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BIOC192 > Lecture 4 - Building Blovks > Flashcards

Lecture 4 - Building Blovks Flashcards

1
Q

What is similar between amino acids and what makes them different

A
  • same common back bone
  • differ by their Side chains
  • varied chemical properties, mostly due to their side chains
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2
Q

In proteins, which part carry’s out the biochemical reactions for which proteins are known

A
  • side chains of amino acids
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3
Q

Properties of amino acids

A
  • amino group
  • carboxyl group
  • side chain
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4
Q

Amino acids are chiral / not chiral

A

Chiral
- most naturally occurring amino acids are L in natures - D form doesn’t really allow formation of a polypeptide bond

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5
Q

Amino acids in solutions are…

A

Zwitterions

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6
Q

Non polar amino acids - how to figure them out

A

Non-polar: • Only C or H at the end of their
side chain. • Hydrophobic.

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7
Q

3 prominent non polar amino acids

A

Glycine:
- R=H
- non chiral
- flexible
- almost on a group by itself

Proline:
- R-group bonds back to main chain N
- Imino acid
- rigid
- almost in a group by itself

Cysteine:
- not really non-polar
- but not polar either

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8
Q

Charged polar side chains - what does the positive and basic mean ? Acidic? Basic?

A
  • positively charged - basic
  • negatively charged - acidic
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9
Q

Polar side chains uncharged

A
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10
Q

How to figure out if an amino acid is polar

A

Polar:
- Also have –OH, –NH2, or –O in their side chain.
- Able to form bonds with other atoms.
- Hydrophilic.

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11
Q

How to know if an amino acid is positively charged polar

A
  • Also have –OH, –NH2, or –O in their side chain.
  • Able to form bonds with other atoms.
  • Hydrophilic.
  • has a +ve charge at ph 7
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12
Q

How to know if an amino acid is negatively charged polar

A
  • Also have –OH, –NH2, or –O in their side chain.
  • Able to form bonds with other atoms.
  • Hydrophilic.
  • has a negative charge at ph 7
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13
Q

Some amino acids have ionisable side groups

A
  • this contributes to the net charge of the protein
  • their charge can change, depending on the pH of the environment
  • the ionisable side chains can be classified by their pka value
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14
Q

What is a pka

A

The pka value for an ionisable group on an amino acid or protein is the pH at which the group is 50% ionised

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15
Q

What is the pI

A

The pI is the pH at which the net charge on an amino acid (or protein) in zero

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16
Q

How can you tell is something is ionisable ?

A
  • it is polar
  • it has an H-atom that can participate in acid-base reactions
  • donates and accepts electrons
17
Q

What is a post-translational modification (PTM)

A
  • almost all amino acids start out as one of the standard 20
  • they are ‘translated’ from RNA into proteins at the ribosome
  • a chemical group can be added to an amino acid residue after translation has occurred (PTM)
  • added via covalent attachment (usually enzyme-mediated)
  • modify the protein is a way that switches it on or off, directs cellular location, targets degration etc
18
Q

How does a disulfide bond form

A

Cysteine can sometimes form a covealonet bond with nearby cysteine

19
Q

Possible amino acid modifications

A
  • phosporylation
  • hydroxylation
  • carboxylation
  • metal binding
  • iodination
  • glycosylation
20
Q

What is phosphorylation used for

A
  • often used to control enzyme activity - like a chemical ON/OFF switch
21
Q

What is hydroxylation used for ?

A

Needed to prevent connective tissues diseases and scurvy, often proline and lysine involved

22
Q

What is carbovylation needed for

A
  • needed for blood clotting, often glutamate is involved
23
Q

Phopholation

A
  • addition of a phosphate group
24
Q

Glycosylation of threonine

A

Glycosylated haemoglobin, know as HbA1c, is used to diagnose and follow patients with diabetes

Asparagiine often glycosylated as well

25
Q

What are peptide bonds

A
  • a covalent bond
26
Q

Rotations of peptide bonds

A
  • planar, trans, dipole
  • flat, a-carbons go on opposite sides, ends have opposite charges
  • partial double bond character (40%)
  • formed via dehydration reaction between C-terminal of one amino acid and N-terminal of another.
27
Q

What is a peptide

A

A short stretch of amino acids joined together by peptide bonds

28
Q

What is a protein

A
  • a longer chain of amino acids joined together, usually with a defined biological function
29
Q

What are amino acid residues

A
  • when amino acids are covalently joined together in a peptide or protein
  • they are no longer complete, individual amino acids
  • their location by residual number e.g met184 refers to a methionine residue at position 184 in a protein or peptide
30
Q

When linked together in a protein,
___ ___ side chains perform the _____ needed to carry out the proteins biochemical reactions

A

When they are linked together in a protein, amino acid side chains perform the chemistry needed to carry out the proteins biochemical reactions

BIOC192 (38 decks)

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