Amino acids, proteins, water and pH Flashcards Preview

Pinciples - biochmistry > Amino acids, proteins, water and pH > Flashcards

Flashcards in Amino acids, proteins, water and pH Deck (35):

What type of molecule is water?

Water is a polar molecule. This means that the electrons are shared unequally as a result of oxygen being more electronegative than either hydrogen molecule.


Describe the structure of water.

Water has a bent structure, which forms a dipole. When you considering the non-bonding electrons also, it presents with a tetrahedral structure.


Which two types of substances dissolve in water?

Ionic and polar substances both dissolve in water as either are hydrophilic.


What types of interactions allow a substance to dissolve in water?

It is all based on electrostatic attraction (affinity of electronegative values), and ion to dipole or dipole to dipole interactions.


What type of charge does hydrogen have when bonded to an electronegative atom like oxygen?

Hydrogen will have a partial positive charge when bound to oxygen as what is created is a polarised bond (hydrogen has less attraction to the bonding electrons so electron will be held closer to the oxygen).


Describe the interaction that is a hydrogen bond.

Hydrogen bonding is based on the fact that it can interact with unshared electrons from another electronegative atom (because it carries a partial positive charge).


Is hydrogen bonding weaker or stronger than a covalent bond?

On its own, hydrogen bonding is weaker than covalent bonding, however collectively it can be stronger.


In knowing that hydrogen atoms are shared between two electronegative atoms, what can these bonds be described as looking like?

The hydrogen bond between a hydrogen and two electronegative atoms can be described as being linear.


What's a word used to describe a non-polar molecule that, as a consequence, doesn't dissolve in water?

The word would be hydrophobic - like a phobia of water (and other substances which are polar).


Would a water molecule 'prefer' to interact with another water molecule or a hydrocarbon?

It would prefer to interact with another water molecule as there is a powerful attraction between water molecules. Also, hydrocarbons are hydrophobic non-polar molecules and they will repeal each other.


What is the 'hydrophobic effect'?

It is when two liquid substances - one polar and the other non-polar - are mixed together and an immicible layer forms separating the water from the hydrocarbon for example.


What is an amphipathic molecule?

It is a molecule which has both a polar component and a non-polar component to it. For example, a phospholipid in a cell membrane as there is s hydrophilic head and hydrophobic tail.


Give examples of hydrophilic heads of an amphipathic molecules.

Choline group, carboxylate acid group etc.


What is a hydrophobic tail of an amphipathic molecule composed of?

It is composed of hydrocarbons.


What does an amphipathic molecule form in water?

It forms a micelle in water, which is where all of the head groups will be in contact with water, and all of the tails will sequestered from the water.


What is the importance of the cell membrane?

It is a selective and controllable barrier to the outside world. It aids in compartmentalisation by isolating organelles.


What two types of lipids does the cell membrane contain?

It contains structural ones (lipid bilayer) and precursors of signalling molecules (DAG, IP3).


As well as lipids, what else does the cell membrane contain?

It also contains proteins which can confer selectivity, may be involved in recognition, and various other things.


What are proteins and polypeptides in humans made up from?

They are made up from around 20 different types of amino acids.


What do the letters 'D' and 'L' refer to when talking about amino acids?

They refer to the stereochemistry of the amino acids and how variations can occur from the alpha carbon of the amino acid.


What four things are attached to the alpha carbon in an amino acid?

There will be an amino group, a carboxyl group, a hydrogen group and any carbon chain.


What is a stereoisomer related to amino acids?

A stereoisomer is when the alpha carbon group of an amino acid is non-superimposible but can be mirrored.


What four types of amino acids do you get?

You can get basic amino acids, non-polar amino acids, acidic amino acids and polar (uncharged) amino acids.


How is a peptide bond formed?

Peptide bonds are formed through an hydrolysis reaction.


What does the direction of a peptide chain go in?

It goes from the N-terminus to the C-terminus.


There are three facts you should know about a peptide bond specifically. What are they?

Peptide bonds have partial double bond character. The peptide bond is planar. Peptide bonds are also strong a rigid which is important for protein folding.


What is it that acid molecules can donate?

Acid molecules can donate a proton (hydrogen ion) to bases which are proton acceptors.


What is the strength of an acid dependent on?

The strength of an acid is dependent on how readily an acid will donate its protons and is so measured using the dissociation constant Ka.


What is the role of the Henderson-Hasselbalch equation?

It connects the dissociation constant of a weak acid with the power of hydrogen of a solution containing this acid. It lets us calculate the properties of a buffer solution.


What is a buffer?

A buffer is a solution used to control the pH of a reaction.


When might a buffer resist a change in pH in addition of moderate amounts of acid or base?

When the dissociation constant is equal to that of the pH.


What is a zwitterion?

A zwitterion is an amino acid without a charged side group in a neutral solution. There will be no net charge. They contain two titration groups.


The pH at which a molecule has no net charge is called what?

It is called the isoelectric pH.


How many dissociation constant values will a zwitterion have?

It will have two as it has two titratable groups.


As the ends of proteins can be ionised, a change in pH can change ionisation of a protei. What can is result in?

It can result in changes to the structure and thereby in the function also.