Reading...
Play button
Play button
Use LEFT and RIGHT arrow keys to navigate between flashcards;
Use UP and DOWN arrow keys to flip the card;
H to show hint;
A reads text to speech;
371 Cards in this Set
- Front
- Back
|
What is the main characteristic of an inorganic compound?
|
lacks carbon
simple compounds like H20 |
|
|
The law of conservation of mass states:
|
mass that enters into a chemical reactions remains unchanged
|
|
|
Mass is neither _____ nor _____ in a chemical reaction.
|
created, destroyed
|
|
|
This law states that elements that compose a compound are present in fixed and precise proportion by mass.
|
law of constant composition
|
|
|
The law of multiple proportions
|
when elements combine they do so in a ratio of small whole numbers
if 2 elements form more than 1 compound, the ratio of the mass of the second element combined with a fixed mass of the first element will also be in ratios of small whole numbers |
|
|
All atoms of an element are ______ and have the same ______.
|
identical, mass
|
|
|
Compounds have constant composition because:
|
they have a fixed ratio of atoms
|
|
|
The periodic table is a tabular representation of all the elements arranged according to their ______ which is representative of the number of ______, and according to their ______ properties.
|
atomic number, protons in the nucleus, chemical
|
|
|
The mass of an atom is the sum of its ____ and ____.
|
protons and neutrons
|
|
|
The number of protons in a given element is fixed and is it's atomic number; whereas, the number of _____ may vary in different _____.
|
neutrons, isotopes
|
|
|
Isotopes are represented as _____ numbers in front of the symbol of the element.
|
superscript
|
|
|
Atomic weights for various elements are the averages of the ____ present in nature, weighted according to ________.
|
different isotopes, abundance
|
|
|
Chemical properties are governed by the _______ of _____ around the nucleus of an atom.
|
arrangement of electrons
|
|
|
# of electrons = # of _____
|
protons
|
|
|
Electrons are arranged into ______, and within these arranged into ______.
|
shells, orbitals
|
|
|
The electrons in the outermost orbital are called ______ determine the ______ of the element.
|
valence electrons, chemical properties
|
|
|
In the periodic table, _____ of elements are those elements with similar numbers and characteristics of valence electrons, and therefore similar ____ properties.
|
columns, chemical
|
|
|
What is an orbital? How many electrons can it hold?
|
3-d space where an electron is found 90% of the time; 2 electrons
|
|
|
What is ionization energy?
|
the energy required to remove the outermost electron from an atom
|
|
|
this is the ability of an atom to attract electrons
|
electronegativity
|
|
|
Covalent bonding
|
sharing of one or more electron pairs between 2 atoms
a molecule is 2 or more atoms held together by covalent bonds |
|
|
ionic bonding
|
electrostatic attraction among ions, formed by the transfer of 1 or more electrons from 1 atom to another
|
|
|
single bond vs double bond
|
single- share 1 pair of valence electrons (h2)
double- share 2 pairs of valence electrons (O2) |
|
|
These are 2 types of diagrams that can be used to represent electron sharing in covalent bonds:
|
lewis and line-bond structures
|
|
|
The more electronegative an atom...
|
the stronger it pulls shared electrons toward itself
|
|
|
Electronegativity (increases/decreases) from left to right across the periodic table.
|
increases
|
|
|
Nonpolar vs Polar covalent bonds
|
nonpolar- share electron equally as atoms have similar electronegativity
polar- share electrons unequally, results in partial positive/negative charges |
|
|
Ions are ___ atoms with more or fewer _____ Than usual.
|
charged, electrons
|
|
|
Anion vs cation
|
anion- negative charge
cation- positive charge |
|
|
Ionic compounds often are called _____ which may form _____.
|
salts, crystals
|
|
|
Negatively charged polyatomic ions have more ______ in their covalent bonds than they do ______ in all their collective nuclei
|
electrons, protons
|
|
|
Polyatomic ions associate wiht ions of the opposite charge to produce _____ in the compound.
|
electrical neutrality
|
|
|
In a covalent bond, the S and P orbitals may ______, creating specific molecular shapes.
|
hybridize
|
|
|
Hybridization
|
process in which atomic orbitals are mixed to form new identical orbitals
|
|
|
Molecular shape determines
|
how biological molecules recognize and respond to one another with specificity
|
|
|
A chemical formula is a statement of
|
ratios of elements that make up a compound
|
|
|
Formula weight is the sum of
|
the atomic weights of the constituent atoms of the formula.
frequently called molecular weight |
|
|
This is the number of atoms, ions or molecules that is large enough to see and handle.
|
mole
|
|
|
mole = avogadro's number
|
6.22 x 10^23 molecules
|
|
|
This is the mass in grams numerically equal to the atomic weight of the element in grams
|
molar mass
|
|
|
Molarity is
|
how many ions or molecules of reactants are present in a given volume of solution
|
|
|
a 1 molar (1M) solultion is the concentration of one ____ of a compound in 1 ____.
|
mole, Liter of solution
|
|
|
How do you make a 0.1 M solution?
|
dissolve 1/10 of the formula weight into 1 L of solution
|
|
|
___ are mixtures in which the solvent and solute are intimately associated as molecules or ions.
|
solutions
|
|
|
in aqueous solutions, the solvent is ___. Solutes in aqueous solutions can be _____.
|
water
gases, liquids, solids |
|
|
Water molecules are _____. Solutes that interact with the _____ or _____ ends of the h20 will be soluble in water.
|
polar, positive or negative
|
|
|
Hydrophilic soluble substances have _____ molecules. Hydrophobic insoluble substances have ___ molecules.
|
polar/charged,
not charged/nonpolar |
|
|
miscible vs immiscible
|
dissolve/don't dissolve in water
|
|
|
Gases that dissolve in water do so because they _____ on the surface of water. Gases dissolve in water according to their _____ in the atmosphere above the water.
|
exert pressure, partial pressure
|
|
|
Substances always diffuse down their _____, from ____ concentration to _____ concentration, until all areas have _____ concentration.
|
concentration gradient, high, low, equal.
|
|
|
This is diffusion across a semipermeable membrane, which is a membrane that will _____.
|
osmosis,
let some components of the solution cross and exclude others |
|
|
The lipids that compose biological membranes prevent _____ substances from crossing.
|
charged/polar
|
|
|
If there are concentration differences across a biological membrane, ___ will cross to equalize them.
|
water
|
|
|
The propensity of water to cross a semipermeable membrane to equalize solute concentration on either side is called:
|
osmotic pressure
|
|
|
If solution A has 3 large molecules and solution B has 15 teeny molecules, into which compartment will water flow to create equilibrium?
|
water will move from A to B due to # of mol. rather than mol. weight
|
|
|
Osmosis equalizes ____ concentration on either side of a membrane regardless of ____ of the solute.
|
water, identity
|
|
|
Exothermic vs endothermic rxn
|
exothermic: product has less energy than reactants (energy supplying)
endothermic:product has more energy than reactants (Energy requiring) endo and exo thermic rxns are often coupled |
|
|
Increasing ____ and ___ speeds up the reaction.
|
concentration of reactants and temperature
|
|
|
Catalysts speed up reactions by
|
lowering activation energy
make productive collisions between reactants more likely, reduce entropy |
|
|
Catalysts are usually ____ molecules called ____.
|
protein, enzymes
|
|
|
Most reactions are reversible, and never go completely _____ or ______.
|
forward, backward
|
|
|
This principle states that any change in status quo prompts an opposing reaction in the responding system.
|
Le Chatelier
|
|
|
When the concentration of one of the reactants is increased, the reaction is pushed toward the _____; when the conc. of one of the products is incr, the reaction is pushed to the _____.
|
right, left
|
|
|
Radioactive isotopes (all element isotopes greater than 83 and some below) have nuclei that are ____ and emit _____ in the form of particles (alpha, beta, positron) or _____ waves (gamma rays).
|
unstable, high energy, electromagnetic
|
|
|
Alpha particle
|
2 protons and 2 neutrons emitted as a group
|
|
|
A beta particle is
|
an electron that comes from the nucleus
|
|
|
a _____ ray is a high energy electromagnetic wave, higher energy than x-rays
|
gamma
|
|
|
positron
|
particle the size of an electron with a positive charge
|
|
|
When alpha and beta particles or positrons are emitted, the nucleus changes its _____ and hence becomes ____.
|
atomic number, another element
|
|
|
Radioactive elements decay according to_____ which is different for each element and isotope
|
half life
very short in nuclear medicine (hours) |
|
|
In radiation medicine, radioactive isotopes have
|
long half lives (Days/weeks/years)
|
|
|
IV radioactive isotopes result in ____, whereas radioactive implants _____.
|
radioactive excreta (handle per protcol),
excreta not radioactive bc confined by sealed implant |
|
|
Radioactivity produces ionization of chemicals that it hits, and in humans, most damaging ionization occurs in ____, resulting in ____.
|
person's DNA, cell death
|
|
|
Patients receiving radiation to treat one cancer have an increased risk for _____ in that area.
|
second malignancy
smaller amts of DNA damage survive as permanent mutations and can combine with other mutations in same cell to produce malignant transformations |
|
|
Enzyme, protein, and cellular functions are maximized when
|
the pH is neutral
|
|
|
Arrhenius
acids and bases produce _____ in water |
acid: H+ or H30+ producer in water
base: OH- producer in water |
|
|
Bronsted-Lowry:
|
acid: proton H+ donor
base: proton acceptor |
|
|
Lewis:
|
acid: electron pair acceptor
base: electron pair donor |
|
|
In neutralization, acids donate ____ And bases donate _____.
|
H+, OH-
|
|
|
In a neutralization reaction:
|
a chemical rxn between an acid and a base that yields a salt and a water
|
|
|
Strong acids ___ dissociate in water, weak acids ____ dissociate in water.
|
completely, partially
|
|
|
H+ comes from an acid and combines with water to form this ion
|
the hydronium ion, H30+
|
|
|
What is the hydronium ion concentration for pure H20?
|
1x 10^-7 M
|
|
|
The pH scale expresses
|
the H+ ion conc. in h20
|
|
|
pH =
|
-log(h30+)
|
|
|
pH of a neutral solution =
|
7.0
H30+ = OH- |
|
|
pH of an acid solution =
|
< 7.0
H30+ > OH- |
|
|
pH of a basic solution =
|
> 7.0
H30+ < OH- |
|
|
These acids have more than one hydrogen and can ionize more than once
|
polyprotic acids
most important is carbonic acid H2CO3 |
|
|
Buffer
|
solution that maintains a constant pH in spite of addition of acid/base
most consist of a solution of a weak acid and its salt most important buffer in blood is carbonic acid H2CO3 |
|
|
Conjugate acid will have ___ than conjugate base.
|
one more proton
|
|
|
This is the equation to express that the physiological activities of a molecule differ with changes in pH and ionization state
|
Henderson-Hasselbach equation
|
|
|
The higher the Ka (equilibrium constant for dissociation), ....
|
the greater the tendency to disscociate, and the stronger the acid
|
|
|
this is the pH at which 50% of the acid is dissociated
|
pKa
|
|
|
when pH = pKa...
|
you will get 50% ionization
|
|
|
pKa =
|
-log(Ka)
|
|
|
carbonic-acid-bicarbonate bufer in the blood equation
|
pH = pK - log(CO2/HCO3-)
|
|
|
if pH < pKa, then
|
weak acids wil be barely dissociated
|
|
|
if pH> pKa, then
|
weak acids will be majority dissociated
|
|
|
At equilibrium, reactions in which acids go to conjugate bases and back again, (and bases to conjugate acids) are constantly taking place, but at
|
equal velocities
|
|
|
Some reactions are ____, such as drug absorption. In this case, the reactant is being _____, and thus the reaction will proceed in a forward fashion according to LeChatelier's principle
|
irreversible, removed
|
|
|
When conditions change in a reaction, such as concentration and temperature, the system will no longer be at equilibrium an dwill try
|
to get there again
|
|
|
ph of a drug solution depends on
|
the pKa
|
|
|
____ stabilize pH. This stabilized acidity determines the form of drug dissociation in systems. The ______ equation conveniently handles drug ionization questions for buffered systems like the body.
|
Buffers, henderson-hassalbach
|
|
|
In a neutralization reaction:
|
a chemical rxn between an acid and a base that yields a salt and a water
|
|
|
Strong acids ___ dissociate in water, weak acids ____ dissociate in water.
|
completely, partially
|
|
|
H+ comes from an acid and combines with water to form this ion
|
the hydronium ion, H30+
|
|
|
What is the hydronium ion concentration for pure H20?
|
1x 10^-7 M
|
|
|
The pH scale expresses
|
the H+ ion conc. in h20
|
|
|
This is the unique about organic componds
|
compounds contain carbon
|
|
|
Carbon can ____ forming rings
|
bond to itself
|
|
|
This type of formula is best used to describe organic compounds, because more than one organic compound can have the same molecular formula, which doesnt explain how they are joined together.
|
structural
|
|
|
saturated hydrocarbons...
|
no double or triple bonds
alkanes: CnH(2n+2) cycloalkanes: CnH2n |
|
|
unsaturated hydrocarbons...
|
have a double or triple bond
Alkenes: general formula is CnH2n (C=C bonds) Alkynes: general formula is CnH2n–2 (CC bonds) Aromatics: usually contain one or more rings of six C atoms called benzene rings (carcinogenic) |
|
|
alkane
|
single bond
saturated hydrocarbon CnH(2n+2) |
|
|
cycloalkane
|
single bond saturated hydrocarbon
CnH2n |
|
|
Alkene
|
unsaturated hydrocarbon
double bond CnH2n |
|
|
Alkyne
|
unsaturated hydrocarbon
triple bond CnH(2n-2) |
|
|
aromatic
|
unsaturated hydrocarbon, double bond,
contain one or more rings of 6 C atoms called benzene rings (Carcinogenic) |
|
|
alkanes are saturated hydrocarbons that consist of only ____ and _____, and have single bonds between carbons.
|
hydrogen and carbon
|
|
|
1 carbon alkane
|
methane
|
|
|
2 carbon alkane
|
ethane
|
|
|
3 carbon alkane
|
propane
|
|
|
4 carbon alkane
|
butane
|
|
|
5 carbon alkane
|
pentane
|
|
|
6 carbon alkane
|
hexane
|
|
|
Structural isomers have the same chemical formulas but different ____, and will have different ______.
|
structure, different properties (boiling and melting points)
|
|
|
As the number of carbon atoms in a molecule increases, so does the number of ____ possible.
|
structural isomers
|
|
|
alkane
|
single bond
saturated hydrocarbon CnH(2n+2) |
|
|
cycloalkane
|
single bond saturated hydrocarbon
CnH2n |
|
|
Alkene
|
unsaturated hydrocarbon
double bond CnH2n |
|
|
Alkyne
|
unsaturated hydrocarbon
triple bond CnH(2n-2) |
|
|
aromatic
|
unsaturated hydrocarbon, double bond,
contain one or more rings of 6 C atoms called benzene rings (Carcinogenic) |
|
|
cycloalkanes are
|
saturated hydrocarbon rings
|
|
|
alkanes are (polar/nonpolar), (soluble/insoluble) in water.
|
nonpolar, insoluble in water (oil and lipid soluble!)
|
|
|
cis and trans isomerism
|
double bond does not have free rotation as the single bond does, so substituents on the carbons that participate in the double bonds can be next to each other or across the molecule from each other
same compound and formula, but different structure means different properties |
|
|
aromatic vs aliphatic
|
aromatic: closed benzene ring (C6H6) as part of their structure; 3 alternating double bonds in the ring
aliphatic: open chain |
|
|
solubility of unsaturated hydrocarbons
|
nonpolar, lipid soluble
|
|
|
Alcohols have an ___ group attached to a saturated carbon (one that is a carbon bonding to 3 other atoms by single bonds).
|
-OH group
|
|
|
Low molec wt alcohols are _____ soluble, and high molec wt alcohols are ____ soluble.
|
water, lipid
|
|
|
Cyclic alkanes can have a -OH group attached to a carbon to become ____
|
cyclic alcohols
|
|
|
Alcohols are more likely to function as ____ because their -OH group is most easily donated.
|
weak bases
|
|
|
_____ have an -OH attached to one of the carbons of a benzene ring. They are chemically different from alcohols in that they are much more likely to donate a ___ in a chemical reaction, making them acids.
|
Phenols, proton
|
|
|
Ethers have a formula of _____, can be ____ or ____.
|
R-O-R', aliphatic or aromatic
(R stands for a Carbon, formaul is "carbon thing - oxygen - carbon thing") |
|
|
Thioalcohol general formula is ____ where S = ____. Thioalcohols can undergo oxidation to form _____ with formula ____.
|
R-SH, sulfur
disulfides, R-S-S-R |
|
|
What is oxidation?
|
addition of oxygen or loss of hydrogen or loss of electrons (Valence becomes more positive)
|
|
|
This is the addition of hydrogen or loss of oxygen or gain of electrons (Valence becomes more negative).
|
reduction
|
|
|
Both aldehydes and ketones contain ____
|
carbonyl group C=O
|
|
|
aldehydes have 1 or 2 hydrogens attached to the carbon of the carbonyl group, whereas ketones have...
|
only carbons attached to the carbon of the carbonyl group
|
|
|
Aldehydes and ketones are soluble in ____ and can be reduced to ____ by addtion of a Hydrogen.
|
water, alcohols
|
|
|
Alcohol can be oxidized to a ____ or ____.
|
aldehyde or ketone
|
|
|
Carboxylic acids have a carboxyl group attached to ____, ____ or ____.
|
hydrogen, aliphatic carbon, or aromatic carbon
|
|
|
Expect a carboxylic acid to react with a ____ to perform this type of reaction:
|
base, neutralization
|
|
|
Esterification reaction is when a carboxylic acid and an alcohol react to form
|
an ester and a h20
|
|
|
Esters can be aliphatic or aromatic, are lipid soluble, and are unique because....
|
low molec wt esters smell good and are used to scent things
|
|
|
Amines
|
Nitrogen bonded to one or more carbons, behave like bases, can form salts
|
|
|
Amides
|
products of a neutralization between organic acid and ammonia or amine (Base)
|
|
|
Amidation reaction is when acid and amine reat to produce
|
amide and h20
links amino acids to one another |
|
|
Isomers can be ____ or ____.
|
structural (connectivity differences),
stereoisomers (configuration differences) |
|
|
The 2 types of stereoisomers are
|
cis (Same side)-trans (opposite/diagonal sides), and optical isomers
|
|
|
Isomers are molecules that have the same molecular formula, but have a different ______ of the atoms in space. That excludes any different arrangements which are simply due to the molecule rotating as a whole, or rotating about particular bonds.
|
arrangement
|
|
|
Cis and trans isomers occur when you have _____ _____ somewhere in a molecule.
|
restricted rotation
C=C |
|
|
Optical isomers are present when a molecule has a _______.
|
chiral carbon (carbon with 4 different substituents)
|
|
|
This is a chiral carbon when 2 molecules possible that are mirror images of one another
|
enantiomers
have same connections but are not superimposable upon each other |
|
|
D and L nomenclature for optical isomers
|
D rotates polarized light to the right (+)
L rotates polarized light to the left (-) D and L are mirror images of each other |
|
|
Enantiomers are _____ with respect to their chemical properties in ordinary chemical reactions. However, binding of enantiomers to enzymes or receptors in the case of drugs ...
|
identical,
may or may not be stereospecific |
|
|
Mirror or optic isomers have ____ properties
|
different
|
|
|
DNA stores info that controls
|
all cellular processes
|
|
|
DNA directs the synthesis and properties of
|
proteins
|
|
|
This is the conduit of the info flow between DNA and protein
|
RNA
|
|
|
DNA is transcribed into ____, who sequence is translated by ____ into proteins.
|
RNA, ribosomes
|
|
|
Genes encode molecular map of ____
|
proteins
|
|
|
Dynamic Functions of proteins
|
catalysis of chemical reactions(enzymes), transport (ATPase), metabolic control (hemoglobin, hormoes), and contraction (actin/myosin)
-enzymes, receptors, pores, channels |
|
|
Structural functions
|
provide the matrix for bone and connective tissue (Collagen and elastin), provide structural strength and elasticity to organs and vascular system
|
|
|
Protein
|
molecules composed of over 50 amino acids
|
|
|
Peptide
|
molecules composed of less than 50 amino acids
ex: adenocorticotropic hormone, ADH, glucagon, calcitonin |
|
|
Codon:
|
sequence of 3 adjacent nucleotides, constituting the genetic code, that determines the insertion of a specific amino acid in a polypeptide chain during protein synthesis or the signal to stop protein synthesis
|
|
|
transcription and translation of the DNA code result in polymerization of _____ into specific linear sequence characteristic of a protein.
|
amino acids
|
|
|
Genes containing codons for amino acids ---> ______ --> mRNA containing codon sequence for amino acids --> _______ ---> protein with specific amino acid sequence
|
transcription, translation
|
|
|
primary structure:
|
amino acid residues
how proteins come together in linear space |
|
|
derived amino acid:
|
proteins contain these, which are formed by an enzymatic rxn on a common amino acid after that amino acid has been incorporated into a protein structure
|
|
|
secondary structure:
|
alpha helix
how amino acid residues fold together in 2-d space |
|
|
tertiary structure
|
polypeptide chain
how alpha helices fold together in 3-d space |
|
|
quaternary structure:
|
how polypeptide chains come together as subunits
|
|
|
ryanodine receptor
|
main ca channel in heart, skeletal muscle and brain cells
|
|
|
Common amino acids contain a central alpha carbon to which these 4 things are covalently bonded
|
carboxylic acid, amino acid, hydrogen, R group side chain
|
|
|
____ uniquely defines each of the 20 common amino acids
|
R group
|
|
|
In mammalian cells, only the _____ enantiomers are found.
|
L
|
|
|
The ______ of amino acid sidechains is critical for the folding of a protein to its native structure and for stability of the folded protein.
|
hydrophobicity
|
|
|
Ionization is the likelihood to have a _____
|
charge
|
|
|
pKa
|
pH at which 1/2 of the molecules are charged and 1/2 are uncharged
|
|
|
basic amino acids have R groups containing _____.
|
nitrogen atoms
high pKa |
|
|
acidic amino acids have R groups containing _____.
|
carboxylic acid groups
low pKa |
|
|
Proteins can be characterized based on the ratio of ____ and ___ amino acids in that protein.
|
acid and basic
|
|
|
glycosylation
|
metabolic process in which small chains of CHO are bound to AAs in proteins through N or O linkages
|
|
|
fatty acylation:
|
lipid groups are attached to an AA in a protein vi an ether linkage
|
|
|
regulatory modification
|
can alter the binding o an AA to a polypeptide and thus change its structure/activity
|
|
|
phosphorylation
|
addition of a phosphate group from ATP to an OH group adding a negative charge to an AA
|
|
|
the polypeptide sequence is predetermined by the nucleotide sequence of its
|
gene (codon)
|
|
|
The unique ______ enables a polypeptide chain to fold into a specific 3-d structure that gives the protein its ____ and ____ properties.
|
primary structure, chemical and physiological
|
|
|
_______ bond has an important role in stabilizing the folded conformation of proteins
|
covalent
|
|
|
chaperone proteins
|
facilitate the rate of protein folding
|
|
|
_____ bonding keeps alpha helix in its helical structure -- stabilized by bonding amino acids within the strucure.
|
hydrogen bonding
|
|
|
in tertiary structure, Hydrophobic side chains occur on the ____, away from water interface.
|
interior
|
|
|
in tertiary structure, Ionized side chains occur on the ____, where they are stabilized by water solvation.
|
exterior
|
|
|
a large number of water molecules form a ____ shell around the outside of the protein
|
solvation
|
|
|
In quaternary structure proteins, the subunits are joined by:
|
hydrophobic interaction forces
electrostatic interaction (salt bridge, ionic linkage) van der waals (dispersion forces) |
|
|
Protein _____ drives its function. This includes its chemical and physical properties, and the energetic forces that hold molecules together.
|
structure
|
|
|
True/false: a single amino acid change in sequence can have deleterious effects on structure and biological fcn.
|
true!
|
|
|
Ligand
|
molecules that bind reversibly to a protein
|
|
|
Binding site
|
site on the protein that a ligand joins at, determines the specificity of the ligand-protein interaction, as it is complementary to the ligand in size, shape, charge, and hydrophobic/philic character
|
|
|
this is a compound permanently associated with a protein and contributes to its function
|
prosthetic group
|
|
|
induced fit
|
structural adaptation that occurs between protein and ligand that makes ligand binding tighter -- conformational change in protein that makes binding site more complementary to ligand
|
|
|
oxygen-binding proteins are needed for living multi-cellular animals because...
|
oxygen is poorly soluble in water and cannot diffuse over enough distance, and cannot be carried into tissues effectively without the protein carrier
|
|
|
This prosthetic group is a protein-bound group incorporated into the globin protein molecule and contributes significantly to oxygen transport function
|
heme prosthetic group, contains iron
|
|
|
Metals such as iron tend to (Gain/lose) electrons to be come (positive/negative) ion.
|
lose, positive
|
|
|
Iron can only bind 02 reversibly in the ____ State. If it is in the ____ state, heme can't bing 02 and the molecule is called methemoglobin
|
ferrous (fe2+), ferric (fe3+)
|
|
|
Heme structure functions to stabilize ____ in the center ofthe molecule.
|
iron
|
|
|
________ can bind heme with greater affinity than O2, making it highly toxic to aerobic organisms
|
carbon monoxide
|
|
|
This is an O2 carying protein that binds and releases O2 with changes in O concentration in the sarcoplasm of muscle cells.
|
myoglobin
myoglobin steals O2 out of blood and gives it to muscle, and the more you have the greater the O2 carrying capacity |
|
|
This is a globular protein containing 4 protein chains with 2 alpha and 2 beta subunits, has 4 total binding sites for 02, and is present in high conc. in RBCs
|
hemoglobin
|
|
|
This is the primary function of Hgb
|
binding O2 in the lungs and transporting O2 into the cells where it is released
|
|
|
Despite amino acid sequence differences between myoglobin and hemoglobin, their ____ and ____ are very similar
|
structure, function
STRUCTURE DRIVES FUNCTION |
|
|
The structure of hemoglobin prevents the formation of _____, which would result in the irreversible conversion of the iron from Fe2+ to Fe3+
|
methemoglobin
|
|
|
Despite amino acid sequence differences between myoglobin and hemoglobin, their ____ and ____ are very similar
|
structure, function
STRUCTURE DRIVES FUNCTION |
|
|
The structure of hemoglobin prevents the formation of _____, which would result in the irreversible conversion of the iron from Fe2+ to Fe3+
|
methemoglobin
|
|
|
Hemoglobin is an ____ protein, in which binding of a ligand to one site affects the binding properties of another site in the same protein.
|
allosteric
|
|
|
Hemoglobin is an ____ protein, in which binding of a ligand to one site affects the binding properties of another site in the same protein.
|
allosteric
|
|
|
T state of a protein
|
tense state, more stable when O2 is absent and molecule is deoxyhemoglobin
|
|
|
T state of a protein
|
tense state, more stable when O2 is absent and molecule is deoxyhemoglobin
|
|
|
Binding of O2 to deoxyhemoglobin triggers change in Hgb subunit to ____ state.
|
R state
|
|
|
Binding of O2 to deoxyhemoglobin triggers change in Hgb subunit to ____ state.
|
R state
|
|
|
____ state is when O2 binds with much higher affinity for Hgb.
|
R state
|
|
|
Why is Hgb sutied for oxygen transportation?
|
Hgb binds O2 cooperatively
|
|
|
The sigmoidal shaped oxyhemoglobin dissociation curve represents that Hgb undergoes transition from a low affinity ___ state to a high affinity ____ state as more oxygen molecules are bound. The sigmoidal curve shows ____.
|
T, R, cooperativity
|
|
|
The Bohr effect:
|
the binding of H+ and CO2 is inversely related to the binding of O2
the binding of O2 to Hgb is pH sensitive! |
|
|
In peripheral tissues, there is a low pH and higher CO2 concentration, causing a ____ in the affinity of Hgb for O2 and O2 is ____ to the tissues.
|
decrease, released
|
|
|
In the lungs, CO2 is excreted causing a rise in blood pH, which _____ the affinity of Hgb for O2, making it possible for Hgb to transport O2 to the peripheral tissues.
|
increases
|
|
|
2,3 DPG binds at site distant from O2 binding site and _____ the affinity of Hgb for O2 by stabilizing Hgb in the T state.
|
reduces
this delivers more O2 to tissues in periphery |
|
|
How does high altitude affect PaO2?
How does the body adapt? |
at higher alt, the PaO2 drops.
the delivery of O2 to tissues adapts to maintain normal levels by increasing 2.3 DPG --> decrease in Hgb affinity for O2 |
|
|
The fetus has a (higher/lower) affinity than maternal Hgb for O2?
|
higher
allows fetus to extract O2 from maternal blood, has gamma subunits rather than beta on its hgb after birth, baby makes beta subunits to get same O2 carrying capacity as adult |
|
|
Sickle cell is (hetero/homo)zygous disease where erythrocytes are ____ and abnormally ____.
|
homozygous, fewer, shaped
|
|
|
The abnormal sickled shape of Hb S cells in sickle cell anemia cause these problems:
|
pain, weakness, dizziness, SOB, blocked capillaries, organ dysfunction and necrosis, 1/2 the normal Hgb level
|
|
|
This is the amino acid substitution that causes sickle cell anemia
|
hydrophobic valine instead of hydrophilic charged glutamate at position 6 in 2 Beta chains
|
|
|
Amino acid sequence is what induces them to ____ into their _____ structure and gives its ability to function.
|
fold, tertiary
|
|
|
Cooperativity is a ___/____relationship!
|
structure, function
|
|
|
The structure and biochemistry of cell function is determined by:
|
proteins
|
|
|
DNA is transcribed into _____, whose sequence is translated by _____ into protein.
|
RNA, ribosomes
|
|
|
genome
|
complete set of info carried by DNA
|
|
|
genomes of eukaryotes are divided into:
|
chromosomes
|
|
|
only ____ % of DNA codes for functional genes
|
2-4%
|
|
|
There are 2 repetitive sequences with special functions:
|
centromeres and telomeres
|
|
|
centromere
|
attachment points for the mitotic spindle for dispersement of chromosomes to the daughter cells in mitosis
|
|
|
teleomere
|
sequence that stabilizes teh ends of the chromosomes, causes it not to unravel or have chemistry done to it, "Caps it off"
|
|
|
intron
|
intervening sequences, not translated into final product, interrupt the otherwise linear seuence
|
|
|
exon
|
coding segment for nucleotide sequences which make up AAs of the peptide it encodes
"recipe for proteins" |
|
|
The ____ are removed during the processing of the RNA transcript, and the remaining ____ are ligated/spliced together.
|
introns, exons
|
|
|
Watson Crick
|
double helix structure of DNA results from interwinding of 2 right-handed polynucleotide strands around a common axis
|
|
|
RNA
|
carries genetic info out of nucleus and into cytoplasm where proteins are made
|
|
|
Most RNA is ____
|
rRNA
|
|
|
Ribosomes
|
large protein complexes that carry out translation
|
|
|
mRNA
|
templates for synthesis of protein, carry info from DNA to cellular protein synthesis sites
|
|
|
tRNA
|
transfer specific AAs from soluble amino acid pools to ribosomes and ensure proper alignment prior to peptide bond formation
|
|
|
RNA is a linear ___ stranded polynucleotide of ribonucleic acids. The property that makes RNA unique is ____.
|
single, the nucleotide sequence
|
|
|
Nucleotides consist of these 3 subunits:
|
1. phophate
2. purine or pyrimidine base 3. pentose if you take away purine/pyrimidine base, it becomes cAMP, if you add 2 phosphates, it becomes ATP |
|
|
The only difference between nucleotides of DNA and RNA is
|
DNA has H on pentose ring, RNA has OH on pentose ring
|
|
|
Nitrogenous bases can be ____ or ____.
|
purines (adenine and guanine)
or pyrimidines (cytosine and thymine -- uracil in RNA) |
|
|
Phosphorylation makes a nucleoside into a ____.
|
nucleotide
|
|
|
3 physical properties of nucleotides:
|
1. soluble in h20 at wide range of pH
2. phophorylation increases aqueous solubility w more polar bonds 3. presence of charged phosphate group provides for sites of electrostatic interaction w positively charged groups(proteins, metal ions) |
|
|
Nucleic acids are strands of nucleotides linked by ___ bonds, linking 5' and 3' groups together.
|
phosphodiester
|
|
|
The nitrogenous base attached to a pentose ring is considered a
|
side chain
|
|
|
The sequence of _____ on a polynucleotide provide the molecule with a unique chemical identity.
|
bases
|
|
|
Other than favorable stacking interactions between neighboring bases, these factors alter structural arrangement and stability of the helix:
|
pH, salt concentration, temp
|
|
|
In polynucelotide strands, nitrogenous bases face outward and are hydro_____, whereas faces of the inner rings are hydro____ and tend to avoid contact w the aqueous environment.
|
philic, phobic
|
|
|
DNA is very (Stable/unstable), making it suitable for long-term storage for genetic info, unlike ____, which is more prone to hydrolysis.
|
stable, RNA
|
|
|
nuclease
|
enzyme that catalyzes phosphodiester scission
|
|
|
exonuclease
|
cleave last nucleotide at 5' or 3' terminus, only clip from the end, cannot clip from a circular polynucleotide, can result in complete degradation
|
|
|
endonuclease
|
cleave phosphodiester bonds in middle of polynucleotide-- sits down on polynucleotide nad searches for a region compatible w enzymatic rxn and clips something specific, can cleave from circular polynucleotide
|
|
|
restriction endonuclease
|
recognize and cleave very specific sequences
basis for recombinant DNA techniques |
|
|
DNA strands run anti-parallel, meaning
|
one runs 5' to 3', one runs 3' to 5'
|
|
|
Base pairing occurs when an acceptor and a donor (purine, pyramidine) are in a position to form a _____ bond.
|
hydrogen
|
|
|
Adenine pairs with ___ and guanine pairs with _____.
|
thymine (uracil in RNA), cytosine
|
|
|
The biologically active form of DNA is ______, created by either underwinding or overwinding the double helix. This process is controlled by ____.
|
superhelical (a coiled coil),
topoisomerases |
|
|
DNA is thermodynamically most stable in ____ structure.
|
circular
|
|
|
Topoisomerase (I & II)
|
enzymes that act by catalyzing the breakage and rejoining of DNA strands, producing a DNA srand more or less superhelical than original
topo I- transient single-stranded break topo II- break both strands simultaneously (hand holding examples) |
|
|
Cellular RNA is linear and (single/double)stranded.
|
single
|
|
|
Protein synthesis takes place on _____, and rRNA is the catalytic component that maintains stability.
|
ribosomes
|
|
|
The _____ of mRNA controls the amount of protein made from each mRNA molecule (demand).
|
short life span
|
|
|
mitochondrial RNA
|
have their own protein synthesizer, including ribosomes, tRNA, and mRNAs. responsible for proteins of electron transport chain and ATP synthase
|
|
|
DNA replication
|
duplication of DNA strands for passing of genetic info to daughter cell in mitosis
|
|
|
semiconservative replication
|
half of parental DNA molecule (one strand) is conserved in each new double helix, paired w new complementary strand (half old/half new)
|
|
|
The addition of nucleotides is performed by DNA ______ which add nucleotides to an existing _____ that provides a 3' OH residue.
|
polymerases, primer
|
|
|
DNA polymerase
|
catalyzes addition of nucleotides during chain elongation, ensure accuracy with enzymatic proofreading
|
|
|
enzymes that catalyze unwinding of DNA for replication
|
topoisomeraase (untwists/folds higher order DNA structure)
helicase (separates parental strands) |
|
|
Origin of replication (ORI) site
|
AT rich region where replication fork initial separation of parental strands occurs
|
|
|
Only the _____ direction can be linearly replicated
|
3' to 5'
|
|
|
No DNA polymerase catalyzes addition of nucleotides to the ____ end of a growing chain
|
5'
|
|
|
The lagging strand is synthesized by a series of short pieces called:
|
okazaki fragments
each fragment needs its own primer |
|
|
After removal of RNA primers leaves a gap, the remaining nick is sealed by ____ by formation of new phosphodiester bonds, requiring energy from ____ or ___.
|
DNA ligase, ATP, NAD+
|
|
|
excision repair, 2 types
|
removal of damaged nucleotides leaving agap in DNA, followed by resynthesis using genetic info on opposite strand and ligation to restore continuity of DNA
base excision repair (BER) nucleotide excision repair (NER) |
|
|
3 major differences between DNA and RNA:
|
1. RNA is single stranded
2. RNA sugar is ribose 3. RNA has uracil instead of thymine |
|
|
gene
|
section of DNA containing recipe for a particular protein - encode primary amino acid sequence of particular proteins
some genes encode for more than 1 protein |
|
|
3 parts of a eukaryotic gene:
|
1. promoter region and upstream regulatory sequences
2. coding region contains exons and introns 3. downstream regulatory regions |
|
|
tRNA
|
interacts with amino acids to assist the ribosome in protein synthesis
|
|
|
RNA polymerases
|
accomplish transciption
primer independent template DNA dependant no proofreading ability depend on DNA characteristics for binding and initiation of transcription |
|
|
RNA polymerases are dependent on DNA characteristics for ______ and _____.
|
binding, initiation of transcription
|
|
|
When a gene is being actively transcribed into mRNA, we say it is..
|
"Turned on"
|
|
|
DNA must be at least partially unwound and relax for ...
|
the transcription complex to bind
relaxed DNA is called "Active chromatin", achieved with binding of transcription factors |
|
|
promoter
|
transcription initiation site
|
|
|
the DNA sequences that transcription factors bind to are called
|
upstream activator sequences/ enhancer sequences
|
|
|
transcription factors influence the likelihood of
|
transcription of a particular DNA segment
|
|
|
a gene may be negatively regulated by a transcription factor that _____ transcription
|
prevents
|
|
|
The decision of which genes should be transcribed depends on: (2)
|
1. combo of specific transcription factors ( transcriptional regulators/enhancers)
2. relaxed state of a DNA region |
|
|
2 common promoter sequences recognized by RNA polymerase II
|
TATA box or CAAT box
|
|
|
RNA polymerase I
|
synthesizes rRNA from multiple sites on multiple chromosomes
|
|
|
RNA polymerase III
|
synthesizes tRNAs and one rRNA (5s)
|
|
|
sense strand of DNA vs antisense strand
|
sense- coding
antisense- non-coding strand, serves as template for mRNA synthesis |
|
|
Transcription starts, continues and ends because of specific _______that promote the initial binding of RNA polymerase, continued binding during elongation, and termination of binding at the end.
|
DNA sequences
|
|
|
DNA structure must be ___ for RNA polymerase to bind to start RNA replication.
|
relaxed
|
|
|
___ are important in the continued unwinding and rewinding of DNA during and after the transcription process.
|
topoisomerases
|
|
|
mRNA have a ____ cap and a ____ poly A tail, added immediately after transcription
|
5', 3'
|
|
|
Small nuclear ribonucleic proteins (snRNPs)
|
enzymes that splice out introns and recognize sequences of intron-exon junctions
|
|
|
Incorrect splicing can occur because the splice site is ____, like in thalassemia.
|
mutated
|
|
|
Different proteins can be formed from the same gene when that gene has multiple: (2)
|
1. alternative splicing sites
2. alternative polyadenylation sites |
|
|
RNAs must be bound to ___ to be exported from nucleus.
|
proteins
|
|
|
Transcription factors may ___ transcription by opening up DNA structure, or ____ transcription by blocking binding of transcription initiation complex.
|
promote, inhibit
|
|
|
The 5' cap and 3' tail are (Translated/untranslated).
|
untranslated
|
|
|
Multiple combinations of bases can code for the same ____.
|
amino acid
|
|
|
5 steps in protein synthesis:
|
1. activation of amino acids
2. initiation at start codon 3. elongation (adds subsequent amino acids) 4. termination and release 5. protein folding and post-translational processing |
|
|
aminoacyl tRNA synthetase
|
enzyme that attaches a particular amino acid to its particular tRNA at binding site, and proofreading ability
|
|
|
2 step reaction for aminoacyl-tRNA synthetase
|
1. amino acid + ATP --> aminoacyl AMP + PPi
2. aminoacyl-AMP + tRNA --> aminoacyl tRNA + AMP |
|
|
When aminoacyl tRNA synthetases recognize they have attached the wrong amino acid to the tRNA,
|
wrong amino acid is excised, leaving binding site open for correct AA to bind, requires additional energy
|
|
|
The ribosome binds to the cap at the ___ end of the mRNA and scns the mRNA sequence until it comes to an initiation codon ____.
|
5', AUG
|
|
|
Protein synthesis is (Rapid/slow).
|
rapid
|
|
|
____ binds to the stop codon
|
protein releasing factor
|
|
|
_____ cleaves the protein from the last tRNA.
|
peptidyltransferase
|
|
|
translation requires energy derived from:
|
2 phosphoanhydride bonds in ATP are cleaved
1 GTP for each: entry of AA into ribosomal site, during each translocation step |
|
|
If the wrong base is at the ____ position of many codos, it might not make a difference in amino acid sequence.
|
3rd/wobble
|
|
|
Even if RNA polymerase makes a mistake and enters wrong base into mRNA, other correct mRNAs can:
|
direct correct protein synthesis
|
|
|
Ribosome has proofreading ability for base-pairing but not for
|
amino acid sequence
|
|
|
The BIG MISTAKE in protein synthesis is when ___ has the wrong sequence, and every molecule of mRNA synthesized from it is wrong, as well as its subsequent protein molecules.
|
DNA
BUT- since there are 2 of most genes, if second copy is OK, only half the protein wound be wrong |
|
|
Mistakes in DNA are called
|
mutations
|
|
|
If a person has 1 mutated gene and one intact one
|
heterozygote
half of protein encoded by that gene will be normal and half with wrong amino acid sequence may or may not exhibit symptoms |
|
|
point mutation
|
single base change
|
|
|
silent mutation
|
change that specifies the same amino acid
CGA to CGG both Arg |
|
|
missense
|
change that specifies different amino acid
CGA to CCA arg to pro |
|
|
nonsense
|
change that produces a stop codon
CGA to UGA arg to stop |
|
|
insertion
|
addition of one or more bases
|
|
|
deletion
|
loss of one or more bases
|
|
|
2 types of frameshift mutations
|
insertion and deletion
|
|
|
2 of the same genes
|
homozygote
if both defective, will exhibit symptoms because none of their protein is correctly formed |
|
|
A heterozygote for sickle cell mutation is a _____ and does/doesn't display symptoms, unless _____.
|
carrier, under stress
|
|
|
folding
|
initial stage of protein processing
may require chaperone proteins to help fold into correct shape, or refold ones that have come undone due to stress (pH, heat) |
|
|
covalent modification
|
phosphorylation, methylation, acetylation
|
|
|
glycosylation
|
attachment of various sugars to proteins
|
|
|
cleavage/activation
|
digestive enzymes, insulin
|
|
|
Rough endoplasmic reticulum
|
membranous structure in cell that has ribosomes to synthesize proteins destined for export
|
|
|
Protein Sorting and packaging in vesicles is mainly done in
|
the golgi apparatus (protein post office)
|
|
|
Secretory proteins like peptide hormones or digestive enzymes must be packaged into
|
secretory vesicles
|
|
|
Some proteins synthesized as precursors must be ______, involving cleavage of some part of the protein (not including RER proteins).
|
activated
|
|
|
Insulin is activated in the secretory vesicles of the ____ in the pancreas.
|
beta cells
|
|
|
Digestive enzymes are activated in the
|
small intestine
|
|
|
Clotting factors are activated in a ______.
|
cascade
domino effect |
|
|
The amount of any biochemical substance in the body is the algebraic sum of ____ and ____.
|
synthesis and degradation
|
|
|
Synthesis of proteins can be manipulated (increased/decreased) by
|
manipulating transcription or translation
|
|
|
Protein degradation is important for
|
regulating amount of protein in cell or extracellular fluid
|
|
|
Protein degradation is accomplished by ____ of the protein into peptide fragments and ultimately into individual _____.
|
digestion (Cleavage),
amino acids |
|
|
Protein digestion is carried out by other proteins, which are _____ that cleave the substrate protein.
|
enzymes
|
|
|
Proteases/proteolytic enzymes
|
proteins hat cleave other proteins
|
|
|
proteasome
|
cellular garbage disposal
|
|
|
This enzyme attaches to a protein to label it for degradation by a proteasome
|
ubiquitin
many molecules of ubiquitin are attached to identify the trash protein as a target for breakdown |
