TugasTersstruktur Biologi Molekuler 2013 |1

TUGAS TERSTRUKTUR BIOLOGI MOLEKULER 2013 SEBELUM UTS KELAS D

NO NIM NAMA MAHASISWA TEXTBOX Learning Outcome (LO) 1. menjelaskan TEXTBOX di depan dosen setelah diskusi dengan TA paling lambat KAMIS, 21 Maret 2013, Jam 16.00 WIB 2. menuliskan dan megirimkan penjelasan TEXTBOX setelah menjelaskan di depan dosen ke hendropram@facebook.com paling lambat KAMIS, 28 Maret 2013, Jam 22.00 WIB.

B1J011088

ASRI NUR RATRI

LO 09: menjelaskan bagaimana kehidupan diarahkan oleh empat basa nitrogen LO 10: menjelaskan sentral dogma biologi molekuler

Life is directed by four nitrogenous bases: adenine (A), guanine (G), cytosine (C), and thymine (T). (15.1) The flow of genetic information is from DNA to RNA to protein, via the processes of transcription (TC) and translation (TL). This concept is known as the Central Dogma of molecular biology. (15.2) Nucleic acids are polymers composed of nucleotides; DNA is deoxyribonucleic acid, RNA is ribonucleic acid. (17.1) In DNA the bases pair A T and G C; this complementary base pairing is the key to information storage, transfer, and use. (18.1) Three important types of RNA are ribosomal RNA (rRNA), messenger RNA (mRNA), and transfer RNA (tRNA). (19.1) The gene is the basic unit of genetic information. Genes are located on chromosomes at a particular genetic locus. Different forms of the same gene are known as alleles (20.1) Genes have several important regions. A promoter is necessary for RNA polymerase binding, with the transcription start and stop sites defining the transcriptional unit (21.1) Genes in prokaryotes tend to be grouped together in operons, with several genes under the control of a single regulatory region (21.2) Eukaryotic genes tend to be more complex than prokaryotic genes and often contain intervening sequences (introns). The introns form part of the primary transcript, which is converted to the mature mRNA by RNA processing (22.1). The codon/anticodon recognition event marks the link between nucleic acid and protein. (25.1) Prokaryotic genes are often regulated in response to external signals such as nutrient availability (25.2)

B1J011090

RYAN PRATAMA

B1J011092

ANI SETIANI

LO 11: menjelaskan struktur DNA dan RNA

B1J011094

NOOR SHIVA SARI

LO 11: menjelaskan struktur DNA dan RNA

B1J011098

KUSNO VIARINI

LO 11: menjelaskan struktur DNA dan RNA

B1J011100

BOENGA NUR CITA

LO 12: menjelaskan organisasi gen

B1J011102

AHMAD IDRIS

LO 13: menjelaskan anatomi gen

B1J011104

PUSPA OKTARIANI

LO 14: menjelaskan struktur gen prokariotik

B1J011106

RANI AZIZAH

LO 15: menjelaskan struktur gen eukariotik

10

B1J011110

DINI ASTRIANIS M

LO 16: menjelaskan ekspresi gen LO 17: menjelaskan regulasi ekspresi gen prokariotik

11

B1J011112

DEVINA ANDAYANI

TugasTersstruktur Biologi Molekuler 2013 |2 LO 18: menjelaskan regulasi ekspresi gen eukariotik LO 19: menjelaskan pengertian genom LO 20: menjelaskan ukuran dan kompleksitas genom LO 21: menjelaskan organisasi genom eukariotik
Eukaryotic genes are often regulated in response to signals generated from within the organism (25.3) The genome is the total complement of DNA in the cell (27.2) Eukaryotic genomes may have a range of different types of repetitive sequences (28.1)

12

B1J011114

SURINIH BAMBANG PRADIYANTO SITI ZULAIKHA

13 14

B1J011116 B1J011118

Genome sequencing has greatly improved our understanding of how genomes work (29.2) Analysis of the transcriptome and LO 22: menjelaskan proteome provides useful information about which genes a cell 16 B1J011122 JOVINA FEBE SUSWATI transkriptom dan is expressing at any given time proteom (30.1) 1. menjelaskan TEXTBOX di depan dosen setelah diskusi dengan TA paling lambat KAMIS, 28 Maret 2013, Jam 16.00 WIB 2. menuliskan dan megirimkan penjelasan TEXTBOX setelah menjelaskan di depan dosen ke hendropram@facebook.com paling lambat KAMIS, 4 April 2013, Jam 22.00 WIB. Cells have to be opened to enable LO 23: menjelaskan nucleic acids to be isolated; opening cells should be done as gently as 17 B1J011124 ADVEN KRISTIANTI tahapan isolasi DNA possible to avoid shearing large dan RNA DNA molecules (35.1). Once broken open, cell preparations can be deproteinised and the nucleic acids purified by a range of LO 24: menjelaskan MIFTAHUL RIZAL techniques. Some applications 18 B1J011126 cara purifikasi DNA dan require highly purified nucleic acid SUSENO RNA preparations; some may be able to use partially purified DNA or RNA (35.2).

15

B1J011120

STENI DWIYANTI

19

B1J011128

RISNA WAHYUNINGSIH

LO 25: menjelaskan cara pengukuran kemurnian dan konsentrasi asam nukleat LO 26: Menjelaskan cara pemekatan asam nukleat LO 27: menjelaskan jenis label dan cara pelabelan asam nukleat LO 28: menjelaskan aplikasi pelacak radioaktif LO 29: menjelaskan prinsip hibridisasi asam nukleat LO 30: menjelaskan prinsip elektroforesis gel dan tipe gel yang digunakan dalam elektroforesis LO 31: menjelaskan prinsip sekuensing

Solutions of nucleic acids are used to enable very small amounts to be handled easily, measured, and dispensed (35.3). Nucleic acids can be concentrated by using alcohol to precipitate the DNA or RNA from solution; the precipitate is recovered by centrifugation and can then be processed as required (36.1). Radioactive isotopes are often used to label nucleic acids, although they are more hazardous than nonradioactive labelling methods (38.1). Radioactive probes are very useful for identifying specific DNA or RNA sequences (38.2). The simple base-pairing relationship between complementary sequences has very far-reaching consequences both for the cell and its functioning and for the scientist who wishes to exploit this feature (39.2). Separation of biomolecules by gel electrophoresis is one of the most powerful techniques in molecular biology (40.1). The principles on which DNA sequencing is based are fairly simple; the procedures required to

20

B1J011130

ASA DAYAH FEBRIANI

21

B1J011132

DEVI FATKULJANAH

22

B1J011134

SEPTI TRISNO ANGGRAINI

23

B1J011136

IRAWATI YASMIN

24

B1J011138

ANDY ROMAETA FITRIANI

25

B1J011140

BUNGA KHALIDA PURI

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achieve the desired result are rather more complex (43.1). Two rapid sequencing techniques were developed in the 1970s: the LO 31: menjelaskan chemical method and the enzymatic 26 B1J011144 SUFRAHA ISLAMIA prinsip sekuensing method. Modern DNA-sequencing DNA technologies are based on the enzymatic method (43.2). The strategy employed to tackle large-scale sequencing projects LO 32: menjelaskan depends on a number of factors, but 27 B1J011146 ANWAR ROVIK preparasi fragmen essentially comes down to a choice DNA between the ordered and shotgun approaches (44.1). 1. menjelaskan TEXTBOX di depan dosen setelah diskusi dengan TA paling lambat KAMIS, 4 April 2013, Jam 16.00 WIB 2. menuliskan dan megirimkan penjelasan TEXTBOX setelah menjelaskan di depan dosen ke hendropram@facebook.com paling lambat KAMIS, 11 April 2013, Jam 22.00 WIB. Restriction enzymes act as a protection system for bacteria in LO 36: menjelaskan that they hydrolyse exogenous DNA 28 B1J011148 SINDI LUKITASARI enzim restriksi that is not methylated by the host modification enzyme (51.1) Restriction enzymes are named SYARIF MAULANA LO 36: menjelaskan according to the bacterium from 29 B1J011150 YUSUF enzim restriksi which they are purified (52.1). Different restriction enzymes generate different ranges of DNA LO 36: menjelaskan fragment sizes; the size of fragment 30 B1J011156 HANIFAH KHOLID B. is linked to the enzim restriksi frequency of occurrence of the recognition sequence (52.2). One very useful feature of restriction enzymes is that they can generate LO 36: menjelaskan cohesive or sticky ends that can be 31 B1J011158 DEMAS PANCAR RIZKY used to join DNA from two different enzim restriksi sources together to generate recombinant DNA molecules (53.1). A physical map of a piece of DNA can be assembled by determining FITRI DIAH LO 37: menjelaskan where the restriction enzyme 32 B1J011160 recognition sequences are relative to PERMATASARI pemetaan restriksi each other; this is known as restriction mapping. (55.1). In addition to restriction endonucleases, there are several LO 38: menjelaskan other types of nuclease enzymes 33 B1J011162 PUTRI nuklease that are important in the manipulation of DNA (56.1). Not all nucleases are helpful! Ribonucleases can be a problem LO 38: menjelaskan when working with purified 34 B1J011164 QURROTU A'YUNIN preparations of RNA, and care must nuklease be taken to remove or inactivate RNase activity (57.1). Polymerases are the copying enzymes of the cell; they are also essential parts of the genetic MUHAMAD REZA LO 39: menjelaskan engineers armoury. These enzymes 35 B1J011166 PUTRATAMA polimerase are template-dependent and can be used to copy long stretches of DNA or RNA.(57.2). A modified form of DNA polymerase I called the Klenow fragment is a LO 39: menjelaskan useful polymerase that is used 36 B1J011168 HABIBAH SUCIATI polimerase widely in a number of applications (58.1). Reverse transcriptase is a key KHAIRINA FEMILIANI LO 39: menjelaskan enzyme in the generation of cDNA; 37 B1J011170 the enzyme is an RNA-dependent YUDIAWAN polimerase DNA polymerase, which produces a

DNA

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DNA copy of an mRNA molecule (58.2). In many applications it is often LO 40: menjelaskan enzim yang digunakan necessary to modify the ends of DNA molecules using enzymes such 38 B1J011172 IIK NURFAGY untuk memodifikasi as phosphatases, kinases, and ujung DNA transferases.(58.3). DNA ligase is essentially molecular glue; with restriction enzymes, it LO 41: menjelaskan provides the tools for cutting and 39 B1J011174 OPIK TAOFIK MUFLIH DNA ligase joining DNA molecules.(59.1). 1. menjelaskan TEXTBOX di depan dosen setelah diskusi dengan TA paling lambat KAMIS, 11 April 2013, Jam 16.00 WIB 2. menuliskan dan megirimkan penjelasan TEXTBOX setelah menjelaskan di depan dosen ke hendropram@facebook.com paling lambat KAMIS, 18 April 2013, Jam 22.00 WIB. Gene cloning utilises the LO 42: menjelaskan sel characteristics of living systems to propagate recombinant DNA 40 B1J008105 ASEP SETIADI inang yang digunakan molecules; in essence this can be dalam kloning gen considered as a form of molecular agriculture (63.1). Gene cloning is achieved by using a vector (carrier) to propagate the LO 43: menjelaskan vektor yang digunakan desired sequence in a host cell. Choosing the right 41 B1J009011 MUKHLISAL IBRAHIM dalam kloning gen vector/host combination is one of the critical stages of a cloning procedure (63.2). The bacterium Escherichia coli is the most commonly used prokaryotic LO 44: menjelaskan sel host cell, with a wide variety of 42 B1J009019 NADIA AYUNINGTHIAS different strains available for inang prokariotik particular Applications (65.1). Microbes (such as yeast) and LO 45: menjelaskan sel mammalian cell lines are two examples of eukaryotic host cells 43 B1J009040 LUCKY ARDIYANTI inang eukariotik that have become widely used in gene manipulation (66.1). Plasmids are extrachromosomal LO 46: menjelaskan genetic elements that are not vektor plasmid yang essential for bacteria to survive but 44 B1J009107 IKA APRIANI often confer advantageous traits digunakan dalam sel (such as antibiotic resistance) on the iang E. coli host cell (66.2). pBR322 is a very famous plasmid and has all the essential LO 46: menjelaskan requirements for a cloning vector vektor plasmid yang relatively small size, useful 45 B1J009111 SHEVITA DWI YANI digunakan dalam sel restriction enzyme sites, an origin of iang E. coli replication, and antibiotic resistance genes (68.1). Multiple cloning sites LO 46: menjelaskan (polylinkers) increase the vektor plasmid yang flexibility of vectors by providing a 46 B1J009161 M ANDRI KURNIAWAN digunakan dalam sel range of restriction sites for cloning inang E. coli (69.1). Plasmid vectors have an upper size limit for efficient cloning, which can LO 46: menjelaskan sometimes restrict their use where a vektor plasmid yang large number of clones is required. 47 B1J009174 ROIHATUL JANNAH In this case it makes sense to clone digunakan dalam sel longer DNA fragments, and a inang E. coli different vector system is needed (69.2). Bacteriophages are essentially LO 47: menjelaskan bacterial viruses and usually consist vektor bakteriofaga of a DNA genome enclosed in a 48 B1J009179 NAILI CAHYANI yang digunakan dalam protein head (capsid). As with other sel inang E. coli viruses, they depend on the host cell

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for their propagation and do not exist as free-living organisms (71.1) Bacteriophage has played a major role in the development of bacterial genetics and molecular biology. In addition to fundamental aspects of gene regulation, has been used as the basis for a wide variety of cloning vectors (72.1). A range of plasmid-based vectors for the yeast Saccharomyces cerevisiae was developed from the naturally occurring yeast 2m plasmid (81.1). Vectors for use in plant and animal cells have properties that enable them to function in these cell types; they are often more specialised than the basic primary cloning vectors such as (82.1). Artificial chromosomes are elegantly simple vectors that mimic the natural construction of chromosomal DNA, with telomeres, a centromere, and an origin of replication in addition to features designed for ease of use, such as selectable markers (83.1).

49

B1J009194

YULLI WAHYU MAHENDRA

LO 48: menjelaskan vektor bakteriofaga yang digunakan dalam sel inang E. coli LO 49: menjelaskan vektor yang digunakan dalam sel inang eukariotik LO 49: menjelaskan vektor yang digunakan dalam sel inang eukariotik

50

B1J009195

WASMID

51

B1J010212

PRIHANTO ARIF HIDAYAT

52

B1J010226

MILA AFRIYANI

LO 50: menjelaskan kromosom artifisial