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Biochem & Cell bio > learning objectives 3.1 > Flashcards

learning objectives 3.1 Flashcards

1
Q

List and describe the 9 functional categories of proteins

A
  1. transport proteins - transport ions and molecules
  2. enzymes - catalyze cellular reactions
  3. scaffold proteins - hold proteins together that interact in catalytic or signaling pathways
  4. signaling proteins - cellular communication
  5. structural proteins - provide mechanical support and structural organization
  6. motor proteins - move along other molecules for transport or synthesis
  7. storage proteins - repositories for ions and molecules
  8. receptor proteins - signal detection and involved in transmission
  9. regulatory proteins - regulate cellular processes
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2
Q

Nonpolar amino acids (9)

A

Valine
Alanine
Methionine
Tryptophan
Proline (contains imino group)
Glycine
Leucine
Isoleucine
phenylalanine

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3
Q

Polar Acid amino acids (2)

A

Aspartate/Aspartic Acid
Glutamate/Glutamic Acid
*Have a net charge of (-1) at ph 7

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4
Q

Polar Basic amino acids (3)

A

Histidine (contains imidozal group)
lysine
Arginine (contains guanidium group)
*have a net charge of (+1) at ph 7

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5
Q

Polar neutral amino acids (6)

A

Serine
Threonine
Asparagine
Glutamine
Cysteine (slightly polar)
Tyrosine (slightly polar)

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6
Q

Aromatic amino acids

A

Tryptophan
Phenylalanine
Tyrosine

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7
Q

Sulfur-containing amino acids

A

Methionine
Cysteine

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8
Q

Carboxyl-containing amino acids (secondary carboxyl)

A

Aspartic Acid
Glutamic acid

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9
Q

Hydroxyl-containing amino acids

A

Serine
Tyrosine
Threonine

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10
Q

special amino acids

A

cysteine (forms disulfide bonds)
Glycine (R-group is just Hydrogen)
Proline (forms a bond to itself)

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11
Q

Hydrophobic amino acids (8)

A

Alanine
Valine
Leucine
Isoleucine
Methionine
Phenylalanine
Tryptophan
Tyrosine

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12
Q

Aliphatic

A

Valine
Leucine
Isoleucine
Methionine

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13
Q

what are the groups that modify amino acids

A

acetyl
phosphate
hydroxyl
methyl
carboxyl
o-GlcNAc

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14
Q

functional groups and linkages

A

Hydroxyl
Acyl
Carbonyl
Carboxyl
Sulfhydryl
Amino
Phosphate
Pyrophosphate
ester
ether
amide

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15
Q

Describe alpha helices

A
  • Right-handed (clockwise)
  • H-bonds b/w peptide backbone
  • H-bonding occurs b/w all peptides. Oxygen in Carbonyl bonds with w/ hydrogen in amino 4 peptides away
  • turns every 3.6 residues
  • h bonds run parallel to axis
  • r-groups determine hydrophobic/hydrophilic character and formation
  • stiff structure
  • often found in membrane proteins
  • contain amphipathic helices (hydrophobic and hydrophilic)
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16
Q

What amino acid do you not see in alpha helices?

A

Proline, because they cannot fit and the steric hindrance

17
Q

What bonds stabilize alpha helices?

A

Hydrogen bonds within the backbone

18
Q

Where do the r-groups point in alpha helices and Beta sheets

A

Alpha helices: point outward
Beta sheets: point out top and bottom

19
Q

What makes up secondary structure?

A

alpha helices and beta sheets, turns

20
Q

Describe beta sheets

A
  • can be parallel or anit-parallel
  • are made of short segments of peptides
  • Hydrogen bonding occurs between adjacent Beta sheets. they can be close by, a little distant, or in a different polypeptide
  • flat but can be bent or twisted
21
Q

Describe beta turns

A
  • 4 residues in a turn
  • often found on the surface of globular proteins. This helps facilitate compact folding
  • Glycine and Proline are commonly found
  • stabilized by H bonds b/w residues 1 and 4
22
Q

describe beta loops

A
  • loops are longer and more complex than turns
  • do not have a regular structure. instead they are unique to each protein
  • usually found on protein surface
  • often involved in specific binding interactions
23
Q

Motifs

A
  • 2 or more repeating structures
  • can be small or large. (small: Helix-loop-helix)
    (large: Beta barrel)
  • associated w/ specific function. Ex.) Helix-turn-helix motif of DNA binding proteins
24
Q

Helix-turn-helix motif

A
  • 2 helices seperated by a turn
  • found in DNA binding proteins
  • found in Ca2+ binding proteins (EFhand)
25
Q

Coiled-coil motif

A
  • 2 alpha helices wrapped around each other
  • stabilized by weak interactions b/w aliphatic side chains
  • amphipatic
  • protein family: fibrous proteins, some transcription factors
26
Q

Zinc finger motif

A
  • a-helix + 2 antiparallel beta strands
  • stabilized by a central Zn2+ bound by 2 cys, and 2 HIs or 4 cys
  • zinc finger = C2H2
  • found in DNA or RNA binding proteins
27
Q

list Protein structure

A

Primary
secondary
tertiary
quaternary

28
Q

describe primary structure

A
  • amino acid sequence
  • stabilized by peptide bonds
  • determines shape and function
29
Q

describe peptide bonds

A
  • usually found in trans configuration
  • formed b/w Amino acids.
  • is a condensation rxn. yields H20
  • two amino acids= 1 peptide bond
  • formed b/w the oxygen of the carboxyl group and the nitrogen of the amino group of the other A.A
  • uncharged. so it can pack tightly
  • NCC-NCC-NCC Backbone
  • formed N-terminus to C-terminus. (from left to right)
  • hydrogen bonding
  • small peptides still have biological activity
  • no rotation around peptide bond b/c of the double bond.
    rotation is possible around the alpha carbon
  • steric hinderance of R-groups affect protein folding
30
Q

describe secondary structure

A
  • made of alpha helices and beta sheets
  • stabilized by H-bonding within the backbone
  • most common is a-helices and Beta sheets +turns
31
Q

describe tertiary structure

A
  • folded protein structure.
  • stabilized by many interactions within the peptide r-groups/residues. (hydrophobic interactions, h-bonds, van der waals, salt bridges, disulfide bridges)
  • can be flexible or stiff
32
Q

describe quaternary structure

A

multiple subunits
- stabilized by non-convalent bonds/interactions
- often required for protein function
- can be identical (homo-) or different (hetero)
- dimer (2 subunits)
- trimer (3 subunits)
- tetramer (4 subunits)

Biochem & Cell bio (20 decks)

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