week 5 - protein structure and function

• Protein functions

  • structure of cells
  • replication of cells (eg. enzymes in cell replication)
  • Transportation (eg. hemoglobin transporting oxygen)
  • catalyzing reactions
  • signaling of messages
  • preventing infection
• how are proteins so diverse

  1. the FUNCTION of a protein depends on its STRUCTURE
  2. its STRUCTURE depends on the protein's SEQUENCE

  sequence --> structure --> function

  • thus, each protein has a different function
• tertiary structure vs quarternary structure

  • tertiary: ONE polypeptide chain
  • quaternary: AT LEAST ONE polypeptide chain
• amino acid groups

  A) nonpolar

  B) aromatic

  C) positively

  D) negatively

  E) polar

  
• conformations - native conformation

  • many conformations are possible for proteins due to the different rotation of peptide bonds
  • the SPECIFIC conformation which provides the SPECIFIC function is called the NATIVE CONFORMATION
• how does structure of a protein form?

  • By weak interactions
  • eg. Hydrogen bonds, Ion-dipole bonds, Ionic bonds, the hydrophobic effect, van der waals
  • these weak interactions are REVERSIBLE
  • meaning that when proteins fold, these interactions break and form constantly to find the most stable state
• weak interactions stabilises protein structure

  • The hydrophobic effect predominates in protein structure and stability
  • The release of water molecules from the structured solvation layer around the molecule as protein folds increases the net entropy

  A) repulsion

  B) hydrophobic

  C) close proximity

  
• weak interactions stabilise protein structures (2)

  • Hydrophobic amino acids are largely buried in protein interior - preventing interactions with water
  • The number of hydrogen bonds and ionic interactions within a protein is MAXIMISED - when forming the native conformation

  A) hydrophobic

  B) hydrophilic

  
• SECONDARY STRUCTURE = LOCAL SPATIAL ARRANGEMENT

  1. alpha helix
  2. beta sheets
  3. beta turns
• THE ALPHA HELIX – MAXIMISED INTERNAL H-BONDING

  • INTRACHAIN H-bonding most important stabilising feature
  • C=O of residue 'i' is H-bonded to N-H of residue 'i+4' (i is the number of the residue in sequence)
  • one turn every 3.6 residues
  • R-groups project outwards - aids stabilisation etc.

  
• THE BETA CONFORMATION

  • b-strands (single) forms b-sheets (multiple)
  • R-groups project above and below
  • antiparallel b-sheet: H-bonds are linear (STRONGER form)
  • parallel b-sheet: H-bonds are bent (WEAKER form)

  A) c

  B) n

  
• BETA TURNS

  • this allows the connection between the ends of 2 anti-parallel strands (U-turn of proteins)
  • Involves FOUR amino acids
  • Glycine is common at position 3
  • Proline common at position 2 (kink - bonded to N)

  A) p

  B) g

  
• types of displaying 3D protein structures

  1. ribbon representation - most common, ribbons = polypeptide
  2. surface contour - the surface of the molecule
  3. ribbon (inc side chain) - highlights side chains
  4. space-filling - least common, highlights atoms
• THE DISULPHIDE BOND

  • Covalent cross-link (disulphide bridge) by cysteine
  • Can be intrachain (within 1 molecule) or interchain (between 2 or more molecules)
  • IS REVERSIBLE depending on environment

  A) cystine

  B) oxidation

  C) reduction

  
• Tertiary strcutre

  1. Fibrous - simple, repeating secondary structure
  2. Globular – several types of secondary structure, more folded, more compact

  A) long

  B) round

  C) repetitive

  D) irregular

  E) insoluble

  F) soluble

  
• protein motif

  • a recognisable folding pattern, linking two or more secondary structures together

  
• protein domain

  • the independently stable parts of a polypeptide chain
  • or the parts that can undergo movement as a single entity of the protein

  
• consequence of protein not folding

  1. loss of function: absence of native conformation = no function
  2. aggregation: formation of larger insoluble molecules

  
• Christian B. Anfinsen's experiments

  • The protein sequence of RNAase A is sufficient for it to fold into its native conformation
  • urea- strong denatuing agent, disrupts H-bonds, unfolds
  • mercaptoethanol - strong reductant, disrupts disulphide link

  steps

  1. added urea and mercaptoethanol to RNAase in native state
  2. RNAase is now unfolded (inactive). Remove urea and M.ethanol
  3. RNAase is now in its native state again, S-S correctly reformed

  A) native

  
• factors impacting the formation of native conformation of proteins

  • Disulphide bonds
  • Weak interactions
  • Enthalpy - decreases when bonds form (ie.weak interactions) because energy is released
  • Entropy - increases when more messy, protein is trying to bury hydrophobic groups and find its native structure

  A) decreases

  B) strong

  C) ordered

  D) spontaneously

  
• entropy

  • replace non-polar tails for non-polar side chains of amino acids
  • in this example: entropy is increasing of WATER
  • in protein structures: entropy is DECREASING as they become more ordered

  
• protein folding via stepwise pathway

  • secondary structures (red) folding against each other
  • they keep coming together, forming a more stable structure

  
• diagram

  • as it reaches the native state,
  • entropy DECREASES - structure is more ordered/stable
  • enthalpy DECREASES - more bonds formed, more energy released
  • unfolded --> globule --> native

  A) unfolded

  B) globule

  C) native

  
• globular proteins

  • eg. Myoglobin (tertiary) & Hemoglobin (quarternary)
  • spherical shape
  • the red "heme" groups binds to oxygen, transporting it from lungs to the rest of body

  A) hemoglobin

  
• Fibrous proteins examples

  • long secodary structures

  A) keratin

  B) fibroin

  C) collagen

  
• Membrane proteins

  • amino acids within the bilayer tend to be hydrophobic amino acids
  • eg. GLUT1 transporter - transports glucose to the cell

  
• Globular proteins -- Myoglobin

  • function: binds oxygen (delivered to tissue via haemoglobin) and supply it to mitochondria
  • structure: tertiary, 8 a-helices, a pocket containing iron which binds oxygen (ie. heme)

  
• Globular proteins -- Haemoglobin (1)

  • structure: quarternary, 4 polypeptide chains (2x a, 2x b)
  • T state: without oxygen, it is TENSE- desperate for oxygen
  • R state: with oxygen, it is RELAXED- relieved to have oxygen
  • when oxygen binds, the conformation of amino acids changes slightly

  A) T

  B) R

  
• haemoglobin (2)

  • cooperative binding -  Binding of oxygen to one subunit increases its affinity for oxygen in the other subunits.
  • Hemoglobin binds to Oxy. in high conc. (ie. in lungs) but releases Oxy. in low conc. (ie. tissues)
  • it allows a trade off in affinity for oxygen, aiding its function
• haemoglobin (3)

  • due to cooperativity of binding, Hb can shift between high-affinity (in lungs) to low-affinity (in tissues), due to the amount of oxygen in the environment
  • x-axis: partial pressure of oxygen
  • y-axis: fraction of hemoglobin bound to oxygen
  • "high affinity state" line: Hb would be tightly binding to oxygen, preventing it from reaching the tissue.
  • "low affinity state" line: Hb would release Oxy. in tissue (desirable), yet unable to bind much oxygen in the lungs (undesirable)

  A) high

  B) low

  
• Fibrous proteins

  • structure: only single secondary structures, long polypeptide chains, joined by cross links, water insoluble
  • keratin: α-helix but it's made of two polypeptides coiled around each other (protofilament->protofibril), in hair
  • collagen: long stretches of 3x α-helices, but these twist in the other direction (right)

  A) filament

  B) fibril

  C) left

  
• Membrane proteins

  • inserted into the lipid membrane of cells
  • hydropathy plots - map the relative hydrophobic/hydrophilic nature of each amino acid
  • in GLUT1, the hydrophilic amino acids within the bilayer enables glucose to flow (creates hydrophilic core)

  
• secondary structure -> b-sheets

  • antiparallel sheet: H-bonds are straight
  • parallel sheet: H-bonds are bent (v-shaped)

  A) antiparallel

  B) parallel