Protein and enzymes

Question 1

R-group

Answer 1

The residue or side-chain on an amino acid.
The R-group is what confers the specific properties of each amino acid. This ultimately dictates the interactions amino acids in a peptide will have and therefore dictates protein structure.

Question 2

Primary structure

Answer 2

The sequence of amino acids in a given protein.

Question 3

Secondary structure

Answer 3

The alpha-helix, or beta-sheet structures formed ONLY through hydrogen bonding.

Question 4

Tertiary structure

Answer 4

Often the final structure of a protein - is the overall folded structure of a peptide in space via bonds between amino acids, such as hydrogen bonding, ionic bonding and hydrophobic interactions.

Question 5

Quaternary structure

Answer 5

Some proteins require two or more peptides to come together to be functional and this is quaternary structure. Classic example is haemoglobin with its four sub-units.

Question 6

Disulphide bond

Answer 6

Strongest bond in protein structures (if they have any disulphide bonds). Forms between two cysteine residues because they contain Sulphur, hence the name.

Question 7

Active site

Answer 7

The site on the surface of an enzyme that is the main site for a reaction to proceed.

Question 8

Substrate

Answer 8

The substance that the enzymes acts upon (i.e. the reactants).

Question 9

Competitive inhibitor

Answer 9

A molecule that closely resembles the substrate and blocks or reduces enzyme activity by filling the active site, thus preventing a reaction proceeding.

Question 10

Non-competitive inhibitor

Answer 10

A molecule that bids to an alternative site on the enzyme rather than the active site. It alters the enzyme shape and therefore changes the specificity of the enzyme for its substrate(s), thereby reducing enzyme activity.

Question 11

What part does hydrogen bonding play in the determination of protein structure?

Answer 11

• H-bonding in secondary structure (a-helix,* b**-sheet). H-bonding in tertiary (and quaternary) structure: between R-groups and between R-groups and water. Stabilisation of H-bonding between water molecules driving shapes of globular proteins.
• At a different level, the H-bonding involved in nucleic acid structure and synthesis indirectly influences amino-acid residue sequence and hence protein shape. It is with this latter point in mind that the comment in brackets was added to the question. Note that they have not yet had lectures on ‘Storing and Using Genetic Information’.*

Question 12

What effect do enzymes have on cellular reactions?

Answer 12

Enzymes, being biological catalysts, increase reaction speeds or allow reactions to proceed at the relatively benign temperature of 37°C (if we are assuming the cells are in the human body). They are able to allow reactions to proceed because they lower the activation energy dramatically. This is usually achieved by bringing reactants closer together in a highly specific way, with one enzyme often only taking part in one reaction within the cell.

Question 13

Human insulin consists of two covalently joined polypeptides

How is the active form of the hormone synthesised in the body?

Answer 13

Insulin is synthesised as a precursor, which is then cleaved. Think about the action of proteinases that cleave proteins, peptide bonds and why insulin has a lot of them for its size, quaternary structure and zymogens. Why should cleavage turn an inactive protein into a hormone? Why make an inactive precursor in the first place?

Question 14

Human insulin consists of two covalently joined polypeptides

How are the two chains covalently linked?

Answer 14

By disulphide bonds (inter- and intra-chain). Which amino-acid residue is involved?

Question 15

In the human body, how many amino acids are there?

Answer 15

there are 20 amino acids required for the synthesis of proteins and other biochemically essential molecules;

Question 16

Amino acids are:

Answer 16

Organic compounds with - NH₂ -COOH groups

Question 17

CLASSES OF AMINO ACIDS

Answer 17

• ALIPATHIC AMINO ACIDS
• AROMATIC AMINO ACIDS
• SULPHUR-CONTAINING AMINO ACIDS
• ACIDIC AMINO ACIDS
• BASIC AMINO ACIDS
• POLAR AMINO ACIDS
• MISCILLANEOUS AMINO ACIDS

Question 18

Amino acid structure

Answer 18

Organic compounds with - NH₂ -COOH groups

Sidechain gives specific properties:

DNA composed nucleotides bases: adenine, guanine, cytosine, thymine —- mRNA adenine, guanine, cytosine, uracil.
Combination of THREE nucleotides code for amino acid or a ‘STOP’ instruction

behaves like zwitterions: Depend pH amino acid subjected to = may take on +/- charge

Question 19

ALIPATHIC AMINO ACIDS

Answer 19

R’ group consisting of hydrocarbons:

• Glycine
• Alanine
• Valine
• Leucine
• Isoleucine

Aliphatic amino acids - ‘r’ group consisting hydrocarbon chains variable length or just hydrogen r group changes behaviour - long hydrocarbon chains will have higher hydrophobic non-polar properties

Question 20

AROMATIC AMINO ACIDS

Answer 20

R - group hydrocarbon ring

Question 21

Name a particularly important aromatic amino acid and condition if it is not present

Answer 21

Phenylalanine

PKU - phenylketonuria - inborn error-metabolism of phenylalanine = accumulates in blood → neurological damage/death - heel-prick test → managed with dietary modification.
treatment - Sapropterin

Question 22

SULPHUR-CONTAINING AMINO ACIDS

Answer 22

The presence of sulphur allows disulphide bridges to form.
Covalently bonded linkages - occur 2x sulphur-containing amino acids = increase strength.

Question 23

ACIDIC AMINO ACIDS

Answer 23

Aspartate

Glutamate

Question 24

BASIC AMINO ACIDS

Answer 24

Lysine

Histidine

Arginine

Question 25

POLAR AMINO ACIDS

Answer 25

Serine

Threonine

Asparagine

Glutamine

Carry charge end of ‘r’ group: serine form hydroxyl group

Question 26

MISCELLANEOUS AMINO ACIDS

Answer 26

Proline unusual ring shape difficult to break - in many tissues needing high strength.

Question 27

Glutamate is:

Answer 27

• One of the 20 amino acids required by our bodies to make proteins. NON-essential amino acid - can be synthesised in the body. It is coded for by the codons GAA and GAG
• plays an important role in metabolism: (clears excess nitrogen)
• Excess nitrogen → converted into urea (part of the urea cycle) Glutamate = non-toxic carrier of ammonium ions - can provide the initial nitrogen into the urea cycle.
• Acts as energy source in the cell → can be converted into α-ketoglutarate, (intermediate in the citric acid cycle)
• Cancers (glioma and glioblastoma) can utilise this mechanism for energy production in the cells ( seen in tumours with an IDH1 mutation)
• Used in synthesis of inhibitory neurotransmitter GABA. Enzyme glutamate decarboxylase (GAD) responsible for this conversion step. Loss of GAD can result in stiff person syndrome.

Question 28

Proteins synthesis process

Answer 28

The process begins in the nucleus → During the process of transcription, DNA helixes found within the nucleus unwind → allows copying of nucleotide sequences, producing a transcript (messenger RNA mRNA) → translated by translation RNA (tRNA) on cell ribosomes. The protein produced on the ribosome → folds into its destined structure

Question 29

Key roles of Protein Synthesis

Answer 29

• Key roles
• cell signalling/cell homeostasis
• acting as mediators of transmembrane transport cell receptors/cell signalling (E.g. seen in the endocrine system. A hormone within the bloodstream is recognised by a cell surface receptor and the hormone binds to the receptor triggering initiation of a G protein-coupled cascade.

Question 30

Proteins function

Answer 30

Proteins function

Structural proteins - Enzymatic - Receptor proteins

• Hormonal protein - Transport proteins
• Defensive proteins - Contractile proteins

The cell receptor, the hormone and the G protein are all examples of proteins.

Question 31

DIGESTION

Answer 31

Proteins can be absorbed in the form of amino acids, dipeptides, or tripeptides (as opposed to carbohydrates)

Proteins → Large polypeptides → smaller polypeptides/peptides → individual amino acids/dipeptides/tripeptides

Question 32

CONJUGATED PROTEINS

Answer 32

Post-translational modification - relates to modification after the protein has been transcribed

co-translational modification: modification occasionally occurs at the same time as translation

Following post/co-translational modification - proteins are termed conjugated proteins.

Question 33

Three types of conjugated proteins:

Answer 33

• Glycoproteins
• Lipoproteins
• Metalloproteins

Question 34

glycoproteins:

Answer 34

glycoproteins

contain oligosaccharide (type carbohydrate) chains covalently attached to amino acid side-chains

Effects: stability, solubility, orientation or cell signalling:

Question 35

Lipoproteins

Answer 35

• Proteins + lipids combined: found on cell membranes - transport hydrophobic molecules (cholesterol)
• Lipoproteins can form complexes each other = apolipoprotein: transport lipids
• can use blood test for levels certain conditions: (hyperlipidaemia)

Question 36

Metalloproteins

Answer 36

Metalloproteins

contains a metal ion cofactor within the structure (co-factor) - Enzymatic, signal transduction, transport and storage. (haemoglobin) 2x α 2x β - haem + iron

Question 37

Hemoglobin:

Answer 37

Haemoglobin - 4 subunits → carry 4 molecules of 02.

• haemoglobin central to respiration/metabolism due to structure + function.
• Amount o2 dissolved in the blood depends on the partial pressure of lung alveoli
• normal function lung plasma leaving lung almost all dissolved.
• Due to 02 low solubility in solution: plasma carry max 3ml/l. whole blood carries approx. 200m;/l due to haemoglobin. O2 concentration measured venous, capillary, arterial blood using near pt. testing = blood gas analysers.

Question 38

Protein structure

Answer 38

Function of a protein is governed by its structure. forming structures within the body such as keratin and collagen. These are integral for support within organisms and as such, are insoluble in water.

(be aware membranous protein too)

Question 39

GLOBULAR Proteins

Answer 39

Globular → wide range roles: -Enzymes - Storage
- Hormones -Transporters -Structural

Multiple regions of Various α-helices and β-pleated sheets → formed from restructuring of the secondary structure & formation of covalent, ionic, disulphide & Van der Waals forces between amino acid side chains → form globular shape unique to each protein
- allows the protein perform particular specific function (e.g. enzyme peptidase)

Question 40

Immunoglobulin

Answer 40

antibodies used to trigger immune response (e.g. globular protein IgG for blood tests)

Question 41

Myeloma

Answer 41

Neoplasm of plasma (myeloma) cells - bone marrow: Overproduction of
M-protein = IgG, IgA (free light chains)

Bone marrow/myeloma cells secrete cytokines interleukins promote proliferation/survival of myeloma cells.

Protein relevance- bloods = ↑ monoclonal proteins ↑IgG ↑IgA

Question 42

FIBROUS Proteins

Answer 42

Elongated shape - sheet-like structures: muscle connective tissue

• fibrous tertiary structure is seen in structural proteins, such as collagen other fibrous proteins tensile strength required
• forms from either multiple beta-pleated sheets or from long chains of alpha-helices.
• Fibrous proteins are insoluble in water

Question 43

Vitamin C deficiency:

Answer 43

insufficient for body’s metabolic needs.
- Vitamin C: essential co-factor for producing collagen

Scurvy: post-translational modification of amino acids proline and lysine can’t occur → can’t convert to hydroxyproline & hydroxylysine = cross-links important for stabilising collagen absent = protein produced weak - treat vit C

Question 44

Scurvy:

Answer 44

post-translational modification of amino acids proline and lysine can’t occur → can’t convert to hydroxyproline & hydroxylysine = cross-links important for stabilising collagen absent = protein produced weak - treat vit C

Question 45

Osteogenesis imperfecta:

Answer 45

Autosomal dominant mutation → glycine substituted larger amino acid→ misfolding collagen proteins = weak collagen produced → brittle bones

Blue sclera: individual with osteogenesis imperfecta.

Question 46

MEMBRANOUS

Answer 46

Membrane transporter membrane enzyme, cell adhesion molecules Transport molecules in and out of cells - aquaporin centre Signalling - glycoproteins in blood types

Question 47

Familial hypercholesteremia

Answer 47

genetic → high levels of cholesterol in the blood fatty deposits in various areas body → causing xanthomas (tendons, eyelids) and atherosclerosis (plaque arteries).

2 types of cholesterol: Low-Density Lipoprotein (LDL) - High-Density Lipoprotein (HDL)

↑ LDL causes plaque formation atherosclerosis = MI, PVD. Stroke risk.

Question 48

Classes of familial hypercholesteremia

Answer 48

Mutations that disrupt controlling LDL blood levels - 5 classes

• *Class 1** - ↓ quantity LDL receptor produced
• *Class 2** intracellular transport LDL receptors to cell surface disrupted
• *Class 3** - affect binding LDL ↔ LDL receptors.
• *Class 4** - LDL ↔ LDL receptors can bind: but not in coated pits = do not internalise
• *Class 5** - affect recycling of LDL receptors doesn’t release LDL