Biochemistry I - Amino Acids And Proteins

Question 1

Central dogma

Answer 1

• James Watson and Francis Crick
• DNA makes RNA makes protein

Question 2

Transcription

Answer 2

DNA to RNA

Question 3

Translation

Answer 3

RNA to protein

Question 4

Reverse transcription

Answer 4

• RNA to cDNA
• reverse transcriptase produces complementary DNA from RNA; replication of retroviruses that use the enzyme to reverse transcribe their RNA to DNA

Question 5

RNA viruses

Answer 5

• have genetic material stored as RNA and can be used as host cell machinery
  e.g. influenza virus, coronavirus, measles

Question 6

Deviation from central dogma

Answer 6

Non coding RNA
RNA viruses
Reverse transcription

Question 7

Non coding RNA

Answer 7

• functional RNA molecule that isn’t translated
  e.g. transfer RNA and ribosomal RNA

Question 8

Epigenetics

Answer 8

Study of heritable changes in gene activity THAT aren’t caused by changes in DNA sequence.
Can be caused by DNA methylation and his tone modification.
Allow for the transcription of only certain DNA

Question 9

3D sequence

Answer 9

The linear sequence of amino acids in a proteins determines its 3D structure. This 3D structure determines its functions

Question 10

Side chains

Answer 10

Different amino acids differ based on the side chain functional groups. Different functional groups have different reactivities.

Side chains can differ based on size, polarity, structure and shape, charge, hydrophobic properties and ability to hydrogen bond.

Question 11

Characteristics of proteins

Answer 11

• proteins don’t usually act by themselves; they form proteins complexes that carry out specific functions e.g. transfer proteins that embed in phospholipid membrane

Question 12

Alpha amino acids and Zwitterions

Answer 12

A center carbon that is an alpha carbon.
Usually contain a chiral carbon except glycine
18/19 chiral amino acids exist in their S - absolute configuration. Only cysteine exists in the R - absolute configuration
Any neutral pH leads amino acids to exist in their dipolar form (Zwitterion); mostly places in our bodies have low pH and so many amino acids exist in this form.

Question 13

In very acidic solutions,

Answer 13

The COO- group becomes protonated, and there’s a positive charge on the NH3

Question 14

As you increase the pH

Answer 14

You get the dipolar amino acid
But if you keep increasing it, the H atom on the NH3 dissociates to add more hydrogen ions to the solution, leaving the negative on COO-. This starts occurring at about pH 9

Question 15

Peptide bond

Answer 15

-Nucleophilic addition elimination reaction between the carboxylate group of one amino acid and the amino group of another amino acid.
-Rigid and planar bond stabilised by resonance delocalisation of nitrogen electrons to the carbonyl oxygen. But an entire polypeptide is not rigid because there is free rotation about carbonyl oxygen.
-Form via a dehydrolysis reaction and is not thermodynamically favourable (requires energy), but they are kinetically stable (the activation energy barrier for the reverse reaction is too high).

Question 16

Residue

Answer 16

Amino acids in a polypeptide chain

Question 17

Hydrolysis

Answer 17

To break the peptide bond.
Helped by strong acids (acid hydrolysis; done with heat; non specific cleavage) or proteolytic enzymes (proteolysis; specific cleavage of peptide bond with the help of protease)
E.g trypsin only cleaves on the carboxyl side of basic amino acids

Question 18

Histidine

Answer 18

The side chain has a pKa of 6.5 which is close to the physiological pH of 7.4
Exists in both protonated and deprotonated form. Useful to have at the active site of a protein

Question 19

pH and pKa

Answer 19

pH<pKa protonated

pH>pKa deprotonated

Question 20

Proline

Answer 20

Secondary alpha amino group; the side chain forms a second covalent bond with the alpha nitrogen
Plays a role in disrupting the alpha helix. It introduced kinks into the alpha helix

Question 21

Glycine

Answer 21

Side chain is a hydrogen atom.
No chiral alpha carbon and so no optical activity
Very flexible
Plays a role in disrupting the alpha helix. It introduces kinks due to its flexibility

Question 22

Cysteine

Answer 22

-Side chain has a thiol group
-If in close proximity with another cysteine from the same polypeptide or another polypeptide, the side chains form a disulphide bridge
-The thiols are found in a reducing environment. If the cysteines are then found in an oxidising environment, you lose the hydrogens and then a bond forms between the two sulfurs.
-The extra cellular space is an oxidising environment; favours the production of disulphide bridges. But you’re more likely to find a reducing environment in the cell.
- cysteine (reduced form), cystine (oxidised form)

Question 23

OIL RIG

Answer 23

Oxidation is loss, reduction is gain

Question 24

Fischer projection

Answer 24

-Emphasises the relationship between the four groups around a chiral carbon
-D and L amino acids are enantiomers (mirror images that are non superimposable)
-If amino group is to the left, it is an L- amino acid. If the amino group is to the right, it’s a D-amino acid.
-Only the L configuration is found in humans

Question 25

Isoelectric Point (pI)

Answer 25

• point along the pH scale at which a molecule exists in a neutral form with zero charge
• knowing the isoelectric point for an amino acid helps us predict if it’s charged at a certain pH
• at low pH, carboxyl group is protonated making the amino acid positive
• at high pH, amino group is deprotonated making the amino acid negative
• to find the pI, we need to take the average of the pKas of the 2 functional groups; amino group is about 9 and the carboxyl group is about 2
• if the side chain also has a functional group, you have to take that into consideration in finding the pI;

Question 26

pKa

Answer 26

pH at which the functional group is half protonated and half deprotonated

Question 27

Classification of amino acids

Answer 27

• we see similarities in the chemical properties of the side chain; hydrogen bonding, acidity, basic, charges
• 2 main groups: polar (hydrophilic) and non polar (hydrophobic)

Question 28

Non polar amino acids

Answer 28

• further broken down into alkyl and aromatic amino acids
• alkyl: glycine (Gly, G), alanine (Ala, A), valine (Val, V), methionine (Met, M), leucine (Leucine, L), isoleucine (Ile, I), proline (Pro, P); their side chains have alkyl groups
• aromatic: phenylalanine (Phe, F), tryptophan (Trp, W); side chains have aromatic chains, smell good

Question 29

Polar amino acids

Answer 29

• further broken down into neutral, basic and acid amino acids
• neutral: serine (Ser, S), threonine, asparagine (Asa, N), glutamine (Gln, Q), cysteine (Cys, C), tyrosine (Tyr, Y); side chains contain oxygen or sulphur; not strongly polar enough
• acidic: aspartic acid (Aspartic, D), glutamic acid (Glu, E); have a carboxylic acid as part of their side chain; very strong hydrogen donors
• basic: histidine (His, H), lysine;(Lys, K), arginine (Arg, R); have nitrogen atoms in their side chains which is a very willing hydrogen acceptor

Question 30

Ionisable amino acids

Answer 30

• at certain pH values, these side chains can exchange hydrogen atoms and can interact via ionic bonds.
• aspartic acid
• glutamic acid
• histidine
• cysteine
• lysine
• tyrosine
• arginine
• all amino acids also contain ionisable alpha carbonyl (always deprotonated at the normal physiological pH) and alpha amino groups (always protonated at the normal physiological pH)

Question 31

Primary structure

Answer 31

• Linear sequence of amino acids
• determined by peptide bond
• determines final 3D conformation of polypeptide
• read from amino side to carboxyl side
• we draw the trans configuration to prevent steric hindrance

Question 32

Secondary structure

Answer 32

• the way the linear sequence of amino acids fold upon itself
• determined by the backbone interactions; hydrogen bonds
• alpha helix: hydrogen bonds run up and down (helix); in the inside of the structure, we have the backbone and the side chain groups are on the outside; right handed helix rotates clockwise, more common than left handed due to less sterics; the screw sense describes the direction in which the helix rotates in respect to its axis. Amino acids here form hydrogen bonds with amino acids 4 residues ahead of them.
• beta sheet: hydrogen bonds run across (zig zag); if amino ends and carboxyl ends line up, it’s a parallel beta sheet; if a single polypeptide sheet wraps upon itself with amino ends lining up with carboxyl ends, it’s an anti parallel beta sheet
• beta turn: suddenly turns in the polypeptide chain; stabilised by hydrogen bonding and usually found on the surface of the protein
• omega loop

Question 33

Tertiary structure

Answer 33

• higher level of folding within a polypeptide change
• depends on distant group interactions
• stabilised by hydrogen bonds, van deer waals interactions, hydrophobic packing, disulphide bridge formation (happens on exterior of a cell due to oxidising environment), ionic interactions

Question 34

Quaternary structure

Answer 34

• bonding between multiple polypeptides
• same interactions from tertiary structure apply here
• each individual polypeptide is called a subunit; dimer, trimer, tetramer, multimeter. Subunits are usually held together by non covalent bonds
• the term for a completely folded up protein is the proper conformation of the protein
• if any level of the structure breaks down, you can have improper folding
• fibrous proteins/ structural: long fingers that play a structural role e.g. keratin and collagen; alpha keratin is a dimer with right handed alpha elides intertwined to form a left handed super coil (alpha coiled coil)
• globular proteins: wide range of functions and relatively spherical e.g. haemoglobin, insulin DNA polymerase

Question 35

Quaternary structure

Answer 35

• bonding between multiple polypeptides
• same interactions from tertiary structure apply here
• each individual polypeptide is called a subunit; dimer, trimer, tetramer, multimeter
• the term for a completely folded up protein is the proper conformation of the protein
• if any level of the structure breaks down, you can have improper folding

Question 36

Conformation

Answer 36

A proteins folded 3D structure; an active protein

Question 37

Denatured proteins

Answer 37

Proteins that have become unfolded or inactive
Can occur by changing temperature (destroys secondary, tertiary and quaternary protein structures), pH (disruption of ionic bonds), adding chemical denaturing agents (disrupt hydrogen bonding, which affects secondary to quarternary structure) or adding enzymes (break peptide bonds, affecting the primary structure)

Question 38

Conformational stability

Answer 38

The forces that keep a protein folded properly; these are the four levels of protein structure.
- another force is the solvation shell which is the layer of solvent surrounding the protein

Question 39

Anfinseni Exoeriment

Answer 39

In the 1950s, Christian Anfinseni conducted exoriments that showed that the information needed to form the 3D active proteins lies in the sequence of its amino acids. Later experiments generalised the idea that the primary structure determines the conformation of the protein.
- he used a ribonuclease (124 amino acids in primary, and 4 disulphide bonds in tertiary). When he added beta mercaptoethanol and urea and disulphide and hydrogen bonds were broken.
- when he removed both agents at the same time, the correct enzymes was reformed
- when he removed the mercaptoethanol first, the enzyme formed was inactive and the wrong disulphide bonds formed because the urea prevented the right non covalent interactions weren’t formed
- when trace amounts of mercaptoethanol was added to the scrambled enzyme, the right structure was eventually reformed. The catalyst breaks the wrong disulphide bonds, and then the correct thermodynamic form is reformed.

Question 40

Prions

Answer 40

• infectious agents made up entirely of protein aggregates
• aggregates of proteins that are found in the body that have misfolded
• causes and cow disease, scrapie in sheep and Creutzfeldt-Jakob disease in humans

Question 41

Alpha amino acid synthesis

Answer 41

• Gabriel synthesis: N-phthalimidomalonic ester; add a base and alkyl halide, then hydrolyse and then add heat
• Strecker synthesis: thought to be more elegant; we start with ammonia, potassium cyanide and aldehyde or ketone;

Question 42

Enzymes

Answer 42

Catabolic enzymes break down their substrates. Anabolic enzymes build more complex molecules from their substrates.