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BIOL 213: EXAM 1
Why study cell and molecular biology? |
-cells are the fundamental unit of life
-all cells have similar chemistry (allows mechanistic understanding of cellular function and dysfunction) |
1st two tenets of Cell Theory proposed by |
Schleiden and Schwann |
third tenet of cell theory added by |
Louis Pasteur |
cell theory |
1. All organisms are composed of one or more cells
2. the cell is the smallest unit of life
3. cells can only arise by division from a pre-existing cell
|
Features common to all cells |
-complex and highly organized
-DNA- genetic program for reproduction
-plasma membrane- selective barrier
-cytosol/cytoplasm
-ribosomes- protein synthesis
-respond to stimuli and adapt to their environment
-small |
two classes of cells (three evolutionary lineages) |
-prokaryotic- relatively simple, no nucleus
---bacteria and archaea
-eukaryotic- more complex, nucleus and other organelles
---animals, plants, fungi, protists |
eukaryotic cells contain _____ organelles |
membrane enclosed |
why is biological chemistry important?
|
an understanding of the structures, properties and quantities of molecules associated with cells is essential to understanding biological function at any level |
why are moles important
|
atoms and molecules are very small so a scale factor is generally used to describe quantities (mole) |
one mole is ____ individuals
|
6 x 10^23 (avogadro's number) |
types of strong chemical bonds |
covalent and ionic |
types of weak chemical bonds |
hydrogen, hydrophobic interactions, Van der Waals Attractions |
covalent bond |
sharing of electrons |
ionic bond
|
transfer of electrons |
Which type of bond is affected by water? why?
|
ionic; weaker, can be pulled apart by polar water molecules |
hydrogen bond |
electrostatic interaction between a H held in a polar covalent bond and another atom (usually O or N) also held in polar covalent bond |
Hydrophobic interactions |
"water fearing" attraction between nonpolar molecules cause by repulsion from water. (phospholipid bilayer in cells)
|
double bond (covalent) |
cannot rotate freely around the bond axis. This restriction has a major influence on the three-dimensional shape of many macromolecules |
an ionic bond can be considered
|
a very polar covalent bond |
van der Waals Attractions |
weak interaction caused by transient electrical charges, dependent on the distance between atoms
-in large numbers can be significant in the attraction between macromolecular surfaces |
-OH group is called a |
hydroxyl group |
C=O group is called a |
carbonyl group |
-COOH is called |
a carboxyl group |
hydrophilic |
water loving |
hydrophobic |
water hating |
The acidity of a solution is defined by |
the concentration of H+ ions it possesses. |
pH= |
-log[H+] |
is a solution of pH 4 more acidic or alkaline than a solution of pH 6 |
more acidic; by 100 fold |
acid |
any molecule capable of releasing (donating) a hydrogen ion (proton) |
strong acids vs. weak acids |
strong acids lose their protons quickly |
base |
any molecule capable of accepting a hydrogen ion (proton) |
strong bases vs. weak bases |
strong bases dissociate readily in water
|
buffers |
weak acids and bases that can release or take up protons near pH 7, keeping the environment of the cell relatively constant under a variety of conditions.
-consists of a mixture of a weak acid and its conjugate base, or a weak base and its conjugate acid |
why are many of the acids and bases important in the cell weak? |
partial dissociation, reversible |
methyl |
-CH3 (nonpolor hydrocarbon) |
hydroxyl |
-OH (alcohol) |
carboxyl |
-COOH (weak acid) |
carbonyl (ketone and aldehyde) |
C=O |
Amino |
-NH2 (weak base) |
Amide |
O=C-NH2 (carbonyl + amine) |
Phosphate |
PO3 (ester and anhydrides) |
Sulfhydryl |
-SH (forms disulfide bonds) |
cells consist of 70% water, and 30% chemicals such as |
ions, small molecules (4%)
phospholipids (2%)
DNA (1%)
RNA (6%)
proteins (15%)
polysaccharides (2%) |
most sugars have the same general formulas (CH2O)n hence the name carbohydrate: |
most sugars have 3-7 carbons, with 6 carbon sugars (hexoses) being especially important. |
polysaccharides function as |
stores of chemical energy and durable biological structural materials |
Glucose- two ring conformations
|
alpha and Beta |
monosaccharides are formed into polysaccharides by |
condensation reaction (gives off water) |
polysaccharides broken up by |
hydrolysis (consumes water) |
cells contain four major families of organic molecules |
sugars, fatty acids, amino acids, nucleotides |
sets of molecules with the same chemical formula but different structures are called
|
isomers |
mirror-image pairs of molecules are called |
optical isomers |
monosaccharides can be linked by covalent bonds called |
glycosidic bonds |
sucrose |
glucose + fructose |
prefix oligo- |
macromolecules made of a small number of monomers (3-50) |
polymers
|
contain hundreds or thousands of subunits |
glucose has a central role as |
an energy source for cells |
fatty acids and lipids ____ in water |
insoluble |
lipids or fats are not really ______ but are ______ |
not really polymers of fatty acids, but are formed by condensation reactions. |
Functions of fatty acids and lipids |
structural: cell membranes
Energy Storage: triacylglycerols |
fatty acids |
long, unbranched hydrocarbon chains with a single carboxyl group on the end |
Amphipathic molecule |
hydrophilic end (carboxyl) and hydrophobic end (hydrocarbon) |
fatty acids typically have ____ number of carbons
|
an even (14-20) number of carbons |
carbon #1 in fatty acid associated with |
carboxylic group |
saturated tails |
no double bonds between its carbon atoms and contains maximum possible number of hydrogens |
unsaturated tails |
one or more double bonds along their length
|
micelle |
formed by fatty acids in water; spherical
e.g. triacylglycerols in cytoplasm |
monolayer |
formed at surface of water by fatty acids
-phospholipids and glycolipids form self-sealing lipid bilayers that are the basis for all cellular membranes |
fatty acids are stored as |
an energy reserve through an ester linkage to glycerol to form triacylglycerol (fat) |
what determines the properties of fat? |
the chain length and level of saturation |
phospholipid |
glycerol + 2 fatty acids + phosphate group linked to another hydrophilic molecule |
triacylglycerols vs. phospholipids (in water) |
triacylglycerols are predominately hydrophobic; phospholipids are strongly amphipathic |
proteins are |
polymers of amino acids
-formed by condensation reactions |
functions of proteins |
-enzymatic
-signaling
-structural |
peptide bonds formed by |
condensation reactions that link one amino acid to the next |
functionality of proteins derives from |
side groups:
-acidic or basic
-polar or nonpolar
-other features |
amino acid side chains (R groups) |
-profound influence on structure/function of proteins |
side chains (R groups) classified as |
-charged (acidic, basic)
-uncharged polar (hydrophilic)
-nonpolar (hydrophobic) |
pyrimidines |
Cytosine, Thymine, Uracil (5 membered ring) |
Purines |
Adenine, Guanine (6 membered ring + 5 membered ring) |
nucleotide |
base + pentose + phosphate |
nucleic acids are polymers of |
nucleotides (formed by condensation reactions) |
functions of nucleic acids |
-storage and transmission (expression) of genetic information
-nucleotides also function as energy carriers and as signaling molecules |
nucleotides are joined together by |
a phosphodiester linkage to form nucleic acids. condensation reaction |
nucleic acids have structural polarity: |
the 5' end has a free phosphate group, the 3' end has a free hydroxyl group |
central dogma of biology |
replication--> transcription -->translation |
sequence defines.... which defines.... |
structure; function |
noncovalent bonds specify |
structure and intramolecular interactions |
pyrimidines |
Cytosine, Thymine, Uracil (5 membered ring) |
Purines
|
Adenine, Guanine (6 membered ring + 5 membered ring) |
nucleotide |
base + pentose + phosphate |
nucleic acids are polymers of |
nucleotides (formed by condensation reactions) |
functions of nucleic acids |
-storage and transmission (expression) of genetic information
-nucleotides also function as energy carriers and as signaling molecules |
nucleotides are joined together by |
a phosphodiester linkage to form nucleic acids. condensation reaction |
nucleic acids have structural polarity: |
the 5' end has a free phosphate group, the 3' end has a free hydroxyl group |
central dogma of biology |
replication--> transcription -->translation |
sequence defines.... which defines.... |
structure; function |
noncovalent bonds specify |
structure and intramolecular interactions |
First law of Thermodynamics |
energy cannot be created or destroyed, but it can be converted from one form to another |
Second law of thermodynamics |
energy spontaneously tends to disperse |
entropy is |
dispersal of energy |
cells use energy to |
create and maintain order |
molecules of a living cells possess energy because
|
of their vibrations, rotations, and movement through space, and because of the energy that is stored in the bonds between individual atoms.
|
the free energy, G, measures |
the energy of a molecule that could in principle be used to do useful work at constant temperature (as in a living cell) |
energetically favorable reactions have
|
a negative delta G |
delta G depends of |
the energy stored in chemical bonds and also on the concentration of the molecules in a reaction |
delta G = |
delta G* + RTln [products]/[reactants] |
delta G*, the standard free energy, reflects |
the intrinsic energy stored in bonds and is defined under standard conditions (25* C; 1 atm; 1 M concentration; pH7) |
at equilibrium, the forward and reverse ____ for a reaction are equal, but not necessarily the ____ |
rates; concentrations |
Keq= |
[AB]/[A][B] |
the greater the value for Keq, the |
more negative delta G*
|
delta G* and Keq values can be used to predict: |
1. ratio of reactants to products at steady state
2. direction of reactions |
2 different ways to couple reaction |
sequential "siphon" and activated carrier (ATP) |
activated carriers store energy in the form of... |
a transferable chemical group or as high-energy electrons |
NAD and NADP are electron carriers that |
facilitate oxidations and reductions |
Where do cells get the energy required to create and maintain order? |
environment:
-light (electromagnetic energy)
-food (chemical bond energy) |
Cells obtain energy from |
the oxidation of organic molecules |
oxidation |
loss of electron |
reduction |
gain of electron |
electron transfer often also involves |
a proton |
Hydrogenation |
reduction |
Dehydrogenation |
oxidation |
Reduced organic compounds yield
|
more energy (electrons) for chemical work: fats>sugars |
enzymes increase the rate of reactions by |
reducing the activation energy |
KM |
the Michaelis' constant Intrinsic value; ability to 'grasp' substrate |
competitive inhibition |
interferes with active site of enzyme so substrate cannot bind |
noncompetitive inhibitor |
changes shape of enzyme so it cannot bind to substrate |
enzyme regulation- allosteric effects |
-more than one binding site
-binding of one ligand alters protein conformation, which changes activity
-can be positive or negative |
feedback inhibition |
inhibited when accumulated to certain level; provides balance |
conformational changes with nucleotide hydrolysis can be used to |
drive a motor protein
(muscle contraction, chromosome spindles, organelle movement)
|
primary structure |
amino acid sequence
-joined through condensation reactions to form peptide bonds
|
unstable folding leads to |
degradations or aggregation |
protein folding constrained by the formation of
|
many weak noncovalent bonds |
protein folding in a cells is often assisted by
|
molecular chaperones, or chaperonins |
secondary structure |
alpha helix and beta sheet
-stabilized by H bonds forming between the amino and carbonyl groups in the polypeptide backbone
|
alpha helix |
the carbonyl group of one peptide bond is H bonded to the amino group of a peptide bond four amino acids away. |
alpha helix can span a membrane bilayer |
shielded from the hydrophobic lipid hydrocarbons (stable H bonding)
|
B sheet ligand |
the polypeptide strands are extended, giving the backbone a pleated shape. These strands associate through hydrogen bonding between peptide bonds in different strands |
Tertiary structure |
the conformation formed by an entire polypeptide including alpha helixes, beta sheets, other loops and folds |
ligand
|
anything that binds with a protein |
Quaternary Structure |
complex of more than one polypeptide |
extracellular proteins are often stabilized by |
covalent cross-linkages: disulfide bonds (Cystine)
these bonds do not change the conformation of a protein, just stabilize |