Exam 1 Flashcards
what is biochemistry
study of molecules of life and their chemical reactions in living systems
Cellular architecture falls into two categories
Prokaryotes
Eukaryotes
Prokaryote
single-celled
includes bacteria, eubacteria, archaea, and cyanobacteria
Eukaryote
Contain a well defined nucleus surrounded by a nuclear membrane
can be single celled or multicelled
Mosaic character
All living things make use of the same types of biomolecules, and use energy to make them. What is the result of this
all living things can be studies using the methods of biochemistry
What are the most common elements in the cell
Carbon
Oxygen
Hydrogen
Nitrogen
(phosphorus)
Biomolecules are ___ based
carbon
Covalent bonds
the glue that holds compounds together
C
carbon
CO
carbon monoxide
CO2
Carbon Dioxide
H2CO3
Carbonic Acid
product of CO2 and H2O
How many bonds does carbon make
4
How many bonds does H make
1
How many bonds does O make
2
How many bonds does S make
2
How many bonds does N make
3
How many bonds does P make
5
Chirality
Alpha carbon has 4 different groups attached
Large biomolecules are generally polymers of
simpler biomolecular units
monomers
Monomeric biomolecules
Nucleotide
Amino acid
Carbohydrate
Acetyl group
Biopolymers
Nucleic acids/DNA/RNA
Proteins
Polysaccharides
Lipids
Amino acids contain
an amino group
a carboxylic acid group
a side chain
Amino acids are the monomers of
Proteins
Carbs are a monomer of
Polysaccharides
Nucleotides are monomer of
Nucleic Acids
DNA
RNA
Acetyl group is monomer of
Lipids
ATP contains
Triphosphate
Ribose sugar
Nitrogen base-Adenine
A single monomer in a polymer is called a
residue
Functions of proteins
Major- Enable metabolic reactions
support cellular structures
Minor- store energy
Functions of Nucleic Acids
Major-encode information
Minor- enable metabolic reactions
support cellular structures
Functions of Polysaccharides and Lipids
Major- Store energy
Support cellular structures
Macromolecules
a molecule with a large number of atoms
Information is passed on from one molecule to another by
Sequence of DNA-> RNA->Protein->3D shape of protein molecule->Function of the proteins
Where do cells get their energy
Light from the sun
Photosynthetic organisms use light energy to make carbs
non-photosynthetic organisms consume these carbs
some archaebacteria us chemical or geothermal energy
Enthalpy
the heat content of a system
Entropy
a measure of the system’s disorder or randomness
Gibbs free energy
a measure of the free energy of a system based on enthalpy and entropy
Low entropy means
work is needed to organize
less likely to occur
higher in energy invested
High entropy
More likely to occur, favorable
lower in energy
Gibbs free energy equation
Change in G= Change in H- T times change in S
H=enthalpy
S=entropy
When change in G is less than 0 (negative)
the reaction is spontaneous or exergonic
When change in G is more than 0 (positive)
the reaction is nonspontaneous or endergonic
G less than 0 is
favorable
Reduction
gain of electrons
Oxidation
loss of electrons
The most essential nutritional component needed for life
water
Why is water important
the solvent for biological systems
to understand biochem it is essential to understand water and its interactions
Hydrophilic
water loving
examples of hydrophilic compounds
Polar
Ionic
Hydrophobic
water fearing
Examples of hydrophobic compounds
non-polar
oils and fats
water has what type of bonds
polar
In polar bonds,
electrons are unequally shared, more negative charge found closer to one atom (the more electronegative one. In water it is the Oxygen molecule)
Electronegativity
tendency of an atom to attract electrons
Covalent bond examples
Non-polar bonds-electrons are shared equally between atoms of the same electronegativity
Polar bonds-Electrons are Not shared equally between atoms of different electronegativity
amphipathic
polar on one end and non-polar on the other end
Ionic compounds readily dissolve in water because of the
ion-dipole interactions
Non-ionic compounds dissolve in water because of the
dipole-dipole interactions
Hydrogen bond
a dipole-dipole bond that exists between and electronegative atom and a hydrogen atom
A hydrogen bond is _____
non-covalent
weak bond, but strong with lots of them present
Strength of bonds from strongest to weakest
Covalent bonds
-OH
-HH
-CH
Non-covalent bonds
hydrogen bond
ion-dipole interactions
hydrophobic interaction
Van der Waals interactions
H bonds provide what to macromolecules while still being _____
Organization
weak enough to be readily broken
Which are longer- H bonds or covalent bonds
Hydrogen bonds (2) Longer
Covalent bond (1) Shorter
Acid
a molecule that behaves as a proton donor which occurs as a result of its ionization
Base
a proton acceptor
Strong acid
a compound that completely ionizes in aqueous solution
Weak acid
a compound that is incompletely ionized in aqueous solution
Water is a ____ acid and a ____ base
weak acid and weak base
Kw
the ionization constant of water
pH is
-log10[H+]
pH is what type of log scale
negative
Because the pH scale is logarithmic, a difference of one pH unit is equivalent to
a 10-fold difference in [H+]
Something more acidic on the pH scale has
more H+
Something more basic on the pH scale has
more OH-
Acid dissociation constant (Ka)
numerical value for the strength of an acid
[H+][A-] over [HA]
The larger the Ka value the
stronger the acid
pKa=
-log Ka
Buffer
a weak acid whose pH resists change upon addition of either more acid or more base
A buffer consists of
a weak acid and its conjugate base
How do buffers resist changes in pH
able to resist changes in free H+ by either binding H+ when an acid is added, or releasing H+ when a base is added
The maximum buffering capacity of a buffer is when
pKa is equal to the pH, the acid is 50% dissociated
[HA]=[A-]
If pH is below the pKa
more protons are on the acid
[HA]>[A-]
If the pH is above pKa
more protons are off the acid
[HA]<[A-]
The Henderson-Hasselbalch equation
pH=pKa + log of [A-] over [HA]
The Henderson-Hasselbalch equation tells us
if the concentration of [A-] is higher than [HA], the pH is higher than the pKa
if the concentration of [A-] is lower than [HA], the pH is lower than the pKa
A buffer is effective in a range of about
1 pH unit above or below the pKa of the weak acid
Principle buffer in cells
H2PO4-/HPO42-
Buffer in blood
H2CO3/HCO3-
Hyperventilation can result in
increased blood pH
Hypoventilation can result in
decreased blood pH
Carbon dioxide in water is
an acid
Carbonic acid
Amino acids are
building blocks of proteins
monomers of proteins
Most amino acids are _____
chiral
are L in proteins
What distinguishes one amino acids from another
R group
There are how many amino acids
20
10 essential
What is the only non-chiral amino acid
Glycine
has two hydrogens
Proline is really a ____ since it has a secondary amine
an imino acid
Classifications of amino acids
polar/non-polar
charged/uncharged
acidic/basic
aromatic (has a 6-carbon ring structure)
Non-polar amino acids
Ala
Val
Leu
Ile
Pro
Phe
Trp
Met
Neutral Polar Side chains
Ser
Thr
Tyr
Gys
Gln
Asn
Acidic Amino Acids
Asp
Glu
contain carboxyl groups
Basic amino acids
Lys
Arg
His
Amine groups
All amino acids have at least how many pKas
Two
Amino group of an amino acid pKa is
9.5
carboxylic acid group of an amino acid pKa is
2
when an amino acid is titrated
titration curve represents the reaction of each functional group with the hydroxide ion
Zwittrion
mid point where the amino acid is neutral
Many important biological reactions/functions depend on the
charge and acid/base properties of proteins
Essential amino acid
Phenylalanine
valine
tryptophan
threonine
isoleucine
methionine
histidine
arginine
lysine
leucine
Peptide bond
the special name given to the amide bond between the carboxyl group of one amino acid and the amino group of another amino acid
When a peptide bond is formed what is released
a water molecule
There is little rotation around the peptide bond because
it has partial double bond nature
peptide bonds are between the carbonyl carbon of the _____ and the N of the _____
N-terminal residue
C-terminal residue
Peptide
realatively short string of amino acid
polypeptide or protein
longer string of amino acids, often 100 or more
N-terminus
start, or left end, of a peptide or protein- free amiNo terminus
C-terminus
end, or right end, of peptide or protein- free Carboxyl terminus
Side chains of amino acids contribute most to
localized charges on proteins
What is the 3-D structure of a protein
the final form of a polypeptide chain
Why is 3-D structure important
form determines function
Why is it important to understand ho a protein is formed
understanding protein structure allows for understanding of biological processes
The final structure of a protein is determined by
the amino acid sequence of the protein
Primary structure of a protein
the amino acid sequence of the protein
Secondary structure of a protein
the localized arrangement in space of the peptide backbone of a protein
Tertiary structure of a protein
final 3-D arrangement of all the amino acids
Quaternary structure of protein
arrangement of separate peptide chains with each other to form an active protein (enzyme)
The peptide bond is rigid and does not rotate giving the peptide bond a ____
planar configuration
Two main types of secondary protein structure
alpha-helix
beta-sheet
alpha helix
polypeptide chain is twisted by the same angle about each of its C atoms
The C=O group of one residue will ____ with the N-H group of the 4th amino acid
H-bond
Amphipathic helix
polar on one side, non-polar on the other
common in transmembrane proteins
what can disrupt the alpha helix
proline
cyclic structure does not allow for rotation of the angle
N in the imino group cannot H bond
terminates the alpha-helix
Beta sheet
sheet is a straight extension of the polypeptide backbone
H-bonding occurs between neighboring polypeptide chains
Beta sheets can be
Parallel or Anti-Parallel
Parallel
both polypeptide chains run in the same direction
Antiparalled
polypeptide chains run in opposite directions with respect to N and C terminus
Tertiary structure of proteins
the 3-D arrangement of a protein
the folding of regions of secondary structure
is stabilized by interactions such as H-bonding and disulfide bonds
Proteins fall into two categories
Globular or Fibrous
Globular proteins
folding of the peptide backbone to form a spherical shape
most proteins are globular
water soluble
shape allows for amino acids that are far apart in primary structure to be close in tertiary structure
Myoglobin
primary oxygen storage protein in the muscle tissue
Heme group
a cyclic organic ring containing iron
porphyrin
a heme group without Fe
Quaternary structure
the structure associated with the interaction of multiple polypeptide chains
individual polypeptides are termed
subunits
1 sub unit
monomer
2 sub unit
dimer
3 sub unit
trimer
Example of Quaternary structure
Hemoglobin
oxygen transport in the blood, compared to storage of myoglobin
Positive cooperativity
when O2 molecule is bound it is easier for the next to be bound. Changes in subunit interactions increases affinity for the next O2
Allosteric
changes in one region affect another region
O2 binding curve of myoglobin
hyperbolic
O2 binding curve of hemoglobin
sigmoidal due to cooperativity
The Bohr Effect
As the pH goes down, O2 affinity for hemoglobin decreases
activity respiring cells create acid, this increases the release of O2 from hemoglobin to these cells
Sickle Cell Anemia
Mutation of a particular Glutamate to Valine occurs
causes RBC to become oblong in shape
Polymers of actins are called
microfilaments
Fibrous proteins
highly elongated proteins with secondary structure as dominant structure
Two types of fibrous proteins
alpha helix
beta sheet
Keratin
durable, chemically resistant protein
found in higher vertebrates, hair, wool, horn, nails, hooves
All the information needed to correctly fold a protein is contained in the
one prime sequence
Hydrophobic interactions
hydrophobic regions of proteins tend to aggregate and dispel water as with membranes.
inner portion of globular proteins
Salt (electrostatic) interactions
attractive forces between opposite charges (+ and - charges in R groups, N or C terminus, or metal ligands)
acidic amino acids are attracted to basic amino acids
disulfide bonds
bonds between sulfurs of two different cysteines
Forces involved in protein folding
hydrophobic interactions
salt (electrostatic) interactions
hydrogen bonds
disulfide bonds
Folding in proteins occurs so that
nonpolar hydrophobic side chains tend to be on the inside
polar side chains are on the outside and have access to the aqueous environment
Liposomes
spherical aggregates of lipids arranged so the polar head groups are in contact with water and nonpolar tails are hidden form water
Two layers of a globular protein
hydrophilic surface
hydrophobic core
Misfolding of proteins plays an important part in neurodegenerative diseases
alzheimer’s disease
parkinson’s disease
“Prion Diseases” (Mad cow, etc.)
APP
amyloid precursor protein
in Alzheimer’s disease it is incorrectly clipped by enzymes, aggregated peptide accumulates over decades, killing neurons
PrP
Prion protein
in prion diseases the infectious agent
Ways to increase the rate of chemical reactions
increasing the temperature
increasing the concentrations of the reacting substances
adding a catalyst
What is the fastest way to increase the rate of chemical reactions
adding a catalyst
Enzyme
a biological catalyst
Catalyst
something that speeds up a reaction without being used up (changed)
Enzymes are considered
proteins
Enzymes can increase the rate of a reaction by a factor of
10 to the 20th power
Most enzymes are proteins but a few are made of
RNA (ribozymes)
Enzymes contains a specific fraction of the structure where reactions take place, this is called
the active site
Most enzymes work in what type of conditions
mild
Many chemical enzymes require
extremely high temperatures and pressures for optimal performance
Activity of many enzymes are
regulated so that the organism can respond to changing conditions or follow genetically determined programs
Enzymes selectively recognize proper substrates over
other molecules
Specificity of enzymes is controlled by
enzyme structure
the unique fit of substrate with the enzyme controls the selectivity for substrate and the product yield
Functional groups on the active site can
distinguish its substrates from among many others that are similar in size and shape
Reactions that have an energy barrier to overcome called the
activation energy or G degree ++
Energy states differ between reactants and products this difference gives us
the energy change for that reaction termed the Gibbs standard free energy change or delta G degree
Activation energy requires
an energy input to start a reaction
Enzymes do what to the activation energy
lowering it
making the reaction more likely to happen and more favorable
they stabilize the transition state of the reaction
A reaction is spontaneous if
Delta G degree is negative
Delta G degree doesn’t say… and cannot…
anything about how fast the reaction will proceed
be altered by a catalyst
Delta G degree is negative, reaction is
spontaneous
Delta G degree is positive, reaction
requires external energy input and is not spontaneous
The rate of reaction depends on
its activation energy
Spontaneous
characteristic of a reaction or process with a negative free energy change
For an enzyme-catalyzed reaction, what must bind to the enzyme
substrate
The substrate fits in a special pocket of the enzyme called the
active site, where the reaction occurs
Binding of substrates to the active site is usually
non-covalent and reversible
Non covalent means
H-bonds, ionic bonds, hydrophobic and van der Waals contacts
Two models to describe the formation of the enzyme-substrate complex
Lock and key
induced fit
Lock and key model
substrate binds to that portion of the enzyme with a complementary shape
Induced fit model
binding of the substrate induces a change in the conformation of the enzyme that results in a complementary fit
Seven major classifications of enzymes
Oxidoreductasis
transferases
hydrolases
lyases
isomerases
ligases
translocases
Oxidoreductases
enzymes in oxidation-reduction reactions
transferases
enzymes in transfer of functional groups
hydrolases
enzymes in hydrolysis reactions
lyases
enzymes in group elimination to form double bonds
isomerases
enzymes in isomerization reactions (change the shape of something)
Ligases
Enzymes in bond formation coupled with ATP hydrolysis
Translocases
Enzymes in solute transport through the membrane
Many enzymes are named
after the reaction they catalyze
Enzymes often use _____ to aid in catalysis
cofactors
Two categories of cofactors used by enzymes
metal ions
coenzymes- further cut into cosubstrates and prosthetic groups
Coenzymes are derived from
vitamins
Three kinds of chemical catalytic mechanisms used by enzymes
Acid-base catalysis
Covalent catalysis
Metal ion catalysis
Acid base catalysis
a proton is transferred between the enzyme and the substrate
Covalent catalysis
a covalent bond forms between the catalyst and the substrate during formation of the transition state
Metal ion catalysis
metal ions mediate oxidation-reduction reactions or promote the reactivity of other groups in the enzyme’s active site through electrostatic effects
Amino acids that can be ____ play a role in acid-base catalysis
ionized
Amino acids that act as covalent catalysts
Ser, Tyr
Cys
Lys
His
Nucleophile
Nucleus seeking atom
slight negative charge
attacks positive charges
Electrophile
electron seeking atom
has slight positive charge
Catalytic triad
hydrogen-bonded arrangement of the Asp, His, and Ser residues of chymotrypsin and other serine proteases
How does the catalytic triad of chymotrypsin work?
Hydrogen-bonded arrangement of Asp, His, and Ser residues
bond cleaved by hydrolysis is between the Ser when the substrate binds to the enzyme
His acts as a base catalysts and abstracts a proton from Ser so the oxygen can act as a covalent catalyst
Asp stabilizes
Specifity pocket
a cavity on the enzyme surface at the active site that accommodates the residue on the N-terminal side of the scissile peptide bond
Rates are measured in
units product produced or substrate consumed per time period
Unimolecular reaction has a
velocity (rate) that is dependent on the concentration of only one substrate
Biomolecular reaction has a
velocity (rate) that is dependent on two substrate concentrations
Km is the
concentration of substrate at which half of the enzyme’s active sites are bound to substrate
Km measures the
affinity of the enzyme for the substrate
High Km means
low substrate affinity
Low Km means
high substrate affinity
