AP Biology Protein Structure and Enzymes

Transcription

1 AP Biology Protein Structure and Enzymes

2 Connection to the Nitrogen-cycle Amino acids (protein) Nucleic acids (RNA and DNA) ATP

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4 1. Assimilation of nitrate by photosynthetic eukaryotes 2. Nitrogen fixation by prokaryotes 3. Denitrification by anaerobic prokaryotes

5 1. Assimilation of nitrate by photosynthetic eukaryotes D 2. Nitrogen fixation by prokaryotes A 3. Denitrification by anaerobic prokaryotes E

6 Amino acids (a.a.) are monomers of polypeptides (protein polymer) Amino group has Nitrogen R-groups have different properties: hydrophilic, hydrophobic, etc.

7 Why are these amino acids hydrophobic?

8 Why are these amino acids hydrophilic?

9 Two a.a. join with a peptide bond Dehydration synthesis: H 2 O is released

10 R-group R-group Carboxyl Amine Peptide Bond

11 1. Label the amino groups. 2. Label the carboxyl groups. 3. Label the R-groups. 4. Show how the two molecules would join together to form a peptide bond: 5. Show the molecule that would be released?

12 1. Label the amino groups. 2. Label the carboxyl groups. 3. Label the R-groups. 4. Show how the two molecules would join together to form a peptide bond: 5. Which molecule would be released? H 2 O

13 Primary Structure The unique a.a. sequence This model of the enzyme lysozyme is 129 a.a. long If left to chance, there are different ways to arrange the 20 a.a. into a chain this long The ordering is spelled out in the DNA of a gene

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15 Secondary Structure Coils = alpha helix Result of H-bonding Folds = beta pleated sheet Result of H-bonding

16 What is responsible for the secondary structure of proteins?

17 Tertiary Structure Irregular contortions (tweaking) caused by interactions between R-groups

18 Match the terms to the #s: hydrophobic interactions, hydrogen-bonding, ionic interactions, disulfide bridge

19 Quaternary Structure Two or more polypeptide subunits combine Ex. Collagen has 3 subunits, Hemoglobin 4

20 1. Specific order of amino acids 2: H-bonding resulting in alpha helix and beta pleated sheets 3. Other chemical bonds result in complex pattern of folding 4. 2 or more subunits come together to form finished product

21 1. energy is added, then: 2. Bonds become 3. Bonds 4. Atoms 5. New bonds 6. Matter is 7. Enzymes activation energy (see graph to the right)

22 1. Activation energy is added, then: 2. Bonds become _unstable 3. Bonds _break 4. Atoms rearrange 5. New bonds _form 6. Matter is conserved

23 1. Which number represents the amount of activation energy required without an enzyme? 2. With an enzyme? 3. Summarize the effect of an enzyme on activation energy? reactants products

24 Label your graph with the following: Reactants Products Activation energy without an enzyme Activation energy with an enzyme Change in free energy reactants products

25 Without enzyme With enzyme Reactants Change in free energy reactants products Products

26 1. Is this an exergonic or endergonic reaction? 2. Is this a catabolic or anabolic reaction? 3. Would G be positive or negative?

27 A catalyst is a substance that speeds up a chemical reaction without being consumed in the reaction. Enzymes are biological catalysts they lower activation energy. Enzymes are proteins, having a complex 3-D shape (4-levels of structure).

28 Sucrose Catabolic Enzyme: Sucrase Enzyme Enzyme

29 1. Where, specifically, in the body does sucrose (table sugar) digestion take place? 2. Describe how the structures called the villi and microvilli affect the surface area for nutrient Enzyme absorption: Sucrase 3. Describe the action of the enzyme sucrase on sucrose: 4. Explain how the enzyme (sucrase) and substrate (sucrose) fit together, using the vocabulary terms: lock-and-key, and induced fit.

30 The complex 3-D shape of the enzyme is critical to its function because of the lock-key-fit that is necessary for the enzyme s function Induced fit is like a clasping handshake the enzyme changes shape to grip the substrate

31 Enzyme-Cycle Diagram

32 1. Calculate the rate of reaction 0 10 min. 2. Calculate the rate of reaction min. 3. Make a claim with justification for which represents V max :

33 1. Calculate the rate of reaction 0 10 min. (5.1 μm 0 μm)/(10 min. 0min.) = 0.51 μm/min. 2. Calculate the rate of reaction min. (8.6 μm 5.1 μm)/(20 min. 10min.) = 0.35 μm/min. 3. Make a claim with justification for which represents V max : 0 10 min. because the rate of 0.51 μm/min. is larger than 0.35 for min.

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36 Amount of Product Formed 1. Describe the rate at A - D 2. Explain the rate at A D 3. Calculate V max D C B A

37 Amount of Product Formed Slow rate due to lag-time substrate must be transported in, processed, and product transported out Rate zero because enzyme ran out of substrate Rate slows as substrate starts to run out Highest rate (Vmax) is steepest slope, between 5 and 20 min. because substrate is abundant: rate = 17.3 µmol/ml min.

38 Enzymes are, they speed up chemical reactions in biological systems. They lower, that is needed for molecules to react with one another. Catabolic enzymes act on substrates such that they:. For example lactase. Anabolic enzymes act on substrates such that they:. For example ATP synthase.

39 Enzyme Peroxidase Investigation Enzyme = peroxidase Found in peroxisomes membranous sack that buds off the ER and is full of digestive enzymes (the liver is rich in peroxisomes) Peroxidase performs the following chemical reaction: 2 H 2 O 2 2 H 2 O + O 2 Hydrogen peroxide is a byproduct of metabolism and it is highly-reactive and is thus a toxin that cells must eliminate.

40 We will use an indicator called guaiacol Guaiacol has a high affinity for oxygen in solution, it binds instantly to form tetraguaiacol, which is brownish, as O 2, the darker the color

41 Time (Min.) Observed Color (1 10) Baseline is used to establish a reference so we can compare treatments to infer an increase, decrease, or no change in rate. 1. Which time will serve as your baseline? Why? 2. Which variables could you manipulate to change the rate of reaction? Which would you hold constant?

42 Take one color measurement at baseline time for each of six test-tubes (ph 3, 4, 6, 7, 8, 10) The color chart can be used to infer increase, decrease, or no change in rate; this inference is called the relative rate of the reaction.

43 The darker (brown) the sample the more light is absorbed (absorbency goes up)

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45 ph above or below optimal will break Hydrogen and ionic bonds, causing the enzyme to denature.

46 1. Describe the relationship between ph and reaction rate for pepsin 2. What is the optimal ph for each enzyme? 3. Suggest why there is this difference:

47 Describe & explain how the reaction rate is changing form A, to B, to C: A B C

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51 1. What is the optimal temp. for humans enzymes? 2. Why is this the optimal temperature? 3. What is the optimal temperature for heat-tolerant bacteria? 4. Why is this the optimal temperature? 5. Why is there a difference in optimal temp. between the two organisms shown?

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53 Substrate was exhausted This scenario does not assume a large excess of substrate

54 Cofactor = nonprotein enzyme-helpers Some are inorganic such as metal atoms: zinc, iron, copper Some are organic (called coenzymes) most vitamins are examples of coenzymes

55 Enzyme Inhibitors Resembles substrate Toxins & poisons often act as irreversible enzyme inhibitors: sarin gas, DDT, penicillin But, inhibition also helps to regulate (control) enzyme activity (which is good)

56 Allosteric enzymes (protein) can experience a 3-D shape change May be turned on (active) or off (inactive) in this way

57 Regulation of Enzyme Activity Tryptophan = a.a. After meal, supply (demand for construction ) Rapid response by feedback inhibition Tryptophan inhibits the first enzyme in the pathway Between meals: supply & demand and the pathway is active making Tryptophan