Download File

Biology 12
Assignment #1: Biological Molecules & the Chemistry of Life
A. Important Inorganic Molecules
Water
1.
Explain why water is considered a polar molecule.
The partial negative charge of the oxygen and the partial positive
charge of the hydrogen create separation of charge.
2.
What holds a water molecule together? A covalent bond
What type of bond holds several water molecules together? Hydrogen
bond
Where will this bond form? Between the “O” of one water molecule
and the “H” of another water molecule
How would you describe this type of bond? a strong intermolecular
force (between 2 molecules). Its not stronger than ionic or covalent
but stronger than other intermolecular forces (London force or dipoledipole forces)
3.
List 4 functions of water in the body. Give an example of each
function.
-acts as a solvent- helps to break down substances for transport in
blood
-lubricates- surrounds food when traveling down the esophagus
-temperature buffer- hydrogen bonds absorb energy without affecting
temperature
-cohesive/ adhesive- when blood (55% water) travels it pulls the blood
behind it because of the hydrogen bonding
Biology 12
Acids and Bases
4.
Give the major characteristics of an acid and relate acids to the pH
scale. Acids release a hydrogen ion (H+) when dissolved in water. pH
of acids will be less than pH of 7
5.
Give the major characteristic of a base and relate bases to the pH scale.
Bases release a hydroxide ion (OH-) when dissolved in water. pH of
acids will be greater than pH of 7
6.
How many more H+ (in terms of concentration) would there be in a
solution of pH3 than in a solution of pH8? pH is based on a logarithm
(x10) scale. Every level of pH you go up you multiply it by 10
ex) 3 to 4 = x10, 3 to 5 = x100, 3 to 8 = x 100 000
Buffers
Hemoglobin in red blood cells acts as a buffer by preventing a drop in
pH of the blood. It is a tertiary protein that bonds to iron, which gives it
its red hue when carrying oxygen.
7.
a. Give another example of a buffer
Bicarbonate (HCO3-) can take a H+ ion to create H2CO3 to increase the
pH
b. What makes this buffer effective? The H2CO3 can also release the
H+ to lower the pH
B. Some Important Organic Molecules
Look at the dehydration and hydrolysis reactions in order to answer the following
questions
8. Look carefully at the bonds formed during synthesis of a large molecule. Water is
produced, where does it come from (be specific)? The OH- from one molecule
and the H+ from the other molecule come together to create water (lose water =
dehydration)
9.
When the reaction is reversed (hydrolysis) water is needed. What are the 2 roles
water molecules play in this reaction? The water breaks apart the molecule into 2
molecules. The water also breaks apart and the OH- is added to one molecule
while the H+ is added to the other side.
Biology 12
Proteins
10. Although many proteins are enzymes, there are many other types of proteins in
our bodies. Give 4 other types of proteins (HEATS: acronym to remember types)
and their role in living things.
Hormones- messengers in the body ex) Insulin sends a signal to the liver to store
glucose
Enzymes- speed up chemical reactions ex) lactase enzyme speeds up the break
down of lactose sugar
Antibodies- involved in the immune response. They target specific foreign bodies
Transport- carry substances throughout the body ex) Hemoglobin carries oxygen
to the cells
Structural- help build the parts of the body ex) collagen in lips/ joints
11. Draw the structural formula of a typical amino acid. Circle the amino group,
acid group and remainder (side chain). Label them.
12. Why are there twenty types of R groups?
There are 20 different amino acids so there needs to be 20 different R groups
13. What is the difference between the amino acid cysteine and the amino acid
alanine, be specific. Think “R-Group” (you will have to look this up).
Cysteine’s R-group is CH2-SH while Alanine is CH3
14. Diagram the joining of 2 amino acids together through dehydration synthesis to
form a dipeptide with a peptide bond. Highlight the peptide bond.
Biology 12
15. a)
When does a polypeptide become a protein? tertiary structure
b) Where does this occur in a cell (think protein synthesis from bio 11)?
in the cytoplasm
16. Describe the four structures proteins can assume in terms of what they are made
of and the bonds holding them together. Make a sketch (very simple), for each,
labeling relevant bonds.
Primary- linear chain of amino acids joined by peptide bonds
Secondary- Alpha helix or Beta Sheets created by hydrogen bonds
Tertiary- Multiple Alpha and beta folded and joined by ionic, covalent or disulfide bonds
Quaternary- multiple polypeptides joined together
Biology 12
17. What is meant by protein denaturation and what is its significance in living
organisms (specifically enzymes). The bonds that allow the protein to fold break
and the protein unravels. This protein loses its function
Carbohydrates
18. By looking at a structural formula of a molecule, how would you know you were
looking at a carbohydrate? CH20 ratio
19. How is a monosaccharide converted to a disaccharide? Give examples. What is
the molecular formula for glucose?
dehydration reaction…C6H12O6
20. How are monosaccharides converted to polysaccharides?
Dehydration reaction to create a disaccharide then another dehydration reaction to
create 3, 4, 5 etc
21. Distinguish between starch and glycogen and sugars (e.g. sucrose). Why is
glucose such an important molecule?
Starch and glycogen are both polymers of glucose. Glycogen is highly branched.
Glucose is used in cellular respiration which produces ATP
22. How would you distinguish a cellulose molecule from a starch molecule? Why
is cellulose indigestible? cellulose uses alternate bonding while starch is on the
same side. Humans do not have the cellulose enzyme
Biology 12
Lipids
23. Explain how a neutral fat (triglyceride) is synthesized (created).
3 dehydration reactions to join 3 fatty acids to the glycerol (3 water molecules
created)
24. Explain how a neutral fat (triglyceride) is hydrolyzed (broken apart). Hydrolysis
reaction…3 water molecules used
25. Define what saturated and unsaturated fats mean. A “C – H” bond is considered
energy rich. How much more energy do fats carry per gram than carbs? You will
have to look this on up
Saturated- single bonds only. Maximum number of hydrogens
Unsaturated- double bonds as well.
26. Compare trans unsaturated fats to unsaturated fats and explain why one is more
healthy than the other. The double bond of trans fat causes a linear molecule to
be created unlike the unsaturated which kinks. These contribute to “low-density
lipoprotein levels” which clog arteries and can lead to heart attack or stroke
Phospholipids
27. Differentiate between a lipid and a phospholipid (phosphate group)
28. Where are phospholipids found in our body? The cell membrane, vesicles,
lysosomes
Steroids
29.
a. What is the base molecule of steroids? 4 fused carbon rings How are
steroids different from other lipids? function and structure
b. Where are they made in the cell? SER In the body? Testes, ovaries,
kidneys
c. List 2 examples of steroids. Cholesterol, testosterone
Biology 12
Nucleic Acids
DNA, RNA & nucleotides- we will be going into more detail with these polymers in the
future but you must know their basic structure and function now
30. What molecules make up the DNA backbone? Phosphate and deoxyribose sugar
Are they the same in RNA? no…phosphate and ribose sugar
31. What are the 3 components of a nucleotide? phosphate, pentose sugar, nitrogen
base
32. Which nitrogen bases are complimentary in DNA? A-T, G-C In RNA? A-U, G-C
33. Sketch a molecule of ATP and describe its structure. Adenine base, ribose sugar
and 3 phosphate molecules
34. What process produces ATP? Cellular Respiration How many ATP molecules
can be made from a single glucose molecule? 36-38 Gross…30-34 Net
35. Why is ATP the “energy currency” of the cell? All cells use ATP for energy
36. Copy out the ATP cycle. Since this is a cycle what does this tell you about this
molecule? It is recycled not destroyed
37. How does our body use ATP? Breaks off a phosphate to release energy
ENZYMES: BIOLOGICAL CATALYSTS
38.
What is the general role of enzymes? To speed up chemical reactions How do
they aid digestion? Allow molecules to be broken down so they can be absorbed
39.
To what group of biological molecules do they belong? Proteins
Biology 12
40.
What process in the cell synthesizes enzymes? Protein synthesis
41.
What is the name for the reaction type that includes all digestive reactions?
Hydrolytic
42.
Explain thoroughly why the reaction is called hydrolysis, and as part of your
answer make a diagram as given in Fig. 6.6, Pg. 107. Use a dipeptide as the
substrate, Label the active site, substrate (and its name), the actual enzyme for
dipeptide digestion, and its source in your diagram. Also label:
enzyme/substrate complex, products induced fit, “lock & key fit”, H2O, H+, OH-,
and hydrolysis.
43.
Describe what an active site is and why it is significant (lock and key)? The area
of the enzyme where the chemical reactions takes place. It has a specific shape
that a specific substrate match (lock and key)
44.
What is meant by the term “optimal temperature”? (don’t simply use the word
“best”, but rather explain why it is the best temperature) Temperatures that are
too low cause the active site to shrink…lock and key and induced fit will be
affected. Temperatures that are too high can cause the active shape to expand and
no longer fit the substrate
45.
What is meant by the term “optimal pH”? (as above). The specific pH that the
enzyme works the best. If pH fluctuates it affects the active site and may cause
the enzyme to denature. no function
46.
Will an enzyme catalyze a reaction if its active site is deformed? (i.e. if the
enzyme is said to be denatured). Why? No, Lock and key fit and induced fit no
longer available
47.
Name 2 ways that an enzyme could become denatured. Just did…see above
48.
Once denatured, can an enzyme regain its 3D shape? Not likely. The folding
process is very specific while a protein is being produced.
Biology 12
49.
What do COFACTORS do? How do they work? They are vitamins or minerals.
They bind to the allosteric site on enzymes and change the shape of the active site
so it BETTER fits the substrate
50.
What is the name of organic cofactors? vitamins
51.
Contrast competitive and non-competitive inhibitors
Competitive inhibitors bind to the active site and prevents the substrate from
joining. No enzyme action.
Non-competitive inhibitors bind to the allosteric site of the enzyme which
changes the shape of the active site so it no longer fits the substrate. No enzyme
function