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BCH 4024 Exam 1 > Lecture 5: Peptide & Bonds > Flashcards

Lecture 5: Peptide & Bonds Flashcards

1
Q

What is formed when a molecule of water is released from 2 AA’s?

A

Peptide Bond

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2
Q

What is the remaining portion of the AA in a peptide after water is released?

And how do we determine the amount of it?

A

AA residue

# of AA’s

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3
Q

What are the end terminals of a peptide?

A

N –> C

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4
Q

A peptide forming rxn is catalyzed by the (1) ________.

(2) _RNA molecules transport (3) _____ _____ to the (1) ________.

______ group from the (3) _____ ______ is added to the _________ group of the growing peptide.

ie. (3) _____ _____ are added successively to the ________ terminal end of the growing peptide.

A

A peptide forming rxn is catalyzed by the (1) ribosome.

(2) tRNA molecules transport (3) amino acids to the (1) ribosome.

Amino group from the (3) amino acids is added to the carboxyl group of the growing peptide.

ie. (3) Amino acids are added successively to the carboxyl terminal end of the growing peptide.

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5
Q

Estimating the # of residues is based on a proteins ______ ________.

A

Estimating the # of residues is based on a proteins moleculuar weight.

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6
Q

Avg MW of an AA is ~ ____.

Avg AA residue weight ~ ____.

How can we estimate the # of residues in a protein?

MW of protein?

A

Avg MW of an AA is ~ 128.

Avg AA residue weight ~ 110.

MW/110 = AA residues

AA x 110 = MW

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7
Q

What is the total # of possible sequences of a protein?

A

20n

n = # of residues w/in a peptide

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8
Q

In a peptide, what titrates first and why?

What occurs when the peptide titrates?

A
  • The strongest acid titrates first as it has the highest pK.
  • A proton is removed from the carboxyl group.
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9
Q

As a proton is removed during titration, what happens to the net charge of the peptide?

A

Net charge of a protein decreases as protons are removed.

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10
Q

How is the isoelectric point for a peptide or protein found?

A
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11
Q

What are the important roles proteins play in cells?

  1. ________ Elements: collage, histones, etc
  2. ________: catalysts needed for metabolism
  3. __________: needed for immune serveillance
  4. _______ & ________: signal transduction
  5. _________: cell import/export
  6. ________ _______: force generation
  7. __________ Factors: gene control
A
  1. Structural Elements: collage, histones, etc
  2. Enzymes: catalysts needed for metabolism
  3. Antibodies: needed for immune serveillance
  4. Receptors & Channels: signal transduction
  5. Transporter: cell import/export
  6. Molecular Motors: force generation
  7. Transcription Factors: gene control
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12
Q

For proteins to carry out important roles in cells, they must adopt a _____ (_____) form. Why?

This requires regular _______ of _________ atoms.

__ structure (______ protein) is needed for biological activity

A

For proteins to carry out important roles in cells, they must adopt a compact (globular) form. Why? As a sphere, it contains the smallest surface to volume ratio that can be packed to have the least amt of surface exposed.

This requires regular packing of constituent atoms.

3D structure (folding protein) is needed for biological activity

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13
Q

What type of proteins often gain a regular 3D structure only after they bind to well-folded proteins?

A

Intrinsically Disordered Proteins

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14
Q

How many hierarchical levels of protein structure is there?

Is this a time-ordered sequence of events?

A

4

No

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15
Q

Describe the 4 Hierarchical levels of protein structure:

  1. Primary Structure
  2. Secondary Structure
  3. Tertiary Structure
  4. Quaternary Structure
A
  1. Primary Structure:
    • AA sequence
  2. Secondary Structure
    • Alpha helix & Beta-structure, formed by the interaction of polypeptide bonds w/in polypeptide chains
  3. Tertiary Structure
    • Polypeptide chain: 3D fold of a single polypeptide chain, globular protein
  4. Quaternary Structure
    • Assembled subunits: 3D spatial arrangement of 2/+ polypeptide subunits
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16
Q

What are the 2 ways AA sequencing is determined?

  1. ____ Sequencing
  2. _________/_________ Fragmentation, followed by Fragment _________ & Automated __________
A
  1. cDNA Sequencing
  2. Enzymatic/Chemical Fragmentation, followed by Fragment Separation & Automated Sequencing
17
Q

Fragmenting Proteins:

  1. Enzymes
    • Trypsin cleaves on _______ side of ____ & ____
    • Chymotrypsin cleaves on _______ side of ____, ____, _____
    • AA sequences are always written w/ __-terminus on the left, cleavage occurs ______ specific residue, freeing _____ group
A

Fragmenting Proteins:

  1. Enzymes
    • Trypsin cleaves on carboxyl side of Arg & Lys
    • Chymotrypsin cleaves on carboxyl side of Phe, Tyr, Try
    • AA sequences are always written w/ N-terminus on the left, cleavage occurs after specific residue, freeing COOH group
18
Q

Fragmenting Proteins:

  1. Cyanogen Bromide (CNBr) Fragmentation
  • Cleaves only _____ Met to produce __ peptides, one w/ _________ _______ at its __-terminus
  • Cleanly fragments protein into a set of _______ CNBr has ___ effect when Methionine is on __-terminus bc?
A

Fragmenting Proteins:

  1. Cyanogen Bromide (CNBr) Fragmentation
  • Cleaves only after Met to produce 2 peptides, one w/ homoserine lactone at its C-terminus
  • Cleanly fragments protein into a set of proteins CNBr has NO effect when Methionine is on C-terminus bc there’s no bond to cleave it to
19
Q

What is repetitive removal of AA’s from N-terminus & Identification?

A

Edman’s Sequencing

20
Q

In Edman’s sequencing, __ is different for each AA.

PTH-AA (?) is identified by ___/______ chromatography

A

In Edman’s sequencing, R is different for each AA.

PTH-AA (Phenyl isothiocyanate) is identified by gas/liquid chromatography

21
Q

Why bother w/ chemical sequencing w/ easy DNA sequencing?

  • Many proteins have different ______ _________ than predicted by DNA coding sequence.
  • _RNA can be _______, removing sequencing and thus changing the expressed _______ structure.
  • Some proteins are _______ to from more than one __________ ______.
  • Some proteins are post-___________ ________, so final sequence is altered
  • ***It’s the _____ sequencing that is physiologically _____.
A
  • Many proteins have different primary structures than predicted by DNA coding sequence.
  • mRNA can be spliced, removing sequencing and thus changing the expressed protein structure.
  • Some proteins are cleaved to from more than one polypeptide chain.
  • Some proteins are post-translationally modified, so final sequence is altered
  • ***It’s the final sequencing that is physiologically active.

BCH 4024 Exam 1 (10 decks)

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