Quiz 2 Flashcards
Name this major functional group
Alcohol
Name this major functional group
Aldehyde
Name this major functional group
Ketone
Name this major functional group
Ether
Name this major functional group
Acid Anhydride
Name this major functional group
Sulfhydryl group
Name this major functional group
Disulfide
Name this major functional group
Amino group
Name this major functional group
Ester
Name this major functional group
Thioester
Name this major functional group
Phosphoester
Name this major functional group
Amide (Peptide bond)
Where do essential amino acids come from?
Our diets since we cannot produce them ourselves like we can with nonessential amino acids
What are the 5 basic groups of amino acids?
Nonpolar (aliphatic) Aromatic Polar, Uncharged Positively charged (basic) Negatively charged (acidic)
Draw the basic structure of an amino acid at physiological pH.
What does it mean to be chiral and are amino acids considered chiral?
To be chiral means that there are 4 different groups coming off of the alpha carbon (the carbon between the carboxyl group and the amino group)
Draw a Glycine. Would this want to be exposed to aqueous solution or buried in the core?
Buried in the core (nonpolar and hydrophobic)
Draw an Alanine. Would this be polar or non polar?
Nonpolar (CH3 has no dipole and is hydrophobic)
Draw Phenylalanine. Would this be buried in the core or exposed to the aqueous solution?
Buried in the core (aromatic - ring with double bonds) (hydrophobic and nonpolar)
Draw a Proline. Where would you find this in relation to the lipid membrane of a cell?
You would find this buried inside the lipid bilayer of the membrane with the non-polar hydrophobic tails
What is the only Amino acid that is NOT chiral?
Glycine (2 Hydrogens coming off of the alpha carbon)
Which aliphatic amino acid would cause a kink in the structure?
Proline due to it connecting to the alpha carbon and the N in the amino group
Draw a Valine. Would this be polar or non polar?
Non polar (remember valine is shaped like a V coming off of the alpha carbon)
Draw a Leucine. How is this structure different from a Valine?
It has an extra carbon coming off of the alpha carbon (shaped like a Y not a V)
Draw an Isoleucine. Is this polar?
No it is nonpolar
Draw a methionine. What makes this group non polar?
The methyl group attached to the sulfur.
Draw a Tryptophan. What group of amino acids does this belong in?
Aromatic
Draw a Tyrosine. What is unique about this group?
It is amphipathic (the H in the OH group can get donated and create a positive charge on one end and negative charge on the other end)
Draw a serine. Is this polar or unpolar?
Polar uncharged
Draw a threonine. Where would you find this amino acid in terms of aqueous or buried.
Out towards the aqueous solution (polar)
Draw a cysteine. What kind of bonds can this amino acid group form?
It is a weak acid and can form a disulfide bond (the S)
Draw an asparagine. Is this polar or nonpolar?
Polar (A comes before G so A has one less C than G)
Draw a Glutamine. What is the abbreviation for this?
Gln
Draw Lysine. What charge does this carry at pH 7.4?
Positively charged
Draw Arginine. Draw where the positive charge would be.
Draw Histidine. What is unique about this amino acid?
Both the charged and uncharged forms are present at neutral pH
Draw aspartate and glutamate at pH 7.4. What are their abbreviations?
Asp, Glu
Negatively charged
What is the isoelectric point (pI)?
The pH at which the amino acid is neutral
How are peptide bonds formed?
Condensation reactions between the amine and carboxylic acid groups
What reaction can break apart the peptide bonds in amino acids?
Hydrolysis (enzymatic assisted by proteases)
Why is Cysteine important in stabilizing the folded tertiary structure of proteins?
It can form disulfide bonds or bridges with adjacent thiols and especially with another cysteine
Remember a thiol is r-s-h
Draw how you would create Cystine from two cysteine residues.
What is the native fold?
The 3-D structure of a protein that is able to fulfill a specific biological function
(has a large number of favorable interactions within the protein -stable)
What are the 4 favorable interactions in a protein?
Hydrophobic effect (driving force for a proteins 3D structure - pushes them together) Hydrogen bonds London Dispersion Electrostatic interactions
What are the 3 forms of a secondary structure of a protein?
Alpha helix
Beta Sheet
Beta Turn
What amino acid is known as an alpha helix disrupter?
Proline due to its kink
What 2 amino acids are known as strong alpha helix formers?
Alanine and Leucine due to their small size and hydrophobic residues
Which are stronger, Parallel or Anti-parallel beta sheets?
Anti-parallel due to their straight hydrogen bonds which cause atoms to be positioned in the same plane (linear bonds)
The hydrogen bond is between the carbonyl group and the amide group
What 2 amino acids are used in order to create beta-turns?
Proline (kink changes directions) and Glycine (small and hydrophobic - only have an H bond)
What kind of interactions are tertiary protein structures held together by?
Weak interactions and disulfide (covalent) bonds
Why does Glycine act as a helix breaker?
Its small side chain allows for other confirmations
Quaternary Protein Structures have multiple _____.
Subunits (more than one polypeptide chain)
Homodimer vs. Heterodimer
Homodimer - two identical protein subunits
Heterodimer -Contains subunits from different gene products
What does a quaternary structure do for the protein’s function?
Provides a mechanism for regulation of protein function through conformational changes. Think about how active sites change shape to bind to substrate
Differences between fibrous proteins and globular proteins.
Fibrous is less water soluble (more stable), has to do with structure and flexibility of a protein
Globular proteins have a hydrophobic core and are less stable and have to do with the function of the protein (enzymes)
What is the folding pattern of a polypeptide chains mainly determined by?
Primarily by the amino acid sequence
Is protein folding random or nonrandom?
Nonrandom
What are the purposes of chaperone proteins when it comes to protein folding?
Help newly synthesized proteins fold
Rescue misfolded proteins
Disrupts protein aggregates
What do enzymes do for a reaction?
They speed up or catalyze a reaction without being consumed in the process
What is the difference between an apoenzyme and a holoenzyme.
Apoenzyme is the enzyme without its cofactor
Holoenzyme is the enzyme with its cofactor (completely active)
What is a prosthetic group?
A coenzyme or cofactor that is bound tightly or covalently to the enzyme
What kind of ions are cofactors usually?
1 or more inorganic ions (Fe2+, K+, Mg2+)
What are coenzymes and what do they do?
They are complex organic or metalloorganic molecules that act as transient carriers of specific functional groups (carry NADH or NAD) (not covalently bound to the enzyme)
Where are coenzymes derived from?
Vitamins (vitamin B12,6,2)
What is the common formula to name an enzyme (new ones)?
substrate+reaction performed+ “ase”
What enzymes are in class 1 and what do they do?
Oxidoreductases (catalyze oxidations and reductions)
OIL RIG
What enzymes are in class 2?
Transferases (transfer of groups like methyl and phosphoryl groups)
What class of enzymes are hydrolases in and what do they do?
Class 3 enzymes that hydrolytic cleavage of bonds with C,O,N or other covalent bonds
(use of water to cleave bonds)
What class of enzymes would lyases be under and what do they do?
Class 4 of enzymes and they cleave C,O,N bonds by elimination and leave double bonds or rings
What kind of enzymes would be in class 5 of enzymes and what do they do?
Isomerases (transfer of groups within molecules to yield geometric or structural changes)
(Make an isomer of original molecule)
What class of enzymes form C-C, C-S, C-O, and C-N bonds by condensation reactions and what are they called?
Ligases , class 6 (coupled to hydrolysis of ATP to ADP or similar cofactor)
Where on the enzyme do catalyzed reactions take place?
Within the active site
How would you describe the active site?
A pocket in the enzyme formed by 1 or more regions of the polypeptide chain
“pocket in the enzyme that catalyzes reactions”
“where the substrate and cofactors bind on the enzyme”
Where in the active site do substrates bind?
Their substrate recognition sites (creates enzyme specificity so it can discriminate among possible substrate molecules)
What does the specificity of an active site depend on?
The precise arrangement of atoms in the active site
Is the pocket of the active site mainly polar or nonpolar?
Mostly nonpolar (think it is kind of buried away from the aqueous solution in a globular protein so it would be nonpolar)
What do polar residues in the active site help with?
Help stabilize the interaction between the substrate and the active site
What type of interactions bind substrates to enzymes?
Weak reversible interactions (van der waals, hydrogen bonds, electrostatic interactions, hydrophobic interactions)
SHORT RANGE SO THIS PULLS THE SUBSTRATE CLOSE TO THE ENZYME
How would you explain the transition state?
Where the substrate is strained and unstable
We lower the activation energy to avoid this strained and unstable condition
What does the free energy have to be in order for a reaction to occur spontaneously?
Negative (no energy input is required to start the reaction, the reaction releases energy)
EXERGONIC
What would the free energy be if the reaction did not occur spontaneously?
Positive (input of free energy is required to drive the reaction to completion)
ENDERGONIC
“Using an enzyme in a reaction will speed up the reaction time and increase the amount of products at the end of the reaction” - what is wrong with this statement?
Addition of the enzyme will increase the reaction rate but will NOT increase the amount of product being produced
THE REACTION REACHES EQUILIBRIUM MORE QUICKLY WITH AN ENZYME
What does rate law show?
The relationship between the reaction rate and the concentration of the reactants.
How is “k” determined?
K is the proportionality constant that relates the concentration of substrate to the rate of the reaction - it is determined experimentally
What are the 4 major strategies used by enzymes for catalysis?
General acid-base catalysis
Covalent catalysis
Metal-Ion catalysis
Catalysis by Approximation
What type of catalysis is occurring when the active site contains a reactive group that temporarily forms a covalent bond to part of the substrate?
Covalent Catalysis
What type of catalysis is occurring when a molecule other than water acts as a proton donor or acceptor?
General acid-base catalysis
What type of catalysis is occurring when the enzyme brings 2 distinct substrates close together in the active site to increase the reaction rate?
Catalysis by approximation
Explain metal-ion catalysis
A metal-ion can act as a nucleophile or electrophile or serve as a bridge between enzyme and substrate (used by enzymes that use ATP as their substrate)
What kind of functional groups participate directly in catalysis?
All polar amino acids
Ser, Cys, Lys, and His
Which amino acid would participate in acid-base catalysis and why?
His due to its pKa being around 7 so it can donate or accept protons at neutral pH
What 3 amino acids make up the catalytic triad?
Asp, His, Ser
