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Biochemistry I > AAs, proteins, hemoglobin, collagen > Flashcards

AAs, proteins, hemoglobin, collagen Flashcards

1
Q

What is transamination?

A

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

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2
Q

All natural AAs prevail in which kind of Fischer-projection?

A

L-conformation (D would be the enantiomer)

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3
Q

What is the maple syrup disease?

What are possible consequences if not diagnosed early enough?

A

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

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4
Q

Describe the acid-base character of non-polar AAs.

A

zwitter-ions

  • R-COO-: weak acid → pK ~ 2
  • R-NH3+: conjugated base → pK ~ 10
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5
Q

In which pH range are the functional groups of AA de-/protonated?

Compare to pK.

A
  • pH < pK<span>side group</span> → protonated
  • pH > pKside group → deprotonated
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6
Q

What is the isoelectric point?

How can it be calculated?

In which ranges is the IP of different AAs?

A

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
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7
Q

What is cystine?

A

2 Cys form disulfide bridge → cystine

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8
Q

What are primary, secondary and tertiary alcohols?

A
  • prim. alcohol: –CH2OH group → 1 C
  • sec. alcohol: –CHROH group → 2 C
  • tert. alcohol: –CR2OH group → 3 C

R = carbon-containing group

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9
Q

What is PKU?

What are possible consequences if not diagnosed early enough?

A

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

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10
Q

What is selenocysteine?

Clinical relevance?

A

21st AA

HIV-protein is a selenoprotein → lower Se-conc.

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11
Q

Explain the structure of glutathion.

Function?

A

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
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12
Q

List some example for important peptides.

A
  • thyroprotein releasing factor
  • oxytocin → uterine contractions
  • bradykinin → inhibits inflammations
  • enkephalins (in CNS)
  • insulin/glucagon

<strong>​</strong>rather overview than list to memorize

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13
Q

What is steric repulsion?

A

repulsion btw atoms due to e- clouds

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14
Q

Which bonds stabilize/form the primary structure of proteins?

A

peptide bonds (AA sequence, peptides) + disulfide bonds

NOTE: all atoms of peptide bond in same plane = coplanar

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15
Q

Which bonds stabilize/form the secondary structure of proteins?

A

H-bonds btw atoms of peptide groups + minimized steric repulsion

⇒ polypeptide backbone

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16
Q

Which secondary protein structures do you know?

A
  • right handed α-helix
  • β-sheet
  • β-turn
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17
Q

Explain the structure of an α-helix.

A
  • orientated right-handed
  • 3.6 AA residues needed for one turn
  • stabilized by H-atoms btw 1, 4 peptide group
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18
Q

What decreases the stability of the α-helix?

A
  • interaction of side chains (electrostatic/ionic)
  • bulkiness of side chains
  • Pro
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19
Q

Describe the structure of a β-sheet.

Which structure found in plasma membranes are formed by β-sheets?

A

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

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20
Q

What are β-turns?

A

tight connections btw ends of antiparallel β-sheets

  • 4 AA residues connected by 1,4 H-bond
  • esp. often formed btw Gly, Pro
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21
Q

Which bonds stabilize/form the tertiary, quarternary structure of proteins?

What is the result of the tertiary, quarternary structure?

A

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

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22
Q

What can you say about the polarity of proteins?

A
  • inside: hydrophobic pocket (= hydrophobic R-groups)
  • outside: hydrophilic surface
23
Q

What is a domain on a protein?

A

a special region for a particular task

24
Q

When does protein folding start?

What happens exactly?

A
  • starts during protein synthesis (cotranslational) → short segments folded into secondary units
  • hydrophobic regions turn inside → molten globule is formed
25
Q

Which enzymes assist protein folding?

Briefly explain their function.

A

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
26
Q

What are chaperones?

Explain their function.

A

heat-shock-proteins
→ more produced during high T → prevent protein denaturation

27
Q

Describe the structure of collagen.

A
  • 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
28
Q

Which AAs form the primary structure of collagen?

A

(Gly-X-Y)n, where

X and Y mostly Pro and HyPro

29
Q

What PTM does the primary collagen helix receive?

A
  • hydroxylation of
    • Pro → HyPro
    • Lys → _5-OH-Ly_s
  • ​__​glycolysation of
    • Lys, receives glucose/galactose

​

30
Q

How is HyPro formed?

What type of reaction is it?

A

via oxidative carboxylation w/ hydroxylation

α-KG + Pro + O2 → succinate + HyPro + CO2

31
Q

How do you call the condition when the AA cannot be hydroxylated during the formation of collagen?

How is it caused?

A

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

32
Q

How does the tertiary structure of collagen look like?

Which kinds of bonds stabilize it?

A

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
33
Q

What is the difference btw pro- and tropocollagen?

A

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

34
Q

How is the quarternary structure of collagen formed?

Which kind of bonds stabilize it?

A

by polymerization of tropocollagen

stabilized by ​cov. lysinonorleucin bridges, and to a minor extent also interchain H bonds btw OH-groups of HyPro

35
Q

How are the lysinonorleucin bridges of collagen fibers formed?

A

by Lys oxidase

  1. NH2 groups of Lys converted to aldehydes
  2. condensated w/ second Lys (formation of Schiff base, linking 2 polypeptides)
  3. reduced to lysinonorleucin bridges

​

36
Q

How do you call the condition that causes deficient formation of the quarternary structure of collagen?

Why does it happen?

A

Menke’s syndrome

dietary deficiency of Cu2+ required by Lys oxidase

→ def. of lysinonorleucin bridges btw tropocollagen fibers, causing kinky hair, growth retardation

37
Q

List 2 inherited disease causing abnormalities in collagen formation.

A
  • osteogenesis imperfecta
    incomplete procollagen formation → fragile bones
  • Ehler-Danlos syndrome
    decr. activity of procollagen peptidase → stretchabile skin, hypermobile joints
38
Q

Explain the structure of heme.

A

planar cyclic tetrapyrrole linked by methyne bridges,
has Fe2+ center

39
Q

Explain the structure of myoglobin.

A

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

40
Q

Describe the model of the oxygen binding site in myglobin and hemoglobin.

A

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

41
Q

What are the functions of distal and proximal His?

A
  • proximal His F8:
  • *holds heme**
  • distal His E7:
  • *weakens CO binding** to the heme ring (b/c endogenous CO occupies 1% of all sites)
42
Q

Describe the structure of hemoglobin.

A

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

​

43
Q

Differentiate btw types of hemoglobin.

Structure?

A
  • HbA1 (normal adult Hb): α2β2
  • HbA2 (minor adult Hb): α2δ2
  • HbF (fetal Hb): α2γ2
  • HbS (sickle cell Hb): α2βs2
44
Q

How do you call the phenomenon by which hemoglobin facilitates O2 binding and release?

Differentiate btw the 2 states of hemoglobin.

A

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
45
Q

What is 2,3-BPG?

How does it affect the function hemoglobin?

A

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

46
Q

Explain how Hb changes from T to R state.

A

in deoxyHb (T state) Fe2+ is out of plane of heme

  1. binding of 1st O2 induces Fe2+ to move into plane of heme
  2. 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

47
Q

What is the function of hemoglobin?

Explain w/r/t its O2 dissociation curve.

A

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
48
Q

What is the function of myoglobin?

Explain w/r/t its O2 dissociation curve.

A

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

49
Q

Explain the Bohr effect.

A

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

50
Q

How is HbF different from normal HbA?

A
  • 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

​

51
Q

How is HbM different from normal HbA?

A

proximal His F8 replaced by Tyr
Tyr oxidizes Fe2+ to Fe3+

→ H2O binds instead of O2, lethal

52
Q

How is HbS different from normal HbA?

A
  • 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

53
Q

How is sickle cell anemia inherited?

Why can it provide evolutionary benefits?

A

autosomal co-dominantly inherited

  • heterozygotes: have ∽ 1% HbS, but are resistant to malaria
  • homozygotes: die
54
Q

What is thalassemias?

A

autosomal recessive blood disorder

→ defective synthesis of Hb, causes improper O2 transport, anemia

Biochemistry I (13 decks)

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