This document discusses protein classification and structure. It defines protein classification as grouping proteins based on structure, function or size. Proteins can have domains and subunits. They come in globular, fibrous, and other shapes. Proteins are linked within and between polypeptide chains using covalent bonds. Proteins bind other molecules specifically through interactions like ionic bonds. Binding allows proteins to regulate activity and form complexes with other molecules like opsins.

1. Protein classification
Lecture 8
Chapter 4 (end)

2. Definition -
protein classification
• Grouping of similar proteins based on
their structure, function, or size
– Globular vs filamentous vs helical
– Cataytic vs structural
– Small vs large vs very large

3. Protein Subunits & Domains
• A single polypeptide may have regions
along its length that fold up separately -
domains
• More than one polypeptide coming
together to form a protein - subunit

4. 04_20_protein domains.jpg

5. 04_21_Serine proteases.jpg

6. 04_22_protein subunit.jpg

7. 04_23_asymmetrical as.jpg

8. Protein - shapes
• Globular proteins - polypeptide folds tightly
together on itself - most enzymes
• Fibrous proteins - elongated structure - span
great distances - hair - keratin
– Many subunits attached together
– Actin & collagen
– Strong & rigid (Collagen - ligaments)
– Strong & flexible (elastin - skin)

9. 04_24_complexstructure.jpg

10. 04_26_spherical shell.jpg

11. Proteins linked together
• Domain to domain links (same P’)
• Protein to protein links (between P’s)
• Covalent bonds used to stabilize
• Disulfide bond most common
– Cysteine AA
– No impact of final shape, but stabilze

12. 04_29_Disulfide bonds.jpg

13. Proteins Bind
• Biological properties of proteins result from
interactions with other molecules
– Antibodies, enzymes, structure, etc
• Binding is always very specific
• Ligand - anything that is bound by a protein
• Ligand binding is by ionic bonds only
• Many ionic bonds required to stabilize link -
matching configurations needed - specificity

14. 04_30_selective binding.jpg

15. Proteins - Binding
• A ligand binds to a protein at a binding site
• A protein may have more than one binding
site
– It may bind the same ligand many times or it may
bind different ligands
• Ligands can bind to regulate the activity of
the protein
• Interior amino acids have a say in the
conformation of the molecule too.

16. Proteins - pair with other
molecules
• Some biologically active molecules are
a result of a very cozy relationship
– Rhodopsin & Opsin
• Retinal (a light sensing pigment) + opsin
protein
• Haem (Fe containing molecule) + globin protein

17. Opsin

18. Sample EXAM (Quiz)
Questions
Quiz 1
(Difficulty factor [1-10] = 6)

19. The smallest unit of life is a(n)
(a) DNA molecule.
(b) cell.
(c) organelle.
(d) virus.
(e) protein.

20. For each of the following sentences, fill in the blanks with the best word or phrase selected
from the list below. Not all words or phrases will be used; each word or phrase should be
used only once.
Cells can be very diverse: superficially, they come in various sizes, ranging from
bacterial cells such as Lactobacillus, which is a few ___ micrometer(s) __ in length,
to larger cells such as a frog’s egg, which has a diameter of about one ______
millimeter _______. Despite the diversity, cells resemble each other to an astonishing
degree in their chemistry. For example, the same twenty ____ amino acids ______
are used to make proteins. Similarly, the genetic information of all cells is stored in
their ____ DNA __________. Although _______ viruses _____ contain the same
type of molecules as cells, their inability to reproduce themselves by their own efforts
means that they are not considered living matter.
amino acids viruses
DNA millimeter(s) yeast
fatty acids plants
meter plasma membranes

21. DNA differs from RNA in
(a) the number of different bases used.
(b) the number of phosphates between the sugars in the
sugar-phosphate backbone.
(c) the kind of sugar found in the sugar-phosphate
backbone.
(d) one of the purines used.
(e) the chemical polarity of the polynucleotide chain.

22. Which of the following statements about the basic chemistry of
cells is TRUE?
(a) All cells contain exactly the same proteins.
(b) All proteins are constructed from the same 22 amino
acids.
(c) The genetic instructions in all cells are stored in DNA.
(d) All organisms contain the same genes.
(e) All of the above

23. A. What sets the limit on the size of structure that can
be seen in a light microscope?
The wavelength of light
B. Why are tissues usually cut into thin sections
and stained before examination under a light
microscope? Most tissues are not
transparent enough to be examined directly in a light
microscope. Transparency is increased by slicing them
into thin sections, and staining shows the different
cellular structures in contrasting colors.

24. The most reliable feature distinguishing a eucaryotic cell from
a procaryotic cell is the
(a) presence of a plasma membrane.
(b) presence of a nucleus.
(c) eucaryotic cell’s larger size.
(d) presence of DNA.

25. Circle the appropriate cell type in which the listed structure or molecule can be
found. Note that the structure or molecule can be found in more than one type of
cell.
Structure or Molecule Cell Type
A. DNA animal plant bacterial
B. nucleus animal plant bacterial
C. plasma membrane animal plant bacterial
D. chloroplast animal plant bacterial
E. cell wall animal plant bacterial
F. lysosome animal plant bacterial
G. mitochondrion animal plant bacterial
H. Golgi apparatus animal plant bacterial

26. A. Write out the sequence of amino acids in the
following peptide using the full names of the amino acids.
Pro–Val–Thr–Gly–Lys–Cys–Glu
proline-valine-threonine-glycine-lysine-cysteine-glutamic
acid (or glutamate)
B. Write the same sequence using the single letter code
for amino acids. PVTGKCQ
C. According to the conventional way of writing the
sequence of a peptide or a protein, which is the C-terminal
amino acid and which is the N-terminal amino acid in the
above peptide? C-terminal is glutamic acid (or glutamate);
N-terminal is proline.

27. Which of the following statements about amino acids is TRUE?
(a) Twenty-two amino acids are commonly found in
proteins.
(b) Most of the amino acids used in protein
biosynthesis have charged side chains.
(c) Amino acids are often linked together to form
branched polymers.
(d) D- and L-amino acids are found in proteins.
(e) All amino acids contain an NH2 and a COOH
group.