BIOCH200 Lecture Notes - Lecture 1: Activation Energy, Stereospecificity, Protein Structure

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skycaribou653

24 Nov 2017

School

University of Alberta

Department

Biochemistry

Course

BIOCH200

Professor

Jonathan Parrish

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Document Summary

With few exceptions, enzymes are proteins (typically globular). Biological catalysts that increasing the rate of reaction by 10^6 to 10^20 times. Highly specific and does not catalyse side or secondary reactions. What distinguishes enzymes from non-biological catalysts is that they can be regulated. Their structure is flexible and changing its shape changes its function: des(cid:272)ri(cid:271)e the stru(cid:272)ture of e(cid:374)z(cid:455)(cid:373)es a(cid:374)d state how it is sta(cid:271)ilized. Typically, globular proteins and their structure is stabilised by similar bonds in protein structure. Covalent, ionic, non-covalent, di-sulphide bridges, van der waals forces etc: tate what is (cid:373)ea(cid:374)t whe(cid:374) we des(cid:272)ri(cid:271)e e(cid:374)z(cid:455)(cid:373)es as (cid:862)spe(cid:272)ifi(cid:272). (cid:863) Some enzymes only act on a group of related substrates, some act only on one substrate, some are stereospecific meaning that they only act on one stereoisomer of that substance. Specificity does not allow the formation of toxic and wasteful by-products produced in side reactions: defi(cid:374)e the ter(cid:373) (cid:862)su(cid:271)strate. (cid:863)

Related Questions

________30. If you are investigating the inner structure of a new cell and see that it has a significantly larger amount of RER than other cells. You would conclude the cell does a great deal of____?
A. ATP synthesis

B. protein synthesis
C. DNA synthesis
D. active transport
E. polysaccharide hydrolysis

________31. If a cell comes in contact with a toxic substance such as H2O2, it could survive as long as it has a ___ to digest it.
A. DNA
B. peroxisome

C. mitochondria
D. phospholipids
E. intermediate filaments

________32. Some cells have structures to help them withstand osmotic pressure. For example,
A. Plant cells due to their walls
B. Animal cells due to the sodium/potassium pumps

C. Bacterial cell due to their swimming

D. Viruses due to their protein coats

________33. Evolution occurs only as a cell ____.

A. They undergo mitosis
B. Change in their gene pool
C. They move from one habitat to another

D. They begin to eat different foods

________34. Ribosomes are produced in the

A. nucleoli.
B. chromatin.
C. nuclear envelopes.

D. Golgi complex. E. cisternae.

________35. Algae are often green, but there are red and brown species also. What accounts for this difference in color?
A. The chlorophyll of chloroplasts
B. The pigments in other plastids

C. The presence of a mitochondria
D. The accumulation of cellular wastes

________36. The chloroplast and other like prokaryotes have which of the following that helps with photosynthesis?
A. They live in water based environments
B. They have chloroplasts in their cytoplasm

C. Change color in the dark vs. the sun
D. They have photoreceptor proteins in their membranes or mesosomes.

________37. Located in the membrane, we see a set of proteins called receptors that only connect with or bind to specific substances. This is called __.
A. ligand specificity.
B. hormone selectivity.

C. cell tonicity.
D. water saturation. E. signal resolution.

________38. Of the following statements, we could say that ___ is false.
A. All organisms are composed of cells and cell products.
B. An organism's structure and all of its functions are due to the activities of cells.
C. The cellular organelles are the simplest structural and functional unit of life.
D. Cells come from preexisting cells.
E. Cells are made from nonliving components including the nucleus, cell membrane and cytoplasm.

________39. If it is really true that our cells are the smallest anatomical unit that meets all of the properties of life, then which of the following could imply otherwise?
A. vacuoles
B. centrioles

C. Golgi apparatus
D. mitochondria
E. endoplasmic reticulum

________40. Oxygen is an absolute need for animal and plant cells alike due to the ___.

A. RER
B. Mitochondria
C. Lysosomes

D. DNA

________41. In a plasma membrane, we expect to see the carb/protein structures to extend into the ___, but the secondary messengers to move within the __.
A. extracellular fluid; cytosol
B. cytosol; extracellular fluid

C. intracellular fluid; cytosol

D. cytosol; intracellular fluid

E. extracellular fluid; plasma

________42. Bacteria are found in all of the following habitats:

A. Caves
B. Oceans
C. Animals

D. Everywhere on Earth

________43. Two solutions are separated by a selectively permeable membrane. Solution A has a higher concentration of an impermeable solute compared to solution B. Which of the following do you expect would happen?
A. solute will move from solution A to solution B

B. solute will move from solution B to solution A

C. water will more from solution A to solution B

D. water will move from solution B to solution A E. no movement of solute or water will occur

________44. In the kidney, we notice that almost all of the cells involved in the production of urine have high concentrations of the Na+/K+ pump. Which typically works to push Na+ ___ its concentration gradient by using ___.
A. up; active transport

B. up; facilitated transport
C. up; cotransport
D. down; active transport
E. down; facilitated transport

________45. In the charts of a patient recently admitted to the hospital noted that he was taking a medication called lithium and high doses of calcium supplements. Given this, we would expect the patientâs liver to have a higher than normal amount of __ to purify out the lithium and calcium.

A. lysosomes.
B. centrosomes.
C. mitochondria.
D. peroxisomes.
E. rough endoplasmic reticulum.

________46. We have long observed that our neural cells in the brain cannot replicate or replace themselves due to the lack of ____.
A. produce ATP.
B. divide.

C. produce enzymes.
D. secrete material across their plasma membrane E. conduct electrical signals.

________47. An organismâs structure and function is ultimately due to the structure and function of itâs __.
A. Organs
B. Tissues

C. Cells

D. Nuclei

The people of Malaysia belong to three communities: the local people called Malays, immigrants from South India called Tamils, and immigrants from China. During the early 20th century, the Malays lived mainly in coastal villages, the Tamils worked on rubber estates, and the Chinese worked in tin mines. In general, the people were very poor and they consumed a limited variety of foods.[1] Rice was the staple diet of all three communities and therefore the key source of caloric and nutrient content. Malays typically grew their own rice and dehulled it before consuming it; dehulling partially removes the aleurone layer of the rice seed. Following their South Indian food habits, the Tamils ate parboiled rice, and the Chinese ate polished white rice imported from Thailand. It was found that among the three Malaysian communities, the Chinese community was much more prone to suffer from some degree of sub-optimal thiamin intake. Out of every 1,000 Chinese inhabitants, about 120 had mild thiamin deficiency, about 80 had severe thiamin deficiency, and about 16 people had died of it. Suboptimal intake of thiamin was rare in Malays and was not reported at all in Tamils.[1] Thiamin, also called Vitamin B1, is required for all tissues, and its deficiency causes the disease Beriberi. Less severe deficiency results in non-specific symptoms such as weight loss, malaise, irritability, and confusion. Although the origin of the word Beri-beri is disputed, it is believed to be a Philippine word meaning âI canât, I canâtâ and was probably coined to refer to the lack of neuromotor coordination in people afflicted with this disease.[2] Thiamin is water-soluble and is stable in the acidic medium. It is unstable to heat, oxygen, and UV light in neutral and alkaline medium. The active form of thiamin is thiamin pyrophosphate (TPP). This active form is a cofactor for pyruvate dehydrogenase and transketolase enzymes that are involved in the metabolism of carbohydrates. These enzymes play an important role in the biosynthesis of a number of cell constituents such as neurotransmitters, pentoses, and reduced equivalents, used in oxidant stress. The human body cannot store thiamin and therefore requires a continuous supply of the vitamin. The thiamin in an individual on a thiamin-free diet typically depletes in fewer than two weeks. Thiamin absorption is affected by compounds, called thiamin antagonists or anti-thiamin factors, that alter the structure of thiamin. These compounds include alcohols, polyphenols, flavonoids, and thiaminase, a heat labile enzyme found in certain foods.[2] In affluent countries, where the diet is rich in thiamin, the most common cause of thiamin deficiency is excessive alcohol consumption. Alcohol intake affects thiamin status in two ways. First, alcoholics get a significant percentage of their daily energy intake from alcoholic beverages, which are nutrient deficient. In other words, alcoholics replace their consumption of nutrient dense foods that are part of their normal diet with the consumption of nutrient deficient alcohol. Second, alcohol inhibits the intestinal ATPase involved in the absorption of thiamin.[4] Sub-clinical thiamin insufficiency associated with excessive alcohol consumption produces an encephalopathy called Wernicke-Korsafoff syndrome. Patients with this syndrome have a higher than normal incidence of abnormal transketolase, which has a very low binding affinity to TPP. This problem can be overcome by putting patients on high-dose thiamin therapy. Some patients, however, might have a form of abnormal transketolase that does not bind at all with TPP. Such people do not respond to high-dose thiamin therapy.[4] Thiamin deficiency is observed in individuals who have low thiamin intake and a diet rich in polished rice, especially if their diet also consists of anti-thiamin factors such as tea, coffee, raw fermented fish, and betel nuts. The minimum amount of thiamin needed by the body can increase because of increased physiological or metabolic demands arising from pregnancy and lactation, heavy physical exertion, illnesses like cancer, liver diseases, hyperthyroidism, and surgery. Since TPP is required for carbohydrate metabolism, the recommended dietary allowances for thiamin are based on the assumption that its intake is related to total energy intake. The recommended dietary allowance in the United States is 0.5 mg/1000 Kcal.

Questions
1. Thiamin deficiency was observed only in the Chinese community even though all three
communities had the same staple (rice) diet. Explain.
2. On packages of enriched rice sold in supermarkets, the rice preparation directions state that the
rice should not be washed before cooking. Explain.
3. Severe metabolic acidosis caused by high levels of lactate is often associated with thiamin
deficiency. Explain.
4. Provide two plausible explanations for what might cause above normal levels of pyruvate in blood
and urine. How can one determine which of the two explanations is correct?
5. Why does thiamin utilization increase among cancer patients?
6. A negative correlation exists between the need for thiamin and the amount of fat in the diet.
Explain.

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BIOCH200 Lecture Notes - Lecture 1: Activation Energy, Stereospecificity, Protein Structure

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