introduction to protein biochemistry Flashcards
why are proteins important and diverse
proteins are extremely versatile biomolecules
-wide variety of functions- reflected by a wide variety of structural properties
recognition of specific molecules : hormones
-small proteins that travel round the bloodstream and beds to specific receptors elsewhere in the body
-for communication
-needs a specific shape that going to bind to the receptor
recognition of specific molecules : antibodies
- recognition of foreign material which allows the immune system to respond
recognition of specific molecules : DNA binding proteins
- bind to specific DNA sequences and affect gene expression
what does porin do
-makes holes in outer membrane bacteria which allows diffusion to occur
-sits in the outer membrane of bacteria and allows diffusion of certain molecules to occur
what does ferritin do
-stores, transports and releases iron
-moves iron around for where it needs to be
-has a single protein copy
structural functions of the cytoskeleton
-contains microtubules which are made up of many alpha-beta tubules subunits- to maintain overall shape of the cell
-cytoskeleton is like the ‘scaffolding’ holding the cell into shape
-cytoskeleton separates chromosomes during mitosis (opposite sides of the cells)
-specific structure at base of cilia and flagella (invovled in cells moving around )
-strong yet dynamic
what are enzymes
-proteins that accelerate the rate of a chemical reaction
-doesn’t change the final equilibrium just gets the reaction there quicker
-they do this by reducing the energy needed to carry out the reaction - activation energy - brings things geographically closer
-enzymes have an active site that binds to the substrate and yields a product
what are proteins made up of
-amino acids
-conserved structure
-side chains vary- R chain varies depending on AA
-join to make PP chain
why are proteins side chains different
-shapes and sizes
-electric charges
-polarity
what’s the primary structure of a protein like
- primary structure is the order of AA in the PP
-protein sequence is defined by the gene sequence
-3 DNA bases - 1 AA
how are AA joined into PP chains
-peptide bonds (loss of water molecules)
-N-terminus (Amino group) and C-terminus (carboxylic group) chain has a beginning and an end
-proteins are generally 50-2000 AA long but can be up to 10000+
-rotation is not possible around the petite bond (rigid structure from peptide bonds)- but more flexibility for other bonds
what contributes to how proteins fold into a 3D structure
-based on properties of their component amino acid
-their charges and shape also contribute
-unfolded= denatured, folded= native
-simple AA thermodynamically unstable -> bonds form between AA-> final folded form is thermodynamically stable
-some proteins can do this spontaneously and other require chaperones to help them into the right shape
what’s the secondary structure of a protein
-regular, repeating structure
-between AA close together in the primary sequence
-stabilised by H bonds
-example: water
-water is polar, relatively negative electrical charge at oxygen end and relatively positive electrical charge at H ends therefore weak attraction
what’s the secondary structure made up of
-alpha helix
-beta sheets
whats the alpha helix
-H bonds between amino(+) and carboxyl (-) group of AA 4 residues apart
-helical spiral structure with side chains on outside
-side chain variable groups are visible
what’s the beta sheet
-H bond between the amino and carboxyl groups of AA further away from each other in the primary sequence- on different strands
-parallel: adjacent stands running in the same direction
-antiparallel: opposite directions
what’s the tertiary structure like
-tightly- packed thermodynamically stable 3 D structure of the protein
-determined by non covalent interactions between side chains (slightly different strengths)
-electric charges: similar charges repel/ opposite charges attract
-size and shape of side chain also constrains
how do different AA interact different with polar water molecules
- hydrophilic: side chains- can form H bonds/ ionic interactions
-hydrophobic: side chains- non-polar so no H bonds/ ionic interactions
where are hydrophobic amino acids normally found on the tertiary structure
-inside
-polar residues end up on outside where they can interact with polar water molecules
-non-polar residues fold into centre of the protein away from aqueous environment of the cell
where do disulphide bridges normally form
-between cysteine residues as cysteine has sulphur in it
-interactions between sulphur atoms in cysteine AA
-oxidation leads to crosslinks between different parts of the primary sequence
-strengthen the tertiary structure
-covalent bonds formed
what are protein domains
-some proteins fold into simple compact structures but many fold into several domains- regions that fold tightly
-separated by flexible region that are less tightly folded
-domains often carry out specific part of the proteins function
-same domain can appear in several evolutionarily linked proteins
-domains have different jobs in the body
what’s the quaternary structure
-more than one PP
-PP come together to form a more complex structure
-subunits can be identical or different
-dimer, trimer, tetramer= quaternary structures made of two, three or four subunits
what are the factors in post-translational modifications
-removal of specific parts of the sequence
-addition of molecules, modulating protein function e.g.
=methylation: addition if CH3 group, methylation of histones (beads which DNA is wrapped around) is used in controlling which parts of the genome are expressed
=glycosylation: addition of various sugars, especially on cell surface and secreted proteins
=uniquitination: addition of 76-aa PP, ubiquitin polymers mark out a protein fro deviations (not reversed;e like the other 2)
what’s phosphorylation
-reversible addition of phosphate groups
-by a class of enzymes called kinases
-an important way in regulating enzyme function
-phosphorylation of AA in or around the act site can change the properties of the region and alter the substrate
what’s protein targeting
-different organelle require different types of proteins
-some proteins need to be moved to cell membrane, or secreted from the cell altogether
-many proteins contain short signals or localisation sequences to show where they need to go
-some proteins are completely synthesised in the cytoplasm and then delivered to their desired location
why are some proteins targeted to the cell membrane
-can occur via secretory pathway- ribosomes associate with the endoplasmic reticulum
-some proteins span the membrane - hydrophobic regions go through the membrane, soluble regions on the inside and outside
-others associate with a trans-membrane protein (forms complex with another membrane)
-or directly with the polar heads on the membrane
what are post translational modifications to anchor membrane proteins
-other proteins are anchored in the membrane by additional hydrophobic groups to the protein sequence
-e.g. addition of fatty acid groups to small G proteins- insert into membrane
-when at the membrane: involved in signalling pathways
-modification allows them to be removed from the membrane: inactive in the cytosol
