UM1010 Protein Biochemistry 2024 Student PDF

Dr Katja Vogt Cell Biology / Biochemistry @katjetz School of Medicine [email protected] [email protected] 1 [email protected] BSc Medical Sciences Dr Katja Vogt  Dr Katja Vogt...

Dr Katja Vogt Cell Biology / Biochemistry @katjetz School of Medicine [email protected] [email protected] 1 [email protected] BSc Medical Sciences Dr Katja Vogt  Dr Katja Vogt Protein Biochemistry Learning objectives Explain how proteins are structured Illustrate how proteins are detected Describe the functions of proteins [email protected] [email protected] 3 BSc Medical Sciences  Dr Katja Vogt Proteins Complex biopolymers, who’s structure is determined by the sequence of amino acids [email protected] [email protected] 4  Dr Katja Vogt α - amino acids Differentiated by different side- chains (R-group) 20 different types typically found in proteins “zwitter ion” = both a positive and negative charged ion [email protected] [email protected] Stretch out both of your ands in front of you, Palms up!  Dr Katja Vogt α - amino acids contain an asymmetric carbon 2 stereoisomers exist → enantiomers / optical isomers Proteins in all life only contain L-amino acid enantiomers The surface of proteins is asymmetric = highly specific molecular recognition Plays important role in the formation of protein ‘secondary structure’ [email protected] [email protected]  Dr Katja Vogt [email protected] [email protected]  Dr Katja Vogt Methionine and Cysteine are special both contain sulphur Methionine is always the first amino acid in a polypeptide chain The free suphydryl group of cysteine is highly reactive and is often used in enzyme active sties to attach various chemical groups to proteins Cysteine can form disulfide bonds [email protected] [email protected]  Dr Katja Vogt Primary Protein Structure: Peptides and the Peptide Bond Carboxyl group of one amino acid is linked to the amino group of another amino acid Cannot rotate freely The primary structure of a peptide or protein is the linear sequence of amino acid residues [email protected] [email protected] from the N- to the C-terminus.  Dr Katja Vogt From Primary to Secondary Structure Primary structure determines how the peptide folds into a 3D shape G D N C L V A I G C N D H K R K R K H K D D K H K R K G V R A I K D L G N C CD H N [email protected] [email protected]  Dr Katja Vogt Secondary Protein Structure: Dependent on hydrogen bonding involving the peptide bonds α Helix β Sheets U Turns The secondary structure of a protein is the folding pattern of the polypeptide chain. [email protected] [email protected]  Dr Katja Vogt α Helix Hydrogen bonds hold the structure in the correct conformation Where are the peptide bonds? Alpha-Helix = right-handed [email protected] [email protected] 13  Dr Katja Vogt β Sheet Which elements do the circles represent? Beta-Sheet Parallel or Hydrogen bonds hold the structure anti-parallel in the correct conformation [email protected] [email protected] 14  Dr Katja Vogt U turns 3-4 amino acids, commonly glycine and proline Form a short loop [email protected] [email protected]  Dr Katja Vogt Tertiary Structure Specifies the special arrangements of the secondary Acidic AA arrangement Q V Basic AA K [email protected] [email protected] V A  Dr Katja Vogt Quaternary Protein Structure Several subunits Held together by non- covalent bonds [email protected] [email protected]  Dr Katja Vogt Haemoglobin – one example Glutamic acid Low hemoglobin levels usually indicate that a person has anemia (reduced level of red blood cells). [email protected] [email protected]  Dr Katja Vogt Sickle cell disease  Dr Katja Vogt Abnormal primary structure can affect protein function - (point) mutations leading to misfolding: Sickle cell disease - (point) mutations leading to trapping of protein in the ER: Cystic Fibrosis - (point) mutations leading to premature stop codons, and hence unfinished proteins: Duchene Muscular Dystrophy [email protected] [email protected]  Dr Katja Vogt Insulin - synthesis Proinsulin contains the AA sequence of insulin plus the 31- amino acid C (connecting) peptide In Golgi disulphide bonds are established aided by C-peptide Sorting and packaging due to special surface proteins that cause them to aggregate with one another under the ionic conditions (acid pH and high Ca2+) in the trans Golgi network Insulin is stored in vesicles in zinc-bound crystals Proteases that cleave proinsulin (convertase-2 and -3) are packaged within the secretory vesicle Because the entire contents of the granule are released, equimolar amounts of insulin and C peptide are secreted, as are small amounts of proinsulin. [email protected] [email protected]  Dr Katja Vogt Abnormal secondary structure can affect protein function Amyloidosis Prions Accumulation of amyloid (collective name for proteins that have folded abnormally and aggregated together. They are not easily broken down) Folded into beta sheets, they form extracellular deposits. 30 different proteins form amyloid deposits Aβ: β-amyloid is associated with Alzheimer's Disease Rajendran et al 2006 [email protected] [email protected]  Dr Katja Vogt Abnormal secondary structure can affect protein function Amyloidosis Prions Prions: proteinaceous infectious particles (No DNA / RNA) Prion protein (PrPC) normal neuronal protein thought to be involved in cell adhesion, ion channel activity and neuronal excitability. Normally mainly alpha-helical secondary structure. In abnormal form alpha helix changes to beta sheet Abnormal PrPC can convert normal PrPC into abnormal form in chain reaction. Molecular models of the structure of normal PrPC (left) and abnormal PrPC (right) [email protected] [email protected]  Dr Katja Vogt Histopathology In humans: Creutzfeldt-Jakob Disease (CJD) Gerstmann-Straussler-Scheinker Syndrome Kuru In animals: Scrapie in sheep Bovine Spongiform Encephalopathy (BSE) in cows Transmissible Mink Encephalopathy in mink Histopathology showing spongiform appearance Feline Spongiform Encephalopathy in cats [email protected] [email protected] BSc Medical Sciences  Dr Katja Vogt Protein detection SDS Page gels – 1D and 2D – Staining techniques – Immunoblotting Mass spectrometry Crystallography Edman sequencing [email protected] [email protected]  Dr Katja Vogt Protein detection SDS Page gels – 1D and 2D – Staining techniques – Immunoblotting Mass spectrometry Crystallography Edman sequencing [email protected] [email protected]  Dr Katja Vogt Protein detection SDS Page gels – 1D and 2D – Staining techniques – Immunoblotting Mass spectrometry Crystallography Edman sequencing [email protected] [email protected]  Dr Katja Vogt Protein detection SDS Page gels – 1D and 2D – Staining techniques – Immunoblotting Mass spectrometry Crystallography Edman sequencing [email protected] [email protected]  Ubiquitin Phosphorylation Glycosylation  Dr Katja Vogt Ubiquitination Ubiquitin is a 8.5kDa protein marks proteins for degradation via the proteasome binds to lysine, cysteine, threonine residues along the length of the target molecule or to the N-terminus of the protein Regulates major cellular processes such as cell division, immune responses and embryonic development [email protected] [email protected]  Dr Katja Vogt Protein breakdown Important way for the cell regulates expression of proteins The proteasome Figure 2: Mark Hochstrasser Nature 458, 422-429(26 March 2009) doi:10.1038/nature07958 [email protected] [email protected]  Dr Katja Vogt Functions of Proteins Structural proteins Catalytic proteins – Enzymes Signaling Proteins Proteins involved in cell adhesion and recognition Membrane transport proteins [email protected] [email protected]  Dr Katja Vogt Functions of Proteins Structural proteins – Extracellular Matrix Proteins (ECM) like collagen, Elastin, lamin and fibronectin – Muscle proteins: actin and myosin – Cytoskeletal proteins – Proteins that participate in immunity (antibodies, complement system…) – Transport proteins including Albumin (50% of plasma protein) – Pro-and anti-coagulant proteins – DNA binding proteins [email protected] [email protected]  Dr Katja Vogt Summary Proteins are organised in 4 different levels (primary to quaternary structure) There are several different detection levels for proteins Proteins can be post translationally modified Proteins fulfil a wide array of functions MBBS Learning outcomes: Define protein and enzyme structure and function including enzyme kinetics and structural/functional proteins Identify different techniques for protein analysis [email protected] [email protected] 35  Dr Katja Vogt Reading list Bhagavan, N. and Ha, C. (2015). Essentials of medical biochemistry. Amsterdam: Elsevier Academic Press. Lieberman, M. and Peet, A. (2015). Marks' essentials of medical biochemistry. Philadelphia: Wolters Kluwer. Alberts, B. (2014). Essential cell biology. New York: Garland Science [email protected] [email protected] 36