S1-L5: Proteins Flashcards
Outline and describe proteins
- Fundamental cellular components vital for all cellualr function
- polymeric–> chain like structures made up of monomers
- macromolecules–> v. large molecules
- 1000’s proteins exist- each with different functions
- ->human body able to generate 2 million different protein types from 20000 genes
For each of the following proteins outline their function and an example of each:
1-Structural 2-Storage 3-Transport 4-Hormonal 5-Receptor 6-Contractile 7-Defensive 8-Enzymatic
1- support--> collagen 2- storage--> casein 3- O2 transport--> hemoglobin 4- metabolism--> insulin 5- cellular response--> B-adrenergic receptor 6- movement--> actin/ myosin 7- protection--> antibodies 8- catalysis--> digestive enzymes
What are polypepetides?
- amino acid monomers linked via peptide bonds
- contain >40 amino acids able to fold in to defined shape
How do polypeptides influence proteins?
-protein sequence of amino acids determines shape + function of protein
What are all proteins composed off?
-standard 20 amino acids–> proteinogenic amino acids
Outline the structure of amino acids (figure 1)
- possess amino (-NH2) + carboxyl (-COOH which acidic)
- amino acids differ based on side R chain
Are amino acids chiral molecules?
- except Ca all amino acids have chiral centre
- -> atom in molecule bonded to 4 different chemical species
Explain the two forms in which amino acids exist and which is more dominant
- able to exist as either of 2 enantiomers–> mirror images L & D
- ->not superimposable (place on each other to be same)
- L form dominates D-amino acids v. rare in nature (left and right-handed)
Which part of amino acids determine the physiochemical properties of amino acids?
-physiochemical properties determined by R group
Outline the 4 different categories in which amino acids can be classed under
- Non-polar hydrophobic (water-hating)
- polar
- acidic
- basic
- last three are hydrophilic (water-loving)
Learn the following non-polar R group amino acids (figure 2)
- Glycine
- Alanine
- Valine
- Leucine
- Isoleucine
- Methionine
- Phenylalanine
- Tryptophan
- Proline
What are acidic R group amino acids?
-Side chains (-) charged at physiological pH (approx 7.4)
Outline the two acidic amino acids (refer to figure 3)
-Aspartic acid AND Glutamic acid
Define basic R group amino acids
-side chains (+) charged at physiological pH (approx 7.4)
What are three basic R group amino acids? (refer to figure 4)
- Lysine
- Arginine
- Histidine
Briefly explain what polar R group amino acids are
-able to form H bond interactions with similar side-chains + peptide bonds
Outline the 6 polar R group amino acids (refer to figure 5)
- Tyrosine
- Asparagine
- Glutamine
- Serine
- Threonine
- Cysteine
With reference to figure 6 describe how cysteine residue can form disulphide bridges
-2 polypeptide chains are covalently linked together (strong bonds)
Describe the formation of polypeptide chains in appropriate detail (figure 7)
- achieved via -COOH and -NH2 group linkage done through dehydration/condensation reaction
- ->removal of H2O molecule
- 2 molecules combine to form larger molecule with small molecule loss
- ->peptide bond forms
What is the significance of this polypeptide chain formation?
- a peptide backbone is formed
- ->side chain project from backbone
Briefly explain what “bond resonance” is
- way to describe bonding in certain molecules/ions by combination of several contributing structures/forms (AKA resonance structures/canonical structures)
- ->in resonance hybrid/ hybrid structure in valence bond theory
What does bond resonance cause? (refer to figure 8)
-causes peptide bond to be rigid AND planar
Why is peptide bonds “trans” form most common?
- rotation around C atom usually limited by steric clashes between bulky R groups
- ->hence trans form most common
What is “directionality” in terms of polypeptides?
refer to figure 9
- means polypeptide chain has two chemically distinct ends from one another
- ->one end has free amino group (Amino terminus)
- read from amino to carboxyl terminal so going from N (amino group) to C (carboxyl group)
Why do polypeptide chains have directionality?
-due to structure of amino acids
Outline the 4 levels of protein structure (figure 10)
- Primary: amino acid sequence
- Secondary: interactions between adjacent amino acids
- ->E.G: a helixes/ B pleated sheet, loops or random coils
- Tertiary: 3D folding of single polypeptide chain
- Quaternary: assembly of multiple proteins into complex
Describe the primary structure of proteins (refer to figure 11)
- amino acid sequence from N-terminus to C (display left to right)
- ->determined by DNA sequence of gene for each protein
How does the primary structure of proteins affect proteins?
-dictates final protein as sequential arrangement of R groups influences subsequent secondary/ tertiary/ quaternary structures
Outline how the primary structure may be effected and the consequences. Include an example.
- Genetic mutation could lead to primary structure changes which may alter structure AND function
- ->E.G: sickle cell diseases
- ->caused by single mutation in HbA hemoglobin gene
Describe the secondary structure of proteins
- parts of polypeptide chains take regular patterns of H-bonding resulting in
- -> a-helixes/ B-pleated sheets
- above patterns connected by short-runs AND longer loops/random coils
Briefly describe the “coiled rod-like” structure of the a-helix
- most common secondary structure
- flexible & elastic
- coil of helix means chain not fully extended
- proline disrupts a-helix structure due to mutation for example (“helix breaker”)
- abundant in hemoglobin
- absent in chymotrypsin (digestive enzyme)
Describe “stabilising by extensive intra-chain H bonding” in the a-helix (figure 13)
- 3.6 amino acids per turn
- right-handed (“clockwise” from N to C-terminal end)
- peptide bonds form backbone
- R groups project outwards to avoid steric (Spatial arrangement) hindrance
Define “amphipathic a-helixes”
-alpha-helix molecule which has both polar and non-polar parts to it
Describe how B-pleated sheets are “flat/short-run and pleated” (figure 14)
- flat sheets/pleated (not as coiled)/short runs (5-10 amino acids)
- parallel AND anti-parallel or mixed
- strands almost fully extended–>surface appears pleated
- strong plus resilient
- multiple sheets connected by short turns OR “hairpin loops”
What are beta plated sheets held together by?
-by H-bonds between peptide bonds on adjacent strands
Outline and explain how length affects B-pleated sheets in comparison to a-helixes
- 1A^o–> equivalent to 10^-10m
- side chains of B-pleated sheets arranged alternately opposite sides of strand
- distance between amino acids is 3.5A^o (1.51A^o in a-helix)
- ->so B-sheets more flexible than a-helixes able to be twisted
- length of B-sheets in protein ranges 2-22 residues
Can b-sheets be amphipathic?
-yes
Describe “loops/random coils” and their relation to proteins
- connect secondary structural elements
- normally located on surface
- rich in polar AND charged residues
- lengths vary 2-20 residues
- frequently part of enzyme active sites
- less conserved than other secondary structural elements
- differences between structurally similar proteins typically occur in loops
What are “structural motifs”?
- arrangements of secondary structures (super-secondary structures) which frequently occur within proteins
- ->AND can be associated with specific biological function
Examples of structural motifs
-B-hairpin/ Helix-loop-helix/ Greek key/ Coiled coil/ Zinc finger/ Beta barrel
Outline and describe the “B-Hairpin” motif (figure 15)
- 2 adjacent anti-parallel B strands joined by hairpin loop
- simplest super secondary structure
- common in globular proteins (spherical + involved in metabolic functions)
- ->no specific function associated with this motif
Briefly explain the “Helix-loop-helix” motif (figure 16)
- 2 a-helixes connected by loop
- function as either DNA-binding (like c-Myc) OR Ca2+ binding motif (like calmodulin)
- ->common in transcription factors (helix-basic loop-helix) AND cell signalling proteins which bind to Ca2+ (EF-hand)
Similarly, explain what the “Greek Key” motif is (figure 17)
- 3 adjacent anti-parallel B-strands connected by hairpin plus 4th strand adjacent to 1st AND linked to 3rd by longer loop
- common in range of proteins–>like proteases (trypsin)/cytokines (TNFa)
- no specific function associated with this motif
Outline and describe the “Coiled coil” motif
- usually contain repeat of 7 residue patterns (hxxhcxc)
- h= hydrophobic/ c=charged/ x= any
- ->resulting amphipathic a-helixes have “stripe” of hydrophobic residues which coil around similar stripes in other helixes
- -> such that hydrophilic residues project outwards
Give examples of the Coiled coil motif (figure 18)
- Leu zippers in transcription factors (like c-Fos)
- structural proteins (myosins)
What are “Zinc Finger” motifs? (figure 19)
- 2 anti-parallel b-sheets followed by 1 a-helix
- ->stabilised by zinc ion
- ->may bind Fe/Zn or no metal at all
- metal binding mediated by Cis (in B-sheets) AND His (in a-helix)
Where may this motif commonly be found?
- common motif in many proteins including transcription factors
- ->E.G: Kruppel-factor 4 (KLF4)
- ->this is protective transcription factor
- can be present frequently within same polypeptide chain
What are the function(s) of this motif?
-binding of DNA/ RNA/ lipid and protein substrates
Describe the “Beta barrel” motif
- multiple anti-parallel B-sheets which twist AND form closed structure
- first strand is H bonded to last
Outline and describe each of the following Beta barrel motifs:
1-Greek Key motif
-Previously discussed
2- Up-and-down barrel (figure 20)
-8 anti-parallel B-sheets connected by hairpin loops (like Retinol-binding protein)
3- Jelly roll barrel (complex)- figure 21
- 8 B-strands arranged as 2 four-stranded antiparallel B-sheets which wrap around hydrophobic interface
- -> example: major capsid protein P2 from bacteriophage PM2
4- Pore-forming- water channels (aquaporins)
- complex of proteins subunits each with 2 four-stranded anti-parallel B-sheets
- ->polar side chains face inwards to form channel for hydrophilic molecules like Porin 1
Give a list of all the motifs outlined
- B-Hairpin
- Helix-loop-helix
- Greek Key
- Coiled coil
- Zinc Finger
- Beta barrel (Greek Key/ Up-and-down barrel/ Jelly roll barrel/ Beta-helix barrel (pore-forming (water channels))
Define and describe “domains”
- polypeptide chain/part of chain which independently folds in to stable structure with its own hydrophobic core
- ->formed from several simple motifs AND secondary structure elements
What is the relation between domains and proteins?
- proteins can have anything between one to several tons of domains
- ->each domain associated with distinct biological function
Describe the following domain example:
Sre homolgy 2 (SH2) domain
- binds phosphor-Tyr residues
- ->important in insulin signalling
Briefly explain the tertiary structure of a protein (figure 23)
- Overall 3D shape of entire polypeptide- held together by
- ->H bonds- between R groups
- ->Ionic bonds (electrostatic attraction)- between CO2 + NH3+ of R groups
- ->Disulfide bridges (covalent cross-links)- between cysteine -SH groups (Cys-S-S-Cys)
- ->Hydrophobic interactions- hydrophobic R groups cluster inside proteins to shield themselves from H2O
Which linkage is the strongest?
-Disulfide bridges
What are Fibrous Proteins?- describe them (figure 24)
- secondary structures form long parallel fibres AND sheets
- ->usually insoluble in water
What important roles do fibrous proteins play?
- providing strength AND support
- ->collagen and keratin
Where are “a-Keratins” and “B-Keratins” found?
- “a-Keratin” mammalian hair and nails
- “B-Keratin” invertebrate silks/reptile scales/ claws
- Avian feathers/beaks and claws
Outline and describe collagen
- Super-helixes OR Gly-rich triple a-helixes (tropocollagen)
- ->assemble in to fibrils
- main protein in connective tissues–> support/connects OR separates tissues AND organs
- v. abundant (25% of total protein)
Why is the “strong and elastic” quality of collagen useful for the human body?
-bone/cartilage/ teeth/ ligaments (skeletal)/ tendons/ skin blood vessels/ eyes (cornea AND lens)
What condition may one develop when collagen “goes wrong”?
- Ehlers Danlos Syndrome (EDS)
- Genetic connective tissue disorder
How may this condition develop and what is it’s affect?
- multiple mutations possible in multiple genes
- ->structure/ production AND OR processing collagen affected
- ->can affect skin/musculoskeletal/cardiovascular
Describe a-Keratins which are found in hair and nails (figure 25)
- composed of coiled-coils of 2 a-helixes which asseble together into larger fibres
- strong & inextensible/insoluble ALSO chemically inert/ disulphide bridges cross link coiled-coils
What is Fibroin? Outline and describe it
- Fibroin found in silk AND spider webs
- ->layers of anti-parallel B-Keratin sheets rich in Ala AND Gly residues
- ->small side chains interdigitate (interlock) to allow close packing of B-sheets
How does the structure of Fibroin allow it to be elastic and strong?
- sheets joined by amorphous (no defined shape/form) stretches
- spider silk able to stretch x30 more than most stretchy nylon
Describe globular proteins
- mixture of irregular folded 2^0 elements to form compact 3D shape
- usually water soluble with inner hydrophobic core transported easily in body fluids
Where are globular proteins often found (also state some examples) ?
- common structure of enzymes
- ->important functions in cellular biochem
- examples- myoglobin/ hemoglobin/immunoglobins
Briefly outline and explain the structure of hemoglobin
- Tetramer (polymer comprising of 4 units)
- 4 polypeptide chains/ subunit (a2B2- adult hemoglobin)
- 4 haem molecules (haem–> porphyrin ring + Fe2+/binds O2)
What is myoglobin?
- related to hemoglobin
- exists as single polypeptide
What is the job of hemoglobin and how is that important?
- transports O2 from lungs to rest of body
- -> released O2 to permit aerobic respiration to provide energy
Outline the possible effect of DNA mutations on hemoglobin
- specific mutations in DNA encoding Hb genes can cause disease
- -> like sickle cell disease/ Thalassaemia
Define Thalassaemia
-produce little/no hemoglobin which used by red blood cells to carry O2 around body
Briefly explain sickle cell disease
- disease caused by single gene defect
- single mutation in DNA coding region within B-globin gene
- non-sense mutation changes primary sequence
Outline the symptoms/ effects mutations (in this particular case) may cause (figure 27)
- changes in RBC shape (sickle-shaped cells)
- RBC’s rigid–> become blocked in capillaries–> Ischaemia/Organ Damage/ Pain
- increased haemolysis (rupture/destruction of red blood cells) leads to RBC destruction –> Anaemia/ Spleen damage (location where red blood cells damaged)
Describe the effect of a single mutation (refer to figure 28 and 29)
- single mutation in B-globin gene (T to A) changes primary sequence (Glu–> Val)
- ->therefore bonding in tertiary structure changes so shape of protein changes
Outline and describe immunoglobins
- Y-shaped proteins of immune system which identify AND combat invading foreign organisms
- 4 chains linked by disulphide bridges
- ->2 large H (heavy) and 2 short L (straight) short chains
What do variable structures in H & L chains form? (figure 30)
- form specific binding sites for non-self targets
- -> antigens
What is the importance of these variable structures?
-antigen recognition by antibody marks it for attack by other components of immune system engaged by constant portions of H chains
Briefly explain “denaturation” of proteins and it’s effect (figure 31)
- process where proteins lose quaternary/ tertiary AND secondary structure present in their native state due to change in environment
- ->results in loss of function
For what possible reasons may protein denaturation occur?
-possibly due to extreme pH/ extreme temp/ organic solvents
During protein denaturation due to pH what is the effect on ionic bonds and then the consequence of that?
- ionic bonds broken as v. sensitive to pH
- disrupts tertiary structure
- can render proteins insoluble in water AND precipitate out of solution
Describe low pH and its effect
- Is high H+ conc (acidic)
- adding H+ neutralises COO part of ionic bond
- -> removing it’s charge (H+ + COO- –> COOH)
Outline what high pH is
- low H+ conc (alkaline)
- removing H+ neutralises NH3+ part of ionic bond-removing its charge
-NH3+ –> NH2 + H+
Explain the denaturation of proteins through heat (increase in temp)
- increase in temp vibrates & breaks H AND ionic bonds
- denaturation able to render (cause) proteins to become water insoluble–> precipitate out of solution
What is pyrexia?
- increase body temp/ fever
- ->ancient anti-viral defence mechanism
How do solvents cause proteins to become denatured?
- ethanol/ acetone/ phenol (organic solvents)
- ->forms new H bonds with protein side chains PLUS backbone
- ->disrupts intra- AND inter- chain H bonds
- ->causes protein to unfold AND denature
Summary of lecture
- Proteins–> polymers of amino acids
- protein function dictated by amino acid sequence
- changes in amino acid sequence may cause disease –> like B-globin/ sickle cell disease
- 4 levels of protein structure–> primary/ secondary/ tertiary/ quaternary
- proteins structure typically either fibrous (like collagen) OR globular (like hemoglobin)
- protein structure may be disrupted (denatured)
- -> by extreme temp/extreme pH/ organic solvents
