proteins structure & functions

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

protein - general functions

transport → hemoglobin, albumin, lipoproteins

muscular contraction → actin & myosin

structure → collagen & elastin

enzymes → catalase

hormones → insulin & glucagon

protection → immunoglobulin (antibody)

storage → ferritin & casein

central dogma

the flow of genetic information in cells

• DNA transcribed into RNA then translated into proteins/peptides

  • expression of mRNA under genetic control of transcription

  • 20 proteinogenic amino acids → functional protein/peptide

protein structure

the sequence and arrangement of amino acids that determines a protein’s folding and ultimately its biological function

• side chains (R‑groups) determine properties (charge, polarity, hydrophobicity)

  • soluble proteins → polar residues on surface

  • membrane proteins → nonpolar residues on surface interacting with lipid bilayer

• amino acid sequence → dictates folding → determines structure → determines function

  • primary → secondary → tertiary → quaternary

fibrous protein

a type of protein characterized by narrow, elongated and strand-like structures that providing structural support and strength

• amino acid sequence: repetitive

• durability: less sensitive to pH and temperature changes

• solubility: generally insoluble in water

• examples: collagen, keratin, elastin, fibrin, actin, myosin

globular protein

a type of protein characterized by compact and round/spherical structures that performs various functions

• amino acid sequence: irregular

• durability: more sensitive to pH and temperature changes

• solubility: generally soluble in water

• examples: enzymes, hemoglobin, insulin, immunoglobulins

covalent bond

strong chemical bonds that stabilize protein structure and provide rigidity and resistance to denaturation

• strength: >50 kcal/mol (very strong)

• only broken during degradation

• maintain primary structure and some tertiary stabilization

  • peptide bonds − link amino acids in the backbone

  • disulfide bonds − between two cysteine residues

noncovalent bond

weak attractive forces between amino acid side chains that specify protein folding, flexibility, and shape

• strength: <1–20 kcal/mol (individually weak, collectively strong)

• essential for tertiary and quaternary structure

• include:

  • hydrophobic interactions (~2–3 kcal/mol)

  • hydrogen bonds (~1–7 kcal/mol)

  • ionic bonds (~1–20 kcal/mol)

  • van der Waals forces (<1 kcal/mol)

hydrophobic forces

noncovalent attractions between nonpolar amino acid side chains that cluster away from water

• strength ~2–3 kcal/mol

• most important force in protein folding → 3° structure

• drive nonpolar residues into the protein core

  • stabilize globular proteins

  • essential for membrane protein orientation

hydrogen (H) bonds

weak attractions between partially charged atoms that occur between hydrophilic R groups or backbone atoms which stabilize protein folding and interactions

• strength ~1–7 kcal/mol

• stabilize secondary structure (α‑helices, β‑sheets)

• contribute to tertiary structure specificity

• easily broken and reformed → allow flexibility

ionic bond

electrostatic interactions between positively and negatively charged amino acid side chains

• strength ~1–20 kcal/mol (can be strong)

• occur between acidic (Asp, Glu) and basic (Lys, Arg, His) residues

• stabilize tertiary and quaternary structure

  • important in active sites and protein–protein interactions

• sensitive to pH changes

van der Waals (London dispersion) forces

very weak, transient attractions between closely packed atoms that arise from temporary dipoles which fine‑tune protein stability

• strength <1 kcal/mol

• contribute to tight packing of the protein interior

• help stabilize tertiary structure

primary (1°) structure

the unique, linear sequence of amino acids in a polypeptide chain determined by the genetic code that ultimately dictates the protein's shape and function

• amino acids are linked by peptide bonds

  • read from N‑terminal → C‑terminal end

  • identical molecules of the same protein fold into the same native conformation

• sequence dictates all higher‑order structure: secondary → tertiary → quaternary

• alterations in sequence → abnormal folding and disease

  • examples: sickle‑cell anemia, cystic fibrosis

peptide bond

a strong covalent bond linking amino acids together from the α‑carboxyl group of one residue to the α‑amino group of the next

• forms the primary structure

• created during translation by ribosomes using mRNA and tRNA

  • directionality: N‑terminus → C‑terminus

• does NOT break during denaturation (only conformational shape changes; backbone remains intact)

• exception: glutathione synthesis uses a non‑standard peptide linkage

secondary (2°) structure

the spatial arrangement of amino acids in a polypeptide chain stabilized by hydrogen (H) bonds between peptide‑bond elements

• determined by primary sequence

• major types: α‑helix, β‑pleated sheet, β‑turns, super‑helical structures, super‑secondary motifs

alpha (α)-helix

a rigid, right-handed coiled secondary (2°) structure stabilized by intrachain hydrogen bonds

• most common and stable secondary structure

• stability arises from maximizing H‑bonds

• 3.6 residues per turn

  • hydrogen bonds run parallel to helix axis

  • side chains project outward

alpha (α)-helix interruptions

amino acid residues or side‑chain patterns that disrupt & destabilize α‑helix formation

• proline (pro) → rigid ring → bends/kinks

• glycine (gly) → too flexible → rotation

• charged residues (glu, asp, lys, arg, his) → electrostatic repulsion or salt‑bridge formation

• bulky residues (trp, val, ile) → steric hindrance

super helical structure

a higher‑order arrangement of α‑helices coiled together into a larger helical structure that provides strength and elasticity

• formed by intertwining multiple helices

• stabilized by hydrophobic interactions and H‑bonds

• seen in structural proteins like keratin and collagen

coiled α-helix - keratin

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

• provides mechanical strength

• stabilized by hydrophobic interactions

coiled α-helix - collagen

a super‑helical cable formed by three helical polypeptide chains wound together

• stabilized by interchain hydrogen bonds

• essential for connective tissue structure

• distinct from α‑helix

beta (β)-pleated sheet

a secondary structure composed of two or more peptide chains or peptide chain segments arranged parallel or antiparallel almost fully extended

• perpendicular interchain hydrogen bonds + side chains alternate above and below plane

  • hydrogen bonds form between adjacent strands

  • appears “pleated” due to zig‑zag backbone

• provides strength and rigidity

beta (β)-turns

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

• involve 4 amino acids

  • hydrogen bond between residue 1 and residue 4

  • often contain glycine (flexible) or proline (kink‑forming)

• commonly found on protein surfaces → essential for compact folding

super secondary structures (motifs)

spatial arrangement of organized secondary level peptide fragments forming intermediate structures between secondary (2°) & tertiary (3°) levels

• stabilized by similar forces as tertiary structure

• often found in active sites

• each motif contributes to a specific domain function

  • ligand binding

  • membrane spanning

  • catalytic activity

  • DNA binding

  • protein–protein interactions

helix-turn-helix motif

a super secondary structure containing two alpha (α) helices joined by a short flexible turn

• one helix = recognition helix (binds DNA major groove)

• classic motif in transcription factors → essential for gene regulation

• homeodomain proteins contain three α‑helices encoded by a 180‑bp homeobox

homeodomain

a DNA-binding domain that typically contains a helix-turn-helix motif enabling the protein to bind DNA and regulate gene expression

• three alpha helices encoded by a 180-base-pair homeobox

zinc (Zn²⁺) finger motif

a DNA‑binding motif consisting of an α-helix and a two-segment antiparallel β-sheet held by a zinc atom and four cysteine or histidine residues

• binds DNA via recognition helix

• found in many transcription factors

• used by all steroid hormone receptors

leucine zipper motif

a DNA‑binding motif with formed by α-helix with regular leucine residues that interacts with another polypeptide in a similar region to coil around each other

• leucines every 7 residues → hydrophobic “zipper”

• helices dimerize through hydrophobic interactions

• forms a Y‑shaped structure that grips DNA

• common in transcription factors (e.g., AP‑1 family)

helix-loop-helix motif

a DNA‑binding motif consisting of a short helix connected by a polypeptide loop to a longer helix

• loop allows movement and proper orientation

• helices dimerize to bind DNA

• important in developmental transcription factors

• regulates cell differentiation pathways

tertiary (3°) structure

the final three‑dimensional arrangement of domains within a single polypeptide chain

• formed by interactions between R‑groups far apart in the primary sequence

• stabilized by hydrophobic interactions, hydrogen bonds, ionic bonds, & disulfide bonds

• determines protein shape, stability, and function

tertiary (3°) structure - folding principles

the forces that drive polypeptide folding into a compact 3D structure

• H₂O molecules interact more strongly with each other → drives hydrophobic collapse

  • hydrophobic side chains collapse inward to form the core

  • polar and charged residues remain on the surface → interact with H₂O

• polar backbone segments buried inside form internal hydrogen bonds generating secondary structure

disulfide bond (S−S)

a covalent bond formed by the oxidation of the thiol groups between two cysteine residues in a protein

• stabilizes the tertiary structure

• two types:

  • inTRAmolecular (intrachain) - forms a bend or loop within a single polypeptide

  • inTERmolecular (interchain) - links two separate polypeptide chains together

tertiary (3°) structure - myoglobin

a protein with tertiary structure containing approximately 80% alpha-helix and no beta-sheet structure

• folds into a compact globular shape around a heme group

• heme is coordinated by a proximal histidine residue

• functions as an oxygen‑storage protein in muscle

quaternary (4°) structure

the spatial arrangement and interaction of multiple polypeptide chains (subunits) within a multi‑chain protein

• each polypeptide chain = monomer / subunit

  • subunits associate through noncovalent interactions

• stabilized by salt bridges (ionic + H bonding)

• enables cooperativity and allostery between subunits

  • example: hemoglobin → oxygen binding to one subunit increases affinity of the others

cooperativity

a property of quaternary structure where ligand binding to one subunit alters the affinity of the remaining subunits

• positive - first binding event increases affinity of other subunits

• negative - first binding event decreases affinity of other subunits

allostery

a property of quaternary structure where ligand binding at one site induces a conformational change that alters activity at a different site

• alters affinity or activity at the functional site (e.g., active site, binding site)

• can be activation or inhibition

• mediated by noncovalent interactions between subunits

steps - insulin synthesis

1. preproinsulin synthesized in RER → contains N‑terminal hydrophobic signal peptide

2. signal peptide cleaved → forms proinsulin

3. proinsulin folds in RER → three disulfide bonds (two inter‑chain, one intra‑chain)

4. proinsulin transported to Golgi → C‑peptide is enzymatically removed

5. mature insulin (A‑chain + B‑chain linked by disulfide bonds) & C‑peptide are released together into circulation

preproinsulin

the initial insulin precursor synthesized in the rough ER containing a signal peptide

• contains:

  • N‑terminal hydrophobic signal sequence (targets protein to RER)

  • A‑chain, B‑chain, and C‑peptide

• signal peptide is cleaved in the RER → forms proinsulin

proinsulin

the insulin precursor formed in the RER after removal of the signal peptide

• contains A‑chain, B‑chain, and C‑peptide

• folds and forms three disulfide bonds

  • two inter‑chain (A ↔ B)

  • one intra‑chain (within A‑chain)

• transported to Golgi, where C‑peptide is removed to form mature insulin

insulin

a mature, globular hormone composed of A‑ and B‑chains linked by disulfide bonds

• formed in the Golgi after removal of C‑peptide

• stabilized by two inter‑chain disulfide bonds + one intra‑chain disulfide bond (A‑chain)

• secreted with C‑peptide into the bloodstream

A-chain

the insulin polypeptide chain containing an intra‑chain disulfide bond required for proper folding and receptor recognition

• part of proinsulin and insulin

• participates in two inter‑chain disulfide bonds with the B‑chain

• essential for correct tertiary structure and receptor recognition

B-chain

the insulin polypeptide chain that pairs with the A‑chain through inter‑chain disulfide bonds

• part of proinsulin and insulin

• connected to A‑chain by two inter‑chain disulfide bonds

• contributes to insulin’s receptor‑binding surface

• no intra‑chain disulfide bond

C (connecting)-peptide

a fragment that ensures proper alignment of A‑ and B‑chains for the proper formation of disulfide bonds in insulin

• present in proinsulin

• cleaved in the Golgi to produce mature insulin & released together with insulin into the bloodstream

• used clinically to assess endogenous insulin production

hydroxylation

a posttranslational modification that attaches an −OH group to proteins

• vitamin C-dependent modification of proline and lysine → essential for structural stability of collagen

acylation

a posttranslational modification that attaches an acyl group (e.g., fatty acids) to proteins

• small G-proteins modification with palmitic acid or myristic acid → affects their attachment to subcellular membranes

ADP ribosylation

a posttranslational modification that attaches an ADP ribose group donated by NAD⁺ to proteins

• mediated by several bacterial toxins → alters protein function and can impact signal transduction pathways

carboxylation

a posttranslational modification that attaches a carboxyl group (−COOH) to proteins

• involved in the activation of vitamin K-dependent blood clotting factors (VII, IX, and X)

methylation

a posttranslational modification that attaches a methyl group (−CH₃) donated by SAM to proteins

• histone modification (tighten)→ inhibits DNA transcription

phosphorylation

a posttranslational modification that attaches a phosphate group (−PO₄) via an ester bond to proteins

• crucial for activating or deactivating many enzymes and receptors→ plays a key role in signal transduction

prenylation

a posttranslational modification that attaches isoprenoids (geranylgeranyl or farnesyl) groups to proteins

• anchors proteins to the inner leaflet to the cell membrane

sulfation

a posttranslational modification that attaches a sulfate group (−SO₄) from PAPS (3′-phosphoadenosine 5′-phosphosulfate) to proteins

• performed on fibrinogen & gastrin

ubiquitination

a posttranslational modification that attaches ubiquitin proteins to target proteins

• covalently attached to the ε‑amino group of a lysine side chain

• signals for protein degradation via the proteasome

glycation

a posttranslational modification that non-enzymatically attaches a glucose molecule to proteins

• high levels to modification to hemoblogin observed in patients with poorly-controlled diabetes

glycosylation

a posttranslational modification that enzymatically attaches a number & variety of sugars to proteins

• modification to erythrocyte membrane proteins define an individual’s blood type

Denatured phenylalanine hydroxylase is able to return to its enzymatic activity after a harmful agent is removed.

This observation is explained by:

the AA content of protein specifies its confirmation

Choose the proper sequence of atoms in the protein backbone:

C-N-C-C

Albumin is a protein composed primarily of which of the following types of secondary structure?

alpha helix

Myoglobin is a protein composed primarily of which of the following types of secondary structure?

alpha helix

Protein molecules have different levels to be organized.

Assembly of multiple subunits into multisubunit molecule is called as which of the following?

quaternary