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BIOLOGY-FY > S1-L5: Proteins > Flashcards

S1-L5: Proteins Flashcards

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1
Q

Outline and describe proteins

A
  • Fundamental cellular components vital for all cellualr function
  • polymeric–> chain like structures made up of monomers
  • macromolecules–> v. large molecules
  • 1000’s proteins exist- each with different functions
  • ->human body able to generate 2 million different protein types from 20000 genes
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2
Q

For each of the following proteins outline their function and an example of each:

1-Structural 
2-Storage 
3-Transport 
4-Hormonal 
5-Receptor 
6-Contractile 
7-Defensive 
8-Enzymatic
A 
1- support--> collagen
2- storage--> casein 
3- O2 transport--> hemoglobin
4- metabolism--> insulin 
5- cellular response--> B-adrenergic receptor 
6- movement--> actin/ myosin 
7- protection--> antibodies 
8- catalysis--> digestive enzymes
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3
Q

What are polypepetides?

A
  • amino acid monomers linked via peptide bonds

- contain >40 amino acids able to fold in to defined shape

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4
Q

How do polypeptides influence proteins?

A

-protein sequence of amino acids determines shape + function of protein

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5
Q

What are all proteins composed off?

A

-standard 20 amino acids–> proteinogenic amino acids

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6
Q

Outline the structure of amino acids (figure 1)

A
  • possess amino (-NH2) + carboxyl (-COOH which acidic)

- amino acids differ based on side R chain

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7
Q

Are amino acids chiral molecules?

A
  • except Ca all amino acids have chiral centre

- -> atom in molecule bonded to 4 different chemical species

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8
Q

Explain the two forms in which amino acids exist and which is more dominant

A
  • able to exist as either of 2 enantiomers–> mirror images L & D
  • ->not superimposable (place on each other to be same)
  • L form dominates D-amino acids v. rare in nature (left and right-handed)
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9
Q

Which part of amino acids determine the physiochemical properties of amino acids?

A

-physiochemical properties determined by R group

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10
Q

Outline the 4 different categories in which amino acids can be classed under

A
  • Non-polar hydrophobic (water-hating)
  • polar
  • acidic
  • basic
  • last three are hydrophilic (water-loving)
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11
Q

Learn the following non-polar R group amino acids (figure 2)

A
  • Glycine
  • Alanine
  • Valine
  • Leucine
  • Isoleucine
  • Methionine
  • Phenylalanine
  • Tryptophan
  • Proline
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12
Q

What are acidic R group amino acids?

A

-Side chains (-) charged at physiological pH (approx 7.4)

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13
Q

Outline the two acidic amino acids (refer to figure 3)

A

-Aspartic acid AND Glutamic acid

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14
Q

Define basic R group amino acids

A

-side chains (+) charged at physiological pH (approx 7.4)

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15
Q

What are three basic R group amino acids? (refer to figure 4)

A
  • Lysine
  • Arginine
  • Histidine
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16
Q

Briefly explain what polar R group amino acids are

A

-able to form H bond interactions with similar side-chains + peptide bonds

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17
Q

Outline the 6 polar R group amino acids (refer to figure 5)

A
  • Tyrosine
  • Asparagine
  • Glutamine
  • Serine
  • Threonine
  • Cysteine
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18
Q

With reference to figure 6 describe how cysteine residue can form disulphide bridges

A

-2 polypeptide chains are covalently linked together (strong bonds)

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19
Q

Describe the formation of polypeptide chains in appropriate detail (figure 7)

A
  • achieved via -COOH and -NH2 group linkage done through dehydration/condensation reaction
  • ->removal of H2O molecule
  • 2 molecules combine to form larger molecule with small molecule loss
  • ->peptide bond forms
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20
Q

What is the significance of this polypeptide chain formation?

A
  • a peptide backbone is formed

- ->side chain project from backbone

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21
Q

Briefly explain what “bond resonance” is

A
  • way to describe bonding in certain molecules/ions by combination of several contributing structures/forms (AKA resonance structures/canonical structures)
  • ->in resonance hybrid/ hybrid structure in valence bond theory
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22
Q

What does bond resonance cause? (refer to figure 8)

A

-causes peptide bond to be rigid AND planar

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23
Q

Why is peptide bonds “trans” form most common?

A
  • rotation around C atom usually limited by steric clashes between bulky R groups
  • ->hence trans form most common
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24
Q

What is “directionality” in terms of polypeptides?

refer to figure 9

A
  • means polypeptide chain has two chemically distinct ends from one another
  • ->one end has free amino group (Amino terminus)
  • read from amino to carboxyl terminal so going from N (amino group) to C (carboxyl group)
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25
Q

Why do polypeptide chains have directionality?

A

-due to structure of amino acids

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26
Q

Outline the 4 levels of protein structure (figure 10)

A
  • Primary: amino acid sequence
  • Secondary: interactions between adjacent amino acids
  • ->E.G: a helixes/ B pleated sheet, loops or random coils
  • Tertiary: 3D folding of single polypeptide chain
  • Quaternary: assembly of multiple proteins into complex
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27
Q

Describe the primary structure of proteins (refer to figure 11)

A
  • amino acid sequence from N-terminus to C (display left to right)
  • ->determined by DNA sequence of gene for each protein
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28
Q

How does the primary structure of proteins affect proteins?

A

-dictates final protein as sequential arrangement of R groups influences subsequent secondary/ tertiary/ quaternary structures

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29
Q

Outline how the primary structure may be effected and the consequences. Include an example.

A
  • Genetic mutation could lead to primary structure changes which may alter structure AND function
  • ->E.G: sickle cell diseases
  • ->caused by single mutation in HbA hemoglobin gene
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30
Q

Describe the secondary structure of proteins

A
  • parts of polypeptide chains take regular patterns of H-bonding resulting in
  • -> a-helixes/ B-pleated sheets
  • above patterns connected by short-runs AND longer loops/random coils
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31
Q

Briefly describe the “coiled rod-like” structure of the a-helix

A
  • most common secondary structure
  • flexible & elastic
  • coil of helix means chain not fully extended
  • proline disrupts a-helix structure due to mutation for example (“helix breaker”)
  • abundant in hemoglobin
  • absent in chymotrypsin (digestive enzyme)
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32
Q

Describe “stabilising by extensive intra-chain H bonding” in the a-helix (figure 13)

A
  • 3.6 amino acids per turn
  • right-handed (“clockwise” from N to C-terminal end)
  • peptide bonds form backbone
  • R groups project outwards to avoid steric (Spatial arrangement) hindrance
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33
Q

Define “amphipathic a-helixes”

A

-alpha-helix molecule which has both polar and non-polar parts to it

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34
Q

Describe how B-pleated sheets are “flat/short-run and pleated” (figure 14)

A
  • flat sheets/pleated (not as coiled)/short runs (5-10 amino acids)
  • parallel AND anti-parallel or mixed
  • strands almost fully extended–>surface appears pleated
  • strong plus resilient
  • multiple sheets connected by short turns OR “hairpin loops”
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35
Q

What are beta plated sheets held together by?

A

-by H-bonds between peptide bonds on adjacent strands

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36
Q

Outline and explain how length affects B-pleated sheets in comparison to a-helixes

A
  • 1A^o–> equivalent to 10^-10m
  • side chains of B-pleated sheets arranged alternately opposite sides of strand
  • distance between amino acids is 3.5A^o (1.51A^o in a-helix)
  • ->so B-sheets more flexible than a-helixes able to be twisted
  • length of B-sheets in protein ranges 2-22 residues
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37
Q

Can b-sheets be amphipathic?

A

-yes

38
Q

Describe “loops/random coils” and their relation to proteins

A
  • connect secondary structural elements
  • normally located on surface
  • rich in polar AND charged residues
  • lengths vary 2-20 residues
  • frequently part of enzyme active sites
  • less conserved than other secondary structural elements
  • differences between structurally similar proteins typically occur in loops
39
Q

What are “structural motifs”?

A
  • arrangements of secondary structures (super-secondary structures) which frequently occur within proteins
  • ->AND can be associated with specific biological function
40
Q

Examples of structural motifs

A

-B-hairpin/ Helix-loop-helix/ Greek key/ Coiled coil/ Zinc finger/ Beta barrel

41
Q

Outline and describe the “B-Hairpin” motif (figure 15)

A
  • 2 adjacent anti-parallel B strands joined by hairpin loop
  • simplest super secondary structure
  • common in globular proteins (spherical + involved in metabolic functions)
  • ->no specific function associated with this motif
42
Q

Briefly explain the “Helix-loop-helix” motif (figure 16)

A
  • 2 a-helixes connected by loop
  • function as either DNA-binding (like c-Myc) OR Ca2+ binding motif (like calmodulin)
  • ->common in transcription factors (helix-basic loop-helix) AND cell signalling proteins which bind to Ca2+ (EF-hand)
43
Q

Similarly, explain what the “Greek Key” motif is (figure 17)

A
  • 3 adjacent anti-parallel B-strands connected by hairpin plus 4th strand adjacent to 1st AND linked to 3rd by longer loop
  • common in range of proteins–>like proteases (trypsin)/cytokines (TNFa)
  • no specific function associated with this motif
44
Q

Outline and describe the “Coiled coil” motif

A
  • usually contain repeat of 7 residue patterns (hxxhcxc)
  • h= hydrophobic/ c=charged/ x= any
  • ->resulting amphipathic a-helixes have “stripe” of hydrophobic residues which coil around similar stripes in other helixes
  • -> such that hydrophilic residues project outwards
45
Q

Give examples of the Coiled coil motif (figure 18)

A
  • Leu zippers in transcription factors (like c-Fos)

- structural proteins (myosins)

46
Q

What are “Zinc Finger” motifs? (figure 19)

A
  • 2 anti-parallel b-sheets followed by 1 a-helix
  • ->stabilised by zinc ion
  • ->may bind Fe/Zn or no metal at all
  • metal binding mediated by Cis (in B-sheets) AND His (in a-helix)
47
Q

Where may this motif commonly be found?

A
  • common motif in many proteins including transcription factors
  • ->E.G: Kruppel-factor 4 (KLF4)
  • ->this is protective transcription factor
  • can be present frequently within same polypeptide chain
48
Q

What are the function(s) of this motif?

A

-binding of DNA/ RNA/ lipid and protein substrates

49
Q

Describe the “Beta barrel” motif

A
  • multiple anti-parallel B-sheets which twist AND form closed structure
  • first strand is H bonded to last
50
Q

Outline and describe each of the following Beta barrel motifs:

1-Greek Key motif

A

-Previously discussed

51
Q

2- Up-and-down barrel (figure 20)

A

-8 anti-parallel B-sheets connected by hairpin loops (like Retinol-binding protein)

52
Q

3- Jelly roll barrel (complex)- figure 21

A
  • 8 B-strands arranged as 2 four-stranded antiparallel B-sheets which wrap around hydrophobic interface
  • -> example: major capsid protein P2 from bacteriophage PM2
53
Q

4- Pore-forming- water channels (aquaporins)

A
  • complex of proteins subunits each with 2 four-stranded anti-parallel B-sheets
  • ->polar side chains face inwards to form channel for hydrophilic molecules like Porin 1
54
Q

Give a list of all the motifs outlined

A
  • B-Hairpin
  • Helix-loop-helix
  • Greek Key
  • Coiled coil
  • Zinc Finger
  • Beta barrel (Greek Key/ Up-and-down barrel/ Jelly roll barrel/ Beta-helix barrel (pore-forming (water channels))
55
Q

Define and describe “domains”

A
  • polypeptide chain/part of chain which independently folds in to stable structure with its own hydrophobic core
  • ->formed from several simple motifs AND secondary structure elements
56
Q

What is the relation between domains and proteins?

A
  • proteins can have anything between one to several tons of domains
  • ->each domain associated with distinct biological function
57
Q

Describe the following domain example:

Sre homolgy 2 (SH2) domain

A
  • binds phosphor-Tyr residues

- ->important in insulin signalling

58
Q

Briefly explain the tertiary structure of a protein (figure 23)

A
  • Overall 3D shape of entire polypeptide- held together by
  • ->H bonds- between R groups
  • ->Ionic bonds (electrostatic attraction)- between CO2 + NH3+ of R groups
  • ->Disulfide bridges (covalent cross-links)- between cysteine -SH groups (Cys-S-S-Cys)
  • ->Hydrophobic interactions- hydrophobic R groups cluster inside proteins to shield themselves from H2O
59
Q

Which linkage is the strongest?

A

-Disulfide bridges

60
Q

What are Fibrous Proteins?- describe them (figure 24)

A
  • secondary structures form long parallel fibres AND sheets

- ->usually insoluble in water

61
Q

What important roles do fibrous proteins play?

A
  • providing strength AND support

- ->collagen and keratin

62
Q

Where are “a-Keratins” and “B-Keratins” found?

A
  • “a-Keratin” mammalian hair and nails
  • “B-Keratin” invertebrate silks/reptile scales/ claws
  • Avian feathers/beaks and claws
63
Q

Outline and describe collagen

A
  • Super-helixes OR Gly-rich triple a-helixes (tropocollagen)
  • ->assemble in to fibrils
  • main protein in connective tissues–> support/connects OR separates tissues AND organs
  • v. abundant (25% of total protein)
64
Q

Why is the “strong and elastic” quality of collagen useful for the human body?

A

-bone/cartilage/ teeth/ ligaments (skeletal)/ tendons/ skin blood vessels/ eyes (cornea AND lens)

65
Q

What condition may one develop when collagen “goes wrong”?

A
  • Ehlers Danlos Syndrome (EDS)

- Genetic connective tissue disorder

66
Q

How may this condition develop and what is it’s affect?

A
  • multiple mutations possible in multiple genes
  • ->structure/ production AND OR processing collagen affected
  • ->can affect skin/musculoskeletal/cardiovascular
67
Q

Describe a-Keratins which are found in hair and nails (figure 25)

A
  • composed of coiled-coils of 2 a-helixes which asseble together into larger fibres
  • strong & inextensible/insoluble ALSO chemically inert/ disulphide bridges cross link coiled-coils
68
Q

What is Fibroin? Outline and describe it

A
  • Fibroin found in silk AND spider webs
  • ->layers of anti-parallel B-Keratin sheets rich in Ala AND Gly residues
  • ->small side chains interdigitate (interlock) to allow close packing of B-sheets
69
Q

How does the structure of Fibroin allow it to be elastic and strong?

A
  • sheets joined by amorphous (no defined shape/form) stretches
  • spider silk able to stretch x30 more than most stretchy nylon
70
Q

Describe globular proteins

A
  • mixture of irregular folded 2^0 elements to form compact 3D shape
  • usually water soluble with inner hydrophobic core transported easily in body fluids
71
Q

Where are globular proteins often found (also state some examples) ?

A
  • common structure of enzymes
  • ->important functions in cellular biochem
  • examples- myoglobin/ hemoglobin/immunoglobins
72
Q

Briefly outline and explain the structure of hemoglobin

A
  • Tetramer (polymer comprising of 4 units)
  • 4 polypeptide chains/ subunit (a2B2- adult hemoglobin)
  • 4 haem molecules (haem–> porphyrin ring + Fe2+/binds O2)
73
Q

What is myoglobin?

A
  • related to hemoglobin

- exists as single polypeptide

74
Q

What is the job of hemoglobin and how is that important?

A
  • transports O2 from lungs to rest of body

- -> released O2 to permit aerobic respiration to provide energy

75
Q

Outline the possible effect of DNA mutations on hemoglobin

A
  • specific mutations in DNA encoding Hb genes can cause disease
  • -> like sickle cell disease/ Thalassaemia
76
Q

Define Thalassaemia

A

-produce little/no hemoglobin which used by red blood cells to carry O2 around body

77
Q

Briefly explain sickle cell disease

A
  • disease caused by single gene defect
  • single mutation in DNA coding region within B-globin gene
  • non-sense mutation changes primary sequence
78
Q

Outline the symptoms/ effects mutations (in this particular case) may cause (figure 27)

A
  • changes in RBC shape (sickle-shaped cells)
  • RBC’s rigid–> become blocked in capillaries–> Ischaemia/Organ Damage/ Pain
  • increased haemolysis (rupture/destruction of red blood cells) leads to RBC destruction –> Anaemia/ Spleen damage (location where red blood cells damaged)
79
Q

Describe the effect of a single mutation (refer to figure 28 and 29)

A
  • single mutation in B-globin gene (T to A) changes primary sequence (Glu–> Val)
  • ->therefore bonding in tertiary structure changes so shape of protein changes
80
Q

Outline and describe immunoglobins

A
  • Y-shaped proteins of immune system which identify AND combat invading foreign organisms
  • 4 chains linked by disulphide bridges
  • ->2 large H (heavy) and 2 short L (straight) short chains
81
Q

What do variable structures in H & L chains form? (figure 30)

A
  • form specific binding sites for non-self targets

- -> antigens

82
Q

What is the importance of these variable structures?

A

-antigen recognition by antibody marks it for attack by other components of immune system engaged by constant portions of H chains

83
Q

Briefly explain “denaturation” of proteins and it’s effect (figure 31)

A
  • process where proteins lose quaternary/ tertiary AND secondary structure present in their native state due to change in environment
  • ->results in loss of function
84
Q

For what possible reasons may protein denaturation occur?

A

-possibly due to extreme pH/ extreme temp/ organic solvents

85
Q

During protein denaturation due to pH what is the effect on ionic bonds and then the consequence of that?

A
  • ionic bonds broken as v. sensitive to pH
  • disrupts tertiary structure
  • can render proteins insoluble in water AND precipitate out of solution
86
Q

Describe low pH and its effect

A
  • Is high H+ conc (acidic)
  • adding H+ neutralises COO part of ionic bond
  • -> removing it’s charge (H+ + COO- –> COOH)
87
Q

Outline what high pH is

A
  • low H+ conc (alkaline)
  • removing H+ neutralises NH3+ part of ionic bond-removing its charge

-NH3+ –> NH2 + H+

88
Q

Explain the denaturation of proteins through heat (increase in temp)

A
  • increase in temp vibrates & breaks H AND ionic bonds

- denaturation able to render (cause) proteins to become water insoluble–> precipitate out of solution

89
Q

What is pyrexia?

A
  • increase body temp/ fever

- ->ancient anti-viral defence mechanism

90
Q

How do solvents cause proteins to become denatured?

A
  • ethanol/ acetone/ phenol (organic solvents)
  • ->forms new H bonds with protein side chains PLUS backbone
  • ->disrupts intra- AND inter- chain H bonds
  • ->causes protein to unfold AND denature
91
Q

Summary of lecture

A
  • Proteins–> polymers of amino acids
  • protein function dictated by amino acid sequence
  • changes in amino acid sequence may cause disease –> like B-globin/ sickle cell disease
  • 4 levels of protein structure–> primary/ secondary/ tertiary/ quaternary
  • proteins structure typically either fibrous (like collagen) OR globular (like hemoglobin)
  • protein structure may be disrupted (denatured)
  • -> by extreme temp/extreme pH/ organic solvents

BIOLOGY-FY (12 decks)

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