Exam 2

Question 1

Insulin: synthesis

Answer 1

In β-cells of the pancreas, proinsulin is cleaved into insulin and connecting peptide (C-peptide). Both are
stored in vesicles and secreted into the blood circulation

Question 2

Insulin: structure and storage

Answer 2

Insulin: primary structure (51 a.a)
2nd: alpha and beta helices
quaternary: zinc-insulin hexamer (6 insulin molecules stabilized by zinc ions)

In β-cells, insulin is first stored in secretory vesicles

Question 3

What determines a proteins function

Answer 3

its structure

Question 4

Formation of a peptide bond

Answer 4

Peptide bond formation: condensation reaction (removal of water) costs energy (GTP, ribosome)

C (w/ =O) binds to N of other a.a
> carboxylic group binds to amine group

Question 5

Polypeptide chain

Answer 5

Peptide chain is amino acids linked through peptide bonds, also called amide bonds
> The properties of a protein is determined by the side chains

N terminus is amine end
C terminus is carboxylic end

Question 6

alpha-helix

Answer 6

Backbone: Formed by polypeptide chain

R-groups (side chains): These stick outwards from the helix, away from the helical axis

Intra-chain Hydrogen Bonds: They form within the same chain between the backbone atoms.

Specifically:
The carbonyl oxygen (C=O) of an amino acid forms a hydrogen bond with the amide hydrogen (N-H) of an amino acid.

These bonds run parallel to the helix axis, holding the coil tightly together

a-helix can anchor proteins in a membrane: pore proteins (transport) and hormone receptors (signal transduction)

helix breakers: Chemical (oxidative) changes in amino acid side chains that disturb structure (loss in structure = loss in function)

Question 7

Collagen

Answer 7

Rigid structure: 3 intertwined a-helices (triple helix)

Primary structure, more than 1000 amino acids is composed of the repeat: Gly-X-Y, with Y often proline or 4-hydroxyproline

Multiple tropocollagen units pack together to form fibrils

In collagen, side chains of prolines and lysines are often hydroxylated
* 4-Hydroxy-proline forms hydrogen bonds to stabilize the triple helix
* 5-Hydroxy-lysine is attachment site for disaccharides, galactose−glucose

Question 8

Collagen suprastructure

Answer 8

In the ER:
1) Synthesis of Pre-procollagen
begins on ribosomes
pre-procollagen includes:
> A signal peptide (helps it enter the ER)
> The actual collagen sequence (with Gly-X-Y repeats)
The signal peptide is cleaved once inside the ER → now it’s procollagen.
2) hydroxylation of proline and lysine residues (via Prolyl hydroxylase and lysyl hydroxylase, with vitamin C as a cofactor) (pro & lys react with alpha-ketoglutarate which turns into succinate once reaction takes place)
3) glycosylation (w/ Galactose or glucose–galactose disaccharides) of selected 5-hydroxylysine residues

In the Golgi Apparatus:
Triple-Helix Formation
> Procollagen is still flanked by propeptides on both N- and C-termini to prevent premature fibril formation.

Secretion into the Extracellular Space
After secretion, procollagen peptidases cleave N- and C-terminal propeptides
This creates tropocollagen, the mature form capable of self-assembly (fibrils into fibers)

Question 9

Synovial joints

Answer 9

Surrounded by ligament (capsule), a fibrous connective tissue with collagen fibers arranged in orderly parallel manner

End of bones at the joint have cartilage, consists of collagen and proteoglycan

Synovial cavity contains synovial fluid, with hyaluronan (also called hyaluronate), to increase the viscosity and elasticity

Question 10

Ehlers–Danlos syndrome

Answer 10

Hyperflexible joints
Mutations in the following can cause EDS:
* Fibrous proteins: COL1A1, COL1A2, COL3A1, COL5A1, COL5A2, and TNXB
* Enzymes: ADAMTS2, PLOD1

PLOD1 = Lysyl hydroxylase (or procollagen-lysine 5-dioxygenase)

Helix-breakers
> Some natural occurring amino acids do not fit in an a-helix, they disturb the structure
> A mutation that introduces a helix breaker can have dramatic effects on protein function
* Skin (COL5A1 and COL5A2)
* Blood vessels (COL3A1)

Question 11

Layers of the arteries and veins

Answer 11

Walls of both are made up of three layers:
tunica intima
tunica media
tunica adventitia

Question 12

Elastic arteries

Answer 12

Have vasa vasorum (networks of small blood vessels that supply the walls of arteries with oxygen and nutrients)

Right under endothelium:
Internal elastic lamina (layer of elastic tissue)

Tunica media (smooth muscle cells
and elastic tissue)

Tunica adventitia (mainly composed of collagen)

Question 13

Collagen versus elastin

Answer 13

Both are structural proteins
Blood vessel walls contain an extracellular matrix with a specific mix of proteins for the right amount of rigidity (collagen) and elasticity (elastins)

Question 14

Disulfide bonds

Answer 14

Extracellular proteins have disulfide bonds to covalently fix the three-dimensional structure made by hydrogen bonds

(SH groups interacting covalently)

Cysteine thiol is a redox group
Oxidation: 2 -SH + O2 <> -S−S- (disulfide bond) + H2O2
> i.e Disulfide-bond formation is an oxidation reaction, reduced to SH thiol groups

Question 15

Vitamin in collagen hydroxylases

Answer 15

Vitamin C (ascorbate) is a reducing cofactor in collagen synthesis
> H of proline or lysine side chain turns into OH

Question 16

Vitamin C dietary deficiency

Answer 16

Results in scurvy
> vitamin C (ascorbic acid) is required for the synthesis of collagen in humans.
> Scurvy leads to the formation of spots on the skin, spongy bleeding gums, and bleeding from the mucous membranes. > The spots are most abundant on the thighs and legs, and a person with the ailment looks pale, feels depressed, and is partially immobilized.
> advanced scurvy: open, suppurating wounds and loss of teeth.

Scurvy does not occur in most animals as most animals can synthesize their own vitamin C

Question 17

Vitamin C: antioxidant

Answer 17

Vitamin C (ascorbate) is the reduced form, which can donate electrons (e − )
to reduce radicals, such as some ROS

The oxidized form dehydroascorbic acid can be reduced back to ascorbate
by glutathione transferases present in most cells.

Question 18

beta-Strands and beta-sheets

Answer 18

Multiple b-stands can form a b-sheet
A β-strand is a single, extended stretch of polypeptide chain
The backbone is zigzagged
> Side chains alternate above and below the strand, creating a pleated sheet appearance when multiple strands are aligned.

beta-sheet
> Formed when two or more β-strands run alongside each other and are linked via hydrogen bonds between the carbonyl oxygen (C=O) of one strand and the amide hydrogen (N-H) of another.

Sheets can be:
Parallel (strands run in the same N → C direction)
Antiparallel (strands run in opposite directions)

Question 19

Protein folding and surface

Answer 19

A polypeptide chain folds into its thermodynamically most stable form.
> polar side chains point outward, can form H-bonds with water
> Hydrophobic core region: apolar side chains pointing inward, H-bonds between different peptide bonds

Charged amino acids at the protein surface, hydrophobic amino acids in the interior

Question 20

Lysozyme: structural domains

Answer 20

a single polypeptide chain that has 2 structural domains:
alpha-helical domain and beta-sheet domain

Question 21

Prion diseases

Answer 21

a group of rare, fatal neurodegenerative disorders caused by the misfolding of a normal protein into a pathogenic form
The normal form of the prion protein: PrPc
The disease-causing form: PrPsc
> change in structure, from a-helices to b-sheet
> has a higher β-sheet content
> results in protein precipitates in brain

Question 22

Domain structure of transcription factor GAL4

Answer 22

has a DNA-binding regions on either end and a regulatory domain in the middle (a regulation RNA-polymerase)

> A protein domain is a structural and functional unit within a single
continuous amino acid chain (usually encoded by single exon)

Question 23

Quaternary structure of proteins

Answer 23

> Many functional proteins consist of more than 1 peptide chain
The subunits can be identical or different (different genes)
They often contain co-enzymes or help-molecules (metal ions)
Hemoglobin archetypal example
- has 4 subunits interacting w/ eachother, 2alpha and 2beta
- each subunit contains a heme group w/ an iron molecule that binds oxygen

Question 24

Hemoglobin quaternary structure

Answer 24

quaternary structure enables cooperativity
When one subunit binds O₂, the entire tetramer changes shape, making it easier for the next subunit to bind O₂.
> This cooperative effect gives hemoglobin its sigmoidal (S-shaped) oxygen-binding curve—perfect for loading oxygen in the lungs and unloading it in tissues.

whereas myoglobin only has a single chain = no cooperative binding

Question 25

A human disorder of hyaluronan metabolism (& example in dogs)

Answer 25

Serum hyaluronan levels are elevated at birth and then decrease to the normal range > This form of cutaneous mucinosis is caused by skin fibroblasts producing abnormally large amounts of acid mucopolysaccharides, usually hyaluronan. > folding and thickening of the skin The thickened and wrinkled skin in Shar-pei dogs is caused by the excessive production of hyaluronan by the hyaluronan synthase 2 (HAS2) gene. > Hyaluronan lubricates the animals’ joints. > Shar-pei dogs are born with wrinkles and lose them as they get older because they literally grow into their skin

Question 26

Proteoglycans

Answer 26

long, highly charged, and repetitive polysaccharides (such as hyaluronan, chondroitin sulfate, and keratan sulfate) attached to core proteins, forming highly hydrated compressible gels Hyaluronan (Hyaluronate) Disaccharide unit = Glucuronic acid + N-acetylglucosamine Linked by β glycosidic bonds Chondroitin 6-sulfate Disaccharide unit = Glucuronic acid + N-acetylgalactosamine-6-sulfate Proteoglycans contain much larger, repetitive sugar polymers than glycoproteins

Question 27

Hyaluronic acid (hyaluronan)

Answer 27

proteoglycan aggregate Hyaluronic acid serves as a scaffold: long, unbranched polysaccharide made up of repeating disaccharide units (Glucuronic acid & N-acetylglucosamine) Core proteins attached to hyaluronan via link proteins. Chondroitin sulfate & Keratan sulfate are covalently attached to the core protein major component of the extracellular matrix found in connective tissue, skin, eyes, and joints cosmetic application: Hylauronic acid fillers

Question 28

Vitamin E

Answer 28

It is an anti-oxidant: Protects amino acids from ROS-damage Affects Maillard (browning) reaction on collagen > Maillard reaction: causes browning and makes collagen stiffer and more prone to degradation = aging > Vitamin E neutralizes free radicals that accelerate Maillard reactions, and reduces oxidative steps that lead to the browning

Question 29

How does selenium neutralize free radicals and other skin-damaging compounds before they can lead to wrinkles?

Answer 29

Glutathione peroxidase reduces hydrogen peroxidase (H2O2) to water > Glutathione peroxidase transfers e- from glutathione (GSH) to hydrogen peroxide Selenium is present in the active site of Glutathione Peroxidase as the amino acid selenocysteine States of selenocysteine 1) Selenolate (E-Se-, active) Attacks hydrogen peroxide (H₂O₂) Selenolate is oxidized to selenenic acid 2) Selenenic acid (E–SeOH) Further oxidized, reacts with GSH 3) Selenosulfide (E–Se–S–G) reduced back to selenolate form by glutathione (GSH) - GSH > GSSG, selenosulfide gives the S & G

Question 30

Protein structure summary

Answer 30

Primairy structure: sequence of linked amino acids Secondary structure: a-helix, b-sheets and loops Tertiary structure: total three-dimensional shape > same sequence gives same shape = conformation Quaternary structure: When a functional protein contains several polypeptide chains (subunits, such as hemoglobin) Large proteins often consist of protein domains (each built from a-helices, b-sheets), linked through unstructured loops that execute distinct parts of function, often encoded by single exons in genes. A single amino acid substitution can lead to serious disease when it disturbs the structure of the protein (such as a helix breaker in collagen, sickle cell anemia Glu>Val).

Question 31

Connective tissue

Answer 31

main function is to support, bind, and protect other tissues and organs Integrins (transmembrane receptor proteins) bind extracellular proteins (fibronectin and collagen) Collagen provides the tensile strength Fibronectin: a large glycoprotein that has binding domains for integrins, collagen etc > Adhesive molecule: connects cells (via integrins) to the collagen Proteoglycans: Provides gel structure, resists compression

Question 32

what can UDP-glucose synthesize?

Answer 32

glycogen, proteoglycans, glycoproteins, glycolipids UDP-glucuronate, UDP-galactose UDP-glucose is activated glucose

Question 33

Glycoproteins

Answer 33

short carbohydrate chains covalently linked to serine or asparagine residues in the protein > most secreted from cells e.g of a branched glycoprotein: fucose contain unique sugar structures > O-glycosylation (serine residues) and N-glycosylation (asparagine residues) of proteins Synthesis reaction: UDP-glucose > glycosylated protein Enzyme: glycosyltransferase Cofactor: Protein-OH > UDP Act as sugar flags outside the cell > Often recognized as “self” by immune system > different 'flags' in diff blood types

Question 34

Conveyer-belt synthesis of N-glycans

Answer 34

1) Initiation on cytosolic side: Sugars like (e.g N-acetylglucosamine) are added one-by-one to dolichol-Phosphate 2) partially assembled glycan flips across the ER membrane (to the lumen side) > More mannose and glucose residues are added 3) N-glycosylation of Secreted Proteins > glycan is transferred from dolichol to the nascent protein > happens whilst the protein in being made (translated) 4) Complete N-glycans are Attached Post-translationally > Although the core oligosaccharide is transferred co-translationally, it undergoes processing and maturation afterward: > In the ER: Glucose and some mannose residues are trimmed. > In the Golgi: Further modification

Question 35

Processing of N-linked glycan

Answer 35

Processing of N-glycans occurs in the endoplasmic reticulum and Golgi apparatus Endo H-sensitive N-glycans are high-mannose glycans or hybrid glycans with at least 5 mannose residues, two of which must be terminal mannose residues

Question 36

What are mucins?

Answer 36

transmembrane glycoproteins > transmembrane mucins are glycoproteins expressed in the GI tract, forming the extracellular glycocalyx of the enterocytes and the inner mucus layer in the colon > have a beta chain and an alpha chain healthy colon mucus layer: inner mucus layer is relatively sterile inner mucus layer limits invasion of enteropathogens, such as Salmonella enterica and Campylobacter jejuni

Question 37

Energy systems at the start of exercise

Answer 37

At the start of sports activities, oxygen uptake increases exponentially, until a steady state is reached During the first few minutes of a cold start, a shortage of oxygen is experienced, limiting oxidative phosphorylation. Substrate-level phosphorylation in the creatine phosphate shuttle and in anaerobic glycolysis is then essential for energy supply > creatine phosphate shuttle: phosphate from creatine phosphate is given to ADP, producing ATP and creatine

Question 38

Overview during oxygen debt

Answer 38

increased NADH/NAD + ratio stopped conversion of: - isocitrate > alpha-ketoglutarate - alpha-ketoglutarate > succinyl co-A - malate > oxaloacetate citrate levels increase due to end-product inhibition

Question 39

Types of MCTs

Answer 39

Monocarboxylate transporter (MCT): * lactate–proton co-transport * acetoacetate–proton co-transport * β-hydroxybutyrate–proton co-transport

Question 40

what determines the rate of biosynthesis of carnosine

Answer 40

availability of beta-alanine

Question 41

What is heme

Answer 41

a prosthetic group in myoglobin and hemoglobin proteins > heme group binds in a hydrophobic pocket through ~16 noncovalent interactions > function of heme is controlled by protein structure

Question 42

Hemoglobin: Binding of O2

Answer 42

Binding of O2 leads to a change in protein conformation of hemoglobin: Deoxyhemoglobin: tense, inactive state Oxyhemoglobin: relaxed, active state cooperativity among the subunits: binding of the first O2 affects the affinity for the subsequent O2 molecules > Cooperativity also occurs in allosteric enzymes consisting of multiple subunits.

Question 43

Myoglobin versus hemoglobin

Answer 43

The difference in affinity for O2 controls binding and release of O2 at different oxygen tensions in the body The saturation curve of monomeric myoglobin shows a hyperbolic relationship The saturation curve of multimeric hemoglobin shows a sigmoidal relationship Myoglobin has a higher affinity for oxygen than hemoglobin > attributed to its role in oxygen storage where it only releases oxygen when O2 levels are very low > hemoglobin plays a role in oxygen transportation from the lungs to tissue and thus its cooperative binding enables efficient binding of oxygen in the lungs and release in the tissues

Question 44

Bohr effect

Answer 44

as the pH decreases, hemoglobin's affinity for oxygen also decreases and thus hemoglobin releases more oxygen than it would at a higher pH at the same partial pressure of O2. During intense exercise: lack of O2, accumulation of CO2 and lactic acid, the blood pH decreases as the proton concentration increases. Since hemoglobin releases more O2 at a lower pH this encourages oxygenation of the muscles and other active tissues that require O2

Question 45

ROS and erythrocytes

Answer 45

oxygen radicals, which have an unpaired electron highly reactive and can react with carbohydrates, fats, proteins, and DNA can damage all cell structures O2- (superoxide), H2O2 (hydrogen peroxide), OH. (hydroxyl radical) can cause hemolysis (destruction of erythrocytes) = important to keep erythrocytes in reduced state met-hemoglobin (Met-Hb is oxidized Hb with Fe 3+ (oxidized state of iron)) leads to the formation of heinz bodies

Question 46

What are heinz bodies

Answer 46

Deposits of oxidized hemoglobin in erythrocytes

Question 47

Broad beans or G6P dehydrogenase deficiency

Answer 47

No G6P DH = no regeneration of NADPH = GSSG cannot be reduced to GSH = accumulation of GSSG = increase in heinz bodies

Question 48

Hemoglobin and heme degradation

Answer 48

Circulating erythrocytes have a lifespan of ~120 days, before they are cleared by macrophages Damaged erythrocytes are phagocytosed by macrophages in the spleen and the liver Heme is degraded to bilirubin, conjugated with diglucuronide, and excreted in bile Iron (Fe 2+ ) is highly toxic as a producer of ROS (Fenton reaction)

Question 49

Local inflammatory response

Answer 49

Major events in a local inflammatory response after infection or injury To destroy pathogens and repair tissue damage, including control of bleeding through blood-clot formation (thrombus) Symptoms: pain, swelling, and fever