Exam 1 Content Flashcards
matter
anything that takes up space and has mass
-made up of elements
element
a substance that cannot be broken down to other substances by chemical reactions
compound
a substance consisting of two or more elements in a fixed ratio
-has characteristics (emergent properties) different from those of its elements
Essential Elements
20%-25% of 92 natural elements are required for life
96% of living matter is
Carbon, Hydrogen, Oxygen, and Nitrogen
Most of Remaining 4% living matter is
Calcium, Phosphorus, Potassium, and Sulfur
trace elements
required by an organism in only minute quantities –> SMALL AMOUNTS
atom
smallest unit of matter that still retains the properties of an element
-composed of subatomic particles: neutrons, protons, electrons
what’s in the atomic nucleus
protons and neutrons
daltons
the measure of neutron and proton mass
electrons
are very small and ignored when calculating the total mass of an atom
atomic number
number of protons in the nucleus
atomic mass
atom’s total mass, can be approximated by the mass number (protons + neutrons)
isotopes
two different atoms of an element that differ in the number of neutrons
-same number of protons
radioactive isotopes
decay spontaneously, giving off particles and energy
-often used as diagnostic tool in medicine
radioactive tracers
can be used to track atoms through metabolism
-they can be used in combination with sophisticated imaging instruments
half-life
a “parent” isotope decays into its “daughter” isotope at a fixed rate
Radiometric dating
Scientists measure the ratio of different isotopes and calculate how many half-lives have passed since the fossil or rock was formed
Energy
The capacity to cause change
Potential energy
The energy that matter possesses because of its location or structure (holds the energy)
Energy levels of electrons
Electrons of an atom differ in their amounts of potential energy based on their distance from the nucleus
- changes in potential energy of electrons can occur only in steps of fixed amounts
Electron shells
An energy level of electrons at a characteristic average distance form the nucleus of an atom
Valence electrons
An electron in the outermost electrons shell
Valence shell
The outermost energy shell of an atom, containing the valence electrons involved int he chemical reactions of that atom
Orbital
The three-dimensional space where an electron is found 90% of the time
-no more than 2 electrons can occupy a single orbital
Chemical bonds
Represent stored potential energy
Covalent energy
The sharing of a pare of valence electrons by two atoms
-may be polar or nonpolar depending on the electronegativity difference of the two involved
Molecule
Consists of two or more atoms held together by covalent bonds
Single bond
The sharing of one pair of valence electrons
Double bond
Sharing of two pairs of valence electrons
Valence
Bonding capacity
Compound
A combination of two or more different elements
Electronegativity
An atoms attraction for the electrons in a covalent bond
-the more electronegative an atom is, the more strongly it pulls shared electrons onward itself
No polar covalent bond
The atoms share the electron equally
Polar covalent bond
One atoms is more electronegative, and the atoms do not share the electrons equally
Ions
The two resulting oppositely charged atoms or molecules
Cation
A positively charged ion
Anion
A negatively charged ion
Ionic bond
Anions and cation attract each other
Ionic compounds
Compounds formed by ionic bonds
Hydrogen bond
Formed when a hydrogen atoms covalently bonded to one electronegative atom is also attracted to another electronegative atom
Van der Waals interactions
Attraction between molecules that are also close together as a result of these charges
Molecular shape and function
Molecular size and shape is key to its function
-molecules shape is deterred by the positions of its atoms valence orbitals
-molecular shape determines how biological molecules recognize and respond to one another
molecules with with similar shapes often have similar functions
Chemical reactions
Making and breaking of chemical bonds
Reactants
That starting molecules of a chemical reaction
Products
The resulting molecules of a chemical reaction
Chemical reactions make and break chemical bonds
All chemical reactions are reversible
just because a reaction can be reversed does not mean it is easily reversible
Chemical equilibrium
Reached when the forward and reverse reactions occur at the same rate
-at equilibrium the relative concentrations of reactants and products do not change
Polar covalent bonds
In water molecules, they spend more time near the oxygen than the hydrogen
Polar molecule
Water is this and the overall charge is unevenly distributed
-polarity allows water molecules to form hydrogen bonds with each other
Water’s four properties
-cohesive behavior
-ability to moderate temperature
-expansion upon freezing
-versatility as a solvent
Cohesion
Hydrogen bonds hold water molecules together
Surface tension
Result of cohesion, its a measure of how difficult its is to stretch or break the surface of a liquid
-contributes to transport of water to roots
Adhesion
Attraction between difference substances
Ex: between water and plant cell walls
Kinetic energy
The energy of motion
Thermal energy
Kinetic energy associated with random motion of atoms or molecules
Temperature
Represents average kinetic energy of molecules in a body of matter
Heat
Thermal energy in transfer form one body of matter to another (unit of cal or J)
Calorie (cal)
The amount of hear required to raise the temperature of 1g of water —> 1 kcal = 1000 cal
Joule
Another unit of energy
1J = 0.239 cal or 1 cal =4.184 J
Specific heat
The amount of heat that must be absorbed or lost for 1g of that substance to change its temperature by 1 degree Celsius
Waters high specific heat is traced to hydrogen bonding
-heat is absorbed when hydrogen bonds break
-heat is released when hydrogen bonds form
—> high specific heat of water minimizes temperature fluctuation to within limits that permit life
Evaporation (or vaporization)
Transformation of a substance form liquid to gas
Heat of vaporization
The heat of a liquid must absorb for 1g to be converted to gas
Evaporative cooling
as a liquid evaporates, its remaining surface cools
-helps stabilize temperatures in organisms and bodies of water
solution
liquid that is a completely homogenous mixture of substances
solvent
the dissolving agent of a solution
solute
the substance that is dissolved
aqueous solution
one where water is the solvent
hydration shell
ionic compound is dissolved in water, eahc ion is surrounded by a sphere of water molecules
hydrophobic
substance doesn’t have an affinity for water
ex: oil –> nonpolar bond
hydrophilic
substance that has an affinity for water
water = solvent of life
-water can dissolve compounds made of nonionic polar molecules
-even large polar molecules like proteins can dissolve in water if they have ionic and polar regions
molecular mass
sum of all masses of all atoms in a molecule
molarity (M)
the number of moles of solute per liter of solution
base
substance that reduces the OH- concentration of a solution
acid
substance that increases the H+ concentration of a solution
-strong acids completely dissociate in water
avagrados number
(6.022x10^-23)
buffers
substances that minimize changes in concentrations of H+ and OH- in a solution
-most contain weak acid and its corresponding base solutions which combine reversibly with H+ ions
hydrogen atom
hydrogen bond between two water molecules can shift from one to the other
valence
the number of covalent bonds it can form
hydrocarbons
organic molecules consisting of only carbon and hydrogen (nonpolar)
-can undergo reactions that release a large amount of energy
organic chemistry
the study of compounds that ocntain carbon, regardless of origin
isomers
compounds with the same molecular formula but different structures and properties
structural isomers
different covalent arrangements of their atoms
cis-trans isomers (geometric isomers)
have the same covalent bonds but differ in their spatial arrangements
enantiomers
isomers that are mirror image of each other
-important in the pharmaceutical industry
functional groups
components of organic molecules that are most commonly involved in chemical reactions
Hydroxyl group (-OH)
alcohol
Carbonyl group (C=O)
keytone, aldehyde
carboxyl group (-COOH)
carboxylic acid, or organic acid
amino group (-NH2)
amine
sulfhydryl group (-SH)
thiol
phosphate group (-OP3^2-)
organic phosphate
methyl group (-CH2)
methylated compound
adenosine triphosphate (ATP)
important organic phosphate
-stores the potential to react with water
-reaction releases energy that can be used by the cell
macromolecules
large polymers
ex: carbohydrate, nucleic acids, protein (have covalent bonds)
polymer
long molecules consisting of many similar building blocks
monomers
repeating units that serve as building blocks
enzymes
specialized macromolecules that speed up chemical reactions such as those that make or break down polymers
-most are proteins
dehydration reaction
when two monomers bond together through the loss of a water molecule
hydrolysis
reaction tat is essentially the reverse of dehydration reaction (making of water molecule)
-polymers are disassembled to monomers
carbohydrates
ex: sugars and polymers of sugars
-simplest carbohydrates = monosaccharides or simple sugars
-carbohydrate molecules are polysaccharides, polymers composed of many sugar building blocks
monosaccharides
have molecular formulas that are usually multiples of CH2O
-glucose = most common
-classified by carbonyl group (aldose or ketose) + number of carbons in skeletons
-serve as major fuel for cells
disaccharide
formed when dehydration reaction joins two monosaccharides
glycosidic linkage
covalent bond between two monosaccharides
-happens in carbohydrates
polysaccharides
polymers of sugars, have storage and structural roles
starch
storage polysaccharide of plants, consists of glucose monomers
-simplest starch = amylose
glycogen
storage polysaccharide in animals
-mainly stored in liver and muscle cells
-hydrolysis releases glucose when the demand for sugar increases
cellulose
major component of the tough wall of plant cells
chitin
another structural polysaccharide, found in the exoskeleton of arthropods
lipids
the one class of large biological molecules that does not include true polymers
-consist of mostly hydrocarbon regions
fats
constructed from two types of smaller molecules: glycerol and fatty acids
glycerol
three carbon alcohol with a hydroxyl group attached to each carbon
fatty acid
consists of a carboxyl group attached to a long carbon skeleton
triacylglycerol
three fatty acids are joined to glycerol by and ester linkage
unsaturated fatty acids (good)
have one or more double bonds
-liquid at room temperature
saturated fatty acids (bad)
have maximum number of hydrogen atoms possible and no double bonds
-solid at room temperature
hydrogenation
the process of converting unsaturated fats to saturated fats by adding hydrogen
hydrogenating
vegetable oils creating unsaturated fats with trans double bonds
trans fats
may contribute more than saturated fats to cardiovascular disease
phospholipid
two fatty acids and a phosphate group are attached to glycerol
-two fatty acid tails and one hydrophilic head
steroids
type of lipid characterized by a carbon skeleton consisting of four fused rings
cholesterol
a type of steroid, a component in animal cell membranes and a precursor from which other steroids are synthesized
-high level of cholesterol in blood may lead to cardiovascular disease
catalysts
speed up chemical reaction
polypeptides
unbranched polymers built from these amino acids
-its the bond between amino acid = peptide bond
protein
biologically functional molecule that consists of one or more polypeptides
amino acids
organic molecules with amino and carboxyl groups
-they differ in properties due to differing side chain (R-groups)
peptide bonds
amino acids linked by covalent bonds
-carboxyl ends in c-terminus
-amino end in n-terminus
primary structure
the sequence of amino acid
secondary structure
coils and folds, result from hydrogen bonds between repeating constituents of the polypeptide backbone
tertiary structure
overall shape of a polypeptide results from interaction between R groups, rather than interaction between backbone constituents
disulfide bridges
strong covalent bonds that may reinforce the protein’s structure
quaternary structure
results when two or more polypeptide chains from one macromolecule
collagen
fibrous protein consisting of three polypeptides coiled like a rope
-accounts for 40% of protein in the human body
hemoglobin
globular protein consisting of four polypeptides
sickle-cell disease
inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin
denatureation
the loss of. protein’s native structure
-protein is biologically inactive
gene
the amino acid sequence of a polypeptide is programmed by a unit of inheritance
polynucleotides
nucleic acids polymers
nucelotide
what a polynucleotide is made of
= nucleoside + phosphate group
pyrimidines
single six-membered ring
ex: cytosine, theymine, uracil
purines
six-membered ring fused to a five-membered ring
ex: adenine, guanine
bioinformatics
uses computer software and other computational tools to deal with the date resulting from sequencing many genomes
genomics
anyalyzing large sets of genes or eve comparing whole genomes pf different species
proteomics
similar analysis of large sets of proteins including their sequences
Enzymatic Proteins
selective acceleration of chemical reactions
ex: digestive enzymes catalyze hydrolysis of bonds in molecules
storage proteins
storage of amino acids
ex: casein the protein of milk is the major amino acids for baby cows
hormonal proteins
coordination of an organisms activities
ex: insulin
contactile and motor proteins
movement
ex: responsible for undulation of cilia and flagella
defensive proteins
protect against disease
ex: antibodies
transport proteins
transport substances
ex: hemoglobin
receptor proteins
response of cell to chemical stimuli
ex: receptors built into the cell membrane
structural proteins
support
ex: keratin, protein of hair, horns, feathers, and other skin appendages
