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General Biology II > lecture 6: proteins > Flashcards

lecture 6: proteins Flashcards

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1
Q

What is a protein?

A

Functional molecule made of one or more polypeptides precisely coiled and folded into a unique shape —> diverse in shape = diverse in functions

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2
Q

8 functional classes of proteins

A
  1. Enzymatic (catalysis)
  2. Communication
  3. Storage
  4. Transport
  5. Regulation
  6. Defense
  7. Motor
  8. Structural
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3
Q

How do cells’ structure correlates with their function (3)? Proteome vs genome?

A

In terms of 3 organization levels:
1. Cell characteristics
2. Organelle characteristics
3. Proteome

  • All cells have same genome, but different proteome depending on their function —> unique development program and gene expression pattern
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4
Q

Gene expression 3 steps

A
  1. DNA (Gene)
    Transcription with RNA polymerase (enzyme) T —> U in RNA
  2. RNA (mRNA) —> message of the gene
    Translation with ribosomes and tRNA —> codons in amino acid language
  3. Protein (polypeptide)
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5
Q

Structure of amino acids? How do they differ?

A

Central carbon bonded to:
1. H
2. R group/side chain
3. Amino group (NH2)
4. Carboxyl group (COOH)

  • unique R group = what makes amino acids different
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6
Q

Why do amino acids ionize (COOH (carboxyl) lose H+ and NH2 (amino) gains H+) in neutral biological fluids? (2)

A
  • Helps amino acids to stay in solution + makes them more reactive
  • Enables proteins to function as buffers in body fluids
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7
Q

All proteins are made from how many AA’s?

A

20

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8
Q

Side chains (R group) are classified as… (3)

A
  1. Non polar: C-H bonds, no electronegative difference/atoms
  2. Polar: electronegative differences (O and N) = polar bonds
  3. Charged (acidic or basic):
    - Acidic = - charge in carboxyl group in R group
    - Basic = + charge in amino group in R group
    —> When added in neutral pH, they will act as a weak acid/base in order to buffer biological fluids
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9
Q

How do side chains differ? (3)

A
  1. Size
  2. Shape
  3. Properties
    - Chemical reactivity
    - The way they interact with water
    - The way they interact with other substances
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10
Q

Non polar vs Polar R groups’ 1. interactions with water and 2. other substances?

A

Non polar =
1. Hydrophobic
2. Less reactive

Polar =
1. Hydrophilic
2. More reactive

don’t worry about reactivity

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11
Q

Stereoisomers of amino acids

A
  • Central carbon = chiral as it is bonded to 4 diff. partners —> gives 2 stereoisomers —> L and R forms
  • Only L (left) forms of AA’S are recognized in cells
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12
Q

Which AA does not have stereoisomers?

A

Glycine, bc its R-group is H —> 2 H so not 4 DIFFERENT partners
- AA has to have 4 diff. partners to have stereoisomers

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13
Q

How are polypeptides formed?

A
  • Polypeptide = chains of amino acids linked by PEPTIDE bonds
  • Small polypeptide chain (fewer than 50 AA’s) = oligopeptides
  • Dehydration reactions (remove water) bonds the carboxyl (COOH) group of one AA to the amino (NH2) group of another AA to form a peptide bond
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14
Q

Polypeptide characteristics (3)

A

Peptide bonds form a “backbone” with 3 key characteristics
1. R-groups extend outwards: are on the side
2. Directionality: C or N terminus = carboxyl or amino group at the end of the chain
3. Flexibility: complete rotation around peptide bonds —> can fold and coil into specific 3D shape

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15
Q

What do proteins look like?

A
  • Most structurally diverse class of molecules known
  • Specific amino acid sequence in polypeptide determine protein’s 3D structure —> primary structure determine rest of higher order structure
  • Proteins’ structure fits its function
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16
Q

4 levels of protein structure + description

A
  1. Primary structure: unique sequence of amino acids in a polypeptide —> all we need is the primary shape to determine 3D structure
    - Encoded by the gene
  2. Secondary structure: coils and folds in polypeptide chain
    - Repeated structures
    - Diff. coils and bends = diff. structures
    - Formed by hydrogen bonds between carbonyl group of one AA and the amino group of another —> interactions between backbone, not the side chains
  3. Tertiary structure: overall complex 3D shape of
    polypeptide
    - Formed from non-covalent interactions and covalent bonds between side chains (or between side chains and peptide backbone)
  4. Quaternary structure: shape of protein and arrangement of subunits when 2+ polypeptide combine to form the functional protein
    - subunits come together in a specific arrangement via same types of non-covalent interactions that govern tertiary structure
17
Q

What are multimers?

A
  • Proteins with quaternary structure = “multimeric”
  • Subunits can be identical (homo) or different (hetero)
    Ex: homo dimer (2 same subunits), homo trimer (3 same subunits), hetero tetramer (4 diff. subunits)
18
Q

What allows diversity in protein structure and function?

A

Combined effects of primary, secondary, tertiary (and sometimes quaternary structure) —> hierarchical
- Each structure is based on the previous structure
—> So all structures are based on the primary structure

19
Q

What is sickle-cell disease?

A
  • Inherited blood disorder
  • Resulting for 1 nucleotide substitution in gene —> 1 single amino acid substitution in the polypeptide
  • Substitution in beta-globin gene required to make one of the beta-subunit of hemoglobin
    —> Change primary structure = change all order structure —> change function —> cause disease
  • Hemoglobin —> crystallize into a fiber = diff. structure and capacity at carrying oxygen is reduced —> get caught in blood vessels bc not smooth

many substitution mutations = neutral and don’t have such drastic effect

20
Q

How does protein folding happen?

A
  • Often spontaneous: folded molecule = more stable than unfolded one
  • Proteins called MOLECULAR CHAPERONES (cylinder shape + cap) help proteins to fold correctly in cells
    1. Unfolded polypeptide enters cylinder
    2. Cap attaches and cylinder changes shape to create hydrophilic environment so the polypeptide folds correctly
    3. Cap removes and properly folded protein is released

several diseases are associated with misfolded proteins

21
Q

What are prions?

A

Improperly folded forms of normal proteins in the brain
- Very slow-acting, virtually indestructible infectious agents that cause brain diseases in mammals
- AA sequence is the same, but shape is radically different —> simply misfolded, primary structure is NOT affected

22
Q

What influences protein structure?

A

First = primary structure determines higher order structures BUT physical & chemical conditions can also influence protein structure
—> Cause proteins to unravel —> DENATURATION
1. Change in temperature
2. pH: H+ more/less available —> can eliminate ionic bonds
3. Salt concentration
4. Detergents: soaps, nurture hydrophobic environment —> changes interactions

23
Q

What is denaturation?

A
  • Loss of protein’s native structure
  • Reversible or not depending on severity of the change
  • Become biologically INACTIVE
24
Q

Why are biologists interested in determining structure of proteins? And how?

A

Bc figuring out protein’s structure leads to figuring out its FUNCTION
1. X-ray crystallography: how we figured out DNA’s double helix structure
2. Nuclear magnetic resonance (NMR) spectroscopy
3. Bioinformatics: use a computer program/code to predict protein structure from data of AA sequences

25
Q

What are protein domains? Difference with “subunits?

A
  • Domains = Distinct units of structure and function in a polypeptide, regions of polypeptide chain
  • Subunits = a polypeptide that joins another polypeptide to form the quaternary structure of a functional protein
26
Q

How can proteins be modified? 2 types of modifications + description ?

A

Modified by enzymes
1. Structural modifications
- PERMANENT, not reversible
- Produce FINAL structure of protein
a) Removal of amino acids
b) Formation of disulfide bridges
c) Additions of carbohydrates (glycosylation) or lipids

  1. Regulatory modifications
    - REVERSIBLE
    - Modifies activity of proteins: makes it more/less functional by removing/adding a group —> turn protein on/off if necessary for a task
    a) Add/remove phosphate groups: phosphorylation
    b) Acetyl groups: acetylation
    c) Methyl groups: methylation
27
Q

What are cofactors?

A
  • Many proteins require an association with non-protein chemicals called cofactors to function normally
  • Cofactors associate with proteins through non-covalent interactions
  • Very important for enzymes

General Biology II (7 decks)

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