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Flashcards in Proteins Deck (43):
1

4 parts of an amino acid

*all are bonded to common carbon core

1. H - hydrogen atom
2. NH2 - amino functional group
3. COOH - carboxyl functional group
4. a distinctive "R-group"

2

What happens to amino acids in water?

They ionize due to the pH of 7

3

What acts as a base in an amino acid?

Amino group (NH2)

4

What acts as an acid in an amino acid?

Carboxyl group (COOH)

The two highly electronegative oxygens pull the hydrogen away

5

What makes the amino acids unique?

The r-group

6

What happens if an R-group just contains carbon and hydrogen?

They will not participate in many chemical reactions

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Hydrophilic R-groups

Polar and electrically charged

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Hydrophobic R-groups

Nonpolar R-groups or highly electronegative atoms capable of forming hydrogen bonds with water

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Does the R-group have a negative charge?

If yes, it is acidic and will lose a proton

10

Does the R-group have a positive charge?

If yes, it is basic and will pick up a proton

11

If the R-group is uncharged, does it have an oxygen atom?

If yes, then the highly electronegative oxygen atom will form a polar covalent bond, thus making it uncharged

12

Dehydration reactions

also called condensation reactions

newly formed bond results in the loss of water

13

What type of bond is a peptide bond?

Covalent

14

What do peptide bonds occur between?

carboxyl group of one amino acid and the amino group of another amino acid

2 hydrogens from (NH2) react with one oxygen from (COOH) to form the peptide bond

15

Are peptide bonds stable?

Yes due to the degree of electron sharing

16

Residues

amino acids that are linked together in a chain

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R-group orientation in residue

Side chains (R-group) stick out which makes it possible for them to react with eachother and to react with water

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What is the directionality of the residue?

N-terminus (amino group) to C-terminus (carboxyl group)

19

Oligopeptide

a polymer with fewer than 50 amino acids

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Polypeptide

a polymer with more than 50 amino acids

21

Primary structure

refers to the distinct amino acid sequence

R-groups affect chemical reactivity and solubility

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Secondary structure

distinctively shaped sections that are stabilized by hydrogen bonding that occurs between the oxygen on the C=O group of one amino acid residue and the N-H groups on another

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a-helix

the polypeptide's backbone is coiled

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B-pleated sheet

segments of the peptide chain fold in the same plane

25

Proline

rarely found in a-helixes

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Tertiary structures

form using a variety of bonds and interactions between R-groups or between R-groups and the backbone

27

Types of interactions used for tertiary structures

1. Hydrogen bonding
2. Hydrophobic interactions
3. van de Waals interactions
4. Covalent bonding
5. Ionic bonding

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Hydrogen bonding

form between polar side chains and opposite partial charges either in the peptide backbone or other R-groups

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Hydrophobic interactions

water molecules force the hydrophobic nonpolar side chains to merge into globular masses

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van der Waals interactions

once hydrophobic side chains are close to one another, electrical attractions take place

constant motion of elections produces tiny asymmetry in charge this makes nonpolar molecules slightly attracted to eachother

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Covalent bonding

can form between two cysteines

disulfide bonds create strong links

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Ionic bonding

form between groups that have full and opposing charges

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Quaternary structure

proteins that involve multiple polypeptides

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Dimers

proteins with two polypeptide subunits

35

Macromolecular machines

groups of multiple proteins that assemble to carry out a particular function

ex: ribsome

36

Is folding spontaneous?

It tends to be

37

Denatured

unfolded proteins

38

How do we know that folding affects function?

Anfinsen studied denatured proteins and found that they could not function

39

Molecular chaperones

special proteins that can facilitate protein folding

40

Prions

proteins that can be induced to fold into infectious, disease causing agents

shapes are different

Ex: mad cow disease

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What are proteins used for?

Catalysis
Defense
Movement
Signaling
Structure
Transport

42

Active site

location where substrates bind to enzyme and react

43

Where can hydrogen bonding occur to form the secondary structure?

Every 4th amino acid

Between carboxyl (-) and amino (+) group