Amino acids and proteins Flashcards
What are the 12 components of a eukaryotic cell?
Plasma membrane, Lysosome, Basal bodies, Golgi complex, Vacuole, Nucleus, Rough endoplasmic reticulum, Cytosol, Free ribosomes, Mitochondria, Smooth endoplasmic reticulum
What does the nucleus consist of?
- Nucleur envelope
- Nucleolus
- Chromosomes
What causes differences in cell types?
Proteins expressed
How does the DNA in every cell differ?
All the same, but not all genes expressed
What does differential expression of DNA mean?
Not all proteins are made
Give 5 examples of specialised cell types
- Nerve cells
- Adipocytes
- Red blood cells
- Muscle cells
- Epithelial cells
What is the simplest cell type?
Prokaryotic cell
What are the 8 components of a prokaryotic cell?
- Capsule
- Cell wall
- Plasma membrane
- Flagella
- Ribosomes
- Cytosol
- Nucleoid
- Pilli
What is the advantage of the differences between eukaryotic and prokaryotic cells?
Can target these differences in the use of antibiotics
What differences can be targeted in the use of antibiotics?
- Bacteria have no separate nucleus
- Bacteria contain cell wall and plasma membrane
- Bacteria lack most organelles
What are the levels of structure in a cell?
Cell/organelle → macromolecular complex → macromolecles → monomeric units
How are monomeric units joined together?
Covalent bonds
How are macromolecules/complexes held together?
By non-covalent interactions
Of what nature are most interactions between biomolecules?
Electrostatic
What do electrostatic interactions involve?
Some sort of charge
What type of interactions are present between biomolecules?
- Hydrogen bonds
- Ionic interactions
- Hydrophobic interactions
- Van der Waals interactions
Where do hydrogen bonds occur?
Between C=O and O-H, and peptide bonds (C=O and N-H)
Why do hydrogen bonds arise?
Because of polarised bonds
Why is the O-H bond polarised?
The hydroxyl group has very strong electronegative oxygen atom that pulls electrons towards it from H
Where do ionic interactions occur?
Between fully charged molecules
Are ionic interactions attraction or repulsion?
Can be either
What do hydrophobic interactions involve?
Exclusion of water
Are van der Waals forces strong or weak?
Weak
Why are van der Waals forces significant?
Because there are lots of them
What does the formation of macromolecules and complexes require?
Weak interactions
What is the result of multiple weak interactions?
They increase the stability of complexes
What is the result of breaking interactions between macromolecules and complexes?
Loss of structure and function
What does solubility depend on?
Ability to form hydrogen bonds
Essentially, what is the ability to be soluble?
The ability to interact with water, not necessarily to form hydrogen bonds
What kind of molecules can form hydrogen bonds?
Polar
Give 3 examples of polar molecules
NAME?
Why is glucose highly soluble?
Because it has lots of -OH groups, which can form hydrogen bonds with water
Are non polar molecules soluble?
No, because they cannot form H bonds
What kind of molecules are insoluble?
Fat like molecules
Why are fat like molecules insoluble?
Because C-C bonds cannot interact with water
Can carbonyl groups interact with water?
Yes, the O can
Why does the presence of a carbonyl group in fats not necessarily mean they are soluble?
Because it doesn’t have much impact compared to the rest of the molecule
What is hydrophilicity?
How much something likes water
What are amphipathic molecules?
Molecules with both polar and non-polar regions
Give an example of amphipathic molecules
Phospholipids
What is the result of amphipathic molecules having both polar and non-polar regions?
One side is very hydrophobic and one side is very hydrophilic
What happens when amphiphatic molecules are placed in water?
Hydrophobic regions cluster together and hydrophilic regions interact with water, forming micelles
Describe a micelle
The hydrophobic groups away from water, with an ordered shell of hydrophilic head groups that interact with water
Why are micelles formed?
Because they are energetically favourable
What model do biological membranes follow?
Fluid mosaic model
What are biological membranes made up of?
Lipid bilayer with proteins embedded in it
How are the proteins associated with the bilayer?
Can be associated on outside or span the membrane
What is it important that membranes have the right amount of?
Fluidity
What regulates membrane fluidity?
Cholesterol
Where do proteins play a crucial role?
Virtually all biological processes
Give 8 roles of proteins
- Catalysts
- Transporters
- Structural support
- Machines
- Immune protection
- Ion channels
- Receptors
- Ligans in cell signalling
What are protein catalysts called?
Enzymes
What do enzymes do?
Speed up rate of reaction
Give an example of a transporter protein
Haemoglobin
What proteins give structural support?
Collagens in skin and bone
What proteins provide immune protection?
Immunoglobulins
What are protein receptors for?
Hormones, neurotransmitters etc
Give an example of a signalling ligand
Growth factors
What kind of molecules are proteins?
Polypeptides
What are polypeptides?
Macromolecules made up of amino acids covalently bonded by peptide bonds to give sequence of protein
Technically, what are amino acids in proteins
Amino acid residues
What is the amino acid sequence encoded for by?
The nucleotide sequence of a gene
What do you have to have to make a protein
A gene
What can each gene make?
More than one protein
How can each gene make more than one protein?
Alternative splicing also transcription of mRNA in different ways
What does the polypeptide chain fold into?
A complex and highly specific 3D struture
What is the folding of a protein determined by?
The amino acid sequence
What does the shape of a protein determine?
Function
What happens to a denatured protein?
It looses its function
What does folding depend on?
The physical and chemical properties of amino acids
Does anything else help proteins fold?
Yes
Where does the ability to fold in the right shape come from?
Solely from amino acid sequence
What are amino acids?
The building blocks of proteins
What is the amino acid made up of?
An amino group, a H, a carboxylic acid and a side chain covalently bonded to the α-carbon
What is the ionised form of an amino acid called?
Zwitterion
What happens to the amino acid in its ionised form>
The amino acid and carboxyl group are ionised, forming NH 3 + and COO -
What is the overall charge on a zwitterion?
None
What acts as the base in a zwitterion?
NH 2
What acts as the acid in a zwitterion?
COOH
Why can amino acids show stereochemistry?
Because there are 4 different functional groups attached to each central carbon
Which isomer is found in humans?
L
What would happen if there was a mixture of isomers in the human body?
Wouldn’t be able to form protein structure
What are amino acids classified according to?
Chemical properties of the R groups
Why are we only really interested in the R groups of amino acids?
Because when amino acids are joined together, we lose the amine group and carboxyl group in peptide bonds, leaving only one α-NH 3 + at N terminal end and one α-COO - at C terminal end, so only R groups impact properties
What do R groups determine?
Acid base behaviour
What kind of things affect an R groups properties?
NAME?
What does aliphatic mean?
Long chains of C’s
What does aromatic mean?
Rings of C’s
Why does size affect properties?
Bulky side chains can cause problems with folding
What are the 3 major types of amino acids?
- Non-polar (hydrophobic)
- Polar, uncharged (hydrophilic)
- Polar, charged (hydrophilic)
Why does the sulphur in methionine not cause polarity?
Because it’s in the middle of the chain
What happens to prolines side chain?
It loops back
What is the result of the polar groups in polar, uncharged amino acids?
They are able to interact with water
What do charged amino acids have?
Whole charges on side chains
Why is histidine classed as a polar, charged amino acid?
Despite having no charge, it’s acid dissociation constant means it’s classed as a positively charged molecule
What is the pK a ?
The acid dissociation constant
What does the acid dissociation constant tell you?
How likely a group is to dissociate/release a proton
What happens if the pH of the solution
The group is protonated, resulting in a positive side chain
What happens when the pH of the solution > the pK value?
The group is deprotonated
What happens in peptide bond formation?
2 amino acids are linked by the removal of water
What is meant by peptide bonds being planar?
C α , C, O, N and H all lie in the same plane
What happens to the R groups when peptide bonds are formed?
They point up and down in different directions
What is the advantage of the R groups pointing up and down alternately?
It allows when to form H bonds
What does the C-N bond of proteins have?
Partial double bond characteristics
What is the advantage of the C-N bond being short?
It means it’s stronger
Why does the C-N bond being short mean its stronger?
Because electrons in the carbonyl bond delocalise across the bond
What is the result of the delocalisation of the carbonyl groups electrons?
Makes the bond rigid and planar
What different ways can peptide bonds be seen?
NAME?
What happens to the R groups in trans formation?
The R groups are on opposite sides
What orientation are peptide bonds in naturally occurring proteins?
Trans
Why are peptide bonds only found in trans formation in naturally occurring proteins?
Prevents steric clashes
What does the amino acid sequence determine?
NAME?
What is the isoelectric point a protein?
The pH at which there is no overall net charge
What is the pI of a basic protein?
> 7
What does a basic protein contain?
A lot of positively charged (basic) amino acids
What is the pI of an acidic protein?
What does a acidic protein contain a lot of?
A lot of negatively charged (acidic) amino acids
What happens if pH
Protein is protonated
What happens if pH > pI?
Protein is deprotonated
How many amino acids are in peptides/oligopeptides?
Few-
How many amino acids are in polypeptides/proteins?
Many
What are conjugated proteins?
Proteins covalently linked to chemical component in addition to amino acids
