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Biochemistry > Week 1 - Protein Structure and Function > Flashcards

Week 1 - Protein Structure and Function Flashcards

1
Q

primary structure protein

A

simply the sequence of amino acids and any modifications made to them. Peptides and Proteins are covalent, linear chains of amino acids.

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2
Q

Secondary structure protein

A

first basic folding patterns that help proteins acquire distinct structure. • Alpha-helices • Beta sheets • Turns/bends

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3
Q

Tertiary structure protein

A

is the assembly of secondary structures into a domain or a fold. This is a typically a discrete functional unit of a protein, and may be the entire protein in some cases (eg cytochrome c, or myoglobin)

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4
Q

Quaternary structure protein

A

is the assembly of several peptides into a functional protein. Usually each peptide is folded through secondary and tertiary (domains) prior to assembly into a quaternary structure. A good example of a protein with a quaternary structure is hemoglobin.

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5
Q

stop codons

A

UAA, UGA, UAG

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6
Q

start codon

A

AUG - methionine

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7
Q

formation and growth of the polypeptide chain - what happens from P site to A site?

A

During formation of a peptide bond, the ester bond in the (P)eptidyl site is cleaved, and peptidyl transferase catalyzes a condensation reaction between its carboxyl terminus and the amino terminus of the amino acid in the (A)mino site. This transfers the P-site amino acid to the A-site amino acid. The polypeptide thus “grows” from the amino terminus to the carboxyl terminus.

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8
Q

what kind of isomers are found in proteins?

A

Only L amino acids are found in proteins

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9
Q

Glycine

A

Glycine, Gly, G

small amino acid

Gly is important in proteins that form twisted helices with other proteins (like collagen) since it has a small R group which allows tight packaging of the strands forming the helix.

  • very flexible backbone
  • smallest AA
  • often found in active sites and turns
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10
Q

Alaline

A

A, Ala

small amino acid

  • Single methyl group
  • Moderately hydrophobic
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11
Q

Proline

A

Pro, P

cyclic amino acid

Pro tends to break the α-helix of protein secondary structure.

– Breaks or kinks α-helices
– Specialized structures
– Major constituent of collagen – Modified (hydroxylated).

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12
Q

Small Amino Acids

A
  • Glycine, Gly, G
  • Alanine,Ala,A
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13
Q

Branched Chain Amino Acids

A
  • Valine, Val, V
  • Leucine, Leu, L
  • Isoleucine, Ile, I
  • muscle protein breaks down to amino acids, the amino group of a BCAA is given to pyruvate to make Ala and the carbons of the BCAA are sent to the TCA cycle to extract energy for the muscles. The BCAAs are hydrophobic and are often in the core of proteins
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14
Q

Serine

A

Ser, S

Hydroxyl AA

  • Ser and Thr and Cys are polar amino acids
  • Serine’s and Threonine’s hydroxyl groups are very reactive and can be phosphorylated or glycosylated easily.
  • They also participate in active sites to carry out covalent chemistry or acid/base chemistry
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15
Q

Threonine

A

Thr, T

Hydroxyl AA

Ser and Thr and Cys are polar amino acids

H-bonding, reactive sites, structural

Serine’s and Threonine’s hydroxyl groups are very reactive and can be phosphorylated or glycosylated easily. They also participate in active sites to carry out covalent chemistry or acid/base chemistry.

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16
Q

Cysteine

A

Cys, C

Sulfur Amino Acids & polar

  • Cysteine can form a “disulfide” bond with another cysteine. This is critical in protein tertiary structure formation and sometimes in quaternary structure.
  • Formation of cys-cys disulfide bond is an oxidation reaction. Reversing it is a reduction:
  • cys-SH + cys-SHcys-S-S-cys + 2H (note – the Hydrogens are incorporated into other molecules).
  • Cys is similar to Ser, but Sulfur reactivity is a little different.
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17
Q

Methionine

A

Methionine, Met, M

Non-polar, sulfur AA

  • Met is hydrophic; it can act as a single methyl group donor.
  • The methyl group that is attached to the sulfur atom of methionine is able to be given to other molecules that need a “1 carbon group” to grow larger.
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18
Q

Aromatics

A
  • Phenylalanine, Phe, F
  • Tyrosine, Tyr, Y
  • Tryptophan, Trp, W

Function:

  • Aromatics are large, generally hydrophobic amino acids.
  • They play special roles in stabilizing the binding of aromatic rings (such as in ATP).
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19
Q
A
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20
Q

Tyrosine

A

Tyrosine, Tyr, Y

  • Tyrosine is a precursor for many other compounds.
  • Tyrosine is phosphorylated during growth factor receptor activation. A phosphate on a tyrosine is a “docking” site for proteins with a “SH2 domain”.
  • Phe can be converted to Tyr by a hydroxylation reaction.
21
Q

Tryptophan

A

Tryptophan, Trp, W

aromatic

Trp can be converted to the B vitamin, niacin

22
Q

Acidic Amino Acids

A

Aspartate, Asp, D

Glutamate, Glu, E

– Generally on the exterior to impart solubility

– In active sites

– Protein modifications

23
Q

Amine AA

A

Acidic residue derivatives:

  • Asparagine, Asn, N
  • Glutamine, Gln, Q
  • Generally polar,
  • Can be reactive,
  • Asn is the site of N-linked glycosylation.
24
Q

Basic AA

A
  • Lysine, Lys, K
  • Arginine, Arg, R
  • Histidine, His, H

Charged at neutral pH
Typically found on the exterior to render the protein soluble

25
Q

Arginine

A

Arg, R

Arg is part of the Urea cycle

26
Q

Lysine

A

Lys, K

undergoes modification

27
Q

Histidine

A

Histidine, His, H

Histidine can bind or release protons (act as a buffer) near physiological pH.

often in active sites, pK is near neutral and can readilybe protonated

28
Q

Hydroxyl functional group

A
  • Ser, Thr, Tyr
  • All of these can be phosphorylated on their side chains
29
Q

Methyl Functional group

A
  • Ala, Val, Ile, Leu, Met
  • Met can donate its methyl group to other molecules that need a carbon atom to make bigger molecules
30
Q

Carboxy functional group

A

Asp, Glu

31
Q

Amino

A

Lysine, K, Lys

32
Q

Sulfhydryl functional group

A

Cysteine, Cys

  • Cys can form disulfide bonds, which can help stabilize tertiary or the quaternary structure of proteins, or serve as redox reaction
33
Q

Aliphatics AA

A
  • Valine, Leucine, isoleucine, methionine, alanine.
  • Provide hydrophobicity, structure. Important in folding.
34
Q

Alcohols

A
  • Serine, threonine, tyrosine.
  • Can be phosphorylated – critical in signaling
  • CCan be glycosylated, important for many functionals and structural aspects of proteins.
  • Important in many enzymatic reactions.
35
Q

Aromatics

A
  • Tyrosine, phenylalanine, tryptophan (histidine also has aromatic ring properties).
  • Structural, hydrophobic often found in binding sites, stabilize other aromatic ring systems
36
Q

Carboxylic acids

A
  • Glutamate and Aspartate
  • Imparts charge
37
Q

Bases Functional Group

A
  • Lysine, Arginine, Histidine
  • Impart charge
  • Participate in enzymatic reactions
38
Q

Sulfhydryl Functional Group

A
  • Cysteine
  • Can form disulfide bonds – critical for tertiary structure and sometimes quarternary structure.
  • Similar to serine; also participates in enzymatic chemistry.
39
Q

pKa Acidic Residues

A

Asp = 3.9

Glu = 4.3

40
Q

pKa Basic Residues

A

His = 6

Arg = 12.5

Lys = 10.5

41
Q

Cysteine pKa

Tyrosine pKa

A

8.3

10

42
Q

Tertiary Structure Bonds

A

4 types of bonds

  • hydrogen bonds
  • disulfide bonds
    • Only the disulfide bond is a covalent bond.
    • Denaturing agents such as heat will disrupt all these bonds except the disulfide bond.
    • Disulfide bonds can be broken by reducing agents
  • hydrophobic interactions
  • ionic bonds (rare)
43
Q

Secondary Structure

A

3 bonds

  • Beta sheet
  • Alphahelix
  • Random coil (turns)

Secondary Structure arises principally from wanting to satisfy Hydrogens Bonds on the main chain carboxyl groups and amide groups.

The side chains, R-groups, determine what kind of secondary structure is favored. Some proteins have all these secondary structures, while other proteins have predominately one kind of secondary structure.

Two alpha-helical proteins, Hemoglobin and rhodopsin.

44
Q

Quaternary Stucture

A

fully functional proteins assembled from individual subunits or domains.

Hemoglobin (Hb) is the carrier of oxygen in the blood. It is assembled from four subunits,

two alpha and two beta.

45
Q

Hemoglobin structure

A

Hemoglobin is composed of four proteins, 2 α-globin subunits and 2 β-globin subunits, which affect one another to synergize the release or the binding of oxygen. Because it is assembled from 4 subunits to form a functional whole, it has quaternary structure.

*composed of α-helices only, and contain no β- sheets.

46
Q

Myoglobin structure

A

Myoglobin is similar in structure to the α-globin proteins and β-globin protein momomer. It is much smaller, has a single peptide, and a single domain. Myoglobin binds and releases oxygen in a non-cooperative fashion. It contains secondary (alpha-helices) and tertiary (globin fold) structure, but no quaternary structure.

* composed of α-helices only, and contain no β- sheets.

47
Q

Cu,Zn-superoxide dismutase

A
  • Superoxide dismutase catalyzes the dismutation of the superoxide (O2.-) radical into either molecular oxygen, O2 or to hydrogen peroxide, H2O2.
  • Each subunit consists of eight antiparallel β- sheets called a β-barrel structure.
  • Superoxide dismutase has a dimeric structure, with a monomer molecular mass of 16,000 Da. Cu and Zn are cofactors.
48
Q

Collagen

A
  • Major Structural protein
  • Unusual Triple Helical structure – Has high % Gly and Pro
  • Atypical 2nd and quaternary structure
  • Other structural proteins also rely on structures atypical for globular proteins.
  • Collagens are a major component of connective tissue such as cartilage, tendons, the organic matrix of bones, and the cornea of the eye.
  • If you have a deficiency in vitamin C, you will be unable to resynthesize collagen, and get the disease scurvy.

Biochemistry (3 decks)

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