Basics of Biological Macromolecules and Cellular Signaling

1. Inside peroxisomes are specialized reactions forming HYDROGEN PEROXIDE as a byproduct. How are peroxisomes involved in fat metabolism?
Peroxisomes catalyse a large variety of different cellular functions of which most have to do with LIPID METABOLISM. Peroxisomes cooperate with the mitochondria for FATTY ACID OXIDATION, converting FAT to ATP. 

2. What is a general summary of what happens in the mitochondria?

Endoxidation of carbohydrates, fatty-acid oxidation, O2 consumption, ATP synthesis by oxidative phosphorylation

3. What happens in the nucleolus?

Synthesis of ribosomal RNA, assembly of ribosomal units

4. What happens in the nucleus?

DNA and RNA synthesis.

5. What happens in the ER and Golgi?

‘Secretory Pathway’, synthesis of membrane lipids, membrane proteins,
and secreted proteins.

6. What happens in the cytoplasm?

Initial catabolism of monosaccharides; storage of glycogen and fat

7. In a 75kg adult, the composition of (%):

Water is – 60

Protein – 16
Triglyceride (fat) – 13
Inorganic salt, insoluble – 5.5
Membrane lipids – 2.5
Carbohydrates – 1.5
Inorganic salt, soluble – 0.7
Nucleic acids – 0.2

8. What is basic make up of cytoskeleton?

ACTIN MONOMERS joined together to form

9. What is the main advantage to most biomolecules forming polymers?


10. Polymerizaion involves what type of reaction?

Dehydration / Condensation (remove water)

11. Peptide bonds are what type of bonds?

COVALENT (this is why it is hard to break them)

12. What reaction is needed to break bonds?

HYDROLYSIS (add water)

13. What are the 4 types of macromolecules?

Proteins, Carbohydrates, Lipids, Nucleic Acids (DNA, RNA)

14. How are amino acids joined together?
Peptide bonds

15. What else is needed for peptide bonds to form? 


16. What are essential amino acids? What are the names?
Cannot be synthesized in the body – get them from our diet.

A HILL Makes People Think TVomit. or PVT TIM HALL

A: Arginine
H: Histidine
I: Isoleucine
L: Leucine
L: lysine
M: Methionine
P: Phenylalanine
T: Threonine
T: Tryptophan
V: Valine

17. What are the non-essential amino acids? What are their names?

Our bodies are able to synthesize them. 

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18. What are the four parts of an amino acid?


BASIC amino group – NH2
ACIDIC carboxyl group – COOH
Side chain – R-group

19. The pH of an amino acid depends on what?

Its location

12. Areas of high concentration of H ions will cause them to want to move where?
Area of lower concentration of H ions.

13. A lower pH would mean more what?
H ions

14. An amine is BASIC – also known as what form?

Deprotonated form

15. An amoonium salt is the CONJUGATE ACID – also known as what?

Protonated form

(There are TWO DIFFERENT FORMS of every amino acid)

If you change the pH of an amino acid, it can act as a buffer. The level
of protonation affects pH.

16. Concerning the general protonation of amino acids, what would we see for

CATION – a low pH (e.g., 1.0)
ANION – a high pH (e.g., 11.0)
ZWITTERIONS – carries both a pos and neg charge (e.g., 6.1)

17. What is the pH of blood?

18. What basic trend do we see in a titration curve?

As you raise the pH, you add OH, and remove H. All free form
H ions will run to OH, forming H2O. The isoelectric point (pI), sometimes abbreviated to
IEP, is the pH at which a particular molecule or surface carries no net electrical charge.

19. What are the amino acid class names, and members?

Aliphatic (straight chain, no phenol rings)
Glycine, Alanine, Valine, Leucine, Isoleucine

Hydroxyl or Sulfur/Selenium-containing
Serine, Cysteine, Selenocysteine, Threonine, Methionine


Aromatic (have phenol rings)
Phenylalanine, Tyrosine, Tryptophan

Basic (fall on higher end of pH scale)
Histidine, Lysine, Arginine

Acidic and their Amide (very acidic, fall on lower end of pH scale)
Aspartate, Glutamate, Asparagine, Glutamine

19. What is very special about the three HYDROXYL amino acids, SERINE, THREONINE-and TYROSINE?
They have a OH group, and thus can be phosphorylated, (can add a P group to OH) part of CELL SIGNALLING.

20. The small amino acids, and the branched chain acids are from what group?


21. What are the two sulfur amino acids?

22. What is unique about CYSTEINE?
Can form disulfide bonds. Cysteine-cysteine

23. What is unique about methionine?
It is the start codon for all amino acids. (It has NO disulfide bonds)

24. What is unique about PROLINE (alpha amino acid)? What type of amino acid is it?
CYCLIC. It can allow proteins to change conformation, and bend.

25. What do you call a protein that phosphorylates another protein?
Kinase – a phosphate group is transferred from ATP and put on another protein.
Remember – only three amino acids can do this…

26. Which of the stereoisomers (amino group moves to the other side), L and D forms can be used in protein synthesis?

The L-form

27. Synthesis of NON-essential amino acids (the ones we can make) depends on what process?
Transamination (transaminase) – exchange of one side chain for another, a reversible RXN

– It depends on the formation of appropriate alpha-keto acids.

28. So…what is the keto acid precursor of the amino acid ALANINE?
Pyruvic acid

29. What serves as the radical storehouse for the above reaction?
Glutamine (Glutamine swaps its amino group for pyruvic acid’s hydroxyl group)

– Remember: for glutamine and pyruvic acid to natrually mix together, might take years!
But with transaminase….much faster!

The players:

Glutamine, Pyruvic Acid, TRANSAMINASE, 
a-Ketoglutamic acid, Alanine

30. How are peptide bonds formed?
The CARBOXYL group of one amino acid connects to the AMINO group of another amino acid.

(dehydration reaction)

31. Do PEPTIDE CHAINS exhibit polarity?
The begining is the amino terminus (methionine)
The end is a carboxyl terminus

32. What should you know about the PRIMARY structure of proteins?
– Not useful for the cell in this form
– It will try to stabilize itself by forming a secondary structure.

33. What should you know about the SECONDARY structure of proteins?
– H bonds are weak
– C bonds are important for maintaining its structure
– Amino acid bonds help to maintain its conformations
– like a SLINKY

34. What should you know about the TERTIARY form of proteins?
– This is usually the final shape
– outside is hydrophillic, inside is hydrophobic
– This is the MONOMER form of the protein
– They fold up to escape the water

35. What should you know about the Quaternary form of proteins?
– Made up of multiple tertiary sub units/monomers/many polypeptides together

Tubulin is normally a dimer in its natural form…two monomers stuck together
Phosphodiester bonds are covalent

36. In carbohydrates, what is the ratio of C-H-O?
1:2:1 e.g., C6H12O6

37. In monosaccharides, different sugars are rearrangements of the same chemical components.

What is the relationship of MANNOSE to GALACTOSE?
Mannose is a C2 epimer of glucose, whereas Galactose is a C-4 epimer.

38. What type of bonds hold monosaccharides together?

Glycosidic bonds (99% of glucose is in a ring structure)

39. Glucose and glucose form what?
What type of bond?
Maltose, alpha (1-4) glycosidic bond

40. What happens when you have glucose and glucose but a beta (1-4) glycosidic bond?
You get celloboise, a type of cellulose, which is NOT usable b/c of the type of bond.
– we do not have the same enzyme cows have to eat grass!

41. How about having the same beta (1-4) glycosidic bond as above, but this time with a
galactose and glucose molecule?
Lactose, this time it is useable b/c we have this enzyme.

42. How about glusocse and fructose?
This time, we get sucrose, but have an alpha-beta (1-2) glycosidic bond.

The direction of the glycosidic bond determines usability – 

can be converted to a usable form of energy.

Polysaccharides act as sites of GLUCOSE STORAGE, or as STRUCTURAL ELEMENTS

43. How many polysaccharides do OLIGOSACCHARIDES have?


44. How many polysaccharides do POLYSACCHARIDES have?

Dozens to thousands

You cannot store as much glucose as you can fat…

45. What makes up starch?

46. Where is glucose produced?

47. What do we know about AMYLOSE? What is its structure?
Where do we find it?
– Unbranched polymer of glucose
– Forms the starch granules in plants

48. What do we know about cellulose?
Where do we find it?
Unbranched polymer of glucose
– The most abundant biomolecule on earth

49. What do we know about glycogen?
– storage form of polysaccharides in animals
– note that this molecule is branched!

50. Basic components of DNA:
– sugar
– nitrogenous base
– phosphate

51. What sugar is important in glycosylation?

52. Four classes of lipids?
– Fatty acids (saturated and unsaturated)
– Glycerides
– Nonglyceride lipids (sphingolipids, steroids, waxes)
Complex lipids (Lipoproteins, glycolipids)

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