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Biochemistry > Unit 1 - Active Recall > Flashcards

Unit 1 - Active Recall Flashcards

1
Q

What range of pH is life tolerable? What happens if lower or higher?

A

Life is only tolerable within a very narrow range of blood pH (7.2-7.6)
- At lower values of pH, proteins
carry a more positive charge
- At high values of pH, proteins
carry a more negative charge

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2
Q

What is the constant for H? 10^14 sum

A
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3
Q

add in more cards from lecture 1 & 2

A
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4
Q

Biomolecules have many _________________ (e.g. NH3+ , COO- ) and change properties with pH

A

ionizable groups

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5
Q

what do you know about acids? strength?

A
  • Strong acids completely dissociate
  • The lower the pKa value, the stronger the acid
  • The higher the pKa value, the weaker the acid (and the stronger its conjugate base)
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6
Q

Explain how the body can compensate to maintain homeostasis?

A
  • Equilibrium shifts right due to excess acid (metabolic acidosis), or low CO 2 (hyperventilation)
  • Equilibrium shifts left due to insufficient HCO 3- (renal problems) or high CO 2 (poor lung function)

Ex:
- HCO3, H2O = Regulated by kidneys
- CO2 = Regulated by breathing
Overall:
Breathing (fast) and kidney function (slow) can be used to regulate the pH of the body, and compensate for different disorders (e.g., acidosis)

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7
Q

Many diseases are due to proteins having one incorrect amino acid like Sickle Cell….How do we explain this?

A

Sickle cell:
- single amino acid mutation in hemoglobin (glutamate to valine)

Why/How?
- mutations are located in the DNA sequence or “gene” that encodes one particular protein.
- inherited mutations affect only that particular protein and its related function.

Note:
- Valine can only make hydrophobic interactions with other amino acids; glutamic acid can make ionic interactions with other basic amino acids and can also interact well with polar uncharged amino acids. Therefore, the tertiary structure of hemoglobin can become significantly changed

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8
Q

Describe four levels of protein structure. Which structure determines all higher order structure?

A

Primary
- amino acid sequence

Secondary
- localized folding

Tertiary
- 3D packing of the protein

Quaternary
- arrangement of protein chains

ANS
- primary structure determines all higher order structure

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9
Q

What are common features of amino acids?

A
  • All proteins are linear polymers of alpha- amino acids (residues in proteins)
  • 20 common amino acids each have a different R group or side chain
  • Two main amino acid categories: non-polar (hydrophobic) and polar (neutral or charged)
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10
Q

Describe what you know about amino acid stereochemistry?

A
  • Most amino acids have a chiral (asymmetric) C-alpha atom: D and L amino acids are enantiomers
  • Amino acids in proteins are in the L configuration, D amino acids are less prevalent
  • For multiple chiral centers, the R, S system must be used (most amino acids are S)
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11
Q

Where are hydrophobic amino acids found? What are the main hydrophobic amino acids?

A

Location?
- inside the protein interior as they have to pack together well

Hydrophobic:
- Ala, Val, Leu and Ile all have aliphatic side chains and are hydrophobic
- Met is one of two amino acids that contains sulfur (S can be oxidized to S=O or O=S=O)
- Trp is the largest amino acid, and its UV absorbance 280 nm can be used to measure protein concentration
- Phe just Ala with a phenyl group
- Pro is the only imino acid: side chain connected to NH group forces “kink” into polypeptide chains (unable to hydrogen bond)

Note:
- Ala is often chosen as a replacement to determine amino acid function using site-directed mutagenesis

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12
Q

What are the polar amino acids?

A
  • Gly is the simplest amino acid
  • Asn and Gln are the corresponding uncharged amides of the acidic amino acids Asp and Glu; they can be H bond donors or acceptors.
  • His has an imidazole side chain, which can be positively charged at acidic pH
  • Ser, Thr and Tyr have hydroxyl (OH) groups that often act as nucleophiles in biochemical reactions

Note:
- Their OH groups can also be covalently attached to other groups (e.g., reversible phosphorylation)
- Tyr is a derivative of Phe, and both are precursors of amino acid neurotransmitters. Tyr also absorbs light at 280 nm.

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13
Q

What does it mean when ‘cysteine residues can form disulfide bonds’? What about its reduction?

A
  • The sulfhdryl (SH) group of Cys can be oxidized to form
    a disulfide bond (S-S) with another Cys
  • Cys is usually reduced (SH) when in the cell and oxidized (S-S) when outside the cell
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14
Q

What amino acids hold a charge? (Are acidic or basic)?

A
  • Asp and Glu have negatively-charged carboxyl side chains at pH 7 (often referred to as acidic AAs)
  • Lys and Arg have positively-charged side chains at pH 7
    (often referred to as basic AAs)
  • His and Cys may also have charged side chains at certain pH
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15
Q

Regarding a titration, consider the following:
For every _________ (peptide, protein) there is an ______________, a pH value where the net charge of the molecule is ______. Whichever is higher (pH or pKa) ‘wins’ the ________.

A

amino acid, isoelectric point (pI), zero, proton

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16
Q

What are some common structures of proteins?

A
  1. Backbone
    - only main chain amino acids shown (overview basically of the molec.)
  2. Wireframe
    - full detail, useful to understand its mechanism and or for drug design
  3. Ribbon
    - emphasizes secondary structure
  4. Spacefill
    - provides general molecule shape
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17
Q

What are peptide bonds?

A

A peptide bond is a chemical bond formed between two molecules when the carboxyl group (C-terminus) of one molecule reacts with the amino group (N-terminus) of the other molecule, releasing a molecule of water (H2O).

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18
Q

What else do you recall about peptide bonds?

A
  • they limit conformational flexibility
  • resonance can be shown (o=c bond turns into c=n bond leaving o with - charge and n with + charge) due to N being the e- withdrawing group
  • peptide bonds have 40% DB character so they are rigid (not very flexible)
  • the only flexibility they have is from the two side C (Φ-C, ψ-C) between the alpha-c bond (dihedral angles define the direction/shape of the peptide chain)

Note:
- there is steric hindrance since only angles exist in specific orientations

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19
Q

Recall the most important aspect(s) of the secondary alpha-helix structure of proteins?

A
  • The H-bond between molecules
  • The R groups of the amino acids determine the surface properties of the α-helix (ex: if all + charge, repulsion would be in effect causing destabilization)
  • main backbone H-bonds inside while R groups are on outside

More detail:
- An α-helix secondary structure is stabilized by hydrogen bonds between carbonyl oxygen and the amino group of every third residue in the helical turn with each helical turn consisting of 3.6 amino acid residues

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20
Q

Recall the most important aspect(s) of the secondary beta-sheet structure of proteins?

A
  • the B-sheet is an extended zig-zag conformation
  • H bonds are between B-sheets while R groups are above and below the sheet
  • B-sheets can be parallel (weaker due to strained H-bonds) or antiparallel (stronger due to straight H-bonds)
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21
Q

Explain motifs and domains in ‘super secondary structure’?

A
  • Protein motifs: Small regions with defined sequence or structure that often serve a common function in different proteins
  • Protein domains: Sub-regions of single polypeptide chains that can fold and function independently (sometimes correlated with exons)
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22
Q

What are the forces that stabilize
protein tertiary structure?

A

Hydrophobic effect and favorable interactions cause proteins to fold

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23
Q

Describe the Anfinsen experiment?

A
  • The lad exposed the native enzyme to excess beta mercaptoethanol and 8.0 M urea and he found that the protein was completely denatured.
  • When he removed the two agents simultaneously via dialysis, he found that the protein refolded back into its original biologically active form.
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24
Q

List some of the things you know about protein folding?

A
  • Native protein structure is encoded by its sequence
  • Most (but not all) proteins can refold on their own
  • Proteins fold much faster than random chance would allow (ms vs. 10 27 years)
  • Initial secondary structure elements guide/restrict protein folding
  • Some intermediates may promote misfolding or aggregation
  • Protein folding is not always guaranteed and misfolding can be irreversible with serious physiological consequences!!!!

Examples of disorders from misfiled proteins:
- Mad cow disease
- Alzheimer’s disease

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25
Q

Describe protein folding as free energy “funnel”.

A
  • an energy landscape theory of protein folding - assumes the unfolded state has the highest energy and the native state has the lowest free energy.

Note:
- proteins fold into their native conformations driven by decrease in Gibbs free energy (negative ΔG)

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26
Q

How is the native state of proteins stabilized? And what is the denatured stabilized by?

A

Denatured stabilized by:
- hydrophobic effect (high entropy)
- enthalpic interactions (all types of bonding)
- static protein chain

Denatured stabilized by:
- high entropy of the protein itself

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27
Q

What are the benefits of the quaternary protein structure? Ex: Hemoglobin

A
  • Easier to fold smaller subunits
  • can reuse subunits in new ways
  • ability to self regulate
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28
Q

Why is DNA anti-parallel?

A
  • Complementary base pairs make DNA anti-parallel
  • In DNA A/T and C/G are complementary
  • Purines (A,G) pair with pyrimidines (T,U,C)
  • By convention DNA sequences are always written 5’ to 3’
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29
Q

Explain DNA double helix structure?

A
  • Consists of two strands of nucleotide polymers, with base pairs in the middle, stacked perpendicular to the helix axis
  • Polar exterior (-ve PO4 ) and non-polar
    interior
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30
Q

Explain what you know about DNA denaturation and renaturation?

A
  • The double helix is stabilized by H-bonds, Mg 2++ binding to PO 4 backbone, and by the
    hydrophobic effect
  • Tm increases with GC content (due to base
    stacking)
  • Denaturation is reversible: renaturation
  • Controlled heating and cooling can make DNA anneal in complex ways (used as a construction material or specific shapes)

Note:
- When heated solutions of DNA are slowly cooled, annealing occurs with return of the coil to helical configuration.
This process is called Renaturation. It involves reannealing or formation of hydrogen bonds between complementary base pairs.

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31
Q

Describe what you know about RNA?

A
  • Contains 2’ hydroxyl on sugar (can be cleaved
    at basic pH)
  • Uracil (U) replaces T (missing methyl group)
  • A single strand can adopt tertiary structure
  • contains an extra hydrogen bond acceptor/donor
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32
Q

What are the 4 types of RNA?

A
  1. mRNA: Codes for proteins (only 5%
    of total cellular RNA)
  2. rRNA: Assists protein synthesis on
    ribosomes
  3. tRNA: Translation adaptors between
    mRNA and amino acids
  4. miRNA: MicroRNAs regulate gene
    expression by blocking mRNA
    translation or stability

Note:
- The nucleotide sequence for mRNA
corresponds to the coding (sense) strand of
the original DNA, and to the codons for
translation

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33
Q

Describe genome structure.

A
  • The nucleosome is the basic structural unit of chromatin
  • Condensation is due to basic histone
    proteins interacting with acidic DNA backbone
  • Histone modifications help regulate packing and gene expression (epigenetics)
34
Q

What are sources of genome variability?

A
  1. Protein coding genes (open reading frames, ORFS)
    - sequence comparison reveals many
    homologous genes (shared ancestry), as well as horizontal gene transfer
  2. Genome sequence variability is ~ 0.1%
    - Single nucleotide polymorphisms (SNPs)
    - Copy number variations (e.g. variable
    numbers of tandem repeats: VNTRs)
    - Insertions, deletions, translocations
    - Mutations are rare, ~60 new mutations per
    person (evolution, disease)
35
Q

What are the types of mutations common in the genetic code?

A
  • Point mutations can be: silent (no amino acid change), missense (different aa), nonsense (premature stop codon) or can also be non-coding
  • Frameshift mutations: addition or deletion of nucleotides (other than multiples of 3) changes translation reading frame
36
Q

Complementary nature of DNA is the basis
of molecular medicine. Give several examples about why or how this is true?

A
  • Site-specific digestion of DNA with restriction endonucleases
  • Amplification and expression of DNA by cloning into vectors
  • Amplification of DNA between specific primers using PCR
  • Creation of genomic or cDNA libraries in a vector collection
  • Manipulation of genes and gene expression (RNA i, CRISPR)
  • DNA sequencing and analysis
  • Probe hybridization to to determine genotype
    (SNPs, Southern blot) or gene expression (microarray, Northern blot)
37
Q

Explain what DNA probes are and what they do?

A
  • Single stranded DNA probes (oligonucleotides) can detect a specific DNA or RNA sequence in a sample
  • DNA binds to target complementary probe
  • Sensitive to as small as a single base pair mutation
  • Genomic or expression probes
  • Fluorescence used for visualization

Notes:
- Probe binds complementary DNA, producing signal
- No binding, no signal
- The DNA probes can correspond to different genes or mutations

38
Q

What are mircoarrays/their purpose? What do you do for normal v. cancerous cells? What do the colours mean?

A

Mircoarrays:
- Microarrays use multiple oligonucleotide probes arrayed at known locations on a 2D
surface to detect the presence or amount of complementary DNA in a sample
- Use for both comparative gene expression analysis (below), and for high density genotyping

Normal vs Cancerous:
- Normal cells: Isolate cDNA, label with green fluorescent molecule
- Cancer cells: Isolate cDNA, label with red fluorescent molecule

Colours:
- Green spot: normal cell produces more of its
message
- Red spot: cancer cell produces more of its
message
- Yellow spot: both cells produce the same amount
of message

39
Q

Explain the idea behind salting in/out of proteins? Ammonium sulphate precipitation?

A

What?
- Controlling protein solubility using
(NH4)2SO4 to isolate proteins by precipitation

Process
- Less salt: salt can interact with protien
- Medium salt: ‘salting in’, equilibrium reached, salt is soluble
- Tons of salt: too much it uses all of the H2O so none can interact with the proteins (becomes non-soluble)

40
Q

Explain general chromatography setup and reason for usage.

A

Chromatography separates molecules based on their relative affinities for the mobile or stationary phase

Set up:
- In the stationery phase, a mixture of molecules and material the molecules may interact with is loaded in a column
- In the mobile phase, the buffer is added and can now interact with the column
- At the end, you will have separated molcules (fractions based on initial sample)

41
Q

Explain size-exclusion chromatography setup and reason for usage.

A

Size exclusion (gel filtration) chromatography separates
proteins based on their size

Set up:
- Stationary phase is porous beads
- Large molecules: do not enter beads so their flow is quick
- Small molecules: do enter beads so their flow is slow
- At the end, you can estimate the molecular weight of a protein based on its retention volume

42
Q

Explain ion-exchange chromatography setup and reason for usage. How can the protein be eluted?

A

Ion exchange chromatography separates proteins based on their charge

Set up:
- stationery phase is charged
- use of anion (+) and cation (-)
- Resin has a (-) charge so (-) molecules move quicker since they won’t be attracted to the charge. If (+) it will stick and slow down.

Can elute the protein by:
- changing the pH (+ –> -)
- adding salt (reduces interactions, making it harder for the protein to stick to the column)

43
Q

Explain affinity chromatography setup and reason for usage.

A

Affinity chromatography separates proteins based on
what they bind (function)

Process:
- A mixture of proteins is added to column
- Wash away protein that doesn’t bind
- Ligand solution is added to compete (elute) proteins from column

Basically whatever binds to the ligand will bind to the column

44
Q

Explain what an affinity tag is?

A
  • The column is a matrix with a immobilized ligand attached to it
  • A protien with an affinity tag on it will bind to the column (stationery phase)
45
Q

Explain 6x histidine affinity tag.

A
  • The protien with 6x histidine connects to a resin due to immobilized Ni2+ making bonds with the histidine tags.
  • It is eluted with Imidazole (has similar chain like histidine)
46
Q

Electrophoresis

A

the separation of charged molecules in an electric field Most common method is SDS polyacrylamide gel electrophoresis (SDS-PAGE)
- separation by charge and size (molecular weight)

47
Q

Give the steps that occur in electrophoresis?

A
  1. Incubate protein with SDS and a reducing agent (e.g. β- mercaptoethanol
  2. Separate the protein out by size using a gel and an electric field - smaller moves quicker to (+) end

terms:
- β- mercaptoethanol = reducing agent, breaks disulphide bonds
- SDS (Sodium dodecyl sulfate) = detergent, hydrophobic tail, hydrophilic head, denatures proteins
- gel = polyacrylamide (molec. mesh)

48
Q

What is 2D-Page? Explain the two dimensions?

A

Proteins can be separated by pI and then by size to reveal hundreds of proteins and disease-related differences in protein levels

Dimensions:
1. isoelectric focusing in pH gradient
2. MW separation by SDS-PAGE

49
Q

X-ray crystallography

A

The 3D arrangement of atoms in a protein can be deduced by measuring the diffraction of X-rays in a protein crystal

Note:
~214,000 protein structures are now available in the Protein Data Bank (PDB),
~90% from X-ray crystallograph

50
Q

Cryo-electron microscopy

A
  • Cryo-EM uses electrons to determine high-resolution protein structures (uses frozen samples)
  • Excellent for large proteins and complexes and no crystal is needed!
51
Q

Nuclear magnetic resonance (NMR) spectroscopy

A
  • uses superconducting magnets to measure the magnetic environment of nuclei
  • Can be used to determined protein structure and motions (dynamics)
52
Q

What does the current drug target for Alzheimers disease target?

A

Current drug design targets the surface of the amyloid fibrils

ie: Aβ (1-42) fibrils

53
Q

Oxygen transport overview

A
  • Hemoglobin used for transport of H+, O2, and CO2
  • Myoglobin used by intercellular cells for O2 storage

Note:
- H+ and CO2 out via veins thru lungs
- O2 in via arteries to tissues

54
Q

How do we adapt to high altitude?

A

Our body adapts to low oxygen availability by increasing red blood cell production decreasing the binding capacity of haemoglobin and by increasing breathing rate.

55
Q

Myoglobin structure

A
  • The heme prosthetic group is an integral part of the myoglobin tertiary structure (iron ion (Fe2+) coordinated to the center of a porphyrin ring)
  • heme group is responsible for the binding of oxygen to myoglobin.
  • Monomeric O2 carrier in muscle cells
  • Has eight α-helices (A-H)
  • Fe2+ coordinates to O2 and the proximal histidine (His F8)

See labelled slide in lecture 7 pg 7

56
Q

The binding of O2 to myoglobin (Mb) can be expressed as a dissociation. Write it out. Then recall another important expression for O2 saturation curves.

A

Kd = [Mb] [O2] / [MbO2]

Note:
- [O2] is usually expressed as a partial pressure (units of mmHg or torr).

Y = [pO2] / [p50] [pO2]

57
Q

Explain what P50 is?

A

P50 is the oxygen pressure when myoglobin is 50% bound. It is inversely proportional to the affinity of myoglobin for O2.

58
Q

Explain myoglobin O2 saturation curve.

A
  • Oxygen binding to myoglobin is hyperbolic
  • Myoglobin can effectively store and release intracellular oxygen
59
Q

Overall, how would you read right and left shifts in O2 binding curve.

A
  • right shift of either a hemoglobin or myoglobin oxygen binding curve corresponds to a larger P50 and hence a lower affinity for oxygen.
  • left shift in the oxygen saturation curve corresponds to a smaller P50 and higher affinity for oxygen.
60
Q

Hemoglobin & its structure

A
  • also used in oxygen transport
  • Area around heme is most conserved
  • Hemoglobin is a heterotetrameric protein (a2b2) that transports O2 from lungs to tissues
  • O2 binding causes a structural change
61
Q

Explain the two states hemoglobin can occupy?

A

T State
- tense
- deoxygenated
- low O2 affinity
- salt bridges (ion-ion interaction) between subunits favour low affinity conformation

R State
- relaxed
- Oxygenated
- High O2 affinity
- salt bridges broken

62
Q

Explain hemoglobin O2 saturation curve.

A
  • Hb can transport (ΔY) much more O2 than myoglobin
  • Sigmoidal behavior on graph indicates cooperative interactions due to protein allostery (regions of proteins communicating with each other)
63
Q

Hemoglobin O2 binding cooperativity

A

O2 binding to one subunit in the R state encourages other subunits to adopt the R state (allostery)

64
Q

Describe the function of an antibody. Use immunoglobulin G as an example.

A
  • antigen binding sites are variable (binds to foreign molecules in body)
  • Stabilized by intra- and inter-chain disulfide (S-S) bonds
  • Antigen binding (Fab) region
  • Complement (FC) region (binds to body cells)
  • IgG consists of two heavy (50 kDa) and two light (25 kDa) chains

Note on immunoglobulins:
- Antigen binding regions are formed from both light and heavy chains
- Immunoglobulins and related proteins contain many immunoglobulin domains

65
Q

Describe immunochemical detection

A
  • Antibodies bind an epitope* by having a complementary surface (right shape), and stabilizing interactions (e.g. H-bonds, and electrostatic forces) with the epitope
  • Antibodies are used to detect and quantify antigens, either directly (e.g. ELISA) or following SDS-PAGE (Western blotting)

Terms:
- epitope = molec. surface of antigen that antibody detects

66
Q

ELISA

A

Enzyme Linked ImmunoSorbent Assay (ELISA) uses multiple antibodies to specifically capture, label, and detect antigen on a microtiter plate. It is the most used lab diagnostic method for proteins and other molecular biomarkers.

Process (wash between each step):
1. Immobilization of the capture protein.
2. Block any unbound sites on the plate.
3. Incubate with the sample (serum, urine, saliva, or spiked research solution).
4. Incubate with detection antibody
5. Apply substrate for chemical colorimetric or chemiluminiscent reactions, or apply incident light for fluorescent reactions, and quantify the signal

Why washes?
- wash away unbound antigen

67
Q

Western blotting

A

uses antibodies to label and detect proteins
following separation by SDS-PAGE

Overview:
- target protien to membrane blot
- anti-target antibody attaches to pr.
- Secondary antibody against primary antibody (Can also be conjugated to a fluorophore instead of an enzyme)
- Enzyme covalently attached to secondary antibody
(e.g, Horse radish peroxidase)
- Light emitted

68
Q

Fluorescence

A
  • Fluorescent molecules absorb light at certain wavelengths and then emit light at a longer wavelength
  • Molecule absorbs light (excitation into excited electronic state)
  • Molecule then emits light (emission; lower
    energy relaxation back to ground state)
  • FITC: common fluorophore, has conj. double bonds
69
Q

Cytoskeletal proteins (_______________________) are essential for cellular structure and _________.

A

microtubules, actin, intermediate
filaments

movement

70
Q

Actin filaments (microfilaments)

A
  • Actin is dynamic, part of the cytoskeleton and essential for cellular motility
  • Reversibly polymerizes to form F actin (faster at + end)
  • F-actin is organized into cables, meshes, etc., by over 100 different actin binding proteins
  • G-actin and F-actin are in equilibrium (~1:1)
  • ATP incorporated into G-actin, ATP hydrolyzed to
    ADP in F-actin
  • Hydrolysis of ATP also allows F-actin to treadmill, with net polymerization at (+) end and removal at (-) end
71
Q

Capping proteins vs severing proteins

A

Capping proteins: can block F-actin polymerization
Severing proteins: break filaments

72
Q

Actin (cell motility)

A
  • Hundreds of actin binding proteins organize and regulate actin assembly
  • Myosin binds to actin (actomyosin) to drive muscle contraction
  • Skeletal muscle cells use actomyosin to contract

Scale:
Individual muscle cell (myofiber) -> Myofibrils (see nucleus) -> Actin filament

73
Q

Actomyosin sliding filament model

A
  1. ATP hydrolysis triggers conformational change
  2. Myosin now reattaches to the actin
  3. Release of ADP and Pi causes conformational change (power stroke)
  4. ATP binds, myosin releases

Overall:
Chemical energy of ATP is transformed into mechanical energy

74
Q

Microtubules (MTs)

A
  • Microtubules are the largest cytoskeletal element (~250 Å) and are hollow (i.e. rigid)
  • provide straight and rigid tracks for movement of chromosomes and vesicles, and form cilia and flagella
  • Microtubules polymerize and depolymerize from the (+) end (regulated by GTP)
  • The (-) end is often anchored to an organizing centre (e.g. centrosome)

Notes:
- the target of some anti-cancer drugs (e.g. taxol, colchicine)
- are reversible aggregates of tubulin dimer and are regulated by GTP

75
Q

Kinesins transport cargo along microtubules. Explain this process.

A
  1. ATP binds leading head and causes conformational
    change
  2. The new leading head releases ADP and snaps
    onto tubulin
  3. The trailing head hydrolyses ATP to ADP and
    detaches from tubulin
76
Q

Intermediate filaments (IFs)

A
  • IFs are rope-like proteins that lack polarity, nucleotide binding, and are built from coiled-coils
  • large heterogeneous family of insoluble fibrous proteins (~100 Å in diameter) that provide mechanical strength and shape
  • Examples include: lamins underlying the nuclear membrane and keratin in epithelial cells
77
Q

Coiled-coil structure - IFs

A
  • The coil forms due to non-polar residues between helices
  • The fundamental unit of intermediate filaments is an a-helical coiled-coil
78
Q

Fibrous proteins: collagen

A
  • Twisted braid of three extended chains (~1,000 AA)
  • Collagen (25% of the body) forms strong cables and meshes in the extracellular matrix, connective tissue, and bone

Note:
- Diseases of collagen include scurvy (lack of vitamin
C), Ehlers-Danlos (stretchy skin), and osteogenesis
imperfecta (brittle bone)

79
Q

Collagen triple helix (not an α-helix)

A
  • Glycine at every 3rd residue is critical for triple
    helix to form
  • Interchain hydrogen bonds are strengthened by hydroxylysine and hydroxyproline residues (ascorbic acid is required for hydroxylase reaction)

Why glycine?
- Since glycine is the smallest of all the amino acids, it allows the chain to form a tight configuration, and and it can withstand stress.

80
Q

Fibrous proteins: elastin

A
  • Elastin is a deformable protein found in elastic tissues
    (e.g. lung, blood vessels)
  • Lys cross-linking (Lys oxidase) connects chains

Note:
- Decreased α1-AT activity in emphysema
can be caused by genetic (e.g. E342K mutation) or environmental (e.g. M358 oxidation) factors

Biochemistry (13 decks)

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