Proteins 1

Which amino acid is used to make proteins but is notable for not being included in the standard genetic code?

Selenocysteine

How many amino acids are considered 'essential' for humans because the body cannot synthesize them?

9

What are the essential amino acids

Valine, Leucine, Isoleucine, Phenylalaine, Methionine, Threonine, Tryptophan, Lysine, Histidine

What is the nutritional significance of L enantiomers compared to D enantiomers in amino acids?

L enantiomers are the form that is nutritionally important.

In a zwitterion at physiological pH, what is the specific state of the amino group?

It is protonated to form NH₃⁺​

In a zwitterion at physiological pH, what is the specific state of the carboxyl group?

It is deprotonated to form COO⁻

What chemical byproduct is removed during the formation of a peptide bond (amide bond)?

H₂​O

The primary structure of a protein is held together exclusively by which type of bond?

Peptide bonds

Which part of the amino acid is involved in the hydrogen bonding that stabilizes secondary structures like the α-helix?

The backbone (not the side chains)

In an α-helix, a hydrogen bond forms between a carboxyl group and an amino group located how many amino acids away?

4 amino acids away

What distinguishes the tertiary structure of a protein from the secondary structure regarding the involvement of amino acid components?

The amino acid side chains are now involved in bonding

Where are hydrophobic amino acids typically located within the tertiary structure of a protein?

They cave toward the center of the structure

What defines the quaternary structure of a protein?

The combination of two or more tertiary structures (subunits)

Two protein examples that possess a quaternary structure

Insulin or Immunoglobulins

Which specific level of protein structure is NOT broken during the process of denaturation?

Primary structure (polypeptide chain)

What are the two hydroxylated amino acids that has sites for post-translational phosphorylation?

Serine and Threonine

Which sulfur-containing amino acid is used as the precursor for glutathione (GSH) synthesis?

Cysteine

In what specific food group is Methionine typically the limiting amino acid?

Legumes

Which aromatic amino acid is used by the body to synthesize Tyrosine?

Phenylalanine

Tryptophan serves as a precursor for the synthesis of which neurotransmitter and which B-vitamin?

Serotonin and Niacin (B3)

What is the primary structural role of the amino acid Proline in the human body?

Collagen production

Post-translational modifications (PTMs) occur on which form of amino acids?

Amino acids within polypeptide chains (not free AAs)

Which mineral is required for the hydroxylation of Lysine to form hydroxylysine in elastin?

Copper

The hydroxylation of Proline to form collagen subunits is dependent on which vitamin?

Vitamin C

Which post-translational modification is critical for calcium homeostasis and blood clotting?

γ-Carboxylation

The γ-carboxylation of proteins is a process dependent on which vitamin?

Depends on Vit K

Which specific chemical element is essential for the iodination of amino acids to form thyroid hormones?

Iodine

ADP-ribosylation of proteins depends on which vitamin to form NAD+?

Niacin (Vit B3)

Under the condition of Phenylketonuria (PKU), which amino acid becomes conditionally essential?

Tyrosine

In the context of liver cirrhosis, which two amino acids become conditionally essential?

Tyrosine and Cysteine

Impairs Phe and Met catabolism

Why can basic amino acids interact effectively with DNA?

They have a positive charge on the NH₂​ group of their side chain

Which basic amino acid is a precursor for the production of Carnitine for fatty acid metabolism?

Lysine

In which population is the amino acid Arginine considered conditionally essential?

Preterm infants

Which basic amino acid is the direct precursor used to produce histamine?

Histidine

Acidic amino acids like Aspartate and Glutamate possess what charge on their side chain?

Negative charge

What is the role of Aspartate in the Urea Cycle?

It serves as a source of Nitrogen

Which neurotransmitter is synthesized directly from Glutamate?

GABA

Which neutral amino acid is utilized by the body to produce porphyrins for heme?

Glycine

What is the primary function of Alanine in the glucose-alanine cycle?

It acts as an inter-organ carrier of Nitrogen to the liver and kidneys

List the three Branched-Chain Amino Acids (BCAAs)

Leucine, Isoleucine, and Valine

What is unique about the catabolism of Branched-Chain Amino Acids (BCAAs) compared to most other amino acids?

They are not catabolized by the liver

What role do BCAAs play in muscle tissue signaling?

They act as anabolic signals to promote protein synthesis

Why does no enzymatic protein digestion occur in the mouth?

There are no enzymes in the salivary glands to break down protein

What are the two primary functions of HCl in protein digestion within the stomach?

It denatures proteins and activates pepsin

Pepsin is secreted in which inactive zymogen form?

Pepsinogen

Which enzyme, located in the small intestine, is responsible for activating Trypsinogen into Trypsin?

Enteropeptidase

Which enzyme acts as the master activator for other pancreatic zymogens like chymotrypsinogen and proelastase?

Trypsin

What is the difference between an endopeptidase (like Pepsin) and an exopeptidase (like Aminopeptidase)?

Endopeptidases target internal peptide bonds

Exopeptidases cleave amino acids from the ends

Which specific exopeptidase is produced in the small intestine and cleaves the amino end of a polypeptide?

Aminopeptidase

Where in the gastrointestinal tract does the majority of amino acid absorption occur?

The duodenum (top of the small intestine)

How does the absorption rate of essential amino acids compare to non-essential amino acids?

Essential amino acids are absorbed faster

Describe the driving force behind facilitated diffusion of amino acids into the enterocyte

The concentration gradient (requires no Na+ or ATP)

Active transport of amino acids depends on the co-transport of which ion?

Na⁺

Which amino acid is the primary energy source used by intestinal enterocytes?

Glutamine

What is the function of Glutamine regarding the bacterial population in the gut?

It drives mucus production to prevent bacterial translocation

When excess amino acids are catabolized in the liver, where is the released NH3​ sent?

Urea Cycle → Kidney

What are the three potential metabolic fates for the carbon skeleton of an amino acid after the NH3​ is removed?

Krebs cycle, gluconeogenesis, or lipogenesis

In the tertiary structure, which specific covalent bond can form between the side chains of two Cysteine residues?

Disulfide bonds

The term 'protein subunit' refers to which level of protein organization?

Tertiary structures within a quaternary complex

Which amino acid is considered a 'limiting amino acid' in grains?

Lysine

What is the functional difference between a 'Native' protein and a 'Denatured' protein?

Native is active and functional

Denatured is inactivate, no bio-activity

How does HCl in the stomach affect the chemical bonds of a protein?

It breaks hydrogen bonds and electrostatic bonds

Which enzyme specifically targets neutral aliphatic amino acids during digestion?

Elastase

What is the primary role of Aminopeptidase in the small intestine?

Cleaving the amino end of the polypeptide chain

How is Na+ removed from the enterocyte after being used for active transport of amino acids?

It is kicked back out using ATP

Why is Glutamine essential for enterocyte regeneration?

It stimulates cell proliferation

Which protein structure involves the folding of a peptide chain onto itself, often in a parallel or anti-parallel fashion?

β-pleated sheet

What makes an amino acid 'conditionally essential' due to genetic factors?

A genetic problem (like PKU) that prevents the conversion of one amino acid to another

Which amino acid has an aliphatic side chain but is technically categorized with aromatic amino acids in some contexts due to its ring structure?

Proline

The process of 'sparing' an amino acid refers to what biochemical relationship, using Methionine and Cysteine as an example?

Consuming Cysteine reduces the amount of Methionine needed by the body

What is the relationship between Tyrosine and Phenylalanine regarding 'sparing'?

Tyrosine 'spares' Phenylalanine

Which enzyme class is responsible for the post-translational phosphorylation of amino acids?

Kinase enzymes

How does the liver handle BCAAs during the 'first pass' of amino acid metabolism?

It takes up most amino acids but allows BCAAs to pass through to other tissues

What happens to a protein's quaternary structure when it is denatured?

The subunits break apart

Which amino acid is transaminated to α-ketoglutarate during catabolism?

Glutamate

What is the role of Asparagine and Glutamine in nitrogen transport?

They carry Nitrogen between organs (to the liver and kidney)

Which amino acid side chain is characterized as being straight or branched without a charge?

Aliphatic (Neutral AAs)

Which enzyme cleaves the carboxyl end of a polypeptide chain and where is it produced?

Carboxypeptidase; produced in the Pancreas

Basic AAs

Lysine

Arginine

Histidine

Acidic and Neutral AAs

Aspartate

Glutamate

Glutamine

Asparagine

Neutral Aliphatic AAs

Glycine

Alanine

Branched side AAs

Leucine

Isoleucine

Valine

Hydroxylated AAs

Serine

Threonine

Sulfur containing AAs

Cysteine

Methionine

Aromatic AAs

Phenylalanine

Tyrosine

Tryptophan

Proline