Basic structures of protein and protein metabolism

Proteins are made of what basic units?

Amino acids arranged in a linear chain joined by peptide bonds

Which bond joins amino acids in proteins?

Peptide bond between carboxyl and amino groups

What is the primary biological role of proteins in growth?

Building materials for muscle, bone, ligaments, tendons, blood, skin, hair, nails, GI tract cells

Which proteins are involved in repair and wound healing?

Clotting factors and scar tissue proteins

What is the role of proteins as enzymes?

Catalysts that allow reactions to occur more quickly and efficiently

Which protein acts as a hormone example?

Insulin (polypeptide hormone)

How do proteins regulate fluid balance?

By maintaining osmotic pressure through plasma proteins

Which protein regulates acid–base balance?

Hemoglobin

Name blood transport proteins

Albumin, globulins, hemoglobin

Name cell transport proteins

Hormone receptors and transport molecules

Which proteins act as antibodies?

Immunoglobulins

Name protein functions beyond enzymes and hormones

Neurotransmitters, blood clotting factors, visual pigments

Which protein is involved in muscle contraction?

Actin

Why is protein structure important?

Structure determines function; disruption causes loss of function

Give an example of disease due to aberrant protein structure

Sickle cell anemia (Val substituted for Glu in HbS)

What happens in sickle cell anemia?

Rigid HbS polymers cause sickled RBCs → infarction and O₂ obstruction

What is denaturation?

Loss of protein structure leading to loss of function

What is the basic structure of amino acids?

Amino group + carboxyl group + α‑carbon + side chain (R group)

What determines amino acid diversity?

Different side chains (R groups)

Name categories of amino acids

Aliphatic, aromatic, polar, sulfur‑containing, charged

What stabilizes secondary protein structure?

Hydrogen bonds

Which level of protein structure is the 3D folded polypeptide chain?

Tertiary structure

At which level do mutations occur?

Primary structure (sequence of amino acids)

What are consequences of mutations in protein sequence?

Altered folding and function, possible disease

What is the difference between fibrous and globular proteins in purpose?

Fibrous are structural; globular are functional

Shape of fibrous vs globular proteins?

Fibrous long and narrow; globular spherical

Amino acid sequence pattern in fibrous vs globular proteins?

Fibrous repetitive; globular irregular

Resilience of fibrous vs globular proteins?

Fibrous less sensitive to temp/pH; globular more sensitive

Solubility of fibrous vs globular proteins?

Fibrous insoluble; globular soluble

Examples of fibrous proteins

Keratin, collagen, elastin, fibrin

Examples of globular proteins

Hemoglobin, myoglobin, insulin, enzymes

What is hemoglobin’s function?

Carries oxygen to tissues and returns CO₂ and protons to lungs

What determines hemoglobin’s quaternary structure?

Hydrophobic interactions, hydrogen bonds, salt bridges between monomers

Which feature of hemoglobin is crucial for oxygen transport?

Heme groups containing iron

What is protein turnover?

Balance between degradation and synthesis of proteins

Define negative nitrogen balance

Degradation > synthesis; more nitrogen excreted than ingested

Causes of negative nitrogen balance

Illness, convalescence, prolonged starvation

Define positive nitrogen balance

Synthesis > degradation; less nitrogen excreted than ingested

Causes of positive nitrogen balance

Growth, pregnancy, new tissue synthesis

Examples of short‑lived proteins

Regulatory proteins, misfolded proteins (half‑life minutes/hours)

Examples of long‑lived proteins

Structural proteins like collagen (half‑life months/years)

What are the four steps of amino group catabolism?

Transamination, oxidative deamination, ammonia transport, urea cycle

What is transamination?

Funneling amino groups to glutamate

Enzymes of transamination

Alanine aminotransferase (ALT), Aspartate aminotransferase (AST)

Coenzyme required for transamination

Pyridoxal phosphate (Vitamin B6)

What is oxidative deamination?

Removal of amino group from glutamate by glutamate dehydrogenase

Products of oxidative deamination

α‑ketoglutarate + ammonia

Where does oxidative deamination occur?

Liver and kidneys

How much amino acids are deaminated per day?

50–70 g

Why must ammonia be transported safely?

Highly toxic, causes CNS toxicity

Two mechanisms of ammonia transport

Glutamine transport, glucose–alanine cycle

What is the glucose–alanine cycle?

Pyruvate forms alanine, transported to liver for conversion to urea

What is the major disposal form of amino groups?

Urea

What percentage of urinary nitrogen is urea?

90%

Sources of nitrogen atoms in urea

One from ammonia, one from aspartate

Where do first two urea cycle reactions occur?

Mitochondria

Where do remaining urea cycle reactions occur?

Cytosol

Fate of urea

Transported to kidney for excretion in urine

What happens to some urea in intestine?

Cleaved by bacterial urease to CO₂ + NH₃

First enzyme of urea cycle

Carbamoyl phosphate synthetase I

Second enzyme of urea cycle

Ornithine transcarbamoylase

Third enzyme of urea cycle

Argininosuccinate synthetase

Fourth enzyme of urea cycle

Argininosuccinate lyase

Final enzyme of urea cycle

Arginase

Which amino acids are exclusively ketogenic?

Leucine and lysine

Define glucogenic amino acids

Catabolism yields pyruvate or TCA intermediates

Define ketogenic amino acids

Catabolism yields acetoacetate, acetyl‑CoA, or acetoacetyl‑CoA

Define essential amino acids

Cannot be synthesized, must be obtained from diet

Define non‑essential amino acids

Carbon skeletons can be synthesized in body

Conversion of tryptophan

Serotonin → melatonin

Conversion of histidine

Histamine

Conversion of glutamate

GABA

Conversion of serine

Ethanolamine → choline → acetylcholine

Conversion of phenylalanine

Tyrosine → DOPA → dopamine → catecholamines

Conversion of DOPA

Dopaquinone → melanin

Conversion of tyrosine

Thyroid hormones T3, T4

Conversion of glycine

Heme

Conversion of arginine + glycine

Creatine phosphate → creatinine

Summary of protein metabolism

Proteins constantly synthesized and degraded; nitrogen removed → urea; carbon skeletons oxidized for energy

During fasting, what happens to muscle protein?

Degraded to supply amino acids for glucose or ketone body production

Which urea cycle enzyme deficiency causes high NH₃, Gln, Ala, ornithine, low citrulline?

Ornithine transcarbamoylase deficiency