amino acids and protein

Question 1

what are proteins

Answer 1

• proteins are polymers of amino acids

Question 2

function of proteins

Answer 2

• form structural elements within the cell and extracellular matrix
• acts as transport and signalling molecule
• form biological catalysts (enzyme)

Question 3

what is the structure of amino acids

Answer 3

• it has a tetrahedral alpha c atom
• attached to a hydrogen, amine, carboxyl group and a substituted r group
• amino acids are chiral
• left handed L isomers

Question 4

what are the amino acids called that must come from out diet

Answer 4

• essential amino acids

Question 5

what can amino acids be broken down into

Answer 5

• they can be broken down to form glucose as an energy source (emergency source)

Question 6

why must amino acids be broken down

Answer 6

• as they cannot be stored or secreted directly

Question 7

how are amino acids broken down : starting with the carbon skeleton

Answer 7

• carbon skeleton converted to glucose (glycogenic amino acids)
  or acetyl - coA or acetoacetate (ketogenic) which can be fed into the TCA cycle

Question 8

how are amino acids broken down : nitrogen

Answer 8

• nitrogen is removed in three steps
  1. amino group transferred to glutamate
  2. glutamate converted into ammonia by glutamate dehydrogenase in the liver
  3. ammonia then enters the urea cycle - a series of five reactions that results in the formation of urea
  4. which is then excreted in urine

Question 9

what are amides and carboxyl groups and some side chains and what is their state dependent on

Answer 9

• they are ionizable

- their state is dependent on ph

Question 10

what happens when you titrate an amino acid at low ph

Answer 10

• the amino acid carries a positive charge and the carboxyl group is uncharged

Question 11

what happens when the ph increases further

Answer 11

• the proton dissociates from the carboxyl group
• as the ph increases further - the amino acid is zwitterionic with both positive and negatively charged groups
• as the net charge is zero this is called the isoelectric point of an amino acid

Question 12

why are titration curves for amino acids not linear

Answer 12

• as there is resistance to ph changes as amino acid acts as a weak buffer

Question 13

what happens if there is an ionisable side chain

Answer 13

• there would be a third pk value
• amino acids would lose a proton at ph 4 and therefore have a negative charge at neutral ph
• the isoelectric point for these amino acids will be in the middle of positive and negative charge

Question 14

ionisation depends on ph

Answer 14

• acid amino acids have negative charge at neutral ph

- basic amino acids have positive charge at neutral ph

Question 15

what does the substituted side chain do

Answer 15

• this determines the characteristics of the amino acid
• inc. the shape, size, charge, chemical reactivity and hydrogen bonding
• which then also determines the structure and function of the protein

Question 16

how is a peptide bond formed

Answer 16

• two amino acids in a condensation reaction forming a peptide bond using an enzyme peptide transferase
• occurs in the ribosome
• peptide bond is formed between the carboxyl group of one amino acid and the amine group of another amino acid

Question 17

3 properties of peptide bonds

Answer 17

• rigid therefore stable
• planar - peptide bonds form when all atoms are in the same geometric plane
• as it is a strong bond does not breakdown naturally in the body therefore need protease enzyme to hydrolyse the bond

Question 18

2 ways in which amino acid can be classified

Answer 18

• structure (aliphatic, aromatic)

- or chemical nature (polarity, acid, base)

Question 19

what are the hydroxyl group and amide groups capable of

Answer 19

• hydrogen bonding with water and each other meaning these amino acids are hydrophilic and are often found on the surface of water soluble globular proteins

Question 20

polar amino acids

Answer 20

• have uneven charge distribution even though they have no overall charge

Question 21

non polar amino acids

Answer 21

have side chains with evenly distributed electrons therefore do not form hydrogen bonds
- they form hydrophobic cores within the protein

Question 22

what are cysteine and tyrosine examples of and their structure

Answer 22

• examples of polar amino acids
• cysteine - forms covalent disulphide bonds with other amino acids in protein polymer
• tyrosine - aromatic amino acid containing a 6 carbon phenyl ring - contains a hydroxy group therefore can hydrogen bond

Question 23

acidic amino acid

Answer 23

• aspartate and glutamate have carboxylic groups that’s carry a negative charge hence referred to as’-ate’
• as they are negatively charged electrostatic attractions can happen impacting structure and function

Question 24

basic amino acid

Answer 24

lysine and arginine

• highly hydrophobic
• histidine charge is dependent on local environment

Question 25

purpose of spectroscopy

Answer 25

• proteins have a mixture of amino acids ; therefore can estimate the conc of solution without destroying the sample
• allows you to determine purity and conc of solution of proteins
• dna absorbs at 260 nm

Question 26

what is electrophoresis and process

Answer 26

• separate proteins or nucleic acids according to molecular weight

1. soft gel acts as a molecular sieve
2. apply gel to protein, add detergent which coats protein
3. proteins coated in positive charge, breaking disulphide bond
4. due to electric field it will move towards anode
5. smaller proteins move faster and further through the gel

Question 27

what is 2d gel electrophoresis for

Answer 27

• its for the proteins with the same molecular weight
  1. apply protein to gel which has a gradient ph along it
  2. apply electric current
  3. when protein comes to its isoelectric point overall charge is zero therefore won’t move in electric field
  4. as proteins have diff amino acids they have different isoelectric points therefore separate proteins according to their isoelectric points then apply electric current and proteins move according to their weight

Question 28

amino acid and disease ; sickle cell anaemia

Answer 28

• rbc have modified shape meaning gets stuck in circulatory system
• mutation in part of the haemoglobin molecule therefore changing genetic code meaning glutamate transferred into valine in beta globin
• glutamate is negatively charged amino acids and this is changed to a hydrophobic molecule therefore changing the properties where destroying glutamates ability to form hydrogen bonds with water or side chains

Question 29

examples of post translation modifications

Answer 29

• glycosylation
• phosphorylation
• cleavage
• lipid addition
• oxidation/carboxylation/ acetylation

Question 30

what is glycosylation

Answer 30

• adding sugars which can stabilise structure and cells are recognised by their sugars on the surface

Question 31

what is phosphorylation

Answer 31

• adding phosphate to protein
• only three amino acids can be phosphorylated
• adding phosphate makes it negatively charged and can take part in electrostatic attractions affecting shape of protein
• enzyme ending in kinase - adds phosphate
• enzyme ending in phosphates - removes phosphate