Biochemistry Flashcards
_______________
- fundamental subunit of polypeptides/proteins
Amino acid
(AA)
There are ____ amino acids that are coded for by the DNA & there are ____ essential amino acids and ____ nonessential amino acids
20
9
11
Amino Acid Structure includes :
____________ bonded to a hydrogen
____________ group
____________ group
____________ group
Central a-carbon bonded to a hydrogen
Amine group (-NH2)
Carboxyl group (-COOH)
Variable functional group (R-group)
All amino acids are chiral except ____________
Glycine
_______________
- 4 different distinct groups bound to an α-Carbon resulting in non-superimposable mirror-images
- a form of isomer with different configuration around a chiral center (forms 2 isomers)
Enantiomers
Amino acids form __________ at low pH
Amino acids form __________ at high pH
Amino acids form __________ at intermediate pH
Cations
Anions
Neutral zwitterions (contains both positive and negative electrical charges, but the net charge on the molecule is zero COO- & NH3+)
R-group chemical properties :
____________ - aliphatic or aromatic
____________ - pH neutral, acidic, alkaline, 3 with sulfur, or selenium
Non-polar
Polar
____________
- amino acids form peptide bonds by dehydration synthesis between the amino group of 1 amino acid & the carboxyl group of another amino acid
Polypeptide synthesis
Polypeptide synthesis is facilitated by ribosomes during ____________ of mRNA
translation
Proteins are composed of 1 or more long ____________ molecules
polypeptide
Other bonds formed in the synthesis & activation of proteins include __________ linkages between cysteine R-groups and __________ bonds between polar R-groups
Disulfide linkages
Hydrogen Bonds
In protein digestion, the protease or peptidase enzymes break peptide bonds via ____________
Hydrolysis
____________ structure
- actual sequence of amino acids in the protein due to peptide bonds
Primary structure
____________ structure
- 2 common configurations
- a-helix & B-pleated sheet are due to Hydrogen bonds between amine hydrogens and carbonyl oxygen of amino acids
- especially prevalent in fibrous structural proteins
Secondary structure
____________ structure
- 3D shape of entire polypeptide due to interaction among hydrophobic R-groups & hydrophilic R-groups, hydrogen bonds, ionic bonds, & disulfide bridges between cysteine R-groups
Tertiary structure
Structural proteins usually have ________ tertiary structures
Fibrous
Enzymes usually have ________ tertiary structures
Globular
____________ structures
- 2 or more polypeptides combine to form a functional protein or incorporation of ligands
- ex : Fe containing heme groups of hemoglobin
Quaternary structures
Long sequences of (non-polar OR polar) amino acids are found in membrane-bound proteins or membrane-embedded proteins & attach protein to lipid bilayer or folded into the interior to stabilize the 3D structure of proteins dissolved in water
Non-polar
____________
- disruption of protein/polypeptide folding & activity by changes in pH, Temperature, or presence of hydrophobic solvents
Denaturation
____________
- correct refolding of denatured protein
Renaturation
____________
- dissolved proteins are surrounded by water molecules oriented according to the charges of the amino acids in that particular surface of the folded protein
- have properties key to binding of substrates to protein active sites
Solvation layer
____________
- proteins are forced by electric current to pass through a medium that sorts molecules by size, charge, and/or other chemical properties
Electrophoresis
__________________
- proteins have unique combinations of R-groups charged positive or negative
- at a specific pH then a particular protein acquires neutral charge (therefore stops moving due to no electromagnetic field force)
- proteins then separated along a pH gradient gel with cathode & anode charges at either end
Isoelectric focusing
____________ chromatography
- mixtures of proteins dissolved in a solvent pass by gravity or under pressure through a medium that binds with varied affinity to substances in the mixture
- more soluble (lower binding affinity) molecules pass through the column fastest & others lag behind so each can be collected as it passes through the column
Column chromatography
_________________
- different molecules’ mass-to-charge ratios detected by bombarding them with beams of electrons
- magnetic field separates charged molecules by mass & charge
Mass spectrometry
X-ray crystallography & computer modeling can help determine _______________
3D protein folding
True or False
Protein function is due to conformational strength, stability, & binding specificity
True
Functions of ___________
- enzymes, providing structure, facilitating movement, transport, or storage of substances & communication
- membrane bound, dissolved, or suspended in organelles or cytosol or are secreted out of cells
proteins
____________ proteins
- collagen (cartilage, bone, tendon)
- keratin (nails, hair, horn)
- histones (DNA supercoiling)
- cytoskeleton
- bacterial/fungal cell walls
Structural
____________
- catalysts of biochemical reactions
- suffix : -ase
Enzymes
Proteins that help facilitate ____________
- muscle function (actin, myosin, tropomyosin)
- kinesins
- flagella
- cilia
Movement
__________ & _________ proteins
- membrane pumps
- membrane channels
- hemoglobin
- myoglobin
Transport & Storage proteins
___________ & __________ proteins
- peptide hormones (insulin, adrenalin)
- neurotransmitters
- antigens (surface markers)
- antibodies (target non-self antigens)
Communication & Identification proteins
____________
- proteins that catalyze biochemical reactions
- production, activation, & regulation determine the complex biochemical dynamics in living organisms
- not reactants & can catalyze the same reaction repeatedly
- highly substrate specific & enzymes specificity includes stereochemistry
- do not influence the thermodynamics (just kinetic reaction rate)
Enzymes
Energy consumed in ____________ enzyme catalyzed reactions are usually obtained when the enzyme activity is coupled with the __________ catalysis of the reaction ATP –> ADP + Pi
endergonic
exergonic
Enzyme-catalyzed reactions are linked sequentially to form ________________
Biochemical pathways
____________
- series of gradual chemical changes in a reactant to form a particular product
Biochemical pathways
____________
- biochemical reactions/pathways break down complex molecules into simpler molecules or release potential chemical energy stored in chemical bonds
- associated with digestion, hydrolysis, oxidation, & exergonic processes
Catabolism
____________
- biochemical reactions/pathways that synthesize complex macromolecules from simpler subunits and/or form bonds that help store chemical energy
- associated with polymerization, dehydration synthesis, reduction, & endergonic processes
Anabolism
____________ reactions
- anabolic reactions & catabolic reactions together
- dephosphorylation of PEP –> pyruvate coupled with substrate-level phosphorylation of ADP to ATP in glycolysis
Coupled reactions
__________ bond with substrates (reactants) at substrate-specific active sites
Enzymes
____________
- change conformation to form enzyme-substrate complex (lowers the activation energy of reactions that create or break substrate bonds by several ways)
Induced fit
The ____________ lowers activation energy of reactions that create or break substrate bonds by :
- conformationally straining bonds so they break more readily
- placing substrates together in an orientation that causes a chemical reaction
- creating an active site microenvironment that induces a reaction
- forming temporary bonds with the substrate as a step toward formation of the product
enzyme-substrate complex
True of false:
Enzymes function within a limited optimal range of temperature & pH conditions
True
Apoenzymes may require cofactors (metal ions or organic molecules) to become activated ____________
Holoenzymes
Cofactors that are permanently incorporated into the enzyme are called _____________
Prosthetic groups
Cofactors that are temporarily bind to enzymes are called ____________
Coenzymes
(ATP, NAD+, coenzyme A)
Enzyme catalysis involves 2 steps:
1.
2.
- Binding of enzyme to substrate to form E-S complex
- formation of product
The ______________________ (aka the Km value) is the substrate concentration
at which the reaction rate
is half of the maximum rate & it is a measure of how well an enzyme binds to its substrate
Michaelis-Menten constant
A (low OR high) Km = high affinity for enzyme to substrate & low rate of catalysis
Low Km
A (low OR high) Km = low enzyme-substrate affinity & high rate of catalysis
High Km
True or false:
The rate of an enzyme reaction or non-enzyme protein binding (antigen/antibody) is a function of substrate concentration [S], Km value, & maximum catalysis rate Vmax
True
True or false:
Temperature & pH affect conformational stability of enzymes (ability to bind or catalyze substrate declines)
True
Enzyme activity is regulated __________ & __________ control of genes coding for those enzymes
transcription
translation
Activation of enzymes by modification of the inactive forms, which are called ____________
zymogens
True or false:
The activation of enzymes occurs by change in the environment (secretion into stomach acid), addition of organic or inorganic covalently bonded groups (phosphorylation), & presence of inhibitors or activators
True
____________ may be products of enzyme catalysis or products farther down the biochemical pathway, or may be substances not directly related to the enzyme-catalyzed reaction
inhibitors
____________ enhance enzyme activity
activators
_______________
- in multi-polypeptide enzymes the substrate binding to 1 subunit enhances binding to others
Positive cooperativity
_______________
- substrate binding to 1 subunit reduces binding to others
Negative cooperativity
______________ inhibition
- inhibitor to substrate that binds to the same active site as the substrate
- formation of enzyme-substrate complex is reduced and therefore Km increases while Vmax stays the same because higher substrate concentration still increases catalysis
Competitive inhibition
______________ inhibition
- inhibitor that binds to the enzyme but not at the active site (allosteric change to enzyme conformation)
- prevents enzyme-substrate complex from completing catalysis
- enzyme still binds to substrate so Km stays the same but Vmax decreases
Non-competitive inhibition
______________ inhibition
- inhibitor binds to enzyme-substrate complex and prevents enzyme-substrate binding & prevents catalysis
- Km increases and Vmax decreases
Uncompetitive inhibition
The inverse of the _______________ rate yields a linear equation that when graphed it clarifies the effects of enzyme inhibitors on Km or Vmax
Michaelis-Menten
______________
- subunit of nucleic acids
- contains a phosphate, a 5-Carbon Sugar, & a Nitrogenous base (A, G, C, T, or U)
Nucleotide
________ : nitrogenous bases bound to ribose
________ : nitrogenous bases bound to deoxyribose
RNA
DNA
The DNA molecule forms a double helix (twisted ladder structure) :
“Rails” are alternating __________ & __________
“Rungs” are the __________
deoxyribose & phosphate subunits
base pairs
Bonds between the base pairs in DNA molecules are ___________
H bonds
Bonds between alternating deoxyribose & phosphate subunits in DNA molecules are ____________
Phosphodiester bonds
In DNA the phosphodiester linkage is highly stable and the helical structure is maintained by ____________ between nonadjacent sugar molecules as the molecule twists
H bonds
Base pairing : between a purine & a pyrimidine
A pairs to _____
C pairs to _____
A to T
C to G