Exam 2 Flashcards
what is the monomer of a protein?
amino acid
what is the structure of an amino acid
amine group (NH2), carboxyl group (COOH), an R group, all bonded to a central (alpha) carbon
All proteins are built from _____ amino acids
20
how many neutral AA?
15
why are side chains so important?
they enable proteins to perform their functions
are nonpolar side chains hydrophobic or hydrophilic?
hydrophobic, gather into clusters (oil and water)
are polar, basic, and acidic side chains hydrophobic or hydrophilic?
hydrophilic, surface of folded proteins impart water solubility of proteins
how many AA are chiral?
19
which AA is achiral?
glycine
what is the only secondary amine?
proline
what is the importance of intermolecular forces of proteins?
important in determining interactions between amino acids
what are the 4 different intermolecular forces in order from strongest to weakest?
- ionic + covalent bonds
- hydrogen bonds
- dipole-dipole forces (disulfide bond)
- van der waals forces
explain a hydrogen bond b/w AAs
side chains can form hydrogen bonds, connecting different parts of a protein molecule
explain van der waals forces
the overall charge of the molecules brings them together (weak)
explain hydrophobic interactions of AA
hydrophobic (nonpolar) molecules come together and expel the water between them
explain a disulfide bond
creates a covalent bond b/w sulfurs
what is a peptide bond?
an amide bond that links 2 AA together, PLANAR, releases a water molecule
how do you name peptides?
citing AA residues in order
define zitterion
a neutral dipolar ion that has one pos charge and one neg charge
amino acid net charge
0, NH3 is + and COOH is - so cancels = 0
define isoelectric point (pi)
describes the ph at which a sample of an amino acid has an equal number of + and - charges
(AA each have their own pi due to the side chain)
how many essential AA are there?
9
what are essential AA?
amino acids that the human body cannot produce, must be consumed in the diet
define metabolism
chemical reactions maintaining living state
define catabolism
breakdown of molecules to form energy
define anabolism
synthesis of compounds needed by cells
define a primary structure
sequence of AA in a protein chain (order of the AA)
be able to label a primary structure (protein backbone, peptide bonds, and side chains
check notes
why is the primary structure important?
primary function is crucial to the function of the protein that the change of even one AA can drastically alter a proteins biological properties
define secondary protein structure
spatial arrangement of the polypeptide backbones determines the secondary protein structure
what does the alpha helix of the secondary protein structure look like?
coil, stabilized by h bonds along the backbone with r groups positioned on the Purdue of the helix, carbonyl group + amide
what does the beta sheet of the secondary protein structure look like?
flat sheet-like structure, adjacent protein chains held together by h bonds along the backbones
parallel beta sheet
peptide chains in same direction
anti parallel beta sheet
turned around/ladder
2 classes of proteins from the secondary structure
- fibrous (tough, insoluble)
- globular (globe shape, water soluble)
examples of fibrous proteins
wool, hair, fingernails
examples of globular proteins
alcohol dehydrogenase, serum albumin
what is collagen?
secondary structure protein, found in skin, cartilage, blood vessels, bone
–> left handed alpha helix
what disease is associated with collagen?
scurvy, lack of vitamin C causing alpha helix to destabilize
define tertiary protein structure
the way an entire protein chain is coiled and folded into its specific 3D shape (determined by primary structure)
define native protein
a protein with the shape in which it functions in living systems
define simple protein
composed of only AA residues
what are simple proteins?
they can function alone
what are conjugated proteins?
aided by a non-amino acid unit
define quaternary protein structure
the way in which two or more protein chains aggregate to form large, ordered structures
what is hemoglobin?
a protein in a quaternary structure composed of 4 polypeptide chains held together by hydrophobic interactions and 4 heme groups (function: carries O2 around the body and CO2 out of the body)
what is protein hydrolysis?
breaking down proteins, peptide bonds hydrolyzed to yield AA (proteases can do this)
what is chymotrypsin’s function?
hydrolyzes a peptide bond on the carboxyl-terminal side of aromatic AA
what is trypsin’s function?
hydrolyzes peptide bonds on the carboxyl side of lysine and arginine
what is the n-terminal of a peptide?
the AA on the end (left) with amine group on the end
what is the c-terminal of a peptide?
the AA on the end (right) with the carboxyl group on the end
define denaturation
loss of the secondary, tertiary, and quaternary protein structure
agents that cause denaturation
- heat
- mechanical agitation
- detergents
- organic compounds
- ph change
- inorganic salts
what is the connection between protein misfolding and neurodegeneration?
neurodegeneration is often attributed to proteins that are not folded the correct way
what are some causes of protein misfolding/neurodegeneration?
- head trauma
- genetic mutation
- age
what are amyloid fibrils?
stable protein aggregates that form under certain conditions, makes long, stiff fibers of proteins that cause damage to cells and leads to neurodegeneration
what causes Alzheimers?
brain tissue formed from the amyloid B peptides
how to prevent Alzheimers?
- diet/eating healthy
- exercise
- low doses of aspirin
define enzymes
a special class of proteins that act as a catalyst for a biological reaction
What is an enzymatic unit?
the time it takes for an enzyme to perform a task
(number of molecules changed from reactant to product per unit of time)
How are enzymes named?
most end with -ase
How are enzymes catalysts?
- lowers the energy barrier for a reaction
- gives direction to a biochemical reaction
Can enzymes be reused?
yes
explain specificity with enzymes
the limitation of the activity of an enzyme to a specific substrate or type of reaction
- structure of enzyme
- specific to chiral centers
- relates to rate
What is a turnover number?
- measures catabolic activity
- the max number of substate molecules acted upon
- (per enzyme unit time)
define active site
pocket with a specific shape and chemical makeup necessary to bind a substrate
define substrate
a reactant in an enzyme (catalyzed reaction)
How enzymes work, 4 steps written out?
E + S –> ES –> EP –> E +P
- E=enzyme
- S=substrate
- P=product
Why are cofactors needed?
the functional groups of proteins are limited to those of the AA side chains, so by combining with cofactors enzymes gain chemically reactive groups that are not available as side chains
What are cofactors?
METALS
- get from the diet
- bind to the enzyme
- ex: Cu2+, Fe2+, etc.
What are coenzymes?
organic molecules
- NOT BOUND
- ex: NAD
How are vitamins and coenzymes related?
vitamins help to build/synthesize coenzymes
4 major factors affecting enzyme activity
- substrate concentration
- enzyme concentration
- temperature
- ph
How does substrate concentration affect enzyme activity?
- more substrates = higher rate
- less substrates = lower rate
- there is a maximum
(exponential)
How does enzyme concentration affect enzyme activity?
more enzymes in a given volume, the quicker the rate will be
(linear)
How does temperature affect enzyme activity?
- max is when it reaches the optimal temperature
- too hot, will denature
(bell curve)
How does pH affect enzyme activity?
- enzymes vary on optimal ph
- (most enzymes max activity at about 5-)
- most enzymes will denature in extreme ph
(multiple bell curves dependent on enzyme)
6 main classes of enzymes
- oxidoreductases
- transferases
- hydrolyses
- isomerases
- lyases
- ligases
function of oxidoreductases
- oxidoses –> oxidation of O2 to substrate
- reductases –> reduction of a substrate
- require coenzymes
EXAMPLE: NAD –> NADH
function of transferases
- catalyze transfer of a group from one molecule to another
EXAMPLE: ATP –> ADP + PO3^2-
function of hydrolases
- breaking down (lipases, proteases, amylases, etc)
- important in digestion
EXAMPLE: polypeptide chain –> AA
function of isomerases
- rearrange the bond placement (change chirality)
EXAMPLE: A –> B
function of lyases
- addition of simple organic groups (H2O, CO2, NH3) yo a double bond
- no energy required
function of ligases
- addition (bonding 2 substrates)
- NEED ENERGY
- proteins and DNA formed
enzymes act as catalysts because of:
- proximity
- orientation
- catalytic effect
- energy effect
- rate of reaction
what are the 2 theories on how a substate fits into an active site?
- lock and key model
- induced fit model
what is the lock and key model?
- a substrate will only fit into an enzyme with the correct shape
- flaw = assumes enzymes are static
what is the induced fit model?
- enzyme changes shape as substrate fits into active site
is the lock and key model or induced fit model more accurate for how an enzyme fits into an active site?
induced fit model because it accounts for the enzyme moving
3 general enzyme regulators
- activation
- inhibition
- feedback and allosteric control
define an enzyme regulator: activation
any process that starts or increases the action of an enzyme
define an enzyme regulator: inhibition
any process the slows or stops the action of an enzyme
define an enzyme regulator: feedback control
regulation of an enzymes activity by the product of a reaction later in the pathway
- negative feedback = stops reaction
- positive feedback = continues reaction
what is negative feedback?
the product at the end of the pathway stops the reaction
what is positive feedback?
the product at the end of the pathway continues the reaction
define an enzyme regulator: allosteric control
product binds to enzyme in a place separate from the active site and changes shape of the enzyme/active site
- negative = substrate cannot bind
- positive = substrate can now bind
