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Biochemistry > Lecture 1: Amino acids- The building blocks of proteins > Flashcards

Lecture 1: Amino acids- The building blocks of proteins Flashcards

know: - the basic structure of an amino acid - about the properties of the 20 naturally occurring amino acids found in proteins - how a polypeptide chain is formed

1
Q

What is the general structure of the amino acid?

A

NH3 (amino) group and COOH (carboxyl) group bonded to an alpha carbon

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2
Q

What is the reaction which results in the formation of a dipeptide called?

A

dehydration reaction

removal of H2O

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3
Q

true or false; peptide bonds are a form of covalent bonding?

A

true

- a covalent bond forms between the (-H)N terminal of one amino acids and the (-OH) C- terminal of another amino acids

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4
Q

What is an R group?

A
  • bonded to an alpha carbon

- determines the identity of the particular amino acid

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5
Q

What is a stereoisomer?

A
  • same molecular formula
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6
Q

What kind of stereoisomer are amino acids?

A
  • chiral : due to 4 different groups being bonded to the alpha carbon
  • optical isomers
  • non superimposable mirror images
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7
Q

How are amino acids classified?

A
  • L/D classification ( the position of theAMINO group on the left or right side of alpha carbon determines the L or D designation)
  • L: left
  • D: right
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8
Q

What are the functions of proteins?

basic examples:

  • enzymes
  • antibodies
  • receptors
  • carriers
  • hormones
  • materials
A
  1. ) Enzymatic catalysis: eg. hexokinase: ATP -dependent phosphorilation of glucose
  2. ) Transport and Storage : hemoglobin (red blood cells; binds oxygen)
  3. ) Hormones: Insulin (regulates plasma glucose)
  4. ) Immune protection: Immunoglobulins, bind infectious organisms
  5. ) Gene regulation: transciption factors
  6. ) structural: collagen (provides tensile strength to skin and bones
  7. ) Contraction (actin and myosin)
  8. ) Receptors: neurotransmitters
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9
Q

What are proteins involved in? What are their generalized functions?

A
  • cell structure
  • movement
  • storage
  • transport
  • nerve cell signalling
  • blood clotting
  • immune defence
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10
Q

What is a proteins distiguishing feature?

A

abbility to fold into specific patterns to form unique 3D structures

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11
Q

How much dry weight do proteins comprise of?

A

50%

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12
Q

Why is the protein structure important?

A

defines the important property of proteins, an abbility to recognize other molecules

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13
Q

What is a protein?

A
  • have highly specific 3- dimensional structure
  • consists of one or more polypeptide chains
  • each polypeptide chain consists of a long chain of amino acids joined end to end in a linear sequence known as the PRIMARY STRUCTURE
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14
Q

What does it mean by primary structure?

A
  • LINEAR chain of amino acids , as linked by peptide bonds
  • sequence of amino acids is in accordance to the gene translated by ribosomes during protein synthesis
  • determine the other levels of structure
  • its sequence is critical to proper proteins functioning
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15
Q

What does it mean by secondary structure?

- characterized by the repetative organisation of the peptide bond

A
  • the arrangement in space of the atoms in the peptide backbone
  • have repetative interactions resulting from hydrogen bonding between amide N-H and the carbonyl groups of the peptide backbone
  • the conformations of the side chains of amino acids ARE NOT PART OF THE SECONDARY STRUCTURE
  • alpha helix, and beta pleated sheet (examples)
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16
Q

What does it mean by tertiary structure?

A
  • includes the 3D arrangement of all the atoms in the protein
  • including those in the side chain
  • and in any other prostheic groups (other groups of atoms other than amino acids)
  • refers to the complete 3D structure of a protein
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17
Q

What does it mean by Quaternary structure?

- association of two or more polypeptides to make up a protein

A
  • the arrangement of the subunits with respect to each other
  • interactions between subunits is mediated by non covalent interactions such as :
    hydrogen bonds
    electrostatic attraction
    hydrophobic interactions
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18
Q

What factors affect the properties of amino acids?

- nature of the side chain

A
  1. ) polar and non polar nature of side chain
  2. ) presence of acidic or basic group
    etc. .
19
Q

How are amino acids classfied?

- according to two major criteria

A
  1. ) the polarity of the side chain

2. ) the presence of acidic or basic group on the side chain

20
Q

What are the 4 groups of amino acids?

A
  1. ) non polar side chains
  2. ) electronically neutral/ polar side chain
  3. ) carboxyl groups in their side chain
  4. ) basic side chains
21
Q

Describe the properties of glycine

A
  • the smallest amino acid
  • side chain -H
  • the small side chain allows glycine to fit into small spaces thus providing CONFORMATIONAL FLEXIBILITY to proteins
22
Q

True or false; Glycine is the only achiral amino acid?

A

true

23
Q

What are the properties of proline

A
  • has a side chain that is bonded to a nitrogen atom of its amino group
  • this results into greater RIGIDITY to proteins
  • and this can cause KINKS in the protein structure
24
Q

Cysteine

A
  • contains sulphydryl group (-SH)

- this is used to STABILIZE proteins by disulfide bonds

25
Q

What does tyrosine, tryptophan and phenylalanine have in common?

A

they all absorb UV light which can be used to detect the proteins in the solution

26
Q

What are the properties of amino acids?

A
  • variable side chain
  • zwitterion
  • chiral
  • acid base chemistry
27
Q

What does the biological activity of a protein depend on?

A
  • their chemistry

- their structure

28
Q

Why does the charge of some amino acids alter with pH?

A

the presence of ionizable groups

29
Q

What is an ionizable group?

A
  • these groups convey positive and negative charged groups to proteins
  • each ionizable group HAS PH VALUE AT WHICH EQUAL AMOUNTS OF CHARGED AND UNCHARGED FORMS EXIST
  • this is known as pKa
30
Q

what is the significance of the amino acid side chain?

A
  • gives chemical and structural diversity:
  • size
  • charge
  • shape
  • chemistry
31
Q

Amino acid side chains groups?

A
  • acidic
  • basic
  • neutral polar
  • neutral non polar
32
Q

Why is cysteine so special? Describe its properties

A
  • polar side chains consist of a thiol group (-SH-)
  • which can react with OTHER Cysteine groups to form DISULFIDE BRIDGES in proteins during an OXIDATION REACTION
  • thiol group can also lose a proton
  • can form cross links
33
Q

What is the effect of a carboxyl group in an amino acid side chain?

A
  • negatively charged at neutral pH
  • can lose a proton that’s why
    ( glutamate and aspartate)
34
Q

What do the pKa values of amino acids depend on?

A

the environment, and can change significantly in the confines of the protein

35
Q

What does pKa mean?

A
  • the pH at which have equal amounts of protonated (charged) and non protonated forms (uncharged)
36
Q

If an amino acid has a hydrophobic side chain, where does this amino acid tend to be found?

A

are usually located in the interior of the protein away from contact with water

37
Q

hydrophilic side chain and polar side chain? where does amino acid orientate?

A

found usually on the exterior of the protein, in contact with water, where they can be hydrated by the surrounding aqueous environment

38
Q

acid and basic side chain? where found on protein?

A

also on the exterior of the protein

39
Q

give 3 examples of basic side chains?

positively charged; can gain a proton

A

Hist, Arg, Lys

40
Q

give 3 examples of acidic side chains?

negatively charged side chains; because they can lose a proton H+

A 
Asparitc ACID (Asp)
Glutamic acid (Glu)
41
Q

give 3 examples of neutral (uncharged side chain)l, polar side chains?

A

Ser (serine), Thr (threonine), Gln (glutamine)

42
Q

give examples of neutral (uncharged side chain), non polar side chains?

A

aliphatic: Val (valine), ala (alanine), Ile (Isoleucine)
aromatic: Phe (phenylalanine)

43
Q

What are neutral, polar side chains good for?

A

GOOD FOR H-BONDING
Ser, Thr through -OH group
Asn, Gln through C=O or NH2 groups

44
Q

define isoelectric PI

A

The pH at which negative an positive charges on the protein are equal

Biochemistry (5 decks)

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