Protein structure and function Flashcards
What do different side chains of amino acids determine
Determine the properties and dictate protein shape at end
What is an example of a transport protein
Haemoglobin
What are proteins
Large polypeptides that are folded in such a way to carry out a specific function in the body
What are amino acids linked by
Peptide bonds
What are short polypeptides referred to as
Peptides
What groups do all amino acids contain?
C, O2 and N and H
What is a dehydration reaction?
When two amino acids are joined together and lose 2Hs and 1 O2.
A new bond (peptide) is formed between carbonyl group of one amino acid and one amino group of another amino acid.
What is the dehydration reaction catalysed by?
Ribosomes, in a hamburger structure
How are peptide bonds formed?
Through dehydration reactions
What is the bi-product of the formation of a peptide bond?
A water molecule per bond
What is an example of a structural protein
Actin
What is an example of a hormonal protein
Insulin
What is an example of an immune protein
Antibodies
What are examples of digestive enzyme proteins
Amylase, lipase, and pepsin
What is an example of a toxin protein
Cholera toxin
What is an example of a storage protein
Egg white
What is an example of a contractile protein
Myosin
Are polar amino acids hydrophobic or hydrophillic?
Hydrophillic
Are hydrophilic amino acids polar or non-polar
Polar
Are non-polar amino acids hydrophobic or hydrophilic
Hydrophobic
Are hydrophobic amino acids polar or non-polar
Non-polar
Are peptide bonds strong or weak? What kind of bond are they?
Strong, covalent bonds
What are peptide bonds formed between?
The C of the carboxyl group on one amino acid and the N of the amine group of another amino acid.
What is a dipeptide
Two amino acids bonded by a peptide bond
What is a polypeptide
Many amino acids bonded by peptide bonds
What is the only part of the amino acid that makes them differ from each other
R group
What are the two configurations that the R side chains of the two amino acids bonded by a peptide bond can be in
Cis and trans
Is the cis orientation stable or unstable, and why
Unstable: increased steric interactions between the R groups on the same side
Is trans orientation stable or unstable, and why
Stable: decreased steric interaction between R groups on opposing sides
Can peptide bonds rotate, and why
No, peptide bonds are rigid and can’t rotate due to resonance.
What part of the peptide bonds are co-planar
O-C-N-H
Where can rotation occur in polypeptides
At the single bonds between the alpha carbon and its neighbouring atoms
What does variation in structure and shape of proteins allow?
Allows them to carry out diverse functions
What does the unique shape of a protein allow?
Allows it to interact with other molecules to carry out specific functions
What is the shape of a protein determined by?
The sequence of amino acids in the protein and its chemical properties
What shape does the active site of an enzyme have?
Complementary shape to the substrate
What is the shape of the active site of an enzyme driven by?
The chemical properties and amino acids of the protein
What occurs at the enzyme-substrate complex?
The enzyme catalyses the reaction and transforms the substrates into products
What occurs after the product of an enzyme-substrate complex reaction is released?
The enzyme returns to its initial state and is therefore unchanged by the reaction so can go on to catalyse more reactions
What does the unique 3D shape with a specific surface configuration of enzymes allow them to do?
Allows them to recognise and bind to specific substrates
What is the active site of an enzyme?
The part of an enzyme that catalyses reactions
What does the induced fit hypothesis state?
The shape of the active site and substrate can change slightly to ensure a better fit
Order of protein structures
Primary, secondary, tertiary, and quaternary structures
What is the primary structure
The unique sequence of amino acids that make up a protein encoded by DNA
What are the two sides to a polypeptide
N terminus (end with amino acid)
C terminus (end with carbonyl group)
How are amino acids read (of N and C terminus)
Amino acids read from N to C terminus
How can we deduce the primary structure of a protein?
By looking at the DNA sequence of the gene coding for it
What are secondary structures
Amino acids sequence fold together (localised) to form two things - alpha and beta helix.
What type of bonds between polypeptide bonding in secondary structures
Weak hydrogen bonding
What is an alpha helix
Backbone forms spiral shape with 3 or 4 amino acids per turn.
Normally all r groups point on outside of helix.
What is a beta sheet?
The backbone extends one way and does a U-turn in the opposite direction to line up with each.
How does beta-sheet form
Hydrogen bonding between a backbone amine group on one strand, and a backbone carbonyl group on another strand
What is the hydrophobic effect
Describes the interaction of non-polar or hydrophobic side chains with the aqueous environment, and their subsequent burial in the interior of the protein.
How are alpha helix and beta sheets formed and what binds hold it together
Both shapes are held together by H bonds.
Key interactions hold proteins together and proteins rely on these weak interactions to keep their shape.
What is a tertiary structure
Folded 3D shape of the polypeptide chain (fold even further than before)
What drives the formation of tertiary structures
The chemistry of the R side groups and the interactions between them
Is the folding process in tertiary structures random and why
Not random, because have a specific primary structure sequence. DNA tends to fold the same way and give same shape.
What are the two types of beta sheets
Parallel (both going N to C) or antiparallel (one strand going from C to N, the other going N to C)
How does the hydrophobic effect occur
When proteins fold, hydrophobic residues want to go inside. For the hydrophilic residues, surface of the protein interacts with the H2O molecules.
What are the two shapes of proteins
Globular and Fibrous
Describe shape of globular proteins
When proteins are highly folded
Describe the shape of fibrous proteins
When proteins are long and spindly
What is the structure of fibrous proteins
Repeated amino acid sequences from long polypeptide chain, and twists together
Are globular proteins insoluble or soluble in water?
Soluble
What functions do most globular proteins have?
Metabolic functions - transport, enzymes, immunity
What are examples of globular proteins?
Enzymes, antibodies, haemoglobin
Are fibrous proteins stable or unstable?
Extremely stable when subject to changes in temperature or pH for example
Are fibrous proteins soluble or insoluble in water?
Insoluble
What functions do most fibrous proteins have?
Structural
What are examples of fibrous proteins?
Keratin and collagen
What are quaternary structures
When two or more polypeptide chains come together to form even larger structures.
The combination of multiple polypeptide chains forming multiple folded protein subunits
What is hydrogen bonding
Theorces involved in maintaining protein structures
What are hydrogen bonding held together by
Weak interactions
What are electrostatic interactions
Forces involved in maintaining protein structures
What are hydrophobic interactions
Forces involved in maintaining protein structures.
Clustering of polar/hydrophobic side chains away from H2O.
How strong are hydrophobic interactions
Weakest of ionic and hydrogen, but there are strength in numbers
How strong are covalent bonds
Strongest bond, aside from peptide backbones
How do covalent bonds form
Bonds occur spontaneously under mild oxidising conditions.
Which amino acid forms disulphide bonds?
Cysteine
What causes a protein to denature
Change in:
pH
Salt concentration
Temperature
