Lecture 19&20- proteins and amino acids Flashcards
Proteins are …. linked amino acids formed according to the ….
Cavalently
Genetic code
Proteins are …. of amino acids
Polymers
….. of amino acids creates a peptide bond
Condensation
Resonance hybridisation of the peptide bond
Generates partial charge
Double bond switches between locations
Contributes to protein structure
Peptide bond has some ….. mobility
Rotational
Movement of amino acids rotates around C-C and N-C bonds
Rotation depends on steric potential and depends on steric clash
C-C angle of rotation is called …
Psi
N-C bond rotation is called …
Phi
Chains of amino acids in peptide bonds fold into proteins by ….
non covalent forces
Proteins fold into a conformation of ….
Lowest energy
(lost free energy, low ability to occupy different spaces)
Purifies protein is denoted by being exposed to a ….
The denatures protein reforms original protein by…
High concentration of urea
Removing urea
What do protein chaperones do?
Ensure proteins obtain and maintain correct shape
Viruses hijack cells.When the virus infects a bacterial cell it’s genes are transcribed and translated. The virus proteins fold by ………….
Hijacking the bacterial cell’s chaperones
Alpha helix overview
Most commonly occurring protein secondary structure
Very energetically favourable fro any amino acid sequence due to peptide backbone interactions
Right handed helix
Discovered in keratin
Hydrogen bonds in alpha helix
Key to structure
H-bonds between peptide backbone
R-groups not involved
H-bond between backbone carbonyl (C=O) and Avery 4th amino acid nitrogen
H-bonds make all of the alpha helix dipoles all point the same way causing a mega-dipole
Beta strand/sheet overview
Relys on association with other beta strands
Multiple beta strands form beta sheets
Discovered in silk
Hydrogen bonds in the beta sheet
Inter-molecular hydrogen bonds between beta strands give beta sheets
They associate parallel and anti-parallel sheets
Protein turns and loops overview
parts that join alpha helices and strands together
Defined as not H bonding within the main body of the structure
often 3-5 amino acid residues
Motif
Small section of protein characterised by interaction of 2º structures
Conserved amino acid sequence with a specific function
Can be picked out in proteins for diverse organisms
Part of a folded single domain
Small section of protein characterised by interaction of 2º structures
Super-secondary protein structure- coiled coil
-Coiled coil-Alpha helical eg leucine zipper occurs in DNA binding proteins
-Helical wheel coiled coil
Super-secondary protein structure- two stranded beta sheet
Small beta sheet lies across major groove
Beta strands are hydrogen bonded to one another by peptide backbone interactions
Leaves amino acid r-groups free to interact with DNA backbone and bases
Tertiary protein structures are arranged in …
They are …. folding regions of the protein
A protein may comprise of several domains, each with …..
Domains
Autonomously
Different roles
RecA domain of a helicase
The motor of an enzyme
Binds and hydrolyses ATP
Helices are a type of ATPase enzyme
There are multiple … within a domain
Motifs
Structural motif
Different to sequence motif
Folded int he same 2º structure but not usually spotted in a primary sequenceq
protein quaternary structure
When a functional is made up of two or more interacting chains
MCM
Complex multiuser
Part of replisome complex
MCM unwinds DNA and allows DNA replication by polymerases
Major groove
Easily read by proteins
R-groups will hydrogen bond if …
They are charged
