What is transamination?
reaction btw an AA (containing -amino group) and a keto acid (containing -keto group) where groups are exchanged
→ α-keto acid becomes AA + vice versa
All natural AAs prevail in which kind of Fischer-projection?
L-conformation (D would be the enantiomer)
What is the maple syrup disease?
What are possible consequences if not diagnosed early enough?
non-polar AAs Val, Leu, Ile are not transaminated (to α-keto-isovalerate/-capronate resp.)
BUT: accumulation in blood and urine
⇒ sweet maple syrup-like odor of urine
⇒ brain damage, death
Describe the acid-base character of non-polar AAs.
zwitter-ions
- R-COO-: weak acid → pK ~ 2
- R-NH3+: conjugated base → pK ~ 10
In which pH range are the functional groups of AA de-/protonated?
Compare to pK.
- pH < pK<span>side group</span> → protonated
- pH > pKside group → deprotonated
What is the isoelectric point?
How can it be calculated?
In which ranges is the IP of different AAs?
pH when AA has no net charge
pI = (pK1 + pK2)/2
IP in:
- basic range for basic AAs
- 6-8 for neutral AAs
- acidic range for acidic AAs
What is cystine?
2 Cys form disulfide bridge → cystine
What are primary, secondary and tertiary alcohols?
- prim. alcohol: –CH2OH group → 1 C
- sec. alcohol: –CHROH group → 2 C
- tert. alcohol: –CR2OH group → 3 C
R = carbon-containing group
What is PKU?
What are possible consequences if not diagnosed early enough?
Phe hydroxylase needed to metabolize Phe to Tyr
phenylketonuria
⇒ lack of Phe hydroxylase causes accumulation of Phe + conversion into phenyl-lactate/-pyruvate/-acetate (detectable in urine)
→ serious mental retardation
What is selenocysteine?
Clinical relevance?
21st AA
HIV-protein is a selenoprotein → lower Se-conc.
Explain the structure of glutathion.
Function?
γ-Glu-Cys-Gly
BUT: Cys attached to side chain C-terminal of Glu
function:
- reduction of peroxides (by reduction of -SH)
- can form disulfide bridges
List some example for important peptides.
- thyroprotein releasing factor
- oxytocin → uterine contractions
- bradykinin → inhibits inflammations
- enkephalins (in CNS)
- insulin/glucagon
<strong></strong>rather overview than list to memorize
What is steric repulsion?
repulsion btw atoms due to e- clouds
Which bonds stabilize/form the primary structure of proteins?
peptide bonds (AA sequence, peptides) + disulfide bonds
NOTE: all atoms of peptide bond in same plane = coplanar
Which bonds stabilize/form the secondary structure of proteins?
H-bonds btw atoms of peptide groups + minimized steric repulsion
⇒ polypeptide backbone
Which secondary protein structures do you know?
- right handed α-helix
- β-sheet
- β-turn
Explain the structure of an α-helix.
- orientated right-handed
- 3.6 AA residues needed for one turn
- stabilized by H-atoms btw 1, 4 peptide group
What decreases the stability of the α-helix?
- interaction of side chains (electrostatic/ionic)
- bulkiness of side chains
- Pro
Describe the structure of a β-sheet.
Which structure found in plasma membranes are formed by β-sheets?
either parallel (adjacent segments of polypeptide chain in same direction) or antiparallel
- H-bonds btw carbonyl C and amide H of peptide bonds
- R-groups of adjacent AAs point into opposite directions
⇒ can form β-barrels
What are β-turns?
tight connections btw ends of antiparallel β-sheets
- 4 AA residues connected by 1,4 H-bond
- esp. often formed btw Gly, Pro
Which bonds stabilize/form the tertiary, quarternary structure of proteins?
What is the result of the tertiary, quarternary structure?
formed by:
- hydrophobic interactions
- H-bonds
- polar interactions
- salt bridges (= ionic interactions)
⇒ monomers (e.g. myoglobin) → tertiary
⇒ polymers (in case of dimer: homo-/heteromers) → quarternary
What can you say about the polarity of proteins?
- inside: hydrophobic pocket (= hydrophobic R-groups)
- outside: hydrophilic surface
What is a domain on a protein?
a special region for a particular task
When does protein folding start?
What happens exactly?
- starts during protein synthesis (cotranslational) → short segments folded into secondary units
- hydrophobic regions turn inside → molten globule is formed
Which enzymes assist protein folding?
Briefly explain their function.
assisted by:
- chaperones: move hydrophobic regions inside
- protein disulfide isomerase: catalyzes formation/breakdown of disulfide bonds
- proline-cis, trans-isomerase: isomerizes trans to cis peptide groups
What are chaperones?
Explain their function.
heat-shock-proteins
→ more produced during high T → prevent protein denaturation
Describe the structure of collagen.
- prim. structure: repeated (Gly-X-Y)n sequence
- sec. structure: left handed collagen helix
- tert. structure: right-handed triple helix, stabilized by:
- quart. structure: collagen microfibrils/fibrils/fibers
Which AAs form the primary structure of collagen?
(Gly-X-Y)n, where
X and Y mostly Pro and HyPro
What PTM does the primary collagen helix receive?
-
hydroxylation of
- Pro → HyPro
- Lys → _5-OH-Ly_s
-
__glycolysation of
- Lys, receives glucose/galactose
How is HyPro formed?
What type of reaction is it?
via oxidative carboxylation w/ hydroxylation
α-KG + Pro + O2 → succinate + HyPro + CO2
How do you call the condition when the AA cannot be hydroxylated during the formation of collagen?
How is it caused?
scurvy
dietary vit C deficiency bc is cofactor for Pro/Lys hydoxylase
→ severe instability of collagen fiber, causing bleeding gums, swelling joints, poor wound healing, death
How does the tertiary structure of collagen look like?
Which kinds of bonds stabilize it?
3 left handed collagen helices form right handed procollagen, eventually tropocollagen triple helix
- interchain H-bonds btw peptide groups of Gly and Pro
- cross links btw 2 Lys
What is the difference btw pro- and tropocollagen?
both are right handed triple helix formed by 3 left handed collagen helices, BUT
procollagen has globular terminals which need to be cut by procollagen peptidase so the 3 helices can polymerize
→ forming tropocollagen
How is the quarternary structure of collagen formed?
Which kind of bonds stabilize it?
by polymerization of tropocollagen
stabilized by cov. lysinonorleucin bridges, and to a minor extent also interchain H bonds btw OH-groups of HyPro
How are the lysinonorleucin bridges of collagen fibers formed?
by Lys oxidase
- NH2 groups of Lys converted to aldehydes
- condensated w/ second Lys (formation of Schiff base, linking 2 polypeptides)
- reduced to lysinonorleucin bridges
How do you call the condition that causes deficient formation of the quarternary structure of collagen?
Why does it happen?
Menke’s syndrome
dietary deficiency of Cu2+ required by Lys oxidase
→ def. of lysinonorleucin bridges btw tropocollagen fibers, causing kinky hair, growth retardation
List 2 inherited disease causing abnormalities in collagen formation.
-
osteogenesis imperfecta
incomplete procollagen formation → fragile bones -
Ehler-Danlos syndrome
decr. activity of procollagen peptidase → stretchabile skin, hypermobile joints
Explain the structure of heme.
planar cyclic tetrapyrrole linked by methyne bridges,
has Fe2+ center
Explain the structure of myoglobin.
monomer w/ 8 α-helices A-H (4 terminated by Pro) + heme in center
- non-polar side chains inside
- polar side chains outside
BUT: distal His E7, proximal His F8 close to heme iron
Describe the model of the oxygen binding site in myglobin and hemoglobin.
Fe2+ can form 6 coordinate bonds
4 w/ heme, 1 w/ proximal His, 1 w/ O2
BUT: if Fe2+ oxidized to Fe3+ (unphysiological), only able to bind H2O
→ moves towards proximal His F8 when O2 binds
What are the functions of distal and proximal His?
- proximal His F8:
- *holds heme**
- distal His E7:
- *weakens CO binding** to the heme ring (b/c endogenous CO occupies 1% of all sites)
Describe the structure of hemoglobin.
tetramer consisting of
- always pair of α subunits
- + either pair of β, γ, δ, βs
⇒ can carry 4 O2
NOTE: β subunit has high homology to myoglobin
Differentiate btw types of hemoglobin.
Structure?
- HbA1 (normal adult Hb): α2β2
- HbA2 (minor adult Hb): α2δ2
- HbF (fetal Hb): α2γ2
- HbS (sickle cell Hb): α2βs2
How do you call the phenomenon by which hemoglobin facilitates O2 binding and release?
Differentiate btw the 2 states of hemoglobin.
allosteric behavior triggers homotropic cooperativity
- R state = relaxed, Hb can be easily saturated w/ O2, stabilized by secondary bonds
- T state = tense, Hb easily releases O2, able to bind 2,3-BPG, stabilized by ionic bonds
What is 2,3-BPG?
How does it affect the function hemoglobin?
formed from 1,3-BPG (intermediate of glycolysis) in peripheral tissue whith low PO2
binds to center of T state hemoglobin, forming add. ionic bonds
⇒ prevents re-binding of O2 to hemoglobin in peripheral tissue
Explain how Hb changes from T to R state.
in deoxyHb (T state) Fe2+ is out of plane of heme
- binding of 1st O2 induces Fe2+ to move into plane of heme
- movement transmitted to His F8 and F helix, breaks ionic bonds btw all 4 subunits → changes in protein structure = oxyHb (R state)
⇒ increased affinity for O2 of other subunits,
ALSO: 2,3-BPG unable to bind now
What is the function of hemoglobin?
Explain w/r/t its O2 dissociation curve.
transports O2 in blood
sigmoidal curve due to cooperative behavior and 2,3-BPG
- high PO2 in pulm. capillaries: Hb becomes easily saturated due to succ. incr. affinity for O2
- low PO2 in syst. capillaries: 2,3-BPG in those tissue, keeps Hb from binding much O2, facilitates O2 release into tissue
What is the function of myoglobin?
Explain w/r/t its O2 dissociation curve.
storage of O2 in muscle tissue as reserve, has hyperbolic curve
releases O2 only at very low PO<strong>2</strong> (i.e. during exercise)
NOTE: Hb would behave just the same if there were no 2,3-BPG in peripheral tissue
Explain the Bohr effect.
describes the decr. affinity of Hb when PCO2 incr./pH decr. → easier release of O2 in tissue w/ high consumption rates
i.e. during exercise: incr. metabolic activity causes
- ↑ T
- ↑ [CO2], ↓ pH
- ↑ production of 2,3-BPG
⇒ H+ binds to Hb → ionic bonds reform, T state
right shift of dissociation curve
How is HbF different from normal HbA?
- α2γ2
- has weaker BPG binding b/c His143 replaced by Ser143
⇒ higher affinity for O2 in placenta, but also limited O2 delivery → changes structure after birth
How is HbM different from normal HbA?
proximal His F8 replaced by Tyr
Tyr oxidizes Fe2+ to Fe3+
→ H2O binds instead of O2, lethal
How is HbS different from normal HbA?
- α2βs2
- surface Glu6 replaced by Val6 → forming sticky hydrophobic patch on βs
deoxyHb aggregates, forming long sickle shaped fibers which are prone to lysis in splenic sinusoids
⇒ causing sickle cell anemia
How is sickle cell anemia inherited?
Why can it provide evolutionary benefits?
autosomal co-dominantly inherited
- heterozygotes: have ∽ 1% HbS, but are resistant to malaria
- homozygotes: die
What is thalassemias?
autosomal recessive blood disorder
→ defective synthesis of Hb, causes improper O2 transport, anemia