Amino Acids and Proteins Flashcards
how many amino acids are found in nature?
more than 700
how many AA are building blocks for proteins in cells?
22
structure of an amino acid?
amino group, carboxyl group, side chain (defines the chemical characteristics of the amino acid - variable R group)
what can an amino acid be classified depending on?
the chemical characteristics of their side chains
synthesis
essential/non-essential
what are the possible chemical characteristics of the amino acids side chains?
polar
non-polar
charged
non-charged
aliphatic
aromatic
types of synthesis of amino acids?
proteinogenic
non-proteinogenic
types of ‘essential’ of an amino acid?
essential
conditionally essential
non-essential
what makes a side chain polar?
if it has an oxygen or nitrogen on the end of the side chain e.g. OH, NH2
what makes a side chain non-polar?
if there is no polar molecule at the end of the side chain e.g. CH3
what charge does the amino acid have if the side chain is basic?
positive charge
what charge does the amino acid have if the side chain is acidic?
negative charge
proteinogenic amino acids?
they are the building blocks of proteins
20 are encoded by triplets of the genetic code
selenocysteine and pyrrolysine both contain a structural change in the mRNA sequence, what does this allow?
allows a STOP codon not to be recognised as such by a specific tRNA
non-proteinogenic amino acids functions?
can have other biological functions beyond forming proteins
e.g. GABA (neurotransmitter)
Carnitine (transport of fatty acids in the blood)
non-proteinogenic amino acid synthesis?
they are not produced directly and in isolation by standard cellular machinery
when and how are non-proteinogenic amino acids modified?
modified by post-translational modification of the protein in which they are embedded
occurs post-translationally, once the protein has already formed
often linked to the function/activity of the protein
what are the common modifications of non-proteinogenic amino acids?
phosphorylation
methylation
acetylation
hydroxylation
give some example of essential amino acids?
His, Ile, Leu, Lys, Met, Phe, Thr, Trp and Val
give example of conditionally essential amino acids:
Arg, Cys, Gln, Tyr, Gly, Pro and Ser
what are essential amino acids?
the ones that can’t be synthesised by the body and must be obtained through the diet
what are conditionally essential amino acids?
in condition of stress, a surplus of these amino acids need to be uptaken through the diet to cope with body demand
give examples of non-essential amino acids:
Ala, Arg, Agn, Asp, Cys, Glu, Gln, Gly, Pro, Ser and Tyr
what are non-essential amino acids?
CAN be synthesised by the body
what does lignin do?
it reduces the absorption of nutrients
what do herbivores eat?
hay, straw, haylage
what does hay/straw/haylage have high levels of?
lignin
hay/straw/haylage - decreased levels of?
essential AA such as Lys
functions of proteins?
storage, enzyme, transport, protection, hormonal, contractile, receptor, structural
contractile protein example?
actin and myosin
hormonal protein example?
insulin
protection protein example?
immunoglobulin (antibody)
transport protein example?
haemoglobin
enzyme protein example?
Rubisco
storage protein example?
ferritin
structural protein example?
spider silk
receptor protein example?
rhodopsin
primary protein structure?
is a sequence of a chain of amino acids
what are amino acids bound together through?
peptide (amide) bonds
protein?
polypeptide chain
dehydration synthesis reaction?
condensation reaction
the alpha helix structure is not what?
it is not a hollow structure, it is just a very tight spiral
what kind of spiral conformation is the alpha helix?
right hand spiral conformation
what does every backbone NH donate?
donates a hydrogen bond to the backbone C=O group of the amino acid lovated 3-4 residues earlier along the protein sequence
what does the Beta structure consist of?
Beta strands and Beta sheets
What are Beta strands?
portions of the polypeptide chain that are almost fully extended having a ‘zig-zag’ shape
Beta strands are flexible but not?
they are flexible but not elastic
Where can the H bonded Beta strands be found?
on separate polypeptide chains or on different segments of the same chain
how do the Beta strands in a sheet run?
can either be parallel (running in the same N- to C- terminal direction) or antiparallel (running in the opposite N- to C- terminal direction)
what are Beta sheets?
when multiple Beta strands are arranged side-by-side they form Beta sheets
What are beta sheets stabilised by?
by hydrogen bonds between between carbonyl oxygens and amide hydrogens on adjacent B strands
why do proteins rarely contain isolated B strands?
because the structure by itself is not significantly more stable than other conformations
what weak bonds stabilise the proteins tertiary structure?
hydrogen bonds
electrostatic interactions
hydrophobic interactions
where are cysteine bonds found between?
between cysteines
two major classes of proteins tertiary structure?
fibrous and globular
amphipathic?
both hydrophilic and hydrophobic parts to the molecule
tertiary protein structure?
occurs when certain attractions/interactions are present between alpha helixes and pleated sheets
secondary protein structure?
occurs when the sequence of amino acids are linked by hydrogen bonds
primary protein structure?
a sequence of a chain of amino acids
quaternary protein structure?
is a protein consisting of more than one amino acid chain
give examples of hydrophobic amino acids:
leucine and isoleucine
give examples of hydrophilic amino acids:
serine or threonine
alpha anylase?
begins breakdown of carbs in our saliva
what leads to misfolded proteins?
mutation in their amino acid sequence
error in the folding process
harmful effects of protein misfolding?
loss of function e.g. cystic fibrosis
gain of function e.g. alzheimer, parkinson, huntington’s (amyloid structure formation)
sickle-cell anaemia?
mutation in haemoglobin
what happens to untreated mutated (for sickle cell) homozygous?
generally die in childhood
heterozygous individuals for sickle cell often show?
resistance to malaria
how does the mutation result in sickle cell anaemia?
glu6>Val in the side chain of Hb so the new valine side chain can bind to a diffetent Hb molecule to form a strand which sickles the red blood cells
