Week 2 Flashcards
What is the difference between nonessential and essential aa’s in humans?
Non essential are made in the body; essential must be supplied by the diet
What is a peptide bond?
Formed by condensation (taking water out of it) between amine and carboxylic acid
What assists hydrolysis of peptide bonds?
Proteases
What is polypeptide cross linking for?
Formed by cysteine disulfide bonds that stabilizes tertiary and quaternary structures
What is a protein that folds into its specific 3-D structure in order to become a functional protein?
Native fold
What are the favorable interactions in proteins?
- Hydrophobic effect
- Hydrogen bonds
- Londen dispersion
- Electrostatic interactions
Explain the hydrophobic effect.
It minimizes interactions of water by driving the proteins to fold into a 3-D shape resulting to the increase in entropy
What is the importance for hydrogen bonds for protein formation?
Binds a-helices and b-sheets in a protein
What is the importance for London dispersion for protein formation?
Stabilizes the interior of the protein
What is the importance for electrostatic interactions for protein formation?
Stabilizes the protein by salt bridges
Describe the primary structure of a protein
AAs are attached by peptide bounds. Once attached an single aa unit is a residue.
What are the 3 forms of secondary structures of proteins?
- a-helix
- B-sheets
- B-turn
Describe the formation of an alpha helix
Held by H-bonds with a turn of 3.6 residues
Side chains point outward
What are the problems of proline in a-helicases?
The rotation around N-C bond is impossible could create more steric hinderance
What are the problems of glycine in a-helicases?
The tiny R-group supports other conformations
Describe the formation of a B-sheet
Arrangement is held together by inter- and intra-chain H-bonds between backbone amides
What is the difference between parallel and antiparallel sheets?
Parallel sheets’ strands are oriented in the same side while anti- are in opposite directions
Parallel have weaker H-bonds, anti- has stronger
Describe the formation of a B-turn
Gly and Pro are found
H-bond stabilizes from a carbonyl to an amide three residues down the sequence
Describe the tertiary structure of a protein
Stabilized by weak interactions and disulfide bonds
Describe the quaternary structure of a protein
Proteins that consist of more than one polypeptide chain
Chains interact with one another non-covalently via electrostatic attractions, H-bonds, and hydrophobic interactions
What is s molecule that is made of a number of smaller subunits?
Oligomers
What is the difference between homodimers and heterodimers?
Homodimer: simplest, contains identical protein subunits
Heterodimer: contains subunits from different gene products
How does quaternary structure of proteins increase functionality?
- Provide structural properties not present in individual subunits
- Provide a mechanism for regulation of protein function through conformational change
- Bring linked functional components into close proximity
What are the two multi-subunit complexes of proteins?
- Fibrous
2. Globular
What is the difference between fibrous and globular proteins?
Fibrous: provide mechanical support and flexibility in tissues. Less water soluble than globular proteins.
Globular: backbones folds on itself to produce a more or less spherical shape. Soluble in water and salt solutions.
What is the purpose for chaperone proteins?
- Help newly synthesized proteins fold properly
- Rescue misfiled proteins
- Disrupt protein aggregates
What are the 5 functional classes of proteins?
- Structural
- Transport
- Metabolic
- Genomic caretaker
- Cell signaling
What is the importance for enzymes?
Catalyze and speed up biochemical reactions without being consumed
What are co-factors for?
Assists catalysts when amino acid side chains aren’t enough
What are examples of cofactors?
K+: pyruvate kinase
Mg2+: Hexokinase, G6P, Pyruvate kinase
What is an enzyme without a cofactor called?
Apoenzyme
What is a completely catalyzes enzyme called?
Holoenzyme
What is a prosthetic group?
Coenzyme/factor bound tightly or covalently to the enzyme
What is a coenzyme?
Complex organic or metalloorganic molecules that act as transient carriers of specific functional groups
Derived from vitamins and not covalently bound to enzymes
What is the typical enzyme nomenclature?
Substrate + reaction performed + -ase
What are the classes of enzymes?
- Oxidoreductase
- Transferases
- Hydrolases
- Lysases
- Isomerases
- Ligases
How do enzymes work?
Speed up reactions by acting as a catalyst and increase the rate of chemical reactions
What happens at an enzyme’s active site?
Substrates and cofactors bind
What are catalytic groups?
Amino acid residues lined in the active site that help make or break bonds
What is enzyme specificity?
When active sites have the ability to discriminate among possible substrate molecules
What are the features of an active site?
- 3-D cleft or crevice containing polar residues for stabilization
- Takes a small portion of enzyme
- Specificity of binding
- Microenvironement
- Substrate binds by weak interactions
What is an induced-fit model?
Enzymes undergo conformational change upon binding to substrate
Describe the active site of lyase
- Binding of the substrate induces a conformational change in the enzyme
- Residues within the active sites reposition increasing the number of binding interactions
- Repositioning causes a strain between bonds A and B
- Strain facilitates cleavage of bond
Why are enzymes considered catalysts?
Alters the rates of reaction without changing the ratio of substrate and products at equilibrium
What is the condition where the substrate is strained and unstable?
Transition state
What is the difference between the energy of the substrate and the trasition state complex (ES)?
Activation energy
Describe E + S → ES → EP → E + P
- Enzyme binds to substrate to ES
- Substrate reaches the transition state and bonds are rearranged
- Product releases
- Enzyme resets
What is a spontaneous reaction where delta G is negative?
Exergonic
What is a reaction where delta G is positive?
Endergonic
What is the relationship between the reaction rate and the concentration of the reactants called?
Rate law
What is k?
Proportionality constant relating the concentration of substrate to the rate of the reaction
What is zero order?
Rate of reaction is independent of the concentration of the reactants k[S]^0
When [S] is so high that the enzyme is completely saturated
What is 1st order?
Rate of the reaction is directly proportional to the concentration of reactants k[S]^1
The rate doubles, when [S] doubles
What is 2nd order?
Reaction depends on the either the square of the concentration of the reactant or the product of the concentration of the two reactants k[S]^2
Rate quadruples when [S] doubles
Why doesn’t enzymes affect reaction equilibrium?
The reaction reaches equilibrium more quickly and same amount of product is produced
What catalysis occurs where molecules other than water acts as a proton donor and acceptor?
Acid-Base Catalysis
What catalysis where active site contains a reactive group forms a temporary covalent bond?
Covalent catalysis
What catalysis where ions act as a nucleophile or electrophile or serve as a bridge between E and S?
Metal-ion catalysis
What AA’s are involved with catalysis?
- All polar amino acids
2. Ser, Cys, Lys, and His
Why does chymotrypsin possess a highly reactive serine residue?
Serine proteases covalently catalysis
It would cleave peptide bonds on the carboxyl terminal of the large hydrophobic aromatic AAs
Uses a Ser residue to carry out a nucleophillic attack of the carbonyl carbon of the substrate
What amino acids are involved in a triad?
Asp, His, and Ser
What is the importance of serine proteases?
- Abound and many are drug targets
- Thrombin is an important enzyme for blood clots
- Many anticoagulants aim to inhibit the serine protease, thrombin
What are the conditions for proper enzyme function?
- 37C, higher temperatures will denature proteins
- Reaction rates of enzyme increases as pH moves from acidic to physiologic range
- Functional groups in active sites are ionized, and more H-bonds are formed
- Affected by salt concentration, substrate concentration, and inhibitors
