Proteomics Flashcards
Define genome
All the genetic material an organism possesses i.e it’s DNA
Define proteome
Entire set of proteins expressed by a genome
What is the proteome based on?
The genome
Most cells contain the same genome regardless of what?
The cell type
Developmental stage
Environmental conditions
Why does the proteome vary considerably in different circumstances?
Due to different patterns of gene expression and different patterns of protein modification
Why is the proteome larger than the genome?
Alternative RNA splicing
Post-translational modification
What are proteins composed of?
Amino acids
What are the wide range of biological roles proteins carry out?
Structural
Catalytic
Signalling
Immunological
What is the only difference between each amino acid?
The nature of the R group
What do different amino acids have?
Different R groups
What does the R group define ?
The amino acid
What 2 functional groups does an amino acid have?
Amine group
Carboxyl group
What does the R group represent?
A side chain from the central ‘alpha’ carbon atom, and can be anything from a simple hydrogen atom to a more complex ring structure
What name is given to the reaction which forms a dipeptide?
Condensation
What does a condensation reaction for the formation of a dipeptide also form?
Water
What name is given to the bond between 2 amino acids (dipeptide) ?
Peptide bond
What name is given to the breakdown of a dipeptide?
Hydrolysis
What is the primary structure of a protein?
The number,type and sequence of amino acids, that make up a linear chain with peptide bonds holding them together
What kind of group is the Amine group?
Basic group
What kind of group is the carboxyl group ?
Acidic group
What are the 4 main classes of R groups?
Acidic ( negatively charged)
Basic (positively charged)
Polar
Non-Polar
What does the acidic R group generally have?
A carboxyl group
What does the carboxyl group of an acidic R group allow them to do?
Donate a H+ to another atom. Hence they become negatively charged and are strongly hydrophilic
What do basic R groups generally have?
NH2
What does the NH2 of a Basic R group allow them to do?
Accept a H+ and become positively charged and they become strongly hydrophilic
What does the polar amino acid mean?
They have oxygen or nitrogen or sulfur on their R side chain
What are polar r groups said to be?
They are hydrophilic as they form weak hydrogen bonds with water molecules
What do non-polar R groups generally contain?
A hydrocarbon chain
What are non-polar R groups said to be?
Hydrophobic
What is the secondary structure of a protein determined by?
The spatial arrangement of the amino acid that form the backbone of the protein
What bonds hold the secondary structure?
Hydrogen bonds
What do the hydrogen bonds cause the protein to have?
A 3D shape as the linear polypeptide backbone begins to fold
What are the four types of secondary structure?
Alpha helix
Parallel beta sheets
Antiparallel beta sheets
Turns
Describe the alpha helix secondary structure?
The hydrogen bonds form between atoms of the same polypeptide chain. The R groups of the amino acids stick outwards.
Describe the beta-sheet secondary structure?
Parts of polypeptide run alongside each other. R groups sit either above or below
What are turns?
A reverse in the direction of the polypeptide chain
What is the tertiary structure caused by?
Interactions between R groups
What are the 5 types of interactions leading to a tertiary structure?
Hydrophobic interactions Ionic bonds Hydrogen bonds Van Der Waals interactions Disulphides bridges
What do prosthetic groups do?
Give the protein added function
Describe hydrophobic and hydrophilic interactions?
Hydrophobic Amino acids cluster together in the centre of the protein and hydrophilic amino acids are found on the surface of the protein
Describe ionic bonds?
Charge dependant attraction occurring between oppositely charged polar R groups, e.g. Between the amino acids arginine and aspartic acid.
Describe hydrogen bonding?
It is a weak polar interaction that occurs when an electropositive hydrogen atom is shared between two electronegative atoms.
Where are weak intermolecular forces found?
Between adjacent atoms
Describe disulphide bridges?
Covalent bonds that form between adjacent cysteine amino acids
What are prosthetic groups?
Additional non-protein structures that are associated with the protein molecule and gives it its final functionality
Give an example of a prosthetic group?
The haem group in haemoglobin. The haem group contains an iron atom which is the site of oxygen bonding. The iron atom is covalently bound to the haemoglobin
When is a quaternary structure displayed by proteins?
When they consist of more than one polypeptide chain, the chains are held together by all the interactions listed in the tertiary structure.e.g. Haemoglobin consists of four subunits and four haem groups
What can temperature and pH influence?
The interactions of the R groups, changing the shape of the protein
What name is given to a protein if it has lost its shape?
Denatured
What will increasing temperature do?
First disrupt (melt) weaker bonds and then finally stronger covalent bonds
What can pH do?
Shift the acid/base characters of the R groups in particular amino acids and so change the ionic interactions in the chain
What do the R groups at the surface of a protein determine?
It’s location within a cell
What do regions of hydrophobic R groups allow?
Strong hydrophobic interactions that hold integral proteins within the phospholipid bilayer
What does transmembrane mean?
Integral proteins spanning the membrane and held in place by hydrophobic alpha helices
What are the 3 possible functions of transmembrane integral proteins ?
Channels
Transporters
Receptors
What are peripheral proteins?
Proteins which are only helps in place at the surface of the membrane by charged or polar amino acid R groups and have fewer hydrophobic R groups interacting with phospholipids
How are integral proteins held firmly in place within the membrane?
By strong hydrophobic interactions with the lipid tails
What can integral proteins either be?
Transmembrane or they are embedded in one side of the bilayer only
What is the phosphate head of a phospholipid said to be?
Hydrophilic
What is the ionic tail of a phospholipid said to be?
Hydrophobic
What is a Ligand?
A substance that can bind to a protein
What can R groups not involved in protein folding allow?
Binding to these other molecules (ligands)
What will binding sites have?
Complementary shape and chemistry to the Ligand
What can the Ligand either be?
A substrate or a molecule that affects the activity of the protein
Describe DNA as a Ligand
Positively charged histone proteins bind to the negatively charged sugar-phosphate backbone of DNA in eukaryotes
What does DNA wrap around histones to form?
Nucleosides packing the DNA in chromosomes
What does the methylation of histones cause?
Nucleosomes to pack together tightly. As a result, DNA is inaccessible and transcription factors cannot bind to the DNA, and genes are not expressed
What does histone acetylation result in?
Loose packing of nucleosomes, meaning transcription factors can bind to the DNA and genes are expressed
What is metabolism?
Metabolism is the sum of all the anabolic (building up) and catabolic (breaking down) reactions.
What happens when a ligand binds to a protein binding site or a substrate binds to an enzyme’s active site?
the conformation of the protein changes.
What does the change in conformation of the protein cause?
a functional change in the protein
In enzymes, what is the specificity between the active site and substrate related to?
induced fit.
Describe the induced fit model.
The induced fit model of enzyme action states that, when the correct substrate starts to bind to the enzyme, there is a temporary change in the shape of the enzyme active site.
Describe the effect of the induced fit (i.e. the temporary change in the shape of the enzyme active site).
This change in shape increases the binding and interaction of the substrate with the enzyme. The chemical environment that is produced lowers the activation energy which is required for the reaction.
What happens once the reaction has taken place?
the original enzyme conformation is resumed and products are released from the active site.
What are competitive inhibitors?
Inhibitors that resemble the normal substrate molecule and compete for admission to the active site.
What are non-competitive inhibitors?
inhibitors that do not directly compete with the substrate to bind to the active site. Instead they bind to another part of the enzyme (secondary binding site). This causes the enzyme to change shape, resulting in the active site becoming less effective.
What is an allosteric enzyme?
An allosteric enzyme is one which changes conformation upon binding a modulator.
In allosteric enzymes, what do modulators bind at?
In allosteric enzymes, modulators bind at secondary binding sites, known as allosteric sites.
What is important to remember about allosteric sites?
they are separate and distinct from the active site of the enzyme.
Upon binding a modulator what will happen to the allosteric enzyme?
Upon binding a modulator, the conformation of an allosteric enzyme will change and this alters the affinity of the active site for the substrate.
What may modulators be?
Modulators may be positive or negative.
What do negative modulators do?
Negative modulators reduce the enzyme’s affinity for the substrate
What do positive modulators do?
positive modulators increase the enzyme’s affinity for the substrate
Give 4 types of enzymes.
proteases
nucleases
ATPases
Kinases
Describe the action of proteases.
hydrolyse peptide bonds to break down proteins into amino acids
Describe the action of nucleases.
hydrolyse phosphodiester bonds to break down nucleic acid into nucleotides
Describe the action of ATPases.
hydrolyse ATP. Many proteins have ATPase activity which is essential for their function
Describe the action of kinases.
catalyse the transfer of a phosphate group onto a molecule such as a carbohydrate or a protein
What are most enzymes known to be allosterically regulated constructed from?
two or more subunits, each composed of a polypeptide chain and having its own active site.
What does each subunit have?
its own active site
What does the entire complex oscillates between?
two different shapes, one catalytically active and the other inactive.
Where do activating or inhibiting regulatory molecules bind to?
a regulatory site often located where the subunits join.
What does the binding of an activator to a regulatory site do?
stabilises the shape that has functional active sites
What does the binding of an inhibitor to a regulatory site do?
stabilises the inactive form of the enzyme.
Due to the arrangement of subunits in an allosteric enzyme, what is important to note? Explain this.
a shape change in one subunit is transmitted to all others. Through this interaction of subunits, a single activator or inhibitor molecule that binds to one regulatory site will affect the active sites of all subunits.
What is cooperativity?
Binding of the substrate itself to one active site enhances binding at the other active sites.
What does cooperativity do?
This mechanism amplifies the response of enzymes to substrates.
What does a dissociation curve show?
A dissociation curve shows how saturated the haemoglobin is with oxygen at any given partial pressure.
What is covalent modification widely used in?
metabolic regulation
What is one of the most common covalent modifications and describe its effect?
addition of a phosphate group, which can alter the shape of a protein by attracting positively charged r-groups (as phosphates carry two negative charges on the two single-bonded oxygen atoms).
What is a sarcomere described to be?
the basic unit of muscle
What do sarcomeres contain?
fibrous proteins called actin and myosin.
What does the action of actin and myosin sliding past each other allow?
allows muscles to contract and relax.
Describe the structure of myosin
The myosin filament is formed from a number of myosin proteins wound together. Each ends in a myosin head, which contains an ATPase.
Describe the structure of actin
The actin filament is formed from a helix of actin sub-units. Each contains a binding site for the myosin heads
Describe the 5 stages of muscle contraction
- Muscle contraction occurs when the muscle receives an impulse from a nerve cell.
- This impulse causes myosin binding sites on actin to be exposed.
- The myosin heads hydrolyzes ATP to ADP and Pi. Then binds to actin, forming a cross- bridge.
- ADP and Pi are released from the myosin, this moves the actin filament to the centre of the sarcomere. (known as a power stroke)
- ATP binds to the myosin head, which causes it to release the actin.
- The myosin head acts as an ATPase; it breaks down the ATP to ADP + Pi, causing the head of the myosin to flex again and the cycle repeats.
