proteins (b1- SMS)

Question 1

4 organizational levels of proteins + linkages for each

Answer 1

1. primary structure: sequence & number of amino acid residues in the polypeptide chain
   - linkage: peptide bonds
2. secondary structure: configurational arrangement of amino acids in a segment of polypeptide chain that are located 3-4 amino acids apart
   - linkage: non covalent bonds, mainly H-bonds
   - includes: α-helix, β-sheets, β-bends, loops, motifs
3. tertiary structure: relationship of amino acids (bonds) which are far away (5+ AA away)
   - folding of domains
4. quaternary structure: arrangement of polypeptide subunits in the final protein, multiple folded subunits come together (if needed)
   - linkage: hydrophobic bonds, ionic bonds, or hydrogen bonds

Question 2

how are peptide bonds formed?

Answer 2

peptide bond: special covalent bond that links two amino acids together

formed: α-carboxyl group (-COOH) of 1 amino acid reacts w/ α-amino group (-NH₂) of another amino acid
- through condensation reaction (aka dehydration reaction) — molecule of water is removed

Question 3

characteristics of peptide bonds

Answer 3

1. partial double bond character: single bond (C-N) but behaves like a double bond
   - bc of resonance
   - gives rigid structure, no rotation around peptide bond (keeps protein structures maintained)
2. stable to denaturation: not broken by heat, acid, or area
   - to break peptide bonds, need enzymes or strong chemicals
   - in denaturation, only H- bonds break but primary structure remains intact

Question 4

polarity/charge of peptide bonds

Answer 4

peptide bond is uncharged (neutral)

however, polypeptides can carry charge based on:
- N terminal (α-NH2 group)
- C terminal (α-COOH group)
- any charged side chains

so bond itself not charged but overall peptide/protein can carry charge depending on pH & composition

Question 5

naming peptides

Answer 5

1. Start from N-terminal amino acid (one with free –NH₂ group)
2. Change the suffix (-ine) of all amino acids (except the last one) to –yl.
3. The last (C-terminal) amino acid keeps its original name.

start naming N to C always!!

Example:
tripeptide has N terminal valine, a glycine, and a C-terminal leucine = called valylglycylleucine

Question 6

sickle cell disease cause

Answer 6

replacement of a single amino acid

clinical significance example of primary structure mutations = loss/impairment of normal function

Question 7

Edman’s method & Sanger Sequencing

Answer 7

2 methods for primary sequencing of amino acids - to determine the primary structure/order of amino acids

Edman’s method: directly determines sequence of amino acids in polypeptide, starting from N-terminal
- more accurate but prob rlly expensive

Sanger sequencing: indirect protein sequencing by sequencing the genes that come for it

Question 8

5 types of secondary structures

Answer 8

1. α helix: spiral shaped, coil-like
2. β sheets: pleated sheet like arrangement of strands (like zig zag pattern)
3. β bends: connect antiparallel β-sheets, make U turns
4. Loops: connect parallel sheets, are much longer
5. Motifs: combination of β-structures & alpha helixes

Question 9

secondary structures: α helix (significance + structure)

Answer 9

integral part of many membrane receptors, like G protein-coupled receptors (GPCRs)

proteins also bind to DNA via alpha helices, so changes to the helices = stop proper binding to DNA = affects gene expression.

• each turn of α helix contains 3.6 amino acids
• commonly occurring, stable conformation
• abundant in variety of proteins like keratin & myoglobin

Question 10

5 amino acids that disrupt an α helix

Answer 10

Proline: geometrically non compatible, introduces a kink

Glycine: confers high flexibility

Charged amino acids: either form bonds or repel each other

Branched chain amino acids: valine, isoleucine

Amino acids with bulky side chains: Tryptophan

if something goes wrong with alpha helixes, you know substitution had to be one of these

Question 11

secondary structures: β-sheets (+ intrachain vs interchain, parallel vs antiparallel)

Answer 11

• proteins containing these structures are inelastic b/c H-bonds are perpendicular to direction of stretching
• very tough structures + hard to degrade

Intrachain β-sheet: single polypeptide chain folds back on itself

Interchain β-sheet: Involves 2 or more different chains lying side by side

parallel β-sheet: adjacent strands run in same direction

anti-parallel β-sheet: adjacent strands run in opposite directions

Question 12

neurodegenerative diseases are caused by

Answer 12

accumulation of β-sheet-rich aggregates called amyloid fibers (also resistant to degradation = build up)

*neurodegenerative diseases:
- alzheimer’s disease
- Parkinson’s disease
- prion diseases
- Huntington’s disease

Question 13

secondary structures: β-bends

Answer 13

segment of polypeptide chain joining 2 successive strands of antiparallel β-sheets or abrupt U-turns

• are short in length (usually having 4 amino acids- are proline + glycine and 2 others)

imp for compact globular shape of proteins

Question 14

β-sheets are represented by ________

Answer 14

arrows

Question 15

non-repetitive secondary structures aka loops

Answer 15

only diff b/w these & β-bends is that these are longer

Don’t really have a proper structure (have all sorts of things- bends, loops, coils, β-sheets, alpha helixes)

“connect adjacent regions of secondary structures, larger # of amino acids as compared to β-bends”

Question 16

super secondary structures: motifs + common types of motifs

Answer 16

recurring combinations of alpha helices (α-helices) and beta strands (β-sheets) that are connected by loops or turns

can form a bunch of them together to form a domain

significance: involved in DNA- binding, protein-protein interaction

common types:
- α–α Motif (Helix–Loop–Helix): in transcription factors
- β–β Motif (Beta Hairpin)
- β–α–β Motif
- Greek key

Question 17

domains (in proteins)

Answer 17

functional 3D structural unit of polypeptides

independent region of protein = able to perform specific function

core of a domain built from combinations of supersecondary structural elements (motifs)

• each domain has the characteristics of a small, compact globular protein

Question 18

folding of protein molecules

Answer 18

is always in the same manner!!

like how regardless of the shirt you buy you fold it the same way

Question 19

4 forces holding tertiary structures

Answer 19

1. Disulphide bonds: strong covalent bond b/w 2 cysteine residues in polypeptide
   - found in immunoglobulins (antibodies), insulin (has both intra & inter chain disulfide bridges)
2. Hydrophobic Interactions: amino acids w/ nonpolar side chains tend to be on the interior of polypeptide molecule while polar/charged tend to be on the surface
3. Ionic interactions: neg. charged groups (-COO-) in side chains interact w/ pos. charged groups such as amino group (-NH3)
4. Hydrogen Bonds

due to interaction of R groups!!

Question 20

which protein structure is responsible for protein folding?

Answer 20

tertiary structure

Question 21

Which statement is true of β-sheets only, and not α-helices?

Answer 21

they are stabilized by interchain hydrogen bonds

α-helices are stabilized by INTRAchain hydrogen bonds

Question 22

example of protein having tertiary structure

Answer 22

myoglobin

Question 23

Stability of tertiary protein structure is provided in part by:

Answer 23

Disulfide bond formation

Question 24

example of quaternary structure

Answer 24

adult hemoglobin

• globin part of hemoglobin has 4 polypeptide chains in its molecule: 2 alpha and 2 beta

Question 25

molecular chaperones (heat shock proteins- Hsp) + 2 examples

Answer 25

**Hsp/chaperones**: helper proteins that assist in folding of proteins and prevent misfolding/degredation (*require ATP*) *called heat shock proteins b/c their expression increases during stress, like heat which can denature proteins* 2 examples: 1. **Hsp70**: bind to hydrophobic regions of proteins to prevent them from making bonds w/ them themselves through *hydrophobic interactions* - keeps the chain straight 2. **mitochondrial Hsp60 (chaperonins)**: barrel/cage-like structures, protein enters them and is folded inside without interference and leaves - kind of like big *molds* that keep the proteins in shape & make sure folding occurs right *protein folding is imp b/c until the protein is folded properly, it cannot complete its function*

Question 26

protein misfolding diseases

Answer 26

group of disorders characterized by **accumlation of misfolded proteins leading to tissue damage** - usually, misfolded proteins are degraded but some accumulate, esp w/ age *examples*: - **Amyloid disease**: accumulation of β- pleated sheets = degenerative diseases like *parkinson's* and *alzheimer disease* alzheimer's = has enzyme active *secretases* - more synthesis = greater accumulation of β-sheets & neurofibrillary tangles (they're not supposed to be tangled- this is abnormal) containing *tau protein*

Question 27

alpha-synuclein protein

Answer 27

abnormal folding/deposits of amyloid are formed by this protein in **parkinson's disease** basically just know this plays a role in Parkinson's disease (progressive neurodegenerative disease)

Question 28

Alzheimer's disease is associated with _______

Answer 28

the deposition of neurotoxic amyloid β peptide aggregates

Question 29

Prion diseases

Answer 29

is called mad cow in animals but in humans its called **TSE (transmissible spongiform encephalopathies)** **prions**: proteinaceous infectious particles (have no DNA/RNA unlike bacteria/viruses- just misfolded proteins that can spread disease) normal PrP: **contains α-helices** abnormal: has **β-sheets** abnormal ones induce a change in normal prion proteins too (*effect of bad company*) causes **hole-like lesions** in brain (why its called spongiform) - are invariably FATAL & no treatment available

Question 30

what are some things that can cause denaturation of proteins?

Answer 30

- mild heating - X rays - UV rays - vigorous shaking - high pressures

Question 31

what are fibrous proteins + examples you need to know

Answer 31

fibrous proteins exhibit **special mechanical properties** - present in extracellular matrix - Skin, connective tissue, blood vessel walls, sclera and cornea *examples: Collagen & elastin*

Question 32

3 types of collagen

Answer 32

1. Fibril-forming collagens 2. Network-forming collages 3. Fibril-associated collagens *placed into 3 groups based on location & functions*

Question 33

collagen structure

Answer 33

3 polypeptide chains (*called alpha chains*) forming a rope like structures (**triple stranded helix**), stabilized by **interchain-hydrogen bonds** amino acid sequence is **glycine-X-Y** where: X = usually **proline** Y = **hydroxypoline** or **hydroxylysine** alpha chains have **kinks b/c of proline** (*note: alpha chains are NOT alpha helixes*)

Question 34

biosynthesis of collagen (how its formed)

Answer 34

produced by **fibroblasts** 1. **formation of pre pro-α chain**: gene is transcribed & translated - *pre pro-α chain* contains signal peptide (guide polypeptide) to direct entry into RER 2. **pro-α chain**: once inside RER, signal peptide is cleaved and this is now formed 3. **hydroxylation**: carried out by enzymes *prolyl hydroxylase & lysyl hydroxylase* (imp!) - OH group is added to proline & lysine 4. **glycosylation**: some OH groups are further modified by glycosylation (*adding sugars*) 5. **assembly of procollagen**: the disulphide bonds hold the polypeptide chains in place at terminal ends (*called propeptides*) - currently called **procollagen** (when it has the terminal propeptides) *procollagen is whats secreted outside of the cell* then outside the cell: 6. **formation of tropocollagen**: propeptides cleaved off and *crosslinking occurs via Lysyl oxidase* to form stable collagen fibers (were not very strong before!)

Question 35

which enzymes carry out hydroxylation step in collagen synthesis?

Answer 35

prolyl hydroxylase & lysyl hydroxylase have **coenzyme vitamin C** & **cofactor Iron**

Question 36

tropocollagen

Answer 36

final functional unit that forms the building block of collagen fibers

Question 37

what is the underlying problem in a patient with SCURVY?

Answer 37

Decreased prolyl hydroxylase and lysyl hydroxylase activity

Question 38

Ehlers-Danlos Syndrome

Answer 38

- skin is extremely flexible & fragile, hypermobile joints - vascular form (once it reaches the blood vessels) is the most serious caused by **deficiency of lysyl hydroxylase or N-procollagen peptidase** (collagen processing enzymes) OR from **mutations in collagen types I, III, and V**, changing the sequence of amino acids *genetic collagen related disorder*

Question 39

Osteogenesis Imperfecta

Answer 39

aka *brittle bone disease* bones **fracture easily** with mild or even no trauma caused by **genetic mutation in type 1 collagen**: bulky amino acids (fatties) replace glycine (skinny legend) = not proper formation of required triple-helical conformation of collagen **treatment: biphosphonates** - decrease apoptosis of osteoblasts (cells that lay down new bone matrix) - cant fit the genetic mutation but can help strengthen the bone

Question 40

Alport Syndrome

Answer 40

inherited disorder of the **basement membranes** of kidney, cochlea, and the eye - symptoms: progressive kidney disease (blood/proteins in urine-not properly filtering), hearing loss, eye abnormalities result in mutation of **type 4 (IV) collagen genes**

Question 41

3 collagenopathies (disorders due to collagen synthesis)

Answer 41

1. Ehlers-Danlos Syndrome 2. Osteogenesis Imperfecta 3. Alport Syndrome

Question 42

where is elastin found?

Answer 42

lungs, walls of large arteries, elastic ligaments **elastin**: connective tissue protein w/ rubber like properties - can be stretched several times its length *rich in proline & lysine*

Question 43

how is elastin made

Answer 43

1. **lysine modified**: lysine residues are oxidatively deaminated by enzyme *lysyl oxidase* - converts **lysine → allysine** 2. **3 allysine + 1 lysine = desmosine**: form a desmosine cross link which is very imp! **desmosine cross linkage**: special feature of elastin- what allows it to stretch/bend in any direction

Question 44

marfan syndrome

Answer 44

*disorder of elastin* **mutation of fibrillin-1 protein** (enhances elasticity of elastin) - impaired structural integrity in the skeleton, the eye, and the cardiovascular system **symptoms**: abnormally tall, long toes/fingers/arms/legs, have flexible joints, & may have scoliosis

Question 45

globular hemoproteins

Answer 45

group of proteins that contain **heme as a tightly bound prosthetic group** in humans, most abundance globular hemoproteins are **myoglobin & hemoglobin** - their heme group reversibly binds oxygen

Question 46

myoglobin structure (globular hemoprotein)

Answer 46

- found in *heart & skeletal muscle*, reservoir for oxygen & its carrier has only **1 polypeptide chain** thats mostly folded into **8 alpha helices** (labelled A to H) turns are b/w helices caused by **proline** & **β-bends** & loops b/w the helices are stabilized by **hydrogen or ionic bonds** **interior of myoglobin**: all nonpolar amino acids, **1 heme group** inside (that has *2 histidine* present in it)

Question 47

hemoglobin A structure (globular hemoproteins)

Answer 47

**tetramer** made of **2 identical dimers** 1 dimer made of 1 α & 1 composed of β and then they're linked together by **polar bonds** polypeptide chains *within each dimer* held together **hydrophobic interactions** - each subunit is structurally similar to myoglobin

Question 48

different types of hemoglobin

Answer 48

**HbA**: adult hemoglobin (*2 alpha, 2 beta chains*) **HbF**: fetal hemoglobin (*2 alpha, 2 gamma [γ] chains*) **HbA2**: minor adult hemoglobin (*2 alpha (α) + 2 delta (δ) chains*) **HbA1c**: glaciated hemoglobin - *indicator of diabetes - this is imp!!* - *HbA1c levels are proportionate to the amount of glucose present in the blood* - *higher than 6.5% is indicator of diabetes*

Question 49

Which of the following is inherited blood disorder that causes reduction of normal hemoglobin (Hb) levels in the body?

Answer 49

Thalassemia

Question 50

How many heme groups are present in a single hemoglobin molecule?

Answer 50

4

Question 51

How does hemoglobin transport oxygen throughout the body?

Answer 51

It binds to oxygen and releases it in the tissues.

Question 52

Fetal hemoglobin (HbF) is a tetrameter. Which of the following is its composition?

Answer 52

α2γ2