Section 3: Special Topics Flashcards
Second law of thermodynamics
Entropy will increase over time
Early human dev. - three main techniques
Ability to dissociate multi-cellular organisms into single cells
Ability to barcode those cells
Sequence every cell - make a map of where those cells are being derived from
What happens in embryogenesis
Patterning
Major axis laid down
3 germ layers form
Rudiments of major organs
Embryogenesis - patterning
Development process where cells acquire diff identities depending on their relative positions in their embryos
Pattern laid down on a small scale, typically <1cm
Lay down the 3 main germ layers to allow further differentiation to take place
Embryogenesis - major axis
Anterior - head
Posterior - tail
Dorsal - back
Ventral - tummy
Embryogenesis - 3 germ layers
Broad brushstrokes of development
Further differentiation takes place within those germ layers
Ectodermal layer
Mesodermal layer
Endodermal layer
Fate map
Tells you what a cell is likely to become if development continues normally
Ectodermal layer (outside, blue) Mesodermal layer (between, red) Endodermal layer (inside, yellow)
Sperm vs egg size
Sperm quite small in size compared to egg
Sperm - major components
Genetic material
Tail to help it swim towards egg
Sac of enzymes (acrosome) on head - helps the sperm burrow through the layers surrounding the egg (corona radiata)
When is meiosis completed
Post-fertilisation, where 2 nuclei become pronuclei
Placenta is a combination of…
The maternal tissues and tissues from the embryo itself
Types of proteins
Digestive enzyme/catalytic - break down nutrients in food into small pieces that can be readily absorbed
Transport - carry substances throughout the body in blood or lymph
Structural - build diff structures, e.g. cytoskeleton
Hormone signalling - co-ordinate activity of diff body systems
Immunological - protect body from foreign pathogens
Contractile - muscle contraction
Storage - provide food for early development of embryo
Toxins - used by pathogens or other organisms to cause disease
Peptides
Short polypeptides (~less than 50 amino acids) Very short peptides can be referred to as dipeptides, tripeptides or tetrapeptides
Residues
Individual amino acids in a polypeptide/protein
Forms of amino acids
Un-ionised/deionised form
Zwitterionic (doubly ionised) form - dominant form, at physiological pH ~7.4, +ve and -ve charge on either side)
Peptide (amide) bond formation
Condensation / dehydration synthesis reaction
Peptide bond properties
Bonds are rigid and can’t rotate due to resonance
O-C-N-H of peptide bonds are essentially co-planar
Rotation can occur at the single bonds between the α-carbon and its neighbouring atoms
R amino acid side chains can be cis (same side) or trans (one up one down) - typically trans as cis is less stable due to steric repulsion
N and C terminus
N (amino) terminus
C (carboxyl) terminus
Proteins always drawn N to C i.e. the direction they come off the ribosome
Protein structures - complex
To facilitate all varied functions proteins provide, they can adopt complex structures
Shape and function of proteins
Shape of a protein is critical to its function
Shape is driven by chemical properties and sequences of amino acids in the protein
Binding of substrates to an active site can cause…
Conformation changes, which provide a function or strengthen the interaction
Proteins - primary structure
The unique sequence of amino acids of a protein
Entirely driven by DNA sequence of gene encoding protein - can deduce the primary structure of a protein by the DNA sequence of a gene
Proteins - secondary structure
Localised folding of the polypeptide driven by H bonding interactions within the polypeptide backbone
Two common types: β (pleated) sheet, α helix
Diff amino acids have a tendency to favour structures
Can fairly accurately predict regions of secondary structure in a protein by the sequence
β sheets
Can be parallel or anti-parallel
Driven by H bonding between a backbone amine (N-H) group on one strand and a backbone carbonyl (C=O) group on other strand
Large aromatic residues and β-branched amino acids are favoured in β strands
α helices
Right-handed helix
Normally each turn is 3.6 amino acids with a pitch of 5.4Å
Driven by H bonding between a backbone amine or backbone carbonyl group 3 or 4 residues earlier
Tightly packed with almost no free space within the helix
Side chains protrude from helix
Helices - amino acid examples
Methionine, alanine, leucine, glutamate and lysine like to form helices
Proline and glycine don’t
Proline may create unique conformations in polypeptide, and often referred to as a helix breaker as it’s always at the end of a helix
Proteins - tertiary structure
Where secondary structures fold in on themselves
The 3D shape of a protein - primarily driven by the chemistry of side chains and interactions between them
Range of non-covalent interactions - H bonding, ionic bonding, d-d interactions, Van der Walls forces
Ionic: opposite charged R groups attract and like charges can repel
Tertiary structures - hydrophobic interactions
R groups of non-polar amino acids orient themselves towards the center of the polypeptide and cluster to avoid water
In membrane spanning proteins, hydrophobic R groups may be outside interacting with lipid tails
Tertiary structures - disulphide bridge
Amino acid cysteine forms a covalent bond with another cysteine through its R group –> disulfide bond
Thiol (S-H) groups are oxidised, removing the H and forming a covalent linkage between the 2 sulfur atoms
Tertiary structures - H bonds
Polar ‘R’ groups on the amino acids form bonds with other polar R groups
Tertiary structures - hydrophilic interactions
R groups of amino acids orient themselves outward to interact with water and maintain solubility of protein
Tertiary structures - ionic bonds
Positively charged R groups bond together
Relative strength of bonds
Disulfide > Ionic > Hydrogen > Van der Waals
