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BIOL 2321 - Cell Biology > Protein Review > Flashcards

Protein Review Flashcards

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1
Q

What are proteins composed of?

A

A long sequence of amino acids

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2
Q

Describe an amino acid structure at cellular pH (~7)

A

A central carbon

bonded to an H

bonded to an R group

bonded to an amino group (NH3+)

bonded to a carboxyl group (COO-)

                 H
                  |
H3N (+) -- C -- C = O
                  |      |
                 R     O (-)
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3
Q

What is cellular pH?

A

~7 (neutral)

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4
Q

How is the amino acid structure different at cellular pH than outside of cellular pH?

A

It is charged

There is a positive charge on the N of the amino group and a negative charge on the single bonded O of the carboxyl group

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5
Q

What is the only difference between individual amino acids?

A

The R groups attached

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6
Q

How many amino acids are there that form proteins?

A

20

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7
Q

How are amino acids categorized and what are the categories?

A

Categorized based on their R groups/side chains at pH 7

acidic (- charged)

basic (+ charged)

polar but uncharged

non polar

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8
Q

How are each of the 20 amino acids named?

A

With 3 letter names and with 1 letter names

ex. Alanine = Ala = A

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9
Q

Give an example of a positively charged amino acid

A

Lysine (Lys/K)

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10
Q

Give an example of a negatively charged/acidic amino acid

A

Aspartic acid (Asp/D)

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11
Q

Give an example of a polar but uncharged amino acid

A

Serine (Ser/S)

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12
Q

Give an example of a non-polar amino acid

A

Glycine (Gly/G)

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13
Q

What atoms will a polar side chain of an amino acid involve?

A

Oxygen or Nitrogen (no full charge at pH 7)

ex. amide group or hydroxyl group

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14
Q

What are non polar side chains of amino acids usually composed of?

A

hydrocarbons

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15
Q

What do SOME non polar side chains of amino acids have? which ones?

A

Sulphur groups

Methionine and Cysteine

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16
Q

Describe peptide bonds

A

Bonds between two amino acids formed by a dehydration reaction

OH lost from carboxyl group
H lost from amino group to form a peptide bond between carbonyl carbon and amine nitrogen

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17
Q

Why is a string of amino acids flexible?

A

the N-C and C-C bond in the backbone can rotate

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18
Q

Where are peptide bonds formed/located?

A

between the carbonyl carbon (carbon in the carboxyl group) and amine nitrogen (nitrogen in the next amine group)

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19
Q

What is generated when many peptide bonds link many amino acids?

A

polypeptide

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20
Q

What orientation (in regards to N and C) are polypeptides?

A

Head to tail or

Amino group to carboxyl group

There is always a N terminus and a C terminus

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21
Q

What is included in the backbone of a polypeptide?

A

everything except the R groups

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22
Q

What contributes to the polarity of a polypeptide backbone?

A

the chain ends are charged amino (head) and carboxyl (tail) groups

every other amino and carboxyl group in the backbone are involved in peptide bonds so they are not charged

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23
Q

What are the 4 structures of proteins?

A

primary
secondary
tertiary
quaternary

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24
Q

Why is protein structure so important?

A

Structure dictates function

Proteins require a specific shape to do any job

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25
Q

Describe primary protein structure

A

A specific linear sequence of amino acids connected by peptide bonds

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26
Q

T or F: because there’s only 20 amino acids, for a peptide 127 amino acids long, there’s not many possible structures

A

FALSE

there is 20^127 possible primary structures

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27
Q

T or F: 1 change in 1 amino acid at 1 position can dramatically change the protein structure and its function

A

TRUE

28
Q

What direction is primary structure always read/notated?

A

from the amino end (N terminus or head) to the carboxyl end (C terminus or tail)

29
Q

What dictates all other structure levels?

A

the primary structure because all other structure levels are dependent on the specific order of amino acids set out in the primary structure

30
Q

Describe secondary protein structure? What are the 2 structure shapes?

A

Formed by small sections of a primary protein folding into patterns

  1. alpha helices
  2. beta sheets
31
Q

Describe alpha helices in secondary protein structures. How are they formed?

A

Create coils by forming hydrogen bonds between amino acids that are four amino acids apart

formed by hydrogen bonds between a hydrogen on an amino group and an oxygen in a carboxyl group (ON THE BACKBONE)

32
Q

How are the side chains organized in an alpha helix secondary protein structure?

A

the R groups project outwards, away from the helix and all 360 degrees around the helix

(R groups are not localized to one side)

33
Q

T or F: alpha helices are ordered and consistent structures

A

TRUE

34
Q

When are alpha helices amphipathic?

A

ONLY when all the hydrophobic R groups project off one half of the helix and all the hydrophilic R groups project off the other half

35
Q

Describe the structure of beta sheets in secondary protein structures. How are they formed?

A

Composed of flat, pleated strands stacked on top of each other (sheets)

formed when a hydrogen bond occurs between backbone atoms (carbonyl of 1 amino will H bond with the amine of another amino) in adjacent strands

36
Q

How do beta sheets form antiparallel beta strands?

A

If there are a few amino acids between each layer that form a curve/u-turn, the beta strands will go in opposite directions (antiparallel)

37
Q

How are side chains organized in beta sheet secondary structures?

A

they alternate projecting above and below the plane of the sheet

38
Q

Are parallel or antiparallel beta sheets more stable? why?

A

Parallel sheets are less stable because they have angled/distorted hydrogen bonds

Antiparallel sheets are more stable because they have straight hydrogen bonds

39
Q

Describe non-repetitive structures

A

Portions of a polypeptide that are not organized into alpha helices or beta sheets

very flexible, form loops, hinges, or turns

usually drawn by a thick line

40
Q

Describe tertiary protein structure

A

the OVERALL shape of the protein that results from the interactions between SIDE CHAINS

41
Q

How are tertiary protein structures formed?

A

hydrophobic interactions aggregate parts of the protein with hydrophobic R groups

clusters the hydrophobic parts on the inside of the protein to protect from the aqueous environment

42
Q

How do R groups interact within a tertiary protein?

A

ionic bonds between charged R groups

hydrogen bonds between polar R groups

Disulfide bridges between cysteines

43
Q

What is the difference between the folding that occurs in secondary structures vs tertiary structures?

A

Secondary structure folding occurs because of interactions between amino acids that are fairly close together (4 apart)

whereas, folding in tertiary structure can be a result of interactions between R groups that have any distance between them
- ex. amino acid #3 can form an ionic bond with amino acid #140 and pull those regions together

44
Q

Describe conformation

A

the final 3D arrangement of all the atoms in a protein molecule

45
Q

Why is there only realistically a few specific conformations for a folded protein?

A

Because they need to maximize the number of weak interactions to stabilize the protein

46
Q

T or F: the final conformation for a protein should be consistent each time it folds (and refolds)

A

true, the final shape is intrinsic to the molecule

47
Q

Describe conformational changes

A

Every activity a protein engages in is accompanied by a conformational change

essential to the protein’s function

48
Q

Why are conformational changes essential to protein function?

A

Because a protein may need one conformation when bound to something, but may need another when unbound

or may have active and inactive conformations depending on cell conditions

ex. ion channels - proteins will change conformations to allow ions to transport

49
Q

Describe domains

A

Distinct regions within the tertiary structure that have separate functions and are connected by an unstructured portion of the polypeptide

50
Q

Describe quaternary protein structure

A

the overall protein structure when the protein requires more than one polypeptide (aka sub unit)

51
Q

Define monomer

A

a functional protein with one polypeptide

52
Q

Define dimer

A

a functional protein with 2 polypeptide chains

53
Q

Define tetramer

A

a functional protein with 4 polypeptide chains

54
Q

T or F: quaternary structure only exists if proteins have 2+ polypeptides

A

TRUE

55
Q

Give an example of a quaternary protein

A

Hemoglobin

Has two polypeptides with 4 subunits

the quaternary structure allows for O2 binding and release

56
Q

What are the two general shapes for quaternary structure?

A

fibrous

globular

57
Q

Describe fibrous shaped quaternary structures and give an example

A

fibrous proteins form long fibres, usually involved in structural support

ex. collagen is a fibrous trimer

58
Q

Describe globular shaped quaternary structures and give an example

A

roughly spherical in shape

ex. hemoglobin is a globular tetramer

59
Q

Describe denaturation

A

Occurs when the weak chemical bonds (ex. hydrogen bonds) that hold the protein together cannot form or are broken

the protein will unravel into a non-functional state and lose its 2/3/4 level structures and become primary

60
Q

T or F: when a protein denatures it loses all structure

A

FALSE. it will never lose its primary structure!!

61
Q

What can cause denaturation?

A

If chemical and physical conditions of the cell are outside of the range that’s tolerable for the protein to function

ex. pH, salt concentration, temperature

62
Q

Can a denatured protein refold into the same protein if conditions are restored? what does this mean about the shape of the protein?

A

Yes

this means the shape is INTRINSIC to the protein - all the info needed to form a functional protein is located within the primary structure

63
Q

What is a molecular chaperone? How do they work?

A

A protein that assists other proteins in folding if they cannot do it alone

Often they bind to the protein or create the conditions necessary for the protein to fold

64
Q

Is there a difference between a polypeptide and a functional protein? what is it?

A

YES YES YES YES

Polypeptide = long string of amino acids that is not necessarily folded into a protein

protein = MUST BE FOLDED to be functional

65
Q

proteins must be WHAT to be functional?

A

FOLDED

BIOL 2321 - Cell Biology (26 decks)

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