Evals10

SUBJECT: BIOCHEMISTRY TOPIC: EVALUATION #10 Set B (Recombinant DNA and Nutrition 1) LECTURER: DR. UY and Prof. Torres DATE: MARCH 2011

Question #:

Correct Answer:

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A. DNA Ligase + ATP

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A. Somatic Gene Therapy

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C. mRNA

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BONUS

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D. All of the choices

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C. Western Blot

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C. Plasmid

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D. All of the above C. Screening of DNA in the library or on gel D. All of the above D. Restriction fragment length polymorphism B. Degrade foreign DNA that enters the bacterium C. Make staggered double strand cut…..

Explanation: DNA Ligase covalently attaches a free 5' phosphate to a 3' hydroxyl and ATP for energy. DNA polymerase is for elongation. Telomerase is an enzyme for providing telomeres for cell division (telomeres are sequence in a DNA that is removed every cycle of division - parang fuel siya ng car). Recombinase are enzyme promoting DNA recombination and is not for joining DNA fragments. SGT is when the therapeutic genes are transferred into the somatic cells of a patient(for treating); Germ-line gene therapy corrects them invitro/in embryo; cloning creates a copy; Genetic engineering is the modifying/manipulation of certain genes (remember GMO?) Reverse transcriptase uses mRNA (messenger RNA) to synthesize cDNA (complemantary DNA); ssDNA is Single stranded DNA, dsDNA is double stranded DNA both are not used by Reverse transcriptase cDNA library contains only complementary DNA molecules synthesized from mRNA; this complementary DNA has already undergone posttranslation modification removing all unnecessary sequences like introns, promoter sequence, etc. Primarily, cDNA is composed mostly, if not all, of exons or sequences that is functional when expressed. Western blot is used to identify proteins; Northern blot is used for probing RNA; Southern blot is for DNA Plasmids can be good cloning vectors because they carry an origin of replication and are therefore able to replicate independently. Plasmid also is very easy to isolate, abundant (easy to grow) and cheaper. All can be used as a host for recombinant DNA technology. Selfexplanatory Probes are single stranded NA used to hybridize with a target DNA. Usually they are marked radioactively so they can easily be identified. Blood, Bone, egg cell as well as other things from the body (hair, sperm, nails etc.) can be used as a source of DNA or mRNA Mutations change the size of specific sequences in the genome. The different sizes may help in identifying one DNA from another using Southern blotting (DNA remember?). Restriction Fragment polymorphism is also unique to individuals just like fingerprints. PCR or plymerase chain reaction is technique for making new strands for usage in other techniques. cDNA is only a complementary DNA. REverse transcriptase is an enzyme that produces a DNA using mRNA as the primer. Restriction enzymes are made by bacterial cells to protect themselves against foreign DNA (such as viruses) by cutting it up into pieces. Bacterial cells modify their own DNA so that the restriction enzymes will not cut it. Remember that they are usually palindromes so they leave some 5' hanging so that it is complementary to the sticky end of the same site. Restriction enzymes do no cut at the same base pair. Restriction enzymes are also cut at specific sites and can only be annealed by that restriction enzyme only.

BIOCHEMISTRY Evaluations 10 Set B

SUBJECT: BIOCHEMISTRY TOPIC: EVALUATION #10 Set B (Recombinant DNA and Nutrition 1) LECTURER: DR. UY and Prof. Torres DATE: MARCH 2011

Portruding. 14 15 16

D. Transformation … CaCl2 B. Probe A. DNA is amplified at many points w/in….

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B. TCCGA

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C. Vector

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A. 5' GTG 3'

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A. RNA

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A. Normal

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D. All of the above

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C. 4

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A. Tetracycline

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B. Ampicillin resistant

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Heatshock + CaCl2 would make the bacterial cell unstable enabling the entrace of the plasmid into it. Electrophoresis is not always succesful. Infection with a bacteriophage has too many risks and can impede the procedure or experiment. Look at number 9 for definition of probe They are usually amplified at one point to be able to recreate copies of the specific gene. It is not a palindrome. Palindromic sequences are sequences that when reversed is complementary to the original sequence. Example is TTCGAA which has a complement of AAGCTT.\ Vector: Small DNA used for recombinant DNA technology – accessory chromosome, can replicate but not part of host’s genome The Normal DNA (Hb-A) uses Glu which is GAG and in the Hb-S this is Val which is 5' GTG 3' Northern blotting is used for RNA Unlike the mother and the father who carry the gene at 376, the baby does not carry it hence the baby will be normal. Prenatal diagnosis, newborn screening and carrier (heterozygote) detection can use recombinant DNA for human genetic testing. Tip: the father is usually very different from the mother (they aren't related kasi) and the children will probably share DNA samples from the mother and the father so look for one that is completely different from the father. The plasmid although primarily encoded to be resistant to ampicillin and tetracylcin was introduced to PstI which cut the plasmid at a single site in the ampicillin-resistant gene so it will only be tetracycline resistant. Because it was cut at a single site in the ampicillin-resistance gene.

Lac Z is used to determine if the plasmid contains the DNA. White = present, blue = none. It is grown on antibiotic containing-x-gal medium and so it is blue as it is not ampicillin resistant. C. 3' C A G G A First you write down the sequence from 5' to 3' (bottom to top) then get it's G T T 5' complementary strand so that it's 3' - 5' Dna polymerase is the enzyme for the elongation of the sequence, while dNTPs are the source of nucleotides to add in the sequence. ddNTPS (ex. D. ddTTPs are ddATPs and ddGTPs) are used to terminate elongation. In this case since the 3' end is adenosine the ddNTP used is ddATP as oppposed to ddTTP. automated sequencing method as the name implies uses only one reaction A. one tube for efficieny and faster way of determining the sequence. VNTRs are used for testing of individuals like parental testing (since VNTRs are unique to individuals). Hybridization is a process of complementation and not an actual technique for comparison. Western blotting is a specialized B. Microarray technique for determining protein in a sequence. Microarray is the best answer since it is a specialized technique for comparing patterns of expression in two different cell types like a normal and cancerous cell. C. blue

BIOCHEMISTRY Evaluations 10 Set B

SUBJECT: BIOCHEMISTRY TOPIC: EVALUATION #10 Set B (Recombinant DNA and Nutrition 1) LECTURER: DR. UY and Prof. Torres DATE: MARCH 2011

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C. Reducing the intestinal time thus reducing contact… B. can be synthesized by the body in sufficient amts. D. they yield more calories per gram when oxidized D. it contains all the essential amino acids B. negative nitrogen balance B. It is caused by prolonged excessive lack… calories C. Milk A. It is the cheapest source of energy for Filipinos B. Linoleic Acid C High Protein diet C. 2000 - 2300 kcals A. Carbon dioxide and oxygen C. Fatty acids with double bonds in the cis….raise… D. 2200 C. About 15%

Fiber is not digested and it usually passes through the GIT largely intact so there intestinal transit time is reduced since it does not spend time being absorbed etc. while carrying it carcinogens and colonic mucosa along with it. Essential nutrients are supplied b the diet but non-essential nutrients can be synthesized by the body example of which is carbohydrades (cheap and readily available ika nga.) Remember the 4, 4, 9, 7. Fats yield 9 kcal when oxidized but it is not the primary source of energy. The higher the value o the dietary protein, the higher its ability to supply the essential amino acids required for the body. The standard used is the Protein Digestibility Corrected Amino Acid Scoring which is based on the profile of essential amino acids and the digestibility of protein. Catabolism > anabolism = negative nitrogen balance (less nitrogen); Anabolism > catabolism = positive nitrogen balance (nitrogen produced); catabolism = anabolism = equilibrium. Kwashiorkor is due to protein deficiency and not caloric deficiency. It is characterized by hypoalbuminemia, anemia, edema, pot belly, depigmentation of the skin, loss of hair/chage of hair to red and bulky stool. PDCAAS or protein digestablity-corrected amino acids is the standard by which to evaluate protein quality. Milk has 1.00 value in PDCAAS, suggesting that milk is a very good source of protein. 1.00 means that it contains all the essential amino acids.

Since Filipinos are rice eaters, it is the most readily available source.

Palmitic acid and Stearic acid are saturated FA while Arachidonic acid is a Polyunsaturated-omega-6 FA. Kidneys reabsorb protein but if its function is impaired, it will have difficulty reabsorbing protein hence a high protein diet is not appropriate. The energy intake should be more or less proportional to the energy requirement per day to be able to carry out normal body functions. Indirect calorimetry calculates heat prodction based on respiratory gases measured over a unit of time> Oxygen consumption and CO2 production. Correct: Fatty acids with double bonds in the TRANS configuration raise plasma cholesterol levels (kaya nga transfat eh!) (289 x 4) >carb + (70 x 9) >fat + (110 x 4) >protein = 2200 cals The patient's caloric intake is adequate having 2200 calories a day. The

BIOCHEMISTRY Evaluations 10 Set B

SUBJECT: BIOCHEMISTRY TOPIC: EVALUATION #10 Set B (Recombinant DNA and Nutrition 1) LECTURER: DR. UY and Prof. Torres DATE: MARCH 2011

of the calories are derived from the proteins. 46

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D. Lignin C. Patient on impending thyroid storm B. Hypoalbumine mia

patient also conforms to the recommended guidelines for her diet having an increased amount of protein since she is pregnant. The answer is C since 440 calories produced by the protein in the diet represent about 20% of the daily caloric intake. Lignin is a complex polymer; the chief constituent of wood other than carbohydrates; binds to cellulose fibers to harden and strengthen cell walls of plants while dextrins, glycogens and starches are available carbohydrates and can be used by the body. A growing child, a recovering person and a pregnant woman would manifest with a POSITIVE NITROGEN BALANCE. Low protein; Albumin = Protein; HYPOalbuminemia

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C. Ketosis

Inadequate carbohydrates will make the body look for other energy sources which will be in the form of Fats and Proteins. If this happens, there will be an increase in ketone bodies hence ketosis

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C. RQ of less than 1 suggests starvation

RQ < .70 means fat is converted to carbohydrate; RQ> 1 means fat synthesized from carbohydrate; Any RQ greater than 1 indicates net synthesis of fatty acids and triglycerides.

BIOCHEMISTRY Evaluations 10 Set B