Protein and enzymes Flashcards
R-group
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.
Primary structure
The sequence of amino acids in a given protein.
Secondary structure
The alpha-helix, or beta-sheet structures formed ONLY through hydrogen bonding.
Tertiary structure
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.
Quaternary structure
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.
Disulphide bond
Strongest bond in protein structures (if they have any disulphide bonds). Forms between two cysteine residues because they contain Sulphur, hence the name.
Active site
The site on the surface of an enzyme that is the main site for a reaction to proceed.
Substrate
The substance that the enzymes acts upon (i.e. the reactants).
Competitive inhibitor
A molecule that closely resembles the substrate and blocks or reduces enzyme activity by filling the active site, thus preventing a reaction proceeding.
Non-competitive inhibitor
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.
What part does hydrogen bonding play in the determination of protein structure?
- 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’.*
What effect do enzymes have on cellular reactions?
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.
Human insulin consists of two covalently joined polypeptides
How is the active form of the hormone synthesised in the body?
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?
Human insulin consists of two covalently joined polypeptides
How are the two chains covalently linked?
By disulphide bonds (inter- and intra-chain). Which amino-acid residue is involved?
In the human body, how many amino acids are there?
there are 20 amino acids required for the synthesis of proteins and other biochemically essential molecules;
Amino acids are:
Organic compounds with - NH2 -COOH groups
CLASSES OF AMINO ACIDS
- ALIPATHIC AMINO ACIDS
- AROMATIC AMINO ACIDS
- SULPHUR-CONTAINING AMINO ACIDS
- ACIDIC AMINO ACIDS
- BASIC AMINO ACIDS
- POLAR AMINO ACIDS
- MISCILLANEOUS AMINO ACIDS
Amino acid structure
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
ALIPATHIC AMINO ACIDS
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
AROMATIC AMINO ACIDS
R - group hydrocarbon ring
Name a particularly important aromatic amino acid and condition if it is not present
Phenylalanine
PKU - phenylketonuria - inborn error-metabolism of phenylalanine = accumulates in blood → neurological damage/death - heel-prick test → managed with dietary modification.
treatment - Sapropterin
SULPHUR-CONTAINING AMINO ACIDS
The presence of sulphur allows disulphide bridges to form.
Covalently bonded linkages - occur 2x sulphur-containing amino acids = increase strength.
ACIDIC AMINO ACIDS
Aspartate
Glutamate
BASIC AMINO ACIDS
Lysine
Histidine
Arginine
POLAR AMINO ACIDS
Serine
Threonine
Asparagine
Glutamine
Carry charge end of ‘r’ group: serine form hydroxyl group
MISCELLANEOUS AMINO ACIDS
Proline unusual ring shape difficult to break - in many tissues needing high strength.
Glutamate is:
- 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.
Proteins synthesis process
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
Key roles of Protein Synthesis
- 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.
Proteins function
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.
DIGESTION
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
CONJUGATED PROTEINS
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.
Three types of conjugated proteins:
- Glycoproteins
- Lipoproteins
- Metalloproteins
glycoproteins:
glycoproteins
contain oligosaccharide (type carbohydrate) chains covalently attached to amino acid side-chains
Effects: stability, solubility, orientation or cell signalling:
Lipoproteins
- 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)
Metalloproteins
Metalloproteins
contains a metal ion cofactor within the structure (co-factor) - Enzymatic, signal transduction, transport and storage. (haemoglobin) 2x α 2x β - haem + iron
Hemoglobin:
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.
Protein structure
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)
GLOBULAR Proteins
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)
Immunoglobulin
antibodies used to trigger immune response (e.g. globular protein IgG for blood tests)
Myeloma
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
FIBROUS Proteins
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
Vitamin C deficiency:
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
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
Osteogenesis imperfecta:
Autosomal dominant mutation → glycine substituted larger amino acid→ misfolding collagen proteins = weak collagen produced → brittle bones
Blue sclera: individual with osteogenesis imperfecta.
MEMBRANOUS
Membrane transporter membrane enzyme, cell adhesion molecules Transport molecules in and out of cells - aquaporin centre Signalling - glycoproteins in blood types
Familial hypercholesteremia
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.
Classes of familial hypercholesteremia
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
