amino acids and proteins Flashcards
how many amino acids are building blocks for proteins in cells?
22
describe the general structure of an amino acid
Amino group - N terminus end
Carboxyl group - C terminus end
R group
what defines the chemical characteristics of the amino acid?
R
In what ways can amino acids be classified based on chemical characteristics?
All about R group side chain
Polar
Non-polar
Charged
Non-charged
Aliphatic
Aromatic
In which ways can amino acids be classified based on synthesis?
Proteinogenic
Non-proteinogenic
In what ways can amino acids be characterised based on essentiallnes
essential
conditionally essential
non essential
What makes an R group polar?
-OH group
C=O bond
amino acids with ‘polar uncharged R groups” are characterised by what?
polar groups in the side chains, which can form hydrogen bonds. e.g -OH, -SH, -C=O and -NH2
the amino acids with “aromatic R groups” are characterised by what?
an aromatic ring structure, which gives these amino acids there characteristic UV spectra
the amino acids with “acidic R groups” are characterised by what?
the amino acids aspartate and glutamate, the negatively charged side chains can form electrostatic interactions with positively charged basic side chains
the amino acids with “basic R groups” are characterised by what?
lysine, arginine and histidine, positive charged side chains
the amino acids hydroxyproline and hydroxylysine are hydroxylated forms of what? what do they require for their synthesis?
- proline and lysine
- vitamin C as a co enzyme
what is desmosine formed from?
4 lysine residues
how do you know if amino acids are aliphatic?
only carbon and hydrogen in the side chain
What are proteinogenic amino acids?
Building blocks of proteins
20 are encoded by triplets of the genetic code
What is different about selenocysteine and pyrrolysine?
They both contain a structural change in the mRNA sequence allowing a STOP codon not to be recognised as such by a specific tRNA
What are non-proteinogenic amino acids?
Don’t need to bind into a protein to exert their function.
e.g. GABA (neurotransmitter)
Carnitine (transport of fatty acids in the blood)
How are non-proteinogenic amino acids produced?
- are not produced directly and I isolation by standard cellular machinery
- Occurring post-translationally, once the protein has already formed
What are some common modifications of non-proteinogenic amino acids?
Phosphorylation
Methylation
Acetylation
Hydroxylation
What are essential amino acids?
Cant be synthesised by the body so must be obtained through the diet
What are conditional 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
What are non-essential amino acids?
Can be synthesised by the body
What is an issue with herbivores consuming lots of hay/straw/haylage?
High levels of lignin, which reduces the absorption of nutrients. This decreases levels of essential amino acids such as Lysine
What are some types of proteins in body?
Receptor
Contractile
Hormonal
Structural
Enzymes
What are some functions of proteins in the body?
Protection
Storage
Structure
Receptors
Transport
Enzymes
Contractions
Hormones
What is primary protein structure?
Sequence of a chain of amino acids
How do amino acids bind together?
Peptide (amide) bonds
What type of chain is a protein?
polypeptide
How does a peptide bond form?
dehydration synthesis reaction (condensation)
What is secondary protein structure?
What are the 2 types?
When hydrogen bonds form between amino acids
α helix
β pleated sheets
Is an α helix hollow?
NO - just a spiral
Is an α helix hollow?
NO - just a spiral
What type of spiral is an α-helix?
Right-hand spiral
How do α-helix spirals form?
Every backbone NH group donates a hydrogen bond to the backbone C=O group of the amino acid, located 3 or 4 residues earlier along the protein sequence
What does a β structure contain?
β strands and β sheets
What are β strands?
Portions of the polypeptide chain that are almost fully extended, having a zig-zag shape
Are β strands flexible or elastic?
Flexible but not elastic
Describe the structure of β strands
H-bonded β strands can be on separate polypeptide chains, or on different segments of the same chain
β strands in a sheet can either be parallel or antiparallel
How do β-sheets form?
When multiple β strands are arranged side by side, they form β sheets
How do β-sheets form?
When multiple β strands are arranged side by side, they form β sheets
How are β sheets stabilised?
Stabilised by hydrogen bonds between carbonyl oxygens and amide hydrogens on adjacent β strands
What is tertiary protein structure?
- Occurs when certain attractions are present between alpha helices and beta-pleated sheets
- spatial arrangement of atoms
How is protein tertiary structure stabilised?
Numerous weak interactions:
Hydrogen bonds
Electrostatic interactions
Hydrophobic interactions
Disulfide bonds
How is protein tertiary structure stabilised?
Numerous weak interactions:
Hydrogen bonds
Electrostatic interactions
Hydrophobic interactions
Disulfide bonds
What are the 2 major classes of tertiary structure proteins?
Fibrous and globular
Are proteins always either hydrophilic or hydrophobic?
Can be either depending on structure, or amphipathic
What is protein quaternary structure?
When a protein has more than one subunit and sometimes other elements too
Give an example of a quaternary protein
haemoglobin
Describe the structure of haemoglobin
4 chains
4 subunits
A non-protein heme group binding a Fe2+
What is the function of haemoglobin?
Allows aerobic respiration by transporting O2 and CO2
What causes mis-folded proteins?
Mutations in their amino-acid sequence
Error in the folding process
What 2 types of effect can protein misfolding have?
Loss of function and gain of function
What 2 types of effect can protein misfolding have?
Loss of function and gain of function
Give an example of an effect of protein mis-folding which is loss of function?
Cystic fibrosis
Give examples of an effect of protein mis-folding which is gain of function?
Alzheimer’s
Parkinson’s
Huntington’s
What causes sickle-cell anaemia?
Mutation in haemoglobin
What is the process of making RNA from DNA?
Transcription
What is the process of making a protein from RNA?
Translation
what do disulphide bonds consist of?
one cysteine residue
how is the primary structure of a protein always written?
N->C terminal
what structure is a a-helix?
secondary
how many amino acids per tern of the helix are there in a a-helix
3.6
the biological function of myoglobin is determined by the presence of a what?
heme (haem) group
what bonds are formed between b-strands
hydrogen
what amino acid does not have a chiral alpha carbon?
glycine
what is the amino acid desmosine commonly found in?
elastin, a protein found in connective tissue
