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146 Cards in this Set

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What is the law of conservation of mass?
mass is neither created nor destroyed in a chemical reaction
What are the components of an atom?
electron
proton
neutron
nucleus
What is the charge of an atom with 5 protons and 4 neutrons?
+5

Atoms are electrically neutral, so the number of protons are balanced by the same number of electrons.

In this case, 5(+1) + 4(0) = +5
What is an isotope?
have different nuclear properties and masses but the same chemical properties.

Basically, the isotopes have the same number of protons but differ in the number of neutrons.
What is the mass number?
It is the sum of the protons and neutrons of an element.

It is used to distinguish isotopes from each other.
Identify the following groups on the periodic table:
I, II, VII, VIII
I- alkali metals
II - alkaline earths
VII- halogens
VIII- noble gases
What is significant about all of the members of group VII on the periodic table?
VII- halogens

they all have similar properties and they all react with hydrogen to from water soluble compounds.
Types of chemical bonds.
covalent - sharing electrons

ionic - losing or gaining electrons
ionization energy
the energy required to remove an electron from the outer shell of an element
What is a miscible liquid?
Liquids that dissolve in water.

e.g. alcohols
What is an acid?
a substance that can donate a hydrogen ion.
What is a base?
a substance that can donate a hydroxyl ion.
What is a neutralization reaction?
a reaction between an acid and a base that results in a salt and water
what is osmosis?
diffusion across a semi-permeable membrane.

relies on osmotic pressure.
endothermic reaction
reaction in which chemical bonds of the products have more energy than the reactants. Energy is required to make the reaction happen.
ATP is usually the energy source
What are catalysts and why are they important?
Catalysts are usually enzymes.

They speed up a reaction and lower the activation energy
equilibrium constant
the point at which reversible reactions have reached an equilibrium between the forward and backward reactions.
KA = reactants/products
define a strong acid or base
one that is 100% ionized in aqueous solution
what is the equation for pH?
pH = -log(H+)
What is the most important buffer in the blood?
carbonic acid

H2CO3<->H + HCO3<-> H + CO3
Henderson-Hasselbach equation
pH=pKa + log proton acceptor/proton donor
signal transduction
the process of converting electrical information into chemical information
4 features of signal transduction
specificity
amplification
desensitization/adaptation
integration
3 classes of hormones
(that we focused on in class)
peptides
steroids
catecholamines
How do peptide hormones work?

name some examples
They bind to cell-surface receptors.

e.g. insulin, glucagon, LH, FSH
How do steroid hormones work?

name some examples
enter the cell and bind to receptors in the cytoplasm.

work at the level of transcription

e.g. progesterone, estrogen, testosterone
How do catecholamines work?
act through cell surface receptors to activate 2nd messenger
endocrine secretory pathways
endocrine
exocrine
autocrine
paracrine
regulated vs constitutive secretion
regulated secretion- hormones are secreted in bursts, so they can be secreted in large amounts over a short period of time.

constitutive secretion - secreting as its synthesized
Are catecholamines proteins?
NO
How many electrons are in a covalent bond?
2 and their spins are opposite
What is the law of conservation of mass?
the mass that enters into a chemcial reaction remains unchanged.

Chemical reactions do not create or destroy mass.
How do you figure out the mass of an atom?
It's the sum of its protons and neutrons.
How do you find the # of electrons of an element b y looking at the periodic table?
the # of electrons = the # of protons of an element (the atomic number)
What are valence electrons?
Electrons located in the outer-most shell that are available to enter into chemical bonds.
Define atomic number.
The number of protons in a given element.
How are the chemical properties of an element derived?
chemical properties of an element are related to the number and char. of electrons in the outermost shell.
what is an ion?
an atom that has lost or gained an electron. a charged (either + or -) atom
True or False

Elements on the right side of the periodic table lose electrons easily and elements on the left gain them.
FALSE

Elements on the left lose electrons and elements on the right gain electrons easier.
What is meant by an electronegative element?
An element on the right side of the periodic table, which means it GAINS electrons easily
True or False

Electronegativity increases from left to right on the periodic table.
True
What is a polar covalent bond?
a covalent bond that unequally shares electrons. The electrons are pulled toward one element more than the other.
Avagadro's number
6.02 x 10 to the 23rd
molarity
the amount of ions or molecules present in a given volume of solution
1molar solution
1M = one mole of a compound in 1 L of solution

one mole = formula weight in grams
e.g. formula weight of CH4 = (1x12) + (4x1)=16
one mole = 16 grams
True or False

Water molecules are polar.
TRUE
Define solute and solvent.
Solute - component of the solution in the smaller amount; that part dissolved in the solvent.

Solvent - component of the solution in the largest amount and that determines the physical state of the solution
Characteristics of a hydrophobic substance
insoluble/poorly soluble in water
not charged
not polar
Define immiscible.
liquids that do not dissolve in water.

e.g. oil
Fill in the blank.

Gases are (more/less)_______ soluble in water as the temperature rises.
LESS

Gases are less soluble in water as the temperature rises.
Fill in the blank.

Solids that dissolve in water are (more/less)_______ soluble in water as the temperature rises.
MORE

Solids that dissolve in water are more soluble in water as the temperature rises.
What does it mean to have a polar covalent bond?
bond where electrons are shared unequally, partial negative charges by the electronegative atom and partial positive charges by the electropositive atom
True or False

All organic compounds containg the carboxyl group are weak acids.
TRUE

It does not fully dissociate in water.
What is pH?
the negative log of Hydrogen concentration
What is dissociation?
The process of ionization in weak acids and bases.
Bronsted and Lowry theory
acids donate protons.

bases accept protons.

An acid becomes a base once it donates its proton.
Henderson-Hasselbach equation
pH=pKa + log(proton acceptor/proton donor)
Define radioactive isotopes and 4 types of radioactive emissions.
Radioactive isotopes are elements with unstable nuclei that emit energy as particles or rays.
alpha particle - 2 protons and 2 neutrons (helium nucleus)
beta particle - electron from the nucleus
gamma ray - high energy electromagnetic wave with no mass or charge
positron - positively charged particle the size of an electron
Beryllium has atomic number of 4 with an atomic wt of 9. How many neutrons are there?
5 neutrons

atomic weight = protons + neutrons
atomic number = # of protons
True or False

The electrons on the outermost shell are the least energetic and the easiest to lose.
False

The electrons on the outermost shell are the MOST energetic.
CH4 has a formula weight of 16.
What is one mole of CH4?
16

one mole equals the formula weight in grams.
molarity
one mole of a compound in one liter solution
Exothermic reaction
What kind of reaction is this?
Endothermic
What kind of reaction is this?
What 2 things can speed up an inorganic reaction?
increasing the concentration of the reactants

increase the temperature
What is a halide?
Any element in group VII of the periodic table. Chlorine is the most common.
True or False

All elements with more than 83 protons are radioactive.
TRUE
True or False

Organic compounds usually have covalent bonds.
True
True or False

Inorganic compounds usually have covalent bonds.
False

Inorganic compounds usually have ionic or highly polar bonds.
Characteristics of alkanes.
consist of hydrogen and carbon
single bond between carbons
end in -ane
NOT polar
NOT charged
NOT water soluble
ARE oil or lipid soluble
structural isomers
more than one isomer for a particular chemical formula
4 solubility characteristics of alkanes
NOT polar
NOT charged
NOT water soluble
ARE oil or lipid soluble
alcohol
What kind of structure is this?
(alcohol)

methanol
What kind of structure is this?
aldehyde
What kind of structure is this?
aldehyde
What kind of structure is this?
(alkane)

ethane
What kind of structure is this?
alkene
What kind of structure is this?
alkyne
What kind of structure is this?
(alkyne)

acetylene
What kind of structure is this?
amide
What kind of structure is this?
(amide)

ethylamide
What kind of structure is this?
(amine)

methylamine
What kind of structure is this?
aromatic
What kind of structure is this?
carboxylic acid
What kind of structure is this?
(carboxylic acid)

ethanoic acid
What kind of structure is this?
ester
What kind of structure is this?
(ester)

methylethanoate
What kind of structure is this?
ether
What kind of structure is this?
ether
What kind of structure is this?
ketone
What kind of structure is this?
ketone
What kind of structure is this?
What are the 4 nucleotides of DNA?
A G T C
What is DNA replication?
copying of the DNA strand before it divides into daughter strands so each daughter double helix has an original and a newly synthesized strand
In what direction does DNA polymerase read?
3 to 5 prime always
What is the 'leading strand' in DNA replication?
usually the top strand running 3 to 5 prime
DNA polymerase
enzyme that copies the DNA template or leading strand
What kind of bonds are formed between DNA base pairs (A-T; C-G)?
Hydrogen bonds

2 Hydrogen bonds between A-T
3 Hydrogen bonds between C-G
aliphatic vs. aromatic hydrocarbons
aliphatic hydrocarbons lack a benzene ring

aromatic hydrocarbons have a benzene ring as part of their structure
solubility of unsaturated hydrocarbons
insoluble in water
soluble in oil and fat
not polar/uncharged
Are alcohols polar or nonpolar?
Both.

They are polar at the OH end and nonpolar at the hydrocarbon end.
structural difference between aldehydes and ketones.
aldehydes have hydrogen attached to the carboxyl group.

ketones have only carbons attached to the carboxyl group
What's the difference between a primary, secondary and tertiary amine?
The number of hydrogens bound the nitrogen

primary - 2 hydrogens + R group
secondary - 1 hydrogen + 2 R groups
tertiary - 3 R groups (no hydrogen)
stereoisomerism
configuration differences with the same connections between the atoms (cis/trans)
optical isomer
type of stereoisomer with a chiral carbon. The images are not superimposable.
enantiomer
mirror image stereoisomers that are not superimposable
What are the 4 main steps of protein synthesis?
DNA replication
DNA transcription
RNA translation
protein synthesis
peptide vs protein
peptide-molecules comprised of less than 50 amino acids

protein-molecules comprised of more than 50 amino acids
general structure of amino acids
carboxylic acid
an amino group
a hydrogen atom
R group side chain (this defines the uniqueness of the amino acid)
in mammals which enantiomers are present, L or D?
only L
True or False

Amino acids are symmetric.
FALSE

Amino acids are assymmetric because they have 4 different constuents (carboxyl, amine, hydrogen and R-group); except glycine which has 2 hydrogens
What specifies the polarity of an amino acid?
The R group
What is pKa?
the dissociation constant.

pH at which half the molecules of an AA are charged and half are uncharged
what constitutes a basic AA?
R group has a nitrogen
high pKa value (so pH=10-12)
what constitutes an acidic AA?
R group has a carboxyl group
low pKa
negatively charged at physiologic pH
phosphorylation
The addition of a phosphate group from ATP to an OH group of an AA. Makes the AA negative
Which configuration is more common, cis or trans, and why?
Trans because the R groups in the cis configuration tend to repel each other and are too large to be side by side.
What determines the 'primary' protein structure?
amino acid sequence
What determines the 'secondary' structure of a protein?
alpha helix or beta sheet structure
What determines the 'tertiary' structure of a protein?
3-D structure of the folded protein where hydrophobic side chains are internal, hydrophilic or ionized side chains face outward
What is a peptide bond
a dehydration reaction b/w 2 amino acids joining the carboxylic acid of one amino acid to the alpha-amino group of another amino acid.

it is a covalent bond.
True or false

Cis and trans configurations are common in secondary structure of polypeptide bonds.
FALSE

Cis configuration is rare because the R-groups repel each other and are too large to be side by side.
Primary structure
the amino acid sequence of a polypeptide
secondary structure
local 3-D folding of a polypeptide chain
cysteine bond
disulfide covalent bond between two cysteine amino acids
tertiary structure
3-D structure of a polypeptide
What 2 secondary structures are the most observed in naturally occurring polypeptides?
alpha-helix

beta sheet
alpha helix
secondary structure

alpha helix formed by hydrogen bonds with every 4th amino acid down the chain
beta sheet
secondary structure

side-by-side parallel or ant-parallel alignment of polypeptide chains, each bound by hydrogen bonds
True or False

All proteins have a quaternary structure.
FALSE
quaternary structure
noncovalent relationship b/w 2 or more polypeptides to form a multiunit protein
ligand
molecules that reversibly bind to other molecules
What is a prosthetic group?
a compound that permanently associates with a protein and contributes to its function

e.g. heme prosthetic group
oxidation or reduction reaction

ferrous (+2) to ferric (+3)
oxidation reaction
What is the significance of iron (+3) in hemoglobin?
this is methemoglobin. oxygen won't bind to the heme group while iron is in this state.
define: hemoglobin

myoglobin
hgb-oxygen binding molecule in the blood; consists of 4 protein chains and 4 heme groups

myoglobin - oxygen binding molecule in the skeletal muscle
allosteric protein
the binding of a ligand to one site affects the binding properties of another site on the same protein
What is the T-state of Hgb?
the tense state with no oxygen bound to the heme groups
What is the R-state of Hgb?
the relaxed state. As one oxygen binds to a heme group, it results in a conformational change in another heme group increasing its affinity to oxygen until all sites are filled.

Hgb is an allosteric protein!
genome
the complete set of informtion carried by DNA
intron
non translated sequence that interrupts the linear code
exon
coding segment for nucleotide sequence
types of RNA
rRNA-ribosomal

mRNA-messenger

tRNA-transfer
rRNA-
ribosomal RNA

most abundant type of RNA in a cell

carries out translation
topoisomerase
enzymes that break and rejoin strands of DNA, producing a superhelix
True or False

RNA is linear and single stranded.
TRUE