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Biochemistry - Block 1 > Biochem Lecture 2 > Flashcards

Biochem Lecture 2 Flashcards

1
Q

List the bond strength from strongest to weakest

A
  1. Covalent 2. Disulfide 3. Salt Bridge 4. Hydrogen bond 5. Van der Waals
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2
Q

Polypeptide chain that is planar with repeating backbone - Determines the tertiary structure

A

Primary Structure

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3
Q

What is the secondary structure composed of

A

Alpha helices + Beta sheets with hydrogen bonds

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4
Q

Composed of Amino Acid Right-hand spiral w/ R groups facing outward

A

Alpha Helix

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5
Q

Side chains alternate between being above and below the plane

A

Beta Sheets

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6
Q

What is Reverse Turn

A

a hydrogen bond between every 3rd AA

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7
Q

List the characteristics of a Primary Structure

A
  • AA sequence contains all the info required for protein folding
  • Peptide bonds are planar
  • Proteins are also known as polypeptides
  • Repeating backbone
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8
Q

What type of bonding is in Primary Structure

A
  • sequence of covalent bonds in proteins
  • Very stable
  • Covalently joined by amide bonds another name for peptide bonds
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9
Q

Secondary Structure CHaracteristics

A
  • Contains alpha and beta helices
  • Twisted B sheet and Beta barrel
  • Beta Strands make up Beta Sheets
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10
Q

Same Direction

H bonding connects 2 AA to 1 AA on an adjacent strand

A

Parallel Beta Sheet

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11
Q

Tertiary Structure Characteristics

A
  • All other types of non-covalent bonds form 3D structures
  • Have similar sec structures but different tertiary structures

native = Functional

  • Hydrophobic AA = INSIDE
  • Hydrophilic/charged AA = OUTSIDE

Porin - inside out model of AA distribution

Water filled channel

  • Hydrophobic exterior
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12
Q

Example of Tertiary Structure

A

Myoglobin

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13
Q

Quaternary Structure

A
  • More than one polypeptide chain associating with each other
  • Can also establish fxn in certain proteins
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14
Q

Quaternary Structure Bonding

A

Uses noncovalent bonds

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15
Q

Example of Quaternary Structure

A

Hemoglobin

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16
Q

Types of Quaternary Structures

A

Homodimer

Heterodimer

Heterotetamer

heteropentomer

homopentamer

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17
Q

A covalent bond formed when the reduced –S-H groups of 2 Cys residues react with one another to make an oxidized –S-S linkage

A

Disulfide bridge

18
Q

Noncovalent interaction between atoms or groups of atoms due to the attraction of opposite charges

A

Electrostatic interaction

19
Q

a noncovalent interaction between the donor atom, which is bound to a positively polarized H atom, and the acceptor atom, which is negatively polarized

A

Hydrogen bond

20
Q

Protein Denaturation:

To denature a protein from 3/4 –> 1

A

Add 8 M Urea and Beta-Mercaptoethanol

21
Q

Protein Denaturation:

To break disulfide bonds

A

Add Beta-mercaptoethanol

22
Q

Protein Denaturation:

To detect an aromatic

A

Trp and Tyr = 280 nm

Phe = 260 nm

23
Q

Strong acid breaks peptide bonds

Edmans degradation releases N terminal Amino Acid

Uses proteases: Cleave @ C terminal

A

To sequence a peptide

24
Q

To sequence a peptide

A

Trypsin: Arg, Lys

Chymotrypsin: Phe, Tyr, Trp

Bromelain: Lys, Ala, Tyr, Gly

CNBr: Met

25
Q

How do you determine Primary Structure?

A

Mass Spectroscopy

26
Q

How do you determine a Secondary Structure?

A

CD Spectroscopy

27
Q

How do you determine Quaternary Structure?

A

X-ray Crystallography

28
Q

predominantly located on the surface of proteins

A

Hydrophilic amino acids

29
Q

located inside of folded proteins

A

hydrophobic amino acids

30
Q

causes loss of secondary, tertiary, and quaternary structures due to the unfolding of the polypeptide chain

A

Denaturation

31
Q

True or Falso:

A denatured protein is incapable of carrying out its biochemical and biological functions

A

True

32
Q

What determines tertiary structure?

A

Primary Structure and Polypeptide

33
Q

A sequence of covalent bonds in proteins is known as

A

Primary Structure

34
Q

The ultimate 3-dimensional structure of a protein is determined by its:

A

Primary Structure

35
Q

The two most common forms of

protein secondary structure are:

A

Alpha and Beta

36
Q

Denaturation leads to loss of what structures

A

Primary, Secondary and Tertiary Structures

37
Q

In order to determine a protein’s secondary structure, what can be used?

A

CD Spectroscopy

38
Q
A
39
Q
A
40
Q
A

Biochemistry - Block 1 (6 decks)

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