Medical Biochemistry Lecture 2: Proteins Structure and Functions

Comprehensive practice flashcards covering protein structures (primary through quaternary), folding forces, classification, motifs, and posttranslational modifications based on Medical Biochemistry Lecture 2.

Albumin

A plasma protein responsible for transport, primarily composed of alpha helix secondary structure.

Hemoglobin

A globular transport protein in plasma that carries oxygen and exhibits quaternary structure with cooperativity.

Collagen

A fibrous structural protein containing three helical polypeptide chains wound together to form a superhelical cable.

Myosin

A fibrous protein involved in muscular contraction, characterized by a long and narrow shape.

Primary Structure

The sequence of amino acids linked by peptide bonds, read from the N-terminal end to the C-terminal end.

Secondary Structure

The spatial arrangement of amino acids stabilized by hydrogen bonds, such as alpha helices and beta sheets.

Tertiary Structure

The final three-dimensional folding of a polypeptide chain including the interaction of R groups far apart in the sequence.

Quaternary Structure

The spatial arrangement and interaction of multiple polypeptide chains (monomers or subunits) within a protein.

Peptide Bond

A covalent bond formed between the $\alpha$-carboxyl group of one amino acid and the $\alpha$-amino group of the next.

N-terminus

The end of a protein or polypeptide chain terminated by an amino acid with a free $\alpha$-amino group.

C-terminus

The end of a protein or polypeptide chain terminated by an amino acid with a free $\alpha$-carboxyl group.

Disulfide Bond

A strong covalent bond ($>50\,kcal\,mol^{-1}$) formed between the thiol groups of two cysteine residues.

Alpha-helix

A rigid, right-handed coiled secondary structure stabilized by hydrogen bonds with $3.6$ residues per turn.

Beta-pleated sheet

A secondary structure composed of two or more peptide chains arranged parallel or anti-parallel with perpendicular hydrogen bonds.

Beta-turns

A type of secondary structure that allows the polypeptide chain to reverse direction.

Fibrous Proteins

Proteins with a long, narrow shape, repetitive sequences, and general insolubility in water, used for structural purposes.

Globular Proteins

Functional proteins with rounded shapes, irregular amino acid sequences, and general solubility in water.

Hydrophobic Forces

Weak attractive forces of approximately $2-3\,kcal/mol$ that drive the burial of non-polar side chains in the protein core.

Ionic Bonds

Electrostatic interactions between negatively and positively charged R groups providing a stabilizing force of $1-20\,kcal/mol$.

Van der Waals forces

Very weak attractive forces measured at less than $1\,kcal/mol$ in protein structures.

Denaturation

The process of changing a protein's conformational shape without breaking its peptide bonds.

Keratin

A protein with a super-helical structure consisting of two right-handed helices intertwined into a left-handed alpha coiled coil.

Super secondary structures (Motifs)

Organized secondary level peptide fragments forming intermediate structures between secondary and tertiary levels.

Helix-turn-helix motif

A super secondary structure containing two alpha helices joined by a short flexible turn.

Zinc finger motif

A motif consisting of an alpha helix and a two-segment antiparallel beta sheet held by a zinc atom and four cysteine or histidine residues.

Leucine zipper motif

An alpha helix with regular leucine residues that interacts with another polypeptide to coil around each other.

Helix-loop-helix motif

A motif consisting of a short helix connected by a loop to a longer helix, often forming dimers.

Homeodomain

A DNA-binding domain with three alpha helices encoded by a $180$ base pair homeobox.

Myoglobin

A protein with tertiary structure containing approximately $80\%$ alpha-helix and no beta-sheet structure.

Cooperativity

A property of quaternary structure where the binding of a ligand to one subunit increases the affinity of other subunits for that ligand.

Allostery

A property observed in quaternary structures like hemoglobin involving changes in subunit interaction upon ligand binding.

Insulin

A globular hormone held together by two inter-chain disulfide bonds between A- and B-chains.

C-peptide

A fragment needed for the proper formation of disulfide bonds in insulin, later cleaved and released into the blood.

Hydroxylation

A posttranslational modification attaching an $\text{-OH}$ group, such as Vitamin C-dependent modification of proline and lysine in collagen.

Acylation

Attachment of an acyl group (e.g., fatty acids) to proteins, affecting their attachment to subcellular membranes.

ADP ribosylation

Modification where an ADP ribose group is donated by $\text{NAD}^{+}$ to a target protein, often by bacterial toxins.

Carboxylation

A Vitamin K-dependent modification attaching a $\text{-COOH}$ group, essential for activating clotting factors VII, IX, and X.

Methylation

Attachment of a methyl group ($\text{CH}_3$) donated by SAM, often inhibiting DNA transcription by tightening histone-DNA association.

Phosphorylation

Attachment of a phosphate group via an ester bond to activate or inhibit protein functions.

Prenylation

Attachment of isoprenoids to anchor proteins to the inner leaflet of the cell membrane.

Sulfation

Attachment of a sulfate group from PAPS typically performed on fibrinogen and gastrin.

Ubiquitination

Attachment of a small protein that tags other proteins for degradation by the proteasome.

Glycation

The nonenzymatic attachment of glucose to proteins, such as hemoglobin in patients with poorly controlled diabetes.

Glycosylation

The enzymatic attachment of various sugars to proteins, defining blood types on erythrocyte membranes.

Domain

A section of a protein often having a separate function such as binding a ligand or spanning the plasma membrane.

Proline

An amino acid that causes a bend or kink, disrupting the regular alpha-helix structure.

Glycine

A small amino acid that allows for rotation, often disrupting the alpha-helix.

Salt bridges

A combination of ionic and hydrogen bonds that stabilize quaternary protein structures.

Preproinsulin

The initial synthesized precursor of insulin containing a signal sequence and chains A, B, and C.

Proinsulin

The intermediate form of insulin after the signal sequence is removed but before the C-peptide is cleaved.

Elastin

A fibrous structural protein characterized by its durability and insolubility in water.

Catalase

An enzyme protein that functions to break down hydrogen peroxide.

Glucagon

A hormone protein synthesized by translation of mRNA, used as a general example of protein function.

Lipoproteins

Plasma proteins categorized under transport functions in the general classification of proteins.

Sickle-cell anemia

A disease resulting from an alteration in the amino acid sequence of the primary structure.

Cystic fibrosis

A disease example cited to illustrate how alterations in primary amino acid sequence produce abnormal function.

Monomer

A single polypeptide chain that functions as a subunit within a quaternary structure.

Covalent Bonds

Strong chemical bonds ($>50\,kcal\,mol^{-1}$) not meant to be broken other than during protein degradation.

Noncovalent Bonds

Weaker attractive forces ($<1$ to $7\,kcal\,mol^{-1}$) that specify protein folding and conformational changes.

Glutathione

A tripeptide whose synthesis is an exception to the standard ribosomal translation process.