Exam 1 Flashcards
element
a substance that cannot be broken down to other substances by chemical reactions; elements are the basic building blocks or the “legos”
What are life’s major elements?
oxygen, carbon, hydrogen, and nitrogen; CHON
oxygen
required for cellular respiration; present in most organic compounds; component of water
carbon
forms the backbone of organic molecules; each carbon atom can form four bonds with other atoms
hydrogen
present in most organic compounds; component of water; hydrogen ion (H+) is involved in some energy transfers
nitrogen
component of proteins and nucleic acids; component of chlorophyll in plants
calcium
structural component of bones and teeth; calcium ion (Ca^2+) is important in muscle contraction, conduction of nerve impulses, and blood clotting; associated with plant cell wall
phosphorus
component of nucleic acids and phospholipids in membranes; important in energy transfer reactions; structural component of bone
potassium
potassium ion (K+) is a principle positive ion (cation) in interstitial (tissue) fluid of animals; important in fluid balance; important in nerve function; affects muscle contraction; controls opening of stomata in plants
sulfur
component of most proteins
sodium
sodium ion (Na+) is a principle positive ion (cation) in interstitial (tissue) fluid of animals; important in fluid balance; essential for conduction of nerve impulses; important in photosynthesis in plants
magnesium
needed in blood and other tissues of animals; activates many enzymes; component of chlorophyll in plants
chlorine
chloride ion (Cl-) is principal negative ion (anion) in interstitial (tissue) fluid of animals; important in water balance; essential for photosynthesis
iron
component of hemoglobin in animals; activates certain enzymes
atom
an atom is the smallest unit of matter that still retains the properties of an element; smallest form of organization
subatomical particles
atoms consist of even smaller units called subatomical particles; subatomic particles=protons, neutrons, and electrons
electron
each electron has one unit of negative charge; a subatomic particle; mass=about 1/1800 that of a neutron or proton
proton
each proton has one unit of positive charge; a subatomic particle; mass=about 1 dalton; found in the atomic nucleus
neutron
electrically neutral subatomic particles; mass=about 1 dalton; found in the atomic nucleus
atomic number
number of protons in an element; unless otherwise indicated, atoms have equal numbers of protons and electrons
mass number
the sum of the number of protons and neutrons in the nucleus of an atom; protons + neutrons = mass number
atomic weight
a measure of an atom’s mass; can be approximated by the mass number
isotope
different form of a particular element–the number of neutrons is different; isotopes of an element have the same number of protons and electrons but vary in the number of neutrons
energy levels/electron shells
the different states of potential energy that the electrons of an atom can have; the first shell, closest to the nucleus, has the lowest potential energy; electrons in outer shells have more potential energy; electrons can only change their position if they absorb or release a quantity of energy that matches the difference in potential energy between the two levels
valence electrons
the most energetic electrons; found in the outermost electron shell
valence shell
the outermost electron shell; has higher energy levels than ones closer to the nucleus; atoms with full valence shells, such as noble gases, are very stable since their valence shell is full they don’t look to share/gain/lose electrons
1st electron shell
1s shell; can hold 2 electrons
orbital
space where electrons are found
2nd electron shell
can hold up to 8 electrons; after the first shell, which only holds 2 electrons, the rest hold up to 8 electrons
How is the chemical behavior of an atom determined?
the chemical behavior of an atom is determined by its electron configuration–the distribution of electrons in its electron shells
electron configuration
the distribution of electrons in an atom’s electron shells
When is an atom the most likely to lost, gain, or share electrons?
when it’s valence shell is not full because it wants to fill the shell
covalent bond
a bond formed when atoms share electrons to fill their valence shells; a single covalent bond forms when one pair of electrons is shared, a double covalent bond is formed when two pairs of electrons are shared; a covalent bond is denoted by a dashed line, ex: H-H
covalent compound
atoms linked by covalent bonds form a covalent compound
electronegativity
the attraction of an atom for electrons is called its electronegativity; on the periodic table, increasing electronegativity is to the top and to the right
nonpolar covalent bond
if electrons in a covalent bond are shared equally; so, neither atoms are pulling more on the electrons in the covalent bond due to a higher electronegativity
polar covalent bond
if the electrons in a covalent bond are not shared equally by the two atoms, then this is a polar covalent bond; so, one of the two atoms sharing the electron has a higher electronegativity and therefore pulls on the electron more
How is the shape of a molecule determined?
the shape of a molecule is determined by the arrangement of electron orbitals that are shared by the atoms involved in the bond
ion
a particle with an electric charge; atoms can gain or lose electrons to become an ion
cations
atoms with positive charges
anions
atoms with negative charges
ionic bond
forms when opposite charges attract; forms as a consequence of the attraction between the positive charge of a cation and the negative charge of an anion
oxidation
loss of one or more electrons; OIL RIG–oxidation is losing, reduction is gaining; the goal is to fill the valence shell of the atom
reduction
gain of one or more electrons; OIL RIG–oxidation is losing, reduction is gaining; the goal is to fill the valence shell of the atom
solvents vs solute
solVents will dissolVe other things
hydrogen bond
a weak attractive force that exists between a hydrogen atom with a partial positive charge and an electronegative atom (usually oxygen or nitrogen) with a partial negative charge; these bonds are relatively weak on their own, but are collectively strong when presented in large numbers
compound
when atoms of DIFFERENT elements combine, the result is a chemical compound; consists of two or more different elements combined in a fixed ratio; example: water has a 2:1 ratio of H to O; not all compounds are molecules
molecule
the smallest particle of a covalently bonded element or compound; two or more atoms joined by covalent bonds; molecules are characterized by covalent bonds; not all compounds are molecules
characteristics of water
water is essential to life on earth, in fact we are 70% water; water can have extensive hydrogen bonding; characteristics of water include: cohesion, adhesion, surface tension, kinetic energy, capillary action, heat of vaporization, high specific heat, and evaporative cooling
hydrophilic
substances that have an affinity for water are hydrophilic; “water-loving” substances; these substances contain ionic or polar bonds; ex: salt, sugar
hydrophobic
hydrophobic substances do not mix with water; “water-fearing” substances; contain nonpolar bonds; ex: oil
cohesion
property of water; the property of sticking together–water molecules have a strong tendency to stick to one another because of the hydrogen bonds among the molecules
adhesion
property of water; the ability to stick to many other kinds of substances, most notable those with charged groups of atoms or molecules on their surfaces; these adhesive forces explain how water makes things wet
surface tension
property of water; water has a high degree of surface tension because of the cohesion of its molecules which have a much greater attraction for one another than for molecules in the air, thus, water molecules at the surface crowd together and produce a strong layer as they are pulled downward by the attraction of other water molecules beneath them
kinetic energy (high or low?)
property of water; kinetic energy is the energy of motion; ???
capillary action
the tendency of water to move in narrow tubes, even against the force of gravity; a combination of adhesive and cohesive forces accounts for this
heat of vaporization
water has a high heat of vaporization because its molecules are held together by hydrogen bonds; as a sample of water is heated, some molecules are moving much faster than others (they have more heat), these faster-moving molecules are more likely to escape the liquid phase and enter the vapor phase, when they do, they take their heat with them, lowering the temperature of the sample, a process called evaporative cooling
high specific heat
the amount of energy required to raise the temperature of water is quite large
evaporative cooling
as a sample of water is heated, some molecules are moving much faster than others (they have more heat), these faster-moving molecules are more likely to escape the liquid phase and enter the vapor phase, when they do, they take their heat with them, lowering the temperature of the sample, a process called evaporative cooling
How does water maintain a steady temperature?
a lot of the heat that goes in is used to break hydrogen bonds rather than the result being molecules moving faster and the temperature increasing
pH
The negative logarithm of the hydrogen ion concentration of a solution (expressed as moles per liter). Neutral pH is 7, values less than 7 are acidic, and those greater than 7 are basic; each number you go up is 10 times more acidic, so if you go up two numbers it’s 100x more; looking at the scale, going downwards is increasing alkalinity (more basic) and upwards is increasing acidity (more acidic)
Why is water vital for life on earth?
because it has a high specific heat which means that it keeps our bodies at a relatively stable temperature rather than us overheating
pH and acidity/alkalinity***
a neutral solution (pH 7) has equal concentrations of H+ and OH-; acidic solutions, which have a higher concentration of H+ than OH-, have pH values less than 7; pH values greater than 7 characterize basic solutions, which have an excess of OH-
buffer
a substance or combination of substances that resists changes in pH when an acid or base is added
acidic solution
has a hydrogen ion concentration (H+) that is higher than its hydroxide ion concentration (OH-) and has a pH value of less than 7
basic solution
has a hydrogen ion concentration (H+) that is lower than its hydroxide ion concentration (OH-) and has a pH greater than 7
solute
a dissolved substance is referred to as a solute
solvent
something capable of dissolving many substances, particularly those that are polar or ionic, because of the polarity of water molecules
van der Waals interactions
Weak attractive forces between atoms; caused by interactions among fluctuating charges; operate over very short distances and are weaker and less specific than the other types of interactions we discussed; they are most important when they occur in large numbers and when the shapes of the molecules permit close contact between atoms; although a single interaction is very weak, the binding force of a large number of these interactions working together can be significant
redox reaction
The chemical reaction in which one or more electrons are transferred from one substance (the substance that becomes oxidized) to another (the substance that becomes reduced); oxidation and reduction always occur together
ionic compound
a substance consisting of anions and cations bonded by their opposite charges
polar molecule
molecule that has one end with a partial positive charge and the other with a partial negative charge; polar molecules are generally soluble in water
nonpolar molecule
Molecule that does not have a positively charged end and a negatively charged end; nonpolar molecules are generally insoluble in water
orbital hybridization
when an atom forms covalent bonds with other atoms, the orbitals in the valence shell may become rearranged in a process known as orbital hybridization, thereby affecting the shape of the resulting molecule
orbital
Region in which electrons occur in an atom or molecule
atomic nucleus
clustered together, protons and neutrons compose the atomic nucleus
radioisotopes
Unstable isotopes that spontaneously emit radiation when they decay
chemical formula
A representation of the composition of a compound; the elements are indicated by chemical symbols with subscripts to indicate their ratios; example on pg 31
simplest formula
A type of chemical formula that gives the smallest whole–number ratio of the component atoms; example on pg 31
molecular formula
The type of chemical formula that gives the actual numbers of each type of atom in a molecule; example on pg 31
structural formula
A type of chemical formula that shows the spatial arrangement of the atoms in a molecule; example on pg 31
reactants vs products
the reactants are the substances that participate in the reaction and are written on the left side of an equation; products are the substances formed by the reaction and are written on the right side of the equation
covalent compound
A compound in which atoms are held together by covalent bonds; covalent compounds consist of molecules
What is the function of a molecule related to?
it’s shape
What are the three basic themes of biology?
evolution, information transfer, and energy transfer
evolution
Any cumulative genetic changes in a population from generation to generation. Evolution leads to differences in populations and explains the origin of all the organisms that exist today or have ever existed.
information transfer
information must be transmitted within organisms and among organisms, and organisms must be able to receive information from their environment; the survival and function of every cell and every organism depend on the orderly transmission of information; evolution depends on the transmission of genetic information from one generation to another
energy transfer
all life processes require a continuous input of energy, most of the energy for life comes from sunlight, energy from the sun is transferred through living systems from producers to consumers (decomposers obtain energy as they feed on the dead bodies and wastes of both producers and consumers), energy is also continuously transferred from one chemical compound to another within every cell
cell theory
The scientific theory that the cell is the basic unit of life, of which all living things are composed, and that all cells are derived from pre–existing cells
cells
The basic structural and functional unit of life, which consists of living material enclosed by a membrane.
unicellular organisms
each organism consists of a single cell
multicellular organisms
each organism is made up of many, many cells
prokaryotic cells
A cell that lacks a nucleus and other membrane–enclosed organelles; includes the bacteria and archaea
eukaryotic cells
An organism whose cells have nuclei and other membrane–enclosed organelles. Includes protists, fungi, plants, and animals
biological growth
an increase in the size of individual cells of an organism, in the number of cells, or in both
development
includes all the changes that take place during an organism’s life
metabolism
The sum of all the chemical processes that occur within a cell or organism; the transformations by which energy and matter are made available for use by the organism
homeostasis
The balanced internal environment of the body; the automatic tendency of an organism to maintain such a steady state.
stimuli
physical or chemical changes in an organism’s internal or external environment that evoke a response
sessile
an organism that’s unable to move from place to place
asexual reproduction
Reproduction in which there is no fusion of gametes and in which the genetic makeup of parent and of offspring is usually identical.
sexual reproduction
A type of reproduction in which two gametes (usually, but not necessarily, contributed by two different parents) fuse to form a zygote
adaptations
(1) An evolutionary modification that improves an organism’s chances of survival and reproductive success. (2) A decline in the response of a receptor subjected to repeated or prolonged stimulation.
emergent properties
Characteristics of an object, process, or behavior that could not be predicted from its component parts; emergent properties can be identified at each level as we move up the hierarchy of biological organization.
List the hierarchy of biological organization in order
atom, molecule, macromolecule, organelle, cell, tissue, organ, organ system, organism, population, community, ecosystem, biosphere
population
consists of organisms of the same species
community
the populations of different species that populate the same area
ecosystem
a community together with the nonliving environment
biosphere
earth and all of its communities
genes
units of hereditary material
nucleotides
A molecule consisting of one or more phosphate groups, a five–carbon sugar (ribose or deoxyribose), and a nitrogenous base (purine or pyrimidine); make up the chains that form DNA
What are the 4 types of nucleotides in DNA?
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proteins
large molecules that are important in determining the structure and function of cells and tissues
hormones
chemical compounds that signal other cells
cell signaling
Mechanisms of communication between cells. Cells signal one another with secreted signaling molecules, or a signaling molecule on one cell combines with a receptor on another cell
cellular respiration
when cells capture energy released by nutrient molecules through a series of carefully regulated chemical reactions
autotrophs
An organism that synthesizes complex organic compounds from simple inorganic raw materials; also called producer or primary producer.
photosynthesis
The biological process that captures light energy and transforms it into the chemical energy of organic molecules (e.g., carbohydrates), which are manufactured from carbon dioxide and water.
heterotrophs
An organism that cannot synthesize its own food from inorganic raw materials and therefore must obtain energy and body–building materials from other organisms. Also called consumer
Difference between primary consumers and secondary consumers
primary consumers eat producers, whereas secondary consumers eat primary consumers
decomposers
Microbial heterotrophs that break down dead organic material and use the decomposition products as a source of energy. Also called saprotrophs or saprobes
taxonomy
The science of naming, describing, and classifying organisms
systematics
The scientific study of the diversity of organisms and their evolutionary relationships. Taxonomy is an aspect of systematics
species
According to the biological species concept, one or more populations whose members are capable of interbreeding in nature to produce fertile off spring and do not interbreed with members of other species
gene pool
all the genes present in the population
genus
A taxonomic category made up of related species; the first part of a species name when using the binomial system of nomenclature
binomial system of nomenclature
System of naming a species by the combination of the genus name and a specific epithet; each species is assigned a two-part name
specific epithet
The second part of the name of a species; designates a specific species belonging to that genus.
clade
a group of organisms with a common ancestor
List the heirarchical classifications of the taxonomic categories from broadest to narrowest
Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species; To remember the order: Duh! Keep Plates Clean Or Family Gets Sick
What are the three domains of life?
Bacteria, Archaea, and Eukarya
What are the four (?) kingdoms?
Protists, Plantae, Fungi, and Animalia
natural selection
The mechanism of evolution proposed by Charles Darwin; the tendency of organisms that have favorable adaptations to their environment to survive and become the parents of the next generation. Evolution occurs when natural selection results in changes in allele frequencies in a population
What are the four observations that Darwin based his theory of natural selection on?
1) individual members of a species show some variation from one another, 2) organisms produce many more offspring than will survive to reproduce, 3) because more individuals are produced than the environment can support, organisms must compete for necessary, but limited, resources such as food, sunlight, and space. Also, some organisms are killed by predators, diseases, or unfavorable natural conditions such as weather changes, 4) individuals with characteristics that enable them to obtain and use resources, escape predators, resist disease organisms, and withstand changes in the environment are more likely to survive to reproductive maturity. the survivors that reproduce pass their adaptations for survival on to their offspring, thus, the best-adapted individuals of a population leave, on average, more offspring than do other individuals, because of this differential reproduction, a greater amount of the population becomes adapted to the environmental conditions, so the environment selects the best adapted organisms for survival; note: adaptation involves changes in populations rather than in individual organisms
mutations
chemical or physical changes in DNA that persist and can be inherited
scientific method
involves a series of ordered steps that are used to make observations, ask critical questions, and develop hypotheses which are used to make predictions that can be tested to gather data
deductive reasoning
The reasoning that operates from generalities to specifics and can make relationships among data more apparent.
inductive reasoning
The reasoning that uses specific examples to draw a general conclusion or discover a general principle.
hypothesis
A testable statement about the nature of an observation or relationship
What three characteristics does a good hypothesis exhibit?
1) it is reasonably consistent with well-established facts, 2) it is capable of being tested; that is, it should generate definite predictions, whether the results are positive or negative, test results should also be repeatable by independent observers, 3) it is falsifiable, which means it can be proven false
prediction
a deductive, logical consequence of a hypothesis
paradigm/paradigm shift
a set of assumptions or concepts that constitute a way of thinking about reality; a paradigm shift is when a person’s view of reality is changed
What are organic compounds?
organic compounds are those in which carbon atoms form the backbone of the molecule
What element has the largest possibility of bonding?
carbon because there are only 4 electrons in it’s valence shell
What happens when you change the structure of a molecule?
There’s going to be a change in it’s function
structural isomers
differ in covalent arrangement of atoms
geometric isomers
have identical covalent bond arrangements but differ in the spatial arrangement of atoms or groups of atoms (cis=same and trans=across from eachother); to identify geometric isomers look for the double bond!
enantiomers
isomers that are mirror images of each other; to tell if it’s an enantiomer look for a carbon with 4 groups coming off of it
functional groups
memorize what they look like–table 3-1
monomer
individual units of a specific molecule, make up polymers
dehydration/condensation reaction
A reaction in which two monomers are combined covalently through the removal of the equivalent of a water molecule; puts things together
hydrolysis reactions
Reaction in which a covalent bond between two subunits is broken through the addition of the equivalent of a water molecule; a hydrogen atom is added to one subunit and a hydroxyl group to the other; breaks things apart
How are polymers degraded into monomers?
through hydrolysis reactions
polymer
A molecule built up from repeating subunits of the same general type (monomers); examples include proteins, nucleic acids, or polysaccharides; comprised of a chain of monomers
What are the four categories of macromolecules?
lipids, proteins, carbohydrates, and nucleic acids
carbohydrates
major function is energy source/storage and provides structure, example: sugars and starches, cellulose, mainly made up of hydrocarbons; most abundant group of organic compounds on earth; can be dissolved in water because of their hydrophilic properties
lipids
major function is energy storage, example: fats
proteins
the “work horse” of our bodies, actually carries out functions, example: enzymes, proteins do most of the work
nucleic acids
the blue print of life, form DNA
monosaccharides
simple sugars/carbohydrates; in a monosaccharide, each carbon except one is bound to a hydroxyl (OH) group and that one carbon is double-bonded to an oxygen atom forming a carbonyl group
aldoses vs ketoses
aldose: C=O on end of molecule; ketose: C=O in middle of molecule
glucose
most abundant monosaccharide; glucose is metabolized to generate energy that cells can use; cells use glucose for energy by breaking it down; in cells, glucose appears in ring form (99.9% of the time)
alpha glucose vs beta glucose
in alpha the OH group is down, in beta the OH group is pointing up
Polysaccharides
consist of repeating units of monosaccharides, usually glucose; form a glycosidic linkage; glucose and fructose are structural isomers; polysaccharide breakdown involves enzymatic AND hydrolysis reactions
glycosidic linkage
Covalent linkage joining two sugars; includes an oxygen atom bonded to a carbon of each sugar.
starches
starches are polysaccharides that store energy for cells; they are water soluble
cellulose
found only in plants, gives plants their rigidity, human body can’t break cellulose down, hydrogen bonding is saturated in cellulose
chitin
found in animals with an exoskeleton; forms the hard outer layer
lipids
relatively insoluble in water–molecules are mostly nonpolar, consisting mainly of C and H; biologically important groups of lipids include: fats, phospholipids, and steroids; functions include: energy storage and provides structure
fats (aka triacylglycerols)
a single triacylglycerol molecule (fat molecule) consists of glycerol covalently linked to three fatty acids; dehydration reactions facilitate the linkage of glycerol to fatty acids; the bond that forms between the glycerol and a fatty acid is an ester linkage
ester linkage
the bond between glycerol and a fatty acid when making triacylglycerol (aka fat)
saturated vs unsaturated fats
saturated: doesn’t have any double bonds, has maximum number of hydrogens bonded to it, it will be linear; unsaturated: has double bonds, the molecule will be bent due to the double bonds
van der waals forces
forces that occur between molecules
amphipathic molecules
A molecule containing both hydrophobic and hydrophilic regions; phospholipids are examples of these (as in the phospholipids bilayer)
phospholipid bilayer
have hydrophilic heads and hydrophobic tails which make them amphipathic molecules; found in cell membranes, help regulate what goes in and what goes out
steroids
consist of 4 carbon ring structures–individual steroids are distinguished by side chains that extend from the ring structures; the side chains are what distinguish steroids; examples include: cholesterol, bile salts, and hormones; steroids are lipids
proteins
made up of amino acids (amino acids are the single subunit or monomer of proteins), carry out many essential functions in living organisms, are a major determinant in how cells look and function
enzymes
type of protein; catalyze specific chemical reactions
structural proteins
type of protein; strengthen and protect cells and tissues, ex: collagen strengthens animal tissues
storage proteins
type of protein; store nutrients; particularly abundant in eggs and seeds
transport proteins
type of protein; transport specific substances between cells and across cell membranes
regulatory proteins
type of protein; some are protein hormones (ex: insulin) and some control the expression of specific genes
motile proteins
type of protein; participate in cellular movements (ex: actin and myosin are essential for muscle contraction)
protective proteins
type of protein; defend against foreign invaders (ex: antibodies play a role in the immune system)
Are amino acids enantiomers?
Yes, each amino acid exists in both a L- and a D- form which are enantiomers of eachother
How are amino acids joined together? What do they form when they’re joined together?
amino acids are linked by peptide bonds and they form polypeptides; they begin with N-termini and end with C-termini
How is the directionality of a polypeptide determined?
by N-termini and C-termini; begins with N-termini and ends with C-termini
What are the four levels of organization in proteins?
primary, secondary, tertiary, quaternary
primary structure
represented as a linear sequence of amino acids linked by peptide bonds; a chain of amino acids held together by peptide bonds
What are proteins made up of?
amino acids
peptide bonds
link amino acids into proteins
secondary structure
secondary structure is the result of hydrogen bonding; amino acids form alpha helixes and beta pleated sheets; these secondary structures are stabilized by hydrogen bonds; at the secondary level, hydrogen bonds occur as well as peptide bonds
tertiary structure
still maintains either alpha or beta structure, but it becomes “balled up” so it’s more compact and there are side chains coming off of it as well
quaternary structure
multiple polypeptides interacting with each other; the same types of interactions as seen in tertiary structures; made up of subunits put together
denaturation
when the protein unfolds and loses its functioning; if your restore its conditions it can renature though
What determines a protein’s function?
a protein’s structure determines its function
glycoproteins
combination of carbohydrates and proteins; prevalent in cell membranes; most proteins secreted are glycoproteins
nucleic acids
blueprints for life; there are two classes: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA); nucleotides are individual units made up of: a five-carbon sugar (DNA or RNA), phosphate groups, and a nitrogenous base (ring compound, containing N)
pyrimidines
cytosine, thymine, and uracil (in RNA)
purines
adenine and guanine
What nucleotides are in DNA? in RNA?
cytosine, thymine, adenine, and guanine; all the same are in RNA, but it also has uracil
Does RNA have a double helix like DNA does?
no
Nucleotide functions
form DNA and RNA; energy exchange (ATP); cell signaling (cAMP)
Why are cells so small?
it all has to do with surface area, it needs a high surface area to be better able to take things in, it’s more efficient for them to be small because they can send things out more quickly as well
