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

Module 1 - From Polypeptide to Protein Flashcards

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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
Q

hydrogen bond

A

interaction between a partially positively-charged hydrogen atom in a molecular dipole and unpaired electron from another atom

26
Q

hydrophobic effect

A

aggregation of non-polar molecules in an aqueous medium in order to decrease the number of interactions with water

27
Q

van Der Waal forces

A
  • 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
Q

secondary structure

A

conformation of a portion of the polypeptide

29
Q

motifs

A
  • 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
Q

what are the 3 basic secondary structures?

A

alpha helix, beta sheet, turns/loops

31
Q

alpha helix

A
  • 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
Q

beta sheet

A
  • 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
Q

turns/loops

A
  • type of secondary structure
  • connectors
  • bends in polypeptide backbone that lie between alpha helices and beta sheets
  • no specific dimension
34
Q

coiled-coil motif

A
  • 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
Q

zinc-finger motif

A
  • 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
Q

B-barrel motif

A
  • 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
Q

helix-loop-helix motif

A
  • 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
Q

tertiary structure

A
  • 3D arrangement of all amino acid residues of a single polypeptide
  • fundamental unit of the tertiary structure of a protein is the domain
39
Q

domain

A
  • 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
Q

structural domain

A

regions of protein that form compact, largely independent globular domains. ex: proline-rich, acidic domain

41
Q

functional domain

A

regions of a protein that perform a certain activity. ex: DNA binding, enzymatic, protein-protein interaction.

42
Q

how many domains for the Src protein?

A

2 functional domains that form the kinase activity and 2 structural domains (SH2 and SH3)

43
Q

quaternary structure

A

number and organization of subunits in a multimeric protein

44
Q

multimeric protein

A

functional protein composed of multiple polypeptides

45
Q

dimer

A

2 polypeptides or 2 subunits

46
Q

trimer

A

3 polypeptides

47
Q

homodimer

A

2 identical polypeptides

48
Q

heterodimer

A

2 different polypeptides

49
Q

intrinsically unstructured proteins

A
  • 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
Q

examples of post-translational modification

A

acetylation, methylation, phosphorylation, hydroxylation, carboxylation, glycosylation, lipidation

51
Q

acetylation

A
  • type of post-translational modification that allows for the addition of an acetyl group
  • it protects against intracellular protease degradation (80% of proteins)
52
Q

methylation

A
  • type of post-translational modification

- adds methyl group

53
Q

phosphorylation

A
  • 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
Q

hydroxylation

A
  • type of post-translational modification

- addition of a hydroxyl group

55
Q

carboxylation

A
  • type of post-translational modification
  • addition of carboxyl group
  • changes properties of residue by adding negative charge
56
Q

glycosylation

A
  • type of post-translational modification
  • addition of carbohydrates
  • sugars added to -OH groups of serine and threonine
57
Q

lipidation

A
  • type of post-translational modification
  • addition of lipid molecules
  • anchors proteins to membranes
58
Q

native state

A
  • most thermodynamically stable conformation of a protein
  • most functional state of the protein
  • depends on the primary amino acid sequence
59
Q

what are the rules of protein folding?

A

spontaneous, reversible, unique

60
Q

reversible denaturation experiment

A
  • 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
Q

sickle cell anemia

A
  • 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
Q

how do side chains differ?

A

size, shape, charge, hydrophobicity, reactivity

Biology 2B03 (5 decks)

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