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Biology 2 > lecture 1: amino acids > Flashcards

lecture 1: amino acids Flashcards

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1
Q

what are the monomers of proteins?

A

amino acids

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2
Q

what are the polymers of proteins?

A

polypeptide

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3
Q

by which bond are amino acids linked?

A

peptide bond

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4
Q

what are the components to each amino acid?

A

-central carbon
-hydrogen group
-amino group (NH2)
-carboxyl group (COOH)
-R group

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5
Q

what differentiates the 20 different amino acids?

A

the R group

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6
Q

in what form is the amino group more stable? what are the 2 forms it can exist as?

A

it can exist as NH2 or NH3+, but its more stable as NH3+ in our bodies so thats how it exists.

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7
Q

what is common between each amino acid?

A

backbone

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8
Q

what is another word for R group?

A

side chain

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9
Q

what are the properties of a non-basic/acidic hydrophilic amino acid? (polar side chains)

A

the side chains contain hydroxyl (OH), carbonyl (C=O) and sulfhydryl (SH) groups

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10
Q

what happens if you see an oxygen in the side chain of an amino acid?

A

it must be at least polar

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11
Q

what are the properties of a basic hydrophilic amino acid? (electrically charged side chains) what is the charge?

A

the side chain is charged positivly. the charge is due to a positive amino group (NH2/NH3) in the R group. CHARGED AT PH 7

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12
Q

what are the properties of an acididc hydrophilic amino acid? (electrically charged side chains) what is the charge? CHARGED AT PH 7

A

the side chain is charged negatively. this charge is due to a negatively charged carboxyl group (COO/COOH)

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13
Q

how does carboxyl exist in our bodies in the backbone of amino acids?

A

as COO-

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14
Q

what are the properties of a hydrophobic amino acid? (polar side chains)

A

the side chains are made up of carbons, hydrogens and methyl groups (CH3)

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15
Q

What happens to an amino acid in very acidic conditions?

A

Backbone becomes positively charged. The carbonyl group gains an H+, due to the fact that there are more H+ in the environment

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16
Q

What happens to an amino acid in very basic conditions?

A

The amino group loses its proton, therefore it is no longer positively charged and the negative charge of the carboxyl takes over.

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17
Q

What does an amino acid look like at PH 7?

A
18
Q

what is the isoelectric point?

A

PH at which a protein has a neutral charge (charge of 0)

19
Q

by which reaction are peptide bonds formed? how does this happen?

A

dehydration reaction. the H of the amino group of one amino acid is lost along with the OH of the carboxyl group of the next amino acid. this continues until we have a chain

20
Q

what is the directionality of the peptide bond?

A

c terminus first (carboxyl end)
n terminus at the end (amino end)

21
Q

why are proteins able to carry out so many diverse functions in cells?

A

-because they can form many different shapes which makes them really diverse comapred to other structures

22
Q

what are the 4 levels of protein structure?

A

-primary structure
-secondary structure
-tertiary structure
-quaternary structure

23
Q

what type of bonds are peptide bonds? why?

A

covalent bonds. anything formed by a dehydration reaction is a covalent bond.

24
Q

what is a primary structure?

A

-Linear sequence of amino acids coded for by a gene sequence
-Has directionality (N-C terminus)
-linear chain of amino acids

25
Q

what is a secondary structure?

A

spatial arangement of amino acids to form alpha helices of beta sheets.

26
Q

how is a secondary structure formed?

A

by H bonding between amino (N-H) group of one amino acid and carbonyl (C=O) (since we lost OH during dehydration) group of another amino acid

27
Q

are R groups involved in the the formation of secondary structures?

A

NO! only the backbone!

28
Q

what are the characteristics of alpha helix?

A

-H-bonding between amino acids 4 places apart
-R groups oriented away from the axis
-looks like a curl

29
Q

what are the characteristics of beta sheet?

A

-two regions of polypeptide chain lie parallel to each other like a folded sheet

30
Q

what is a tertiary structure?

A

-structure formed when alpha helix and beta sheets interact to form a variety of shapes
-formed through the interactions between amino acid side chains

31
Q

what type of bonds happen in tertiary structure?

A

side chains interact again through covalent and non-covalent interactions to form tertiary structures

32
Q

what type of non-covalent bonds are involved in a tertiary structure?

A

-H bonding (between R groups)
-hydrophobic interactions between hydrophobic amino acids (2 hydrophobic)
-van der Waals (2 hydrophilic or 2 hydrophobic)
-ionic bond (charged amino acids interact through salt bridges)

33
Q

what type of covalent bonds are involved in a tertiary structure?

A

disulphide bridge (amino acids interact with a sulfhydyl group)

34
Q

what are van Der Waals?

A

a way in which 2 polar or 2 hydrophobic amino acids can interact with each other in a tertiary structure.

35
Q

what is a quaternary structure?

A

-more than one polypeptide chain interacting together to form a protein

36
Q

how are polypeptides held together in the quaternary structures?

A

by the same interactions as a tertiary structure

37
Q

what is denaturation?

A

disrupting protein structure. proteins become unfolded as all bonds are broken. we are left with polypeptides.

38
Q

is renaturation possible?

A

sometime possible, but highly unlikely

39
Q

what are the conditions that can denature a protein? why?

A

-temperature (alters vibrational and rotational energy and disrupts non-covalent interactions such as H-bonds
-PH (changes the ionic state of the charged side chains, which disturbs bonds and makes for the protein to unfold)

-salt (changes the ionic environment. there are now more charges in the environment which disrupts the charges of the protein causing it to unfold)

-detergent (disrupts hydrophobic regions)

-reducing agent (breaks covalent disulphide bonds. smells and. something that you add to the protein that causes a reduction)

40
Q

what is the movement od hydrophobic/hydrophilic side chains when we add detergent?

A

-hydrophobic side chains move from the interior of protein to the exterior of protein
-hydrophilic Side chains move to the interior of protein

41
Q

what levels of protein structure are affected by denaturation?

A

4th, 3rd, 2nd, NOT FIRST! (cant break peptide bonds)

42
Q
A

Biology 2 (27 decks)

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