Proteins Flashcards
What is the structure of an amino acid?
Central carbon atom, covalently bound to
- Amino group
- Carboxyl group
- Hydrogen atom
- R group (side chain)
How do amino acids ionise?
Amino group gains hydrogen ion
NH2 + H+ —–> NH3+
Carboxyl group gives up hydrogen ion
COOH —–> COO- + H+
Which group in the amino acid is acidic?
The carboxyl group
Which group in the amino acid is basic?
The amino group
How are amino acids classified? Why?
Based on the properties of the R groups
Because in polypeptide chains, only the hydrogen atom and the R group of the amino acids remains
What is an amino acid residue?
What remains of an amino acid after it has been jointed to another amino acid
- R group
- hydrogen atom
What are the types of properties of the R group?
Chemical properties
Physical properties
What are the possible chemical properties of the R group?
Polar/non-polar
Hydrophobic/hydrophilic
Acidic/basic/neutral
What are the possible physical properties of the R group?
Aliphatic/aromatic
What does the pKa value of amino acids measure?
How acidic the amino acids are
What does a low pKa value mean?
The amino acid is more acidic
What does a high pKa value mean?
The amino acid is less acidic
more basic
What happens to the amino acid if pH > pKa? Why?
Higher pH means fewer hydrogen ions present
amino acid gives up hydrogen ions
becomes deprotonated
What happens to the amino acid if pH < pKa? Why?
Lower pH means more hydrogen ions present
amino acid takes up hydrogen ions
becomes protonated
What is physiological pH?
7.4
What is the primary structure of a protein?
Amino acids joined together in a linear chain
What reaction occurs when two amino acids are joined together?
amino acid1 + amino acid 2 —–> polypeptide + water
What bond joins two amino acids together?
Peptide bond
What is the amino terminus of a polypeptide?
The amino group NH2 end of the polypeptide chain
What is the carboxyl terminus of a polypeptide?
The carboxyl group COOH end of the polypeptide chain
What are the properties of peptide bonds?
Planar
Rigid
Trans conformation
What is meant by peptide bonds being planar?
The central carbon atom
N-H
C=O
are all in the same plane
What is meant by peptide bonds being rigid?
No rotation about the peptide bond
What atoms are involved in a peptide bond?
C-N
C from C=O
N from N-H
What is meant by the peptide bond having a trans conformation?
Heavier groups are on opposite sides of the peptide bond
the heavier groups are the central carbon atom, R group, H atom altogether
What is the importance of the amino acid sequence in the primary structure?
Determines the way the polypeptide chain folds
the structure of the protein
and hence its function
What are peptides/oligopeptides?
Chains of a few amino acids joined together
What are polypeptides/proteins?
Chains of many amino acids joined together
What type of bond is a peptide bond?
Covalent bond
What is the secondary structure?
The spatial arrangement of the polypeptide backbone
What are the types of secondary structures?
Alpha helix
Beta strand
What do layers of beta strands form?
Beta pleated sheet
What holds the alpha helix and the beta pleated sheets together?
Hydrogen bonds between C=O and N-H
What are the types of beta sheets? What do they each mean?
Parallel - run in same direction
Anti parallel - run in opposite directions
How does the polypeptide chain fold up into an alpha helix or beta pleated sheet if peptide bonds are rigid?
Bonds next to peptide bonds are free to rotate
What is the tertiary structure?
Secondary structure folds up to form a 3D conformation
What are the types of tertiary structures? What do they each mean?
Globular - spherical shape
Fibrous - long strand-like shape
What is the general function of fibrous proteins?
Structural support
Maintain shape
How many types of secondary structures are there in fibrous proteins?
Single repeating secondary structure
How many types of secondary structures are there in globular proteins?
Several different types
What is a classic example of a fibrous protein?
Collagen
What is a protein domain?
Part of polypeptide chain that folds into a distinct shape
has a specific function
How do water-soluble proteins generally fold up?
Non-polar hydrophobic side chains are buried within
Polar/charged hydrophilic side chains are on surface
How do integral membrane proteins generally fold up? Why?
Non-polar hydrophobic chains are on the surface
interact with hydrophobic tails
Polar/charged hydrophilic chains form a channel within
interact with water in and out of cell
What is the quarternary structure?
Different polypeptide chains coming together to form a multi-subunit protein
What is an example of a protein with a quarternary structure?
Hb
What is an example of a protein with a tertiary structure?
Myoglobin
What does pI stand for?
Isoelectric point
What is the pI of proteins?
pH at which protein has no overall charge
Do acidic proteins have a low or high pI value? Why?
Low
low pH means more hydrogen ions, neutralises negative charge of acidic amino acid
Do basic proteins have a low or high pI value? Why?
High
high pH means fewer hydrogen ions, because already have positively charged amino acids
What happens to the protein if pH > pI? Why?
High pH means fewer hydrogen ions
amino acid gives up hydrogen ions
becomes deprotonated
What happens to the protein if pH < pI? Why?
Low pH means more hydrogen ions
amino acid takes up hydrogen ions
becomes protonated
What are conjugated proteins?
Proteins covalently linked to additional chemical components that are not amino acids
What are some examples of roles of proteins? Give examples for some roles
Structural support e.g. collagen
Enzymes e.g. hexokinase
Transporters e.g. Hb
Carriers, channels etc.
Receptors, ligands etc.
