biochem ch1 amino acids Flashcards

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1
Q

What are the different groups in an amino?

A

The amine group, the carboxy group, the hydrogen, and the variable side chain

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2
Q

On a fisher projection how can you know if an amino acid is an L or D amino acid

A

In a fisher projection, the amino group will be on the left side in an amino acid L for left

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3
Q

What form of amino acids are found in the body L or D

A

L amino acids

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4
Q

what direction are the vertical and horizontal bonds in a Fischer projection facing

A

The vertical bonds are facing away into the paper or the screen

The horizontal bonds are coming toward you

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5
Q

What are enantiomers

A

Molecules that are mirror images of each other that are non-superimposable

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6
Q

How are peptide bonds formed?

A

Nucleophilic edition elimination reactions between the Amine group of one amino acid and the carboxy group of another amino acid

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7
Q

What are the two types of hydrolysis which can break down peptide bonds?

A

Strong acid hydrolysis breaks down peptides with the use of a strong acid and heat to breakdown peptide bonds non-specifically

Proteolysis is the use of an enzyme called protease to breakdown peptide bonds specifically

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8
Q

what is special about the amino acid histidine

A

It has a pKa of around 6.5 which is close to physiological pH of 7.4 which allows it to stabilize and destabilize substrates at active sites of proteins.

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9
Q

when pH>pKa of an amino acid what be said about the aa

A

the aa will be in it’s deprotonated form.

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10
Q

when pH<pKa of an amino acid what be said about the aa

A

the aa will be in it’s protonated form.

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11
Q

What is special about the amino acids, proline and glycine

A

Proline’s R group wraps around itself and connect to the Amine group

Glycine’s R group is an H

These amino acids are both special because they can cause kinks in the alpha helix secondary structure of proteins. They are known as alpha helix breakers.

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12
Q

What is special about the amino acid cysteine?

A

It’s our group contains a thiol or an SH which can form bridges with other cysteines.

In reducing environments like the intracellular space, they do not form a bridge in

oxidizing environments like the extracellular space They do form a bridge.

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13
Q

What is the isoelectric point?

A

It is the pH of an amino acid when the amino acid is neutral and has zero charge

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14
Q

What is a zwitterion?

A

It is when a molecule has a positive and negative charge present at the same time

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15
Q

Describe the primary structure of an amino acid chain

A

It is the basic linear sequence of amino acids in a polypeptide chain held together by peptide bonds

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16
Q

Describe the secondary structure of proteins

A

It is the folding of linear primary structure, polypeptide chains into structures which include alpha helices, and beta sheets

17
Q

Describe the tertiary structure of proteins

A

It is the overall 3-D shape that takes place after just the localized folding of secondary structure of proteins

Tiri structure bonds include hydrogen, bonding, disulfide, bridges, hydrophobic, interactions, and Vanderwall’s forces

18
Q

Describe the quaternary structure of proteins

A

It is the arrangement and interaction between multiple polypeptide chains with each being called a sub unit

It has the same bonding of tertiary structure proteins, which are hydrogen bonding, disulfide, bridges, hydrophobic, interactions, and Vanderwaal forces

19
Q

What is the proper confirmation of a protein?

A

It is when the first second third and 4th degree structures are properly folded

20
Q

What is protein misfolding??

A

When any level of protein structure begins to breakdown

21
Q

What is protein confirmation?

A

It is the active three-dimensional structure protein

22
Q

What is a denatured protein?

A

A protein that is inactive

23
Q

What is a solvation shell, and how does it relate to protein?

A

Otherwise, known as the hydration shell in Aqua environments, it is the layer of water or solution directly outside of a protein that helps to stabilize it

When the solvation shell is water, the electronegative oxygen of the water interacts with the positive polar amino acids further stabilizing it

24
Q

what are four ways that denaturation can occur

A

By increasing the temperature

By changing the pH

By adding chemical denaturants

By adding enzymes