MODULE 2: Chapter 4.1 Flashcards
What are proteins composed of?
Polymers of amino acids
Proteins are formed from twenty common amino acids, each with unique properties.
What bond links amino acids together in a polypeptide chain?
Peptide bond
The peptide bond is a type of amide bond.
What are short polypeptides usually called?
Peptides or oligopeptides
Short polypeptides typically consist of fewer than 40 amino acids.
What determines the structure and function of a protein?
The precise arrangement of amino acids
Unique chemical and physical properties of amino acids influence protein characteristics.
What drives the folding of proteins into their three-dimensional shape?
Hydrophobic effects
Hydrophobic amino acids tend to cluster inside, minimizing interactions with water.
How many possible protein sequences can an oligopeptide of 10 residues have?
About 10 trillion
The total number of combinations is calculated as 20^10.
What is the average molecular mass of an amino acid residue?
∼110 daltons (Da)
This means a polypeptide chain of 500 amino acids has a mass of about 55 kilodaltons (kDa).
What is the pKa of the α carboxyl group of amino acids?
∼2.3
This indicates that at pH 7, the α carboxyl group is deprotonated and carries a negative charge.
What is the isoelectric point (pI)?
The pH at which the amino acid carries no net charge
For alanine, the pI is 6.0, at which it exists as a zwitterion.
What configuration do most amino acids found in nature have?
L-amino acids
Almost all amino acids in proteins are in the L configuration.
What does the RS system describe?
The absolute spatial configuration of amino acids
It categorizes amino acids as either S or R based on atomic arrangements.
What type of interactions stabilize the macromolecular protein structure?
Weak noncovalent interactions
These interactions occur between atoms within the protein.
What are amino acids with chiral centers called?
α amino acids
All amino acids except glycine have a chiral α carbon.
What is the molecular mass of human titin?
2,993,428 Da
Titin is a large muscle protein with a significant molecular mass.
True or False: The amino acid proline has a primary amino group.
False
Proline’s amino group is part of a pyrrolidine ring.
Fill in the blank: The _______ indicates the pH at which an amino acid carries no net charge.
isoelectric point (pI)
The pI is crucial for understanding the behavior of amino acids in solution.
What is the absolute configuration of L-alanine?
S
The configuration is determined by the counterclockwise arrangement of groups around the chiral Cα when the lowest priority group is oriented away.
Which amino acid has an absolute configuration of R?
L-cysteine
L-cysteine is the only L-amino acid with the R configuration due to the clockwise orientation of its groups around the chiral Cα.
Who developed the single-letter abbreviations for the 20 amino acids?
Margaret Dayhoff
She created this system in the 1960s to facilitate computational analysis of protein-coding genes.
What is the single-letter abbreviation for Valine?
V
Valine is represented by ‘V’ in the single-letter amino acid code.
List the four general subfamilies of amino acids based on their chemical properties.
- Charged amino acids
- Hydrophilic amino acids
- Hydrophobic amino acids
- Aromatic amino acids
True or False: Glycine fits well into the hydrophobic amino acid group.
False
Glycine is included in the hydrophobic group due to its side chain properties, but it does not fit well into any of the defined groups.
What is the pKa value of the side-chain carboxyl groups in aspartate and glutamate?
∼4.0
This low pKa means aspartate and glutamate are negatively charged at pH 7.
What charge do lysine and arginine typically carry at pH 7?
Positive
Lysine has a pKa of ∼10.5 and arginine has a pKa of ∼12.5, leading to their positive charge at physiological pH.
What role does histidine play in enzyme reactions?
It can act as both a hydrogen donor and acceptor
Histidine’s imidazole group has a pKa near neutral pH, allowing it to participate in acid-base reactions.
Fill in the blank: The hydroxyl groups of serine and threonine can be _______ by enzymes called serine/threonine kinases.
phosphorylated
Which amino acids are classified as hydrophilic but generally uncharged at physiological pH?
- Serine
- Threonine
- Cysteine
- Asparagine
- Glutamine
What is the pKa of the sulfhydryl group in cysteine?
∼8.3
Cysteine can form disulfide bonds when oxidized, stabilizing protein structures.
What is the importance of glutamine in nitrogen metabolism?
It buffers toxic ammonia and transports nitrogen to the liver
This process is crucial for urea production.
List the seven hydrophobic amino acids.
- Glycine
- Alanine
- Proline
- Valine
- Leucine
- Isoleucine
- Methionine
What unique property does proline have compared to other amino acids?
It cannot act as a hydrogen-bond donor
This is due to the nitrogen in its pyrrolidine ring lacking a hydrogen.
True or False: Leucine is the most abundant amino acid in proteins.
True
Leucine’s observed level is about 9.1%, which is significantly higher than the expected level.
Which amino acid has the most chemically inert side chain?
Glycine
Glycine’s hydrogen side chain makes it the least chemically active of all amino acids.
What unique property does the nitrogen of proline exhibit in a polypeptide chain?
The nitrogen of proline lacks a hydrogen, preventing it from acting as a hydrogen-bond donor.
Where are proline residues typically found in protein structure?
Proline residues are usually found in regions that separate α helices and β sheets.
What stabilizes α helices and β sheets in proteins?
α helices are stabilized by intrastrand hydrogen bonding, while β sheets are stabilized by interstrand hydrogen bonding.
List the three aromatic amino acids.
- Phenylalanine
- Tyrosine
- Tryptophan
What is the wavelength range at which aromatic amino acids absorb ultraviolet light?
250–280 nm.
Which aromatic amino acid has the highest molar absorbance at 280 nm?
Tryptophan.
What is a key characteristic of tryptophan?
Tryptophan is the largest of the 20 amino acids, with a molecular mass of 204 Da.
What property makes tyrosine more polar than phenylalanine?
The hydroxyl group on the phenyl ring of tyrosine.
What does amphipathic mean in the context of amino acids like tyrosine and tryptophan?
Amphipathic refers to a dual chemical nature—part hydrophobic and part hydrophilic.
What role does the hydroxyl group in tyrosine play regarding phosphorylation?
The hydroxyl group can be phosphorylated by kinase enzymes and dephosphorylated by phosphatase enzymes.
True or False: Phenylalanine has a higher level of ultraviolet absorbance than tyrosine.
False.
What is the absorbance maximum of phenylalanine?
257 nm.
What is the precursor relationship between phenylalanine and tyrosine?
Phenylalanine is the chemical precursor to tyrosine.
What is the function of the green fluorescent protein (GFP) in jellyfish?
GFP emits green light after absorption of blue light.
What causes the fluorescence of GFP?
Fluorescence is stimulated by the absorption of blue light, usually emitted by aequorin.
What is formed from the modification of three amino acid residues in GFP?
The chromophore.
Which amino acids are involved in the formation of the GFP chromophore?
- Serine
- Tyrosine
- Glycine
What is the process by which peptide bonds are formed?
Peptide bonds are formed by a condensation reaction between the carboxylic acid and amino groups of two amino acids.
What do peptide bonds link together?
Amino acids.
What is the typical half-life of a peptide bond in water?
About 10 years.
What are the two termini of a peptide or protein?
- Amino terminus (N terminus)
- Carboxyl terminus (C terminus)
How are amino acid sequences specified?
From the amino-terminal (N-terminal) to the carboxyl-terminal (C-terminal) direction.
What restricts rotation around the peptide bond?
Partial double bond character due to resonance.
What are the torsional angles on either side of the peptide bond called?
- φ (phi) angle
- ψ (psi) angle
What is a Ramachandran plot?
A plot showing the allowable combinations of φ and ψ angles for amino acid residues based on steric hindrance.
Who first identified the energetically favored combinations of φ and ψ angles?
Gopalasamudram Ramachandran.
What does a Ramachandran plot show?
Allowable combinations of φ and ψ angles for amino acid residues based on steric hindrance
Dark blue areas indicate most compatible angles, while uncolored areas are energetically unfavorable.
What is the central dogma of biology?
DNA sequences are transcribed into RNA sequences, which are then translated into proteins
This process involves triplet codons specified by the genetic code.
How many triplet codons are in the genetic code, and how many specify amino acids?
64 triplet codons; 61 specify amino acids
The remaining 3 codons are termination codons.
What is a missense mutation?
A single nucleotide mutation in DNA that changes one amino acid in a protein
Example: An alteration of aspartate to leucine at a substrate binding site.
What is a nonsense mutation?
A single nucleotide mutation in DNA that results in a termination codon in the corresponding mRNA
The termination codons are UGA, UAA, and UAG.
What is a frameshift mutation?
A single nucleotide mutation that changes the codon register, resulting in a new amino acid sequence
Caused by nucleotide insertions or deletions.
What is a silent mutation?
A single nucleotide mutation that does not change the sequence of amino acids in a protein
Occurs due to redundancy in the genetic code.
What is the role of amino acid side chains in a protein?
They determine the overall chemical properties and three-dimensional structure of a protein
Variations in size, charge, and bonding ability influence protein interactions.
Define polypeptide chain.
An extended polypeptide with many amino acids linked by peptide bonds
Found in proteins.
What is an α carbon in an amino acid?
The central carbon atom between the amino group and the carboxyl group
It serves as an attachment point for the amino acid side chains.
What is the isoelectric point?
The pH at which a given amino acid has no net charge
Important for understanding amino acid behavior in different pH environments.
What is a zwitterion?
An electrically neutral but dipolar molecule that contains both positive and negative charges
Common in amino acids at physiological pH.
What are enantiomers?
Stereoisomers that are mirror images of each other and cannot be superimposed
Important in biochemistry due to their different biological activities.
What is the function of serine/threonine kinase?
An enzyme that can phosphorylate serine or threonine residues within proteins
Phosphorylation can alter protein function and activity.
Define disulfide bond.
A covalent cross-link between two cysteine residues that can stabilize the three-dimensional structure of a protein
Also referred to as a disulfide bridge.
What is DNA bioinformatics?
The use of DNA sequence information to predict the function or evolutionary relatedness of a given DNA segment
Essential for understanding protein structure from genetic data.
What is the significance of the informational relationship between DNA and protein sequences?
Links random mutations to protein function, aiding in understanding molecular evolution
Exploited by biochemists to analyze the effects of mutations.
Fill in the blank: The smallest and least chemically active amino acid is _______.
glycine
Fill in the blank: The amino acid that is often positively charged at pH 7 is _______.
lysine
True or False: Multiple triplet codons can specify the same amino acid.
True
What type of amino acid is tryptophan?
The largest amino acid, hydrophobic, aromatic, and strongly absorbs light
Important for protein structure and function.
What is the function of a protease?
An enzyme that catalyzes hydrolysis of a peptide bond
Critical for protein degradation and processing.
