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Biology 2B03 > Module 1 - From Polypeptide to Protein > Flashcards

Module 1 - From Polypeptide to Protein Flashcards

1
Q

what are the functions of proteins?

A
  • structural component of the cell
  • sensors for environmental changes and mechanisms for relaying this information to the cell
  • enzymes/catalysts for chemical reactions
  • gene regulation
  • signalling molecules between cells
  • molecular motors
  • organelle identity and function
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2
Q

N-terminus

A

amino end of basic amino acid structure

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3
Q

C-terminus

A

carboxyl end of basic amino acid structure

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4
Q

peptide bonds

A

these bonds link amino acid residues to form a chain. they form by condensation reactions between a carboxyl group of one amino acids and an amino group of another

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5
Q

what does the basic amino acid structure include?

A

amino group (NH3+), carboxyl group (COO-), hydrogen, and variable R group

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6
Q

how are amino acids usually classified?

A

solubility in water, polarity of side chain

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7
Q

solubility

A

physical property of molecule that can allow for temporary hydrogen bonding with water

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8
Q

hydrophilic molecule

A

charge-polarized and capable of hydrogen bonding in water

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9
Q

hydrophobic molecule

A

not electrically polarized and unable to form hydrogen bonds with water. thus, the water repels them in favour of bonding with itself

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10
Q

saturated hydrocarbons

A

Long chain of carbons linked together by single bonds

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11
Q

hydrophobic amino acids: non-polar side chains

A

aromatic amino acids: phenylalanine (Phe), tyrosine (Tyr), tryptophan (Trp)
aliphatic amino acids: alanine (Ala), valine (Val), isoleucine (Ile), leucine (Leu), methionine (Met)

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12
Q

difference between aromatic amino acids and aliphatic amino acids?

A

aromatic amino acids have an aromatic side chain while aliphatic amino acids have a hydrocarbon side chain

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13
Q

what sorts of molecules are water soluble?

A
  • molecules with an -OH group at one end (or O- at pH of 7.0)
  • molecules with an -NH2 group at one end (or NH3+ at pH of 7.0)
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14
Q

hydrophobic amino acids: charged side chains

A

basic amino acids (positively charged): lysine (Lys), arginine (Arg)
acidic amino acids (negatively charged): Aspartic Acid (Asp), Glutamic Acid (Glu)

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15
Q

hydrophilic amino acids: polar, uncharged

A
  • serine (Ser) and threonine (Thr) are uncharged at neutral pH, but have hydroxyl groups that can participate in hydrogen bonding
  • asparagine (Asn) and glutamine (Gln) are uncharged but have polar amide groups
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16
Q

special amino acids

A
  • cysteine (Cys) can form covalent bonds with other cysteine residues. these bonds are called disulphide bridges
  • glycine (Gly) is very small. since it’s side chain is just hydrogen, it can allow bends in polypeptides
  • proline (Pro) forces a kink in the peptide chain
  • histidine (His) has an imidazole side chain that shifts between a positive charge and a neutral charge depending on the pH of the environment
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17
Q

where does peptide bond formation/translation occur?

A

ribosome

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18
Q

translation process

A
  • ribosome is made up of 1 small subunit and 1 large subunit
  • amino acids are carried into the ribosome attached with tRNAs
  • small subunit of ribosome positions mRNA so it can be read in groups of 3, i.e. codon
  • each codon on mRNA matches with anticodon on tRNA
  • as mRNA passes through the ribosome, it is translated into an amino acid sequence
  • this happens particularly with 3 sites: A site, P site, E site
  • the tRNA enters the A site and is tested for a codon-anticodon match with the mRNA. if the match is correct, the tRNA is shifted to the P site and the amino acid it carries is attached to the end of the amino acid chain. then the spent tRNA is moved to E site to be ejected and recycled
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19
Q

4 levels of protein organization

A

primary structure, secondary structure, tertiary structure, quaternary structure

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20
Q

primary structure

A

the linear arrangement of amino acids

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21
Q

number of different possible polypeptide sequences and how to determine this?

A
  • 20^n polypeptide sequences
  • relies on the number of amino acids found in the peptide and on the fact that there are 20 amino acids that can be a part of the peptide
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22
Q

statistical coil

A

represents the idea that proteins have a collection of structures that they switch between. suggests that a protein spends most of its time in a particular structure, but not 100% of the time

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23
Q

what local interactions stabilize protein structures?

A

ionic bonds, hydrogen bonds, van Der Waal forces, hydrophobic effect

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24
Q

ionic bond

A

attraction between a positively charged cation and a negatively charged anion

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25
hydrogen bond
interaction between a partially positively-charged hydrogen atom in a molecular dipole and unpaired electron from another atom
26
hydrophobic effect
aggregation of non-polar molecules in an aqueous medium in order to decrease the number of interactions with water
27
van Der Waal forces
- results from creation of a temporary dipole when 2 non-covalently bonded atoms are close enough together to disturb the electron distribution in one another - also known as London Dispersion forces - if bonds are not hydrogen bonds and ionic, they are van Der Waal
28
secondary structure
conformation of a portion of the polypeptide
29
motifs
- combinations of secondary structures - exhibit particular 3D architecture that is usually associated with a particular function - ex: coiled-coil motif, zinc-finger motif, B-barrel motif, helix-loop-helix motif
30
what are the 3 basic secondary structures?
alpha helix, beta sheet, turns/loops
31
alpha helix
- type of secondary structure - spiral, rod-like structure - carbonyl oxygen of each peptide bond is hydrogen bonded to the amide hydrogen of the amino acid 4 residues towards the C terminus - forms independently of the side chains (i.e. they do not contribute to the structure) - periodicity of hydrogen bond formation defines the structure - R groups determine hydrophobic/hydrophilic quality of the outer surface of the helix (i.e. they contribute to the properties of the structure)
32
beta sheet
- type of secondary structure. - planar structure composed of alignments of 2 or more strands - hydrogen bonds between carboxyl group and amino groups of backbone in adjacent beta strands - position of hydrogen bonds are not regular like in alpha helices - parallel/antiparallel - can form within a polypeptide or between two polypeptides - forms independently of the side chains (i.e. they do not contribute to the structure) - R groups determine hydrophobic/hydrophilic quality of the structure of the sheets (i.e. they contribute to the properties of the structures)
33
turns/loops
- type of secondary structure - connectors - bends in polypeptide backbone that lie between alpha helices and beta sheets - no specific dimension
34
coiled-coil motif
- 2 alpha-helices wrapped around one another - amphipathic - in an aqueous environment, the hydrophobic effect favours the hydrophobic interactions holding the alpha-helices together - commonly found in DNA binding proteins
35
zinc-finger motif
- consists of an alpha-helix and 2 beta-strands - held in position by the interaction of the amino acid residues - commonly found in DNA binding proteins and can also bind to RNA molecules as well
36
B-barrel motif
- 4 to 10 antiparallel beta-strands form a sheet - the barrel is formed when the last beta-strand forms hydrogen bond with the first strand - useful for forming a channel or pore across a hydrophobic membrane
37
helix-loop-helix motif
- 2 small alpha-helices held together at a specific orientation by non-covalent interactions between specific amino acid residues and a cofactor, calcium - the shape can only be established once polypeptide is interacting with calcium. this means that protein structure and function rely on cofactor
38
tertiary structure
- 3D arrangement of all amino acid residues of a single polypeptide - fundamental unit of the tertiary structure of a protein is the domain
39
domain
- substructure produced by any part of a polypeptide chain that can fold independently into a compact, stable structure - two types of domains: structural and functional
40
structural domain
regions of protein that form compact, largely independent globular domains. ex: proline-rich, acidic domain
41
functional domain
regions of a protein that perform a certain activity. ex: DNA binding, enzymatic, protein-protein interaction.
42
how many domains for the Src protein?
2 functional domains that form the kinase activity and 2 structural domains (SH2 and SH3)
43
quaternary structure
number and organization of subunits in a multimeric protein
44
multimeric protein
functional protein composed of multiple polypeptides
45
dimer
2 polypeptides or 2 subunits
46
trimer
3 polypeptides
47
homodimer
2 identical polypeptides
48
heterodimer
2 different polypeptides
49
intrinsically unstructured proteins
- not folded and lack tertiary structure as isolated subunits - when 2 of these proteins interact with one another, they can form a stable structured protein - they can also assume a structure when they are interacting with their substrate
50
examples of post-translational modification
acetylation, methylation, phosphorylation, hydroxylation, carboxylation, glycosylation, lipidation
51
acetylation
- type of post-translational modification that allows for the addition of an acetyl group - it protects against intracellular protease degradation (80% of proteins)
52
methylation
- type of post-translational modification | - adds methyl group
53
phosphorylation
- type of post-translational modification - transfer of a phosphate group from ATP to the -OH group of serine, tyrosine, or threonine by kinases - removal of phosphate group is done by phosphatase
54
hydroxylation
- type of post-translational modification | - addition of a hydroxyl group
55
carboxylation
- type of post-translational modification - addition of carboxyl group - changes properties of residue by adding negative charge
56
glycosylation
- type of post-translational modification - addition of carbohydrates - sugars added to -OH groups of serine and threonine
57
lipidation
- type of post-translational modification - addition of lipid molecules - anchors proteins to membranes
58
native state
- most thermodynamically stable conformation of a protein - most functional state of the protein - depends on the primary amino acid sequence
59
what are the rules of protein folding?
spontaneous, reversible, unique
60
reversible denaturation experiment
- studied ribonuclease A protein - denatured protein with urea to bring it to its unfolded state - used mercaptoethanol to break disulphide bridges - used dialysis to remove denaturants - when placing protein back it its native conditions, found that the protein folded back into the same conformation - spontaneous
61
sickle cell anemia
- haemoglobin has 2 native states: one with oxygen, the other without oxygen - in those who have sickle cell anemia, there is a single change in the amino acid chain from glutamate to valine at position 6 - this results in a change from charged amino acid residue to a hydrophobic amino acid residue - hydrophobic amino acid residue results in aggregates - these cells can carry oxygen, but there cell shape is dramatically altered
62
how do side chains differ?
size, shape, charge, hydrophobicity, reactivity

Biology 2B03 (5 decks)

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