to make RNA copies of individual genes, and the purpose of translation
is to synthesize proteins, which are used for millions of cellular functions. Translation is
the synthesis of a protein from an mRNA template.
…………………
Unit 7
1. Lock and Key theory of enzyme activity
Answer:
The activation site of on an enzyme is the region where the substrate fits with
the proper geometry for a reaction to occur. This “fit” between the enzyme and substrate is
called the lock and key model. In order for a reaction to occur, the reactants (substrates)
must be brought close together. The substrates bond to the active site on the enzyme, and
are brought close together. Sometimes the active site changes shape to bring the substrates
together. The reaction occurs and the products are released. The enzyme goes back to its
normal tertiary configuration. According to this analogy, an enzyme acts like a key by
combining with a specific substrate and ¨unlocking¨ the substrate for further activity of the
cell. This is a useful analogy because the key (enzyme) must have the correct shape to fit
the lock (substrate). After the lock has been opened (reaction takes place) the key (enzyme)
is free and unchanged so that it may be used repeatedly in the same manner. The portion
of the enzyme that is involved in the reaction is called the active site.
2. Explain denature
Answer: When an enzyme is denatured its three-dimensional shape is altered, typically
such that it no longer compliments its substrate(s) three-dimensional shape(s), and thus,
it can no longer bind to the substrate(s) to lower the reaction's activation energy
and speed up (catalyze) the reaction. Denaturation of proteins involves the disruption and
possible destruction of both the secondary and tertiary structures.
3. List all the factors that would affect enzyme activity and describe how
Answer: Factors Affecting Enzyme Activity
A. Heavy Metals: Such as Pb+2 (lead) or Hg+2. These metals can bond with parts of enzymes and
cause them to change shape (denature them). This bonding is called noncompetitive inhibition.
This is explained by a process in which the inhibitor fits into a place (site) on the enzyme, which
is different from the active site. When this happens, the folding of the enzyme changes a little bit,
and the active site is distorted in a way, which makes it a less effective catalyst. The enzyme can
no longer bond to its substrate so there is no chemical reaction.
B. Competitive Inhibition: Some molecules are shaped like a substrate and compete with the
substrate for the enzyme's active site. A competitive inhibitor fits into the enzyme's active site but
doesn't react with anything there. This prevents the correct substrate from binding with its enzyme.
Example: Cyanide is an electron transport inhibitor.
Since some of the enzymes get bonded to the "wrong" substrate, the amount of "correct"
production is reduced. Sometimes these molecules only bond temporarily with the enzyme, but
sometimes they bond permanently (for the life of the enzyme) rendering the enzyme useless.
If too many important enzymes are inactivated, the organism may die.
C. Temperature: Cold temperature slows down enzymatic reactions (lower the Kinetic Energy).
Warm temp to around 40oC - speed up reactions.
High Temp - denature enzymes and cause reactions to stop.
If we increase the temperature of the solution the enzyme is operating in, we will typically see an
increase in the reaction rate until a point is reached at which the enzyme starts to unfold. This is a
result of breaking hydrophobic bonds as the increase in temperature causes the enzyme's structure
to "wiggle" around. The enzymes active site changes shape so that it can no longer bond to it's
substrate and as a result there is no chemical reaction.
D. pH: Each enzyme operates best at a preferred pH level. (Optimum)
Any other pH affects tertiary structure (shape of the active site) of the enzyme and slows down
reactions. Too much of a change denatures the enzyme so it can no longer bond to its substrate and
stops the reaction.
E. Substrate Concentration: The greater the concentration of substrate, the greater the rate of
reaction.
If we do a series of experiments arranged so the concentration of the enzyme is always the same,
but the substrate (reactant) concentration is increased from one experiment to the next, we find
that in the low substrate concentration experiements the rate increases as we increase substrate
concentration. However as the experiements involve higher and higher substrate concentrations,
we find that we reach a maximum reaction rate. More substrate doesn't increase the rate any more.
At this point, we say that the enzyme is saturated (it can't handle any more). To increase the rate
again, we'd need more enzyme.
F. Enzyme Concentration - more enzyme, greater rate of reaction.
What happens if we change the concentration of an enzyme? More catalyst means a faster reaction,
so the reaction rate increases. (Reaction rate is basically "how much substrate reacts in a particular
amount of time, usually a second).