Week 1 Flashcards
Tertiary protein structures
Proteins fold into a 3 structure that requires lowest energy
What’s used to determine protein structure
X-ray crystallography, NMR
Cryo-EM= cryogenic electron microscopy. At cryogenic temps= -238 to-460 F
Proteins are not rigid structures
Conformation is flexible and dynamic. The function of many proteins relies on changes in conformation
E.g enzyme activation and substrate binding (induced fit hypothesis)
For example: cyclin dependent kinase Cdk in cell cycle- Cdk enzyme is only active when cyclin binds to it and alters in conformation
Protein functions include
Binding
Catalysis
Switching e.g. cell signalling pathways
Structural roles e.g. cytoskeleton elements
Regulation of protein function; localisation in the cell
Majority proteins synthesised on ribosomes rER in cytosol each protein contains a sorting signal to direct it to correct site in cell. Proteins move from cytosol into organelles via transporters located in membrane
The secretory pathway
Proteins transported from one compartment to another via transport vesicles. Specialised cells have secretory vesicles. Store hormones, enzymes for future . Require extracellular signal to fuse and release
Protein modification
Most are post translationally modified in the rER. Includes disulphide bonds and glycosylation (i.e. sugars added)
Further modified in Golgi apparatus
Phosphorylation
Phosphate group is attached covalently to amino acid side chains can inhibit or activate protein
Induces a conformational change in protein
Reaction is catalysed by protein kinase (uses ATP)
Dephosphorylation by protein phosphatase
Unfolded protein response (UPR)
UPR works as a homeostatic response to keep a cell’s folding capacity in balance with its needs
An imbalance in this process leads to ER stress (accumulation of unfolded/misfolded proteins in ER lumen) and an increase in unfolded proteins
Can inhibit translation and lead to cell death
widespread effects on physiology, linked to many diseases:
-Alzheimer’s: caused by increase in protein folding compared to degradation which results in build up of proteins (amyloids) in ER leading to stress and damage
-Parkinson’s and heart disease
How do we study tissues
Fixation-prevents degradation and helps maintain architecture
Dissection
Embedding- in wax or plastic resin, cut thin sections using microtome
Sectioning
Staining -acid/ basic dye
Visualisation
Staining
Can be specific or general most commonly used is H&E- haematoxylin and eosin
Dyes bind to different areas of cell depending on pH
Four main tissue types
Muscle
Epithelial
Connective
Nervous 0
What are the two types of epithelium
Covering - lines cavities and cover surfaces
Glandular- secretory epithelia cells
How do cells join to form a functional epithelium
Join with adjacent cells to form a continuous sheet
Cells form cell to cell junctions and adhere to a basement membrane this side of the cell is referred to as basal
PAS (peiodic acid-Schiff) stain
Specialist stain, stains particular carbohydrates & glycoproteins in the basement membrane
Naming epithelial tissue
Number of layers- simple or stratified
Shape of cells - cuboidal (round cube shape), columnar (taller than wider), squamous (flat)
Specialisation -ciliated, keratinised
Exceptions to classifications epithelium
Pseudostratified -looks like multiple layers but is only one all cells attached to basement membrane
Transitional- changes shape of top layer depending on environment. Urothelium stretches
Apical side (apex/luminal)
Cellular specialisations: keratinisation, cilia, microvilli
Specialised junctions
Basal side
Anchors to basement membrane
Allows cells to receive nutrients
Allows cells to receive nervous innervation
Lateral/ intercellular sides
Connecting epithelial cells together via cell to cell junctions
Different cell junctions
Tight junctions- zonula occludens
Zonula adherens- adherens junctions
Communicating junctions- gap junctions
Desmosomes- macula adherens
Hemidesmosomes
Keratinisation
Certain stratified squamous epithelial cells undergo keratinisation= excess keratin produced
Keratin- cytoskeletal protein
Cells die leaving behind keratin
Keratin is strong but flexible
Forms a protective layer impermeable to water
Epithelial cancers
Carcinomas. Can be invasive if it begins to break through basement membrane
Where does new membrane synthesis take place
The endoplasmic reticulum
Basement membrane definition
A thin layer of extracellular matrix , provides structure and an anchor for cells as well as a channel for nutrient
Carcinoma definition
Abnormal cells that divide uncontrollably found in epithelium
Cilia definition
Tiny hair like projections that beat or waft bodies in a certain direction
Columnar cell
Cell that’s taller than it is wide
Cuboidal cell
Square or circular shaped cell
Dysplasia
The presence of abnormal cells that is not cancerous but could become cancerous
Endothelium
A thin layer of cells lining the internal aspects of organs and/or blood vessels
Metaplasia
One kind of cell transitioning to become another kind of cell
Abnormal change in the nature of tissue
Microvilli
Tiny projections on the surface of epithelial cells, for the purpose of absorption (increased surface area)
Neoplasia
A mass of tissues that has accumulated when cells do not stop dividing or do not die
Psuedostratified
The appearance of multiple cell layers where in fact only one exists
Simple epithelium
A single layer of epithelial cells
Stratified
Multiple layers of cells in epithelium
Squamous cell
Flat shaped cells
Transitional epithelium
Type of stratified epithelium
Cells can change shape in response to stretching
Also known as urothelium, found in urinary system-ureter and bladder
Enable tissue to contract and expand
Protein structure
Primary- amino acid sequence, covalent peptide bonds, polypeptide structure may have projecting side chains with -ve charged or +ve charged groups, also polar (hydrophilic) and non polar (hydrophobic)
Secondary- a helix, b pleated sheet held in place by local hydrogen bonds. Also ionic , instantaneous dipoles (van der waals) and hydrophobic bonds
Tertiary- 3D conformation, final shape of single protein molecule held in place by non-local interactions, electrostatic interactions, van der waals, ionic bonds, disulfide bridges (cysteine), proteins fold into tertiary structure that requires lowest energy so (hydrophilic/ hydrophobic or -ve, -ve wont be next to eachother due to repulsion). Non polar amino acids tend to arrange themselves on inside of protein and polar amino acids on outside
Quaternary- shape of molecule when more than one subunit involved, more than one polypeptide chain. Homomer: same polypeptide chain. Heteromer: different polypeptide chains.
E.g. haemoglobin, 4 chains, 2 dimers (2 chains) dimers are identical each is made of 2 different chains so its a heteromer
Protein structure is related to its a function
Globular-soluble, may be secreted, often enzymes (insulin, haemoglobin etc), hydrophilic molecules on outside
Fibrous -form elongated sheets for structural rigidity (actin, collagen)
Membrane- form pores for passage of solutes (Na/K channels). Contain separated hydrophobic and hydrophilic regions
Protein modification. Growth factor signalling
Membrane receptor activation by a growth factor e.g. tyrosine kinase. Leads to receptor dimerisation and phosphorylation
Cytoplasmic signalling: adaptor protein binds to phosphorylated receptor, Ras(G protein) binds to adaptor
This will build up a cascade that eventually signals through cell to nucleus, telling that cell what to do in response to the molecule that has come in from the outside and been recognised by receptor on the surface
Regulation of protein function
Synthesis (is it present or not)
Localisation (is it where it needs to be)- prevents wastefulness and harm
Modification ( is it active/inactive)
Degradation (is it needed anymore)
Synthesis via up regulating gene expression
Many proteins are only synthesised when and where they’re needed. Controlled by gene expression
For example:
-during cell differentiation/ specialisation
-in the immune response
- in response to signals from other cells
Types of secretion
Constitutive secretion: default pathway and is used primarily to replenish material at plasma membrane and certain membrane bound organelles. Unregulated, continuous, no external signals required
Regulated secretion: requires extracellular signal, terminates in secretory vesicles that store secreted material until signal triggers fusion with plasma membrane
Where does degradation of proteins occur
Lysosomes/endosomes
Proteins that enter endoplasmic reticulum
Begin to cross membrane while still being synthesised
Structure of basement membrane
Basal lamina: lamina lucida then lamina densa
Reticular lamina
