Biology Journal 9/25/2014

Describe this chemical reaction in as much detail as you can!

• Synthesis of two amino acids (aka monopeptides) into a dipeptide.

• Condensation (because it makes H2O out of the H and OH of the amino and carboxyl groups)

• Anabolism (because it is building a larger molecule• It’s making a peptide bond (the bond holding amino

acids to each other in proteins, aka polypeptides)

Schedule

Thursday: review for 2.4 and 2.5 QuizFriday: 2.4 and 2.5 QuizTuesday: 2.6 homework dueWednesday: Notebooks collected, for practice and evidence!

2.4 Proteins:  Proteins have a very wide range of functions in living organisms.

Nature of science: Looking for patterns, trends and discrepancies—most but not all organisms assemble proteins from the same amino acids.

Understandings:•Amino acids are linked together by condensation to form polypeptides.•There are 20 different amino acids in polypeptides synthesized on ribosomes.•Amino acids can be linked together in any sequence giving a huge range of possible polypeptides. Most organisms use the same 20 amino acids in the same genetic code although there are some exceptions. Specific examples could be used for illustration.•The amino acid sequence of polypeptides is coded for by genes.•A protein may consist of a single polypeptide or more than one polypeptide linked.•The amino acid sequence determines the 3-D conformation of a protein.•Living organisms synthesize many different proteins with a wide range of functions.•Every individual has a unique proteome.

Applications and skills:Application: Rubisco, insulin, immunoglobulins, rhodopsin, collagen and spider silk as examples of the range of protein functions.Application: Denaturation of proteins by heat or by deviation of pH from the optimum. Egg white or albumin solutions can be used in denaturation experiments.Application: Proteomics and the production of proteins by cells cultured in fermenters offer many opportunities for the food, pharmaceutical and other industries.Skill: Drawing molecular diagrams to show the formation of a peptide bond.

Aims:  Obtaining samples of human blood for immunological, pharmaceutical and anthropological studies is an international endeavour with many ethical issues.

Topic 2: Molecular biology (21 hours)

2.5 Enzymes:  Enzymes control the metabolism of the cell.

Nature of science: Experimental design—accurate, quantitative measurements in enzyme experiments require replicates to ensure reliability.

Understandings:•Enzymes have an active site to which specific substrates bind.•Enzyme catalysis involves molecular motion and the collision of substrates with the active site.•Temperature, pH and substrate concentration affect the rate of activity of enzymes.•Enzymes can be denatured.

Applications and skills:Application: Methods of production of lactose-free milk and its advantages. Lactase can be immobilized in alginate beads and experiments can then be carried out in which the lactose in milk is hydrolysed.

PRACTICALDesign of experiments to test the effect of temperature, pH and substrate concentration on the activity of enzymes. Students should be able to sketch graphs to show the expected effects of temperature, pH and substrate concentration on the activity of enzymes. They should be able to explain the patterns or trends apparent in these graphs.

Theory of knowledge:  Development of some techniques benefits particular human populations more than others. For example, the development of lactose-free milk available in Europe and North America would have greater benefit in Africa/Asia where lactose intolerance is more prevalent. The development of techniques requires financial investment. Should knowledge be shared when techniques developed in one part of the world are more applicable in another?

Topic 2: Molecular biology (21 hours)

Enzymes Enzymes (almost)(almost) always end in what always end in what 33 letters? letters?

ASEASE

Identify the parts for each of the letters.

State what kind of reaction is occurring in as much detail as you can.

A = SubstrateB = EnzymeC = Active siteD = Enzyme-substrate complexE = Products

This is the enzyme-catalyzed catabolic reaction of A into E’s. We can’t say if it’s hydrolysis (but, it might be)

What determines what the 3D shape of a protein will be?

The sequence of amino acids! These interact and fold up into the final enzyme shape.

Make a drawing of a generalized amino acid.

R group (could be 20 different things in human proteins)

Carboxyl(COOH)

Amine(NH2)

Alpha carbon(the middle C where the R group is attached)

What is a proteome?

Just like a genome is all of the genes an organism has (ATCG’s), a proteome is all of the proteins (sequence of amino acids) that an organism makes.

What is activation energy?

The energy required to start a chemical reaction. The activation energy converts the reactants into a transition state, which then progress to the products.

Activation energy is the energy which must be put into reactants to break some bonds to get a reaction started

Enzymes lower activation energy, making reactions happen faster.

These reactants (TNT) really want to be the products (a bunch of gasses). It just needs the activation energy to do the reaction….

Where does the activation energy come from?

An Explosive Example…

What does the protein insulin do?

Insulin is made by the pancreas. When blood-sugar is high, it is released and decreases the amount of glycogen (blood sugar) in the blood and stores it in the liver, or as fat.

Define what it means for a protein to denature.

TIME

Ene

rgy

in R

eact

ants

/Pro

duct

s

Start(reactants)

Intermediaries

Reaction Complete(products)

Activation Energy

Withoutenzyme

Withenzyme

What do enzymes have to do with activation energy?

This graph shows the enzyme activity (rate of reaction) for salivary amylase, which digests starches in the mouth.

1. Why is the highest rate at 38°C?2. Why does enzyme activity decrease rapidly

at temperatures higher than 38°C?

1. 38°C is the highest rate because the enzyme is optimized to operate fastest at normal human body temperature.

2. At temperatures higher than 38°C, the enzyme denatures.

Optimum Temperature

Reaction rate increases with

increase in temperature, as molecules move

faster

Amylase denatures, and quickly stops

facilitating chemical reaction

What does the protein

RuBisCO do?

RuBisCO (Ribulose-1,5-bisphosphate carboxylase/oxygenase) is a protein used in carbon-fixation (taking carbon from the atmosphere and making carbohydrates out of it). It is found in most plants, and autotrophic single-celled organisms. It’s probably the most abundant protein on Earth!

State the effect of pH on enzyme rate.

All enzymes have an optimal pH. Deviation from this results in the denaturaziation of enzymes, and thus a reduction in reaction rate.

How is lactose-free milk made?

1. Adding lactase to milk.

2. Running milk through an apparatus with immobilized lactase.

Note: This can be done to any substance to treat it with an enzyme!

Describe the lock and key model of enzyme function.

Enzymes are specific to one (although sometimes multiple) substrate. How?1. Structurally: the 3D shape of the active site matches the substrate2. Chemically: the polar / nonpolar parts of the active match the substrate

a. What kind of reaction is this?

b. Write out the reaction as words

c. Which are the reactants?

d. Which are the products?

+ +→ H2O

a. What kind of reaction? Anabolic Condensation

b. Write out the reaction as words: below

c. Which are the reactants? fructose, glucose

d. Which are the products? sucrose, water

+ +→ H2O

fructose + glucose → sucrose + water