Unit 1 - section 2 Flashcards
What is the proteome?
The entire set of proteins expressed by the genome
What is the genome?
Entire hereditary information encoded in DNA
2 processes that are responsible for the proteome being much larger than the genome
Alternative RNA splicing
Post translational modification
Why is the entire genome not expressed in all cells?
Regulation of gene expression
What is the monomer that forms the basic structure of a protein?
Amino acids
What is the polymer formed from amino acids?
A polypeptide (protein)
What level of protein structure is the polypeptide chain?
Primary level
What type of bonds are involved in the basic (primary) structure and how are they formed?
Peptide bonds
Formed by dehydration reactions (between a carboxyl group and amide group)
What are the 4 main classes of amino acid side chains (R groups)
Acidic
Basic
Polar
Non-polar
For acidic amino acid state:
Examples (2)
Hydrophilic or hydrophobic
Common feature
Examples:
Aspartic acid
Glutamic acid
Hydrophilic
Have a carboxyl group which ionises to make them acidic
For basic amino acids state:
Examples (3)
Hydrophilic or hydrophobic
Common feature
Examples:
Arginine
Lysine
Histidine
Hydrophilic
Have an additional amino acid group which ionises to NH3^+
For polar amino acids state:
Examples (6)
Hydrophilic or hydrophobic
Common feature
Examples: Glutamine Tyrosine Asparagine Theonine Cysteine Serine
Hydrophilic
Different functional groups which contain
-OH, -SH, =O
For non-polar amino acids state:
Examples (9)
Hydrophilic or hydrophobic
Common feature
Examples: Isoleucine Tryptophan Phenylalanine Glycine Methionine Alanine Leucine Proline Valine
Hydrophobic
R-group is a hydrocarbon
Name and describe the secondary structures of protein
Alpha helix - protein is a helix shape held together by hydrogen bonds between amino acids
Beta sheets - parts of the polypeptide chain run alongside each other to form a corrugated sheet.
Antiparallel beta sheets horizontal hydrogen bonds
Parallel - beta sheets have diagonal hydrogen bonds
Turns - reverses the direction of the polypeptide chain.
Their exact role has not been determined
What bonds are involved in holding the secondary structure of proteins in place
Hydrogen bonds
Describe the tertiary structure of proteins using globular proteins as an example
The 3D shape of the protein. This further folding is due to the interactions between R-groups
Globular proteins:
Formed due to non polar R-groups clumping together in centre of protein where they are held together by hydrophobic interactions
Amino acids with hydrophobic R-groups usually end up in centre of protein since repelled by water
4 types of bonds that can hold the tertiary structure of proteins in place
Hydrophobic interactions Ionic bonds Hydrogen bonds Van Der Waals interactions Disulfide bridges
Name the non protein part added to some proteins
Prosthetic groups
2 examples of prosthetic groups added to proteins
Carbohydrates
Nucleic acid
Give an example of a protein that contains a non-protein group and describe its function
Haemoglobin contains prosthetic group haeme and has function of supplying red blood cells with oxygen
Describe the quaternary structure
Exists in proteins that have two or more tertiary sub units joined together
Bonding between subunits means that changes to conformational shape of one polypeptide chain can effect the properties of another subunit in the protein
2 factors that can influence the interaction of R groups
pH
Temperature
How does
a)pH
b)temperature
Affect R group interactions
a) Increase temperature Ek of proteins increases, placing stress on bonds and breaking them. Weaker intermolecular bonds are particularly susceptible
b) Changes pH affect concentration H+ and OH- ions in a solution
Changes the relative charge of protein and places stress in polar interactions such as H bonding and ionic bonding
Changes result denaturation of protein and the loss of tertiary structure and function
Define hydrophobic and hydrophilic
Hydrophobic - to repel or fail to mix with water
Hydrophilic- to dissolve or mix with water
What is the current accepted model of the plasma membrane structure?
Fluid mosaic model
What are the main components of the plasma membrane?
Phospholipids
Proteins
What is the significance of hydrophobic and hydrophilic interactions in membrane structure?
Hydrophobic reactions between lupus tails hold the double membrane together
The hydrophilic heads of phospholipids allow the outer layers of the membrane to be surrounded by aqueous solutions
Define the terms integral and peripheral membrane proteins and describe how they are held in position in the membrane?
Integral proteins- penetrate the hydrophobic layer of the membrane. They contain a stretch of non-polar amino acids in the hydrophobic region, which holds them in place
Peripheral proteins - not embedded in the lipid layer but have loose associations with the surface of the membrane
3 examples of integral membrane proteins
Channels
Transporters
Many receptors
What is the function of structural integral membrane proteins?
Attaches to intracellular cytoskeleton to hold together cell structure
What is the function of enzymes?
Integral membrane protein with an active site that is exposed to substrates in the extracellular matrix. Catalyses chemical reactions
What is the function of receptor proteins?
Integral membrane protein that has a specific binding site exposed to extracellular matrix. Received signals from specific molecules for cellular communication
What is the function of marker proteins?
Attach to specific non-protein components. Important functions in cellular immunity
What is the function of cell adhesion proteins?
Allow cells to be held together closely with neighbouring cells. Can allow passage of molecules between cells
What is the function of selective ion transport proteins?
Integral membrane proteins that allow selective passage of molecules across membranes. These proteins include protein channels for diffusion and osmosis and and carrier proteins involved in active transport
Define the term ligand
A substance that binds to a protein
State the regions of proteins that are involved in ligand binding
Free R-groups
What are the similarities between the ligand and the protein binding site
They have complementary shape and chemistry
Name the type of proteins DNA is bound around
Histones
What is the type of charge on the DNA backbone and the proteins with which it is bound?
DNA backbone is negatively charged and the proteins it is bound around are positively charged
What structure is formed from DNA and the proteins it is bound to?
Nucleosomes
What is the name given to the linear structure that results from the tight packaging of DNA in eukaryotes?
Chromosomes
Name and state the functions of other proteins that bind to specific sequences of double stranded DNA
Transcripting factor proteins
Proteins that bind to specific sequences of double stranded DNA and initiate and halt transcription by recruiting DNA polymerase
Describe the changes that occur to a protein following the binding of a ligand
Results in a conformational change to the protein which therefore alters the behaviour of the protein
Name the site where a ligand binds to an enzyme
Active site
Name the different groups of enzymes? (7)
Protease ATPase Phosphatase Nuclease Kinase Synthase Polymerase
What reaction does protease catalyse?
Hydrolysis of peptide bonds (breaking down proteins)
What reaction does ATPase catalyse?
Hydrolysis of ATP
What reaction does phosphatase catalyse?
Removal of phosphate by hydrolysis
What reaction does nuclease catalyse?
Breakdown of nucleus acids by hydrolysis
What reaction does kinase catalyse?
Transfer of a phosphate group to another molecule
What reaction does synthase catalyse?
The joining of two molecules together by dehydration synthase reaction
What reaction does polymerase catalyse?
Addition of molecules in series in a chain
Describe the induced fit model
The active site closely fits the substrate then changes slightly to achieve a perfect fit
What happens to the chemical environment when binding of enzyme and substrate occurs
The chemical environment produced lowers the activation energy required for the reaction
What is the affinity of the enzyme for the
•substrate
•products of a reaction
Substrate - high affinity
Products of the reaction - low affinity
What happens to the conformation of the enzyme after catalysis?
After catalysis the products are released from the active site and the enzyme reverts to its original confirmation
Define allosteric enzyme
An enzyme that can have its activity altered by a ligand called a modulator
Define the term modulator
A modulator is is ligand which binds to a secondary binding site separate from the active site (an allosteric site), leading to a conformational change to the enzyme
What is the difference between positive and negative modulators of enzyme activity
Negative modulators switch off enzymes
Positive modulators switch on enzymes
Name the protein structure that can show cooperativity
Quaternary protein structure
Describe the process of cooperativity
When changes in one protein binding site change the affinity of all other sub groups
Give an example of a protein that shows cooperativity and state what it does
Haemoglobin
Carries oxygen around the body
How do pH and temperature affect cooperativity in enzymes
High temperature reduces affinity
Low pH reduces affinity
What is phosphorylation?
The addition or removal of a phosphate group resulting in a reversible confrontational change to the protein which can regulate activity. It’s is a form of post translational modification
What is the role of:
•kinase
•phosphatase
•ATPase
Kinase transfers a phosphate group (phosphorylation)
Phosphatase removes a phosphate group (dephosphorylation)
ATPase hydrolyses ATP by removing phosphate
Describe the adding or removing of a phosphate from a protein
Results in a conformational change as the position of charged binding is altered
What is the correct term for removing a phosphate from a protein?
Dephosphorylation
Name 2 types of protein that can be regulated using post translational addition of phosphate
Enzymes
Receptors
Name the group of proteins that use ATP for their phosphorylation
ATPase ?
Describe the steps in muscle contraction
Muscle contraction occurs when the muscle relieves impulse from a nerve cell
The impulse causes myosin binding sites on actin to be exposed
The myosin heads form a flexed shape and bind to the actin
ADP and Pi are released from myosin, causing it to return to its relaxed shape. This moves the actin filament to the centre of the sarcomere
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 and Pi causing the head of the myosin to flex again
(Sarcomere basic unit of muscle)
