Amino Acids and Proteins Flashcards by Rosabelle Manton

how many amino acids are found in nature?

more than 700

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how many AA are building blocks for proteins in cells?

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structure of an amino acid?

amino group, carboxyl group, side chain (defines the chemical characteristics of the amino acid - variable R group)

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what can an amino acid be classified depending on?

the chemical characteristics of their side chains
synthesis
essential/non-essential

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what are the possible chemical characteristics of the amino acids side chains?

polar
non-polar
charged
non-charged
aliphatic
aromatic

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types of synthesis of amino acids?

proteinogenic
non-proteinogenic

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types of ‘essential’ of an amino acid?

essential
conditionally essential
non-essential

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what makes a side chain polar?

if it has an oxygen or nitrogen on the end of the side chain e.g. OH, NH2

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what makes a side chain non-polar?

if there is no polar molecule at the end of the side chain e.g. CH3

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what charge does the amino acid have if the side chain is basic?

positive charge

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what charge does the amino acid have if the side chain is acidic?

negative charge

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proteinogenic amino acids?

they are the building blocks of proteins
20 are encoded by triplets of the genetic code

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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

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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)

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non-proteinogenic amino acid synthesis?

they are not produced directly and in isolation by standard cellular machinery

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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

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what are the common modifications of non-proteinogenic amino acids?

phosphorylation
methylation
acetylation
hydroxylation

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give some example of essential amino acids?

His, Ile, Leu, Lys, Met, Phe, Thr, Trp and Val

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give example of conditionally essential amino acids:

Arg, Cys, Gln, Tyr, Gly, Pro and Ser

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what are essential amino acids?

the ones that can’t be synthesised by the body and must be obtained through the diet

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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

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give examples of non-essential amino acids:

Ala, Arg, Agn, Asp, Cys, Glu, Gln, Gly, Pro, Ser and Tyr

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what are non-essential amino acids?

CAN be synthesised by the body

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what does lignin do?

it reduces the absorption of nutrients

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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