Download Make notes using these questions

Discuss the answers to these questions without referring to your notes.
Then check your notes and see if you can improve your answers.
1.
2.
3.
4.
5.
6.
What is the proteome?
Why is the proteome larger than the genome?
What is ‘alternative RNA splicing’?
How does it affect protein function?
What is ‘post translational modification’?
How does it affect protein function?
AH Biology: Unit 1
Proteomics and Protein
Structure 2
Protein Structure
Think
• What are the functions of protein in a cell?
• Why is protein structure important?
• Why do organisms usually live within a narrow range of
temperature and pH?
• If eukaryotic cells are identical in structure relative to their
cellular components why do organisms look different?
• How can a gecko stick to Perspex?
• How do multicellular organisms stay together?
Four levels of
protein
structure
Primary protein structure
• Proteins are polymers of amino acid monomers. A
monomer is the simplest unit of a polymer. There are 20
amino acids in total.
• The primary sequence of a protein is the order in which
the amino acids are synthesised by translation into the
polypeptide.
Zwitterion: amino acids
• Is a base as the N terminus is free to accept hydrogen ions from
solution.
• Is an acid as the C terminus is free to donate hydrogen ions.
• The charge on an amino acid and therefore a protein is pH
dependent.
Primary protein structure
• Interactive amino acids
• Peptide bonding
• Primary structure
Peptide bond formation
• A peptide bond is formed between the carboxylic acid (–COOH)
terminal of one amino acid and the amine (–NH2) terminal of
another.
• This is a condensation reaction as water is produced.
• As a result, all proteins have a carboxyl terminus (end) and an
amine terminus.
Secondary protein structure
• Hydrogen bonding along the backbone of the protein
strand results in regions of secondary structure called
alpha-helices, parallel or antiparallel beta-sheets or
turns. These cause the protein to have a threedimensional shape as the linear polypeptide backbone
begins to fold.
• Alpha-helices and beta-sheets
Alpha-helix
Hydrogen bonding between
the N–H and C=O groups of
every 3.5 amino acid
residues in the polypeptide
backbone.
Beta-sheet
Antiparallel
Parallel
Hydrogen bonding
between the N–H
and C=O groups of
the amino acid
residues in the
polypeptide
backbone.
Beta-sheet
Amino acids and R groups
• R groups are the residues or side chains of the 20
amino acids, which have different functional
groups.
1.
2.
3.
4.
5.
Positively charged, basic
Negatively charged, acidic
Polar
Hydrophobic, non-polar
Uncharged polar
• These functional groups give the protein its
function as they interact with each other and with
other structures associated with the protein.
Amino acids and R groups
• R groups
• R group properties test
Tertiary structure
• The polypeptide folds further into a tertiary structure.
• This conformation (shape) is caused by interactions between
the R groups.
1.
2.
3.
4.
5.
Hydrophobic interactions
Ionic bonds
Hydrogen bonds
Van der Waals interactions
Disulfide bridges.
• Prosthetic groups (non-protein parts) give proteins added
function.
Hydrophobic interactions
• Occur between non-polar R groups along the length of the
polypeptide.
• Folding of these regions occurs so that they form a central
hydrophobic core, separating non-polar hydrophobic R groups
from aqueous solution while the polar hydrophilic R groups
are expressed on the outside of the structure, free to interact
in aqueous solution.
• Hydrophobic sections of proteins are classically found
embedded in the phospholipid bilayer of a cell, while the
hydrophilic polar parts are free to interact with the
extracellular and intracellular solutions.
Hydrophobic protein domains
Ionic bonds
• Charge dependent attraction occurring between
oppositely charged polar R groups, eg between the
amino acids arginine and aspartic acid.
• pH affects ionic bonding and results in denaturation of
the protein at extremes of pH as the H+ and OH– ions in
solution interact with the charge across the ionic bond.
Hydrogen bonds
• Hydrogen bonding is a weak polar interaction that occurs when an
electropositive hydrogen atom is shared between two
electronegative atoms.
• Hydrogen bonding is charge dependent.
• pH affects hydrogen bonding and results in denaturation of the
protein at extremes of pH as the H+ and OH– ions in solution interact
with the charge across the hydrogen bond.
Ionic and hydrogen bonds
Van der Waals interactions
• Weak intermolecular force between
adjacent atoms.
• Geckos and Van der Waals forces.
Disulfide bridges
• Covalent bonds that form between adjacent cysteine
amino acids.
• These can occur within a single polypeptide (tertiary
structure) or between adjacent polypeptides (subunits,
quaternary structure).
Prosthetic groups
• These are additional non-protein structures that are
associated with the protein molecule and give it its final
functionality.
• Examples:
1. chlorophyll (magnesium centre), responsible for light
capture in photosynthesis
2. haem (iron centre), found in red blood cells in
haemoglobin and responsible for oxygen carriage.
Chlorophyll
Haem
Tertiary structure
• Tertiary structure review
Human pancreatic lipase
Quaternary structure
• Quaternary structure exists in proteins with several
connected polypeptide subunits.
• These subunits are held together by all of the
interactions listed in the tertiary structure.
• Quaternary structure review
• Immunoglobulins
• Keratin
Haemoglobin: four subunits and
four haem groups
Effects of temperature and pH
• Temperature increases the kinetic energy of the protein molecule,
placing stress on bonds and breaking them. The weaker
intermolecular bonds are particularly susceptible: Van der Waals,
hydrogen bonds and ionic bonds.
• Changes in pH affect the concentration of H+ and OH– ions in
solution. This in turn changes the relative charge of the protein and
places stress on polar interactions such as hydrogen bonding and
ionic bonding.
• This results in the denaturation of the protein and the loss of tertiary
structure and function.
• Denaturation review
Hydrophobic and hydrophilic interactions
• The R groups at the surface of a protein determine its
location within a cell.
– Protein trafficking animation of Golgi apparatus.
– Protein transport animation and the enzymes involved.
Pepsin structure: globular protein
Make notes using these questions
1.
2.
3.
4.
5.
6.
7.
8.
9.
Draw the structure of an amino acid molecule. Label the key parts.
Draw a diagram to show how amino acids become joined together. Explain why
this is called a ‘condensation’ reaction. What would the opposite reaction by
called?
Amino acid R-groups are described as hydrophilic or hydrophobic. What does this
mean?
Draw a table to show the four levels of protein structure. Include descriptions
and diagrams.
Bonding is extremely important in protein structure. Describe the types of bonds
that would be found at each level of protein structure. Which of these are ionic
and which are covalent?
How does the type of chemical bonding that occurs in a protein affect its
function?
Explain why protein molecules embedded in cell membranes often contain high
numbers of hydrophobic R – Groups.
What is a prosthetic group? Give an example.
Not all proteins have a quaternary structure. Explain why.
The fluid
mosaic model
of membrane
structure
The fluid mosaic model of
membrane structure
1.
2.
3.
4.
5.
6.
7.
8.
Phospholipid
Cholesterol
Glycolipid
Sugar
Intrinsic transmembrane
protein
Intrinsic glycoprotein
Intrinsic protein
anchored by a
phospholipid
Extrinsic glycoprotein
Mitochondria animation for
membrane proteins. Discuss
hydrophobic and hydrophillic
interactions, and ATP synthase.
The fluid mosaic model of
membrane structure
• Regions of hydrophobic R groups allow strong
hydrophobic interactions that hold integral proteins,
those embedded in the membrane, within the
phospholipid bilayer as they are free to interact with the
hydrophobic tails of the phospholipids.
• Some integral proteins are transmembrane and cross
the phospholipid bilayer, for example:
– channel proteins: facilitated diffusion and active transport
– transporters: sodium potassium pump
– receptors: G-proteins.
The fluid mosaic model of
membrane structure
• Peripheral/extrinsic proteins have fewer hydrophobic R
groups interacting with the phospholipids.
• Peripheral/extrinsic proteins are responsible for cell–cell
interactions:
– cell recognition and the immune system
– junctions such as desmosomes and tight occluding junctions
between adjacent cells in tissue are essential for the
maintenance of multicellular organisms
– HIV and cell recognition.
HIV and surface
proteins
Junctions
between
cells
Think
• What are the functions of protein in a cell?
• Why is protein structure important?
• Why do organisms usually live within a narrow range of
temperature and pH?
• If eukaryotic cells are identical in structure relative to their
cellular components why do organisms look different?
• How can a gecko stick to Perspex?
• How do multicellular organisms stay together?