Study Guide The Cell as Biochemical Machinery

PREFACE

The Block “The Cell as Biochemical Machinery” (CBM) has been designed for students at
the first semester in order to understand the concept about cells. Cell is the smallest unit of
the body; grouping with other substances to represent its products to form a bigger unit,
called body tissues. Cell is a protoplasm mass with a nucleus, which is lined by a
membrane. In particular condition, cell can make assimilation, growth, and reproduction.

In this Block, there are three main areas that have to be understood:
1. The structure and function of the cell including plasma membrane, transport of
various substances in cell membrane, receptors, organelles and inclusions, nucleus
and chromosomes, cytoskeleton, and cell cycle.
2. Introduction to biology molecular and its application in medicine, gene expression,
and signal transduction.

Beside these three areas, this Block also defines about the basic characteristics of cell, and
describes about some prominent individuals who have done cell researches, given in the
introductory lecture.

By understanding the concepts of cell, students are expected to have a sufficient basis for
continuing medical studies to further extend their knowledge and skills in the medical
sciences. By doing so, students will be able to keep update with the fast progressing
medical sciences and technologies and apply them properly in their future medical practice.

This Study Guide of “The Cell as Biochemical Machinery” (CBM) contains learning tasks to
be discussed by the students in the small group discussions and individually in order to
achieve the block objectives. Other than that, there are overviews of lectures, student
project to write and to present a paper, practice, items for self-assessment to evaluate
students’ understanding on the concepts.

The Block “The Cell as Biochemical Machinery” (CBM) is undertaken 10 days including
examination. Student-centered learning as the primary approach in the teaching-learning
activities with dynamic group discussions are facilitated by tutors. Individual learning on
campus and at home is also an important part of the learning process. To develop good
understanding of the CBM, learning activities will also be carried out as lectures and
practical works.

The Planner Team

CBM

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 Study Guide The Cell as Biochemical Machinery

TABLE OF CONTENTS

Preface..................................................................................................................... 1
Table of contents …………………………..……....................................................... 2
Curriculum content .................................................................................................. 3
Planners Team ........................................................................................................ 6
Lectures .................................................................................................................. 6
Facilitators ………………………………………………... ………............................... 7
Time Table Class A ……………………………………………………….................... 8
Time Table Class B……………………..………………………………………………. 10
Meeting of students representatives …………………………………………….……. 12
Plenary Session ………………………………………………………………………… 12
Assessment Method…………………………………………………………………….. 12
Student project ........................................................................................................ 12
Abstract ................................................................................................................... 13
Learning Task ……………………………………………………………………………. 21
Practice……………………………………………………………………………………. 26
Self Assessment …………………………………………………………………………. 27
References………………………………………………………………………………… 31
Assessment Form ……………………………………………………………………… 32
Curriculum Map…………………………………………………………………………… 33

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 Study Guide The Cell as Biochemical Machinery

CURRICULUM
THE CELL AS BIOCHEMICAL MACHINERY

Aims:
 To comprehend the molecular mechanisms underlying normal cell function and
disorders
 To apply basic cellular and molecular concepts and principles in dealing with clinical
disorders

Learning Outcomes:

1. Explain the structure of the plasma membrane and differentiate the transport
mechanism of various substances through plasma membrane.

2. Explain the general structure and function of cytoskeleton in relation to endocytosis,

pinocytosis, and locomotion.

3. Differentiate functionally cytoplasmic organelles from cytoplasmic inclusions.

4. Explain the general functional structure of cell nucleus.

5. Explain the principal mechanisms by which genes control general cell functions and
gene expression in normal cells.

6. Explain the energy metabolism of the cell and its clinical implications

7. Explain the signaling mechanism underlying cell to cell communication and its clinical or
practical implications

8. Summarize cell cycle and its clinical implications.

9. Explain applications of molecular biology in medicine

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CURRICULUM CONTENT

1. The Structure of the Plasma Membrane & the Transport Mechanism of Various
Substances
a. The molecular structure of plasma membrane
b. The transport mechanism of common substances (micro molecules) through the
plasma membrane
c. The practical and clinical implication of transport substances
2. Organelles and Inclusions
a. The basic concept of organelles & inclusion body
b. The general principle of post translation modifications on Rough Endoplasmic
Reticulum and Golgi Apparatus
c. The functional structure of the lysosomes, proteasomes, and peroxisomes
d. The mitochondria function underlying energy metabolism
e. The clinical implication of the function of proteasomes, peroxisomes, lysosomes,
and mitochondria
3. Cytoskeleton
a. The components of cytoskeleton
b. The mechanism of macromolecules crossing from extracellular to intracellular
c. The mechanism of cells product release from intracellular to extracellular
d. The common mechanisms of cell locomotion
e. The clinical implication of cytoskeleton disorders
4. Nucleus and Chromosomes
a. The major components of the cell nucleus
b. The structures that compose the nuclear pore complex
c. The structures that compose the nucleosome
d. The clinical implication of nucleus and chromosome disorders
5. Introduction to Molecular Biology
a. The basic concept of gene, genome, and central dogma
b. The functional structure of DNA & RNA
c. The molecular mechanism of genetic inherited
d. The clinical implication of DNA mutation
e. The various mechanism of DNA repair system
6. Gene expression
a. The function of three types of RNA
b. The definition of genetic code and codon
c. The mechanism of transcription
d. The mechanism of translation
7. Bioenergetics and oxidative metabolism
a. Mitochondrial electron transport system
b. Mechanism of ATP synthase
c. Oxidative phosphorylation inhibitors
8. Signal transduction
a. The signaling molecules (ligand)
b. The cell receptors
c. The variety pathways transduction signals from peripheral cytoplasm to the
nucleus by which stimulate inhibit.
d. The function of secondary and the third messenger.

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 Study Guide The Cell as Biochemical Machinery

9. Cell Cycle
a. The basic concept of the cell cycle
b. The two major events in cell cycle
c. The mechanism of the cell division
d. The mitotic and the meiotic cell division
e. The process of cell differentiation
f. The clinical implication of the cell division and cell differentiation disorders
10. Applications of Molecular Biology in Medicine
a. The implications of gene testing
b. The advantages of using recombinant vaccine compared with non-
recombinant/conventional
c. Reproductive cloning

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 Study Guide The Cell as Biochemical Machinery

PLANNERS TEAM

No Name Departement Phone

dr. I G K Nyoman Arijana, M.Si.Med
1 Histology 085339644145
(Pengelola Blok)
Prof.Dr.dr.I Nyoman Adiputra, MOH,
2 Physiology 0811397971
PFK,Sp.Erg.
4 dr. Wayan Surudarma, M.Si Biochemistry 081338486589

5 Dr. dr.Komang Januartha Putra Pinatih, Microbiology 08123831710

M.Kes

LECTURER
No Name Departement Phone
1 dr. IGK Nyoman Arijana, M.Si.Med Histology 085339644145
2 dr. Wayan Surudarma, M.Si Biochemistry 081338486589
3 dr. I Wayan Sugiritama, M.Kes Histology 08164732743
4 Dr. dr. Desak Made Wihandani, M.Kes Biochemistry 081338776244

5 Dr.dr.Komang Januartha Putra Pinatih, Microbiology 08123831710

M.Kes
6 Dr. dr. Ni Made Linawati, M.Si Histology 03518617765

7 Prof.Dr.dr.I Nyoman Adiputra, MOH, Physiology 0811397971

PFK,Sp.Erg.
8 Dr I G A Dewi Ratnayanti, M.Biomed Histology 085104550344
9 Dr. rer. Nat. dr. Ni Nyoman Ayu Dewi, Biochemistry 081337141506
M.Si
10 Dr. Ni Wayan Tianing, S.Si, M.Kes Physiotherapy 08123982504

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FACILITATORS
REGULAR CLASS

NO NAME GROUP DEPT PHONE VENUE

dr. Gede Putu Supadmanaba, 2rd floor:
1 S.Ked
A1 Biochemistry 082146558748
R.2.01
2rd floor:
2 dr. Yuliana, M.Biomed A2 Anatomy 085792652363
R.2.02
dr. I Dewa Ayu Inten Dwi 2rd floor:
3 Primayanti, M.Biomed
A3 Physiology 081337761299
R.2.03
2rd floor:
4 dr I Gde Haryo Ganesha S.Ked A4 DME 081805391039
R.2.04
Clinical 2rd floor:
5 Dr.dr. A.A Ngurah Subawa.,M.Si A5
Phatology
08155735034
R.2.05
2rd floor:
6 dr. Putu Aryani, MIH A6 Public Health 082237285856
R.2.06
2rd floor:
7 dr. IGK Nyoman Arijana, M.Si. Med A7 Histology 085339644145
R.2.07
2rd floor:
8 dr. Oka Negara, FIAS A8 Andrology 085935054964
R.2.08
2rd floor:
9 dr. I Made Krisna Dinata, M.Erg A9 Physiology 08174742566
R.2.22
2rd floor:
10 dr. Putu Yuliandari, S.Ked A10 Microbiology 089685415625
R.2.23

ENGLISH CLASS

NO NAME GROUP DEPT PHONE VENUE

dr. Ida Ayu Dewi Wiryanthini, 2rd floor:
1 M.Biomed
B1 Biochemistry 081239990399
R.2.01
2rd floor:
2 dr. IGA Dewi Ratnayanti, M.Biomed B2 Histology 085104550344
R.2.02
2rd floor:
3 dr. Agung Nova Mahendra, MSc. B3 Pharmacology 087861030195
R.2.03
2rd floor:
4 dr. I Gede Wirata, S.Ked B4 Anatomy 081239791628
R.2.04
2rd floor:
5 dr. I Putu Adiartha Griadhi, M.Fis B5 Physiology 081999636899
R.2.05
2rd floor:
6 dr. Luh Ariwati, S.Ked B6 Parasitology 08123662311
R.2.06
Clinical 2rd floor:
7 Dr.dr.I Nyoman Wande,Sp.PK B7 Phatology
08124686885 R.2.07
dr. Wayan Citra Wulan Sucipta 2rd floor:
8 Putri, MPH
B8 Public Health 087761838141
R.2.08
dr. I Wayan Gede Sutadarma, 2rd floor:
9 M.Gizi
B9 Biochemistry 082144071268
R.2.22
2rd floor:
10 dr. Made Agus Hendrayana, M.Ked B10 Microbiology 08123921590
R.2.23

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 Study Guide The Cell as Biochemical Machinery

TIME TABLE
CLASS A

Day/
Time Activity Venue Lecturers
date
1 08.00 – 10.00 PPKN C UPT. PPKB
Fri 10.00 – 12.00 SGD DR Facilitator
12.00 – 13.00 Lecture 1. The Structure of plasma C Adiputra
24 membrane & transport mechanism
Nov of various substances
17 13.00 – 13.30 Break
13.30 – 14.00 Independent learning
14.00 – 15.00 Plenary C Adiputra

2 08.00 – 09.00 Lecture 2. Organelles and Inclusions C Linawati

Mon 09.00 - 10.30 Independent Learning
10.30 – 12.00 SGD
27 12.00 – 12.30 Break
Nov 12.30 – 14.00 Student Project
17 14.00 – 15.00 Plenary C Linawati

3 08.00 – 09.00 Lecture 3. Cytoskeleton C Sugiritama

Tue 09.00 - 10.30 Independent Learning
10.30 – 12.00 SGD DR Facilitator
28 12.00 – 12.30 Break
Nov 12.30 – 14.00 Student Project
17 14.00 – 15.00 Plenary C Sugiritama

4 08.00 – 09.00 Lecture 4. Nucleus and chromosome C Arijana

Wed 09.00 - 10.30 Independent Learning
10.30 – 12.00 SGD DR Facilitator
29 12.00 – 12.30 Break
Nov 12.30 – 14.00 Student Project
17 14.00 – 15.00 Plenary C Arijana

5 08.00 – 09.00 Lecture 5. Introduction to molecular C Januartha

Thu biology
09.00 - 10.30 Independent Learning
30 10.30 – 12.00 SGD DR Facilitator
Nov 12.00 – 12.30 Break
17 12.30 – 14.00 Student Project
14.00 – 15.00 Plenary C Januartha

6 08.00 – 10.00 PPKN C UPT. PPKB

Fri 10.00 – 12.00 SGD DR Facilitator
12.00 – 13.00 Lecture 6. DNA mutation and repair C Wihandani
01 system
Dec 13.00 – 13.30 Break

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17 13.30 – 14.00 Independent learning

14.00 – 15.00 Plenary C Wihandani

7 08.00 – 09.00 Lecture 7. Gene expression C Surudarma

Mon 09.00 - 10.30 Independent Learning
10.30 – 12.00 SGD
04 12.00 – 12.30 Break
Dec 12.30 – 14.00 Student Project
17 14.00 – 15.00 Plenary C Surudarma

8 08.00 – 09.00 Lecture 8 Application of molecular C Ayu Dewi

Tue biology techniques in medicine
09.00 - 10.30 Independent Learning
05 10.30 – 12.00 SGD
Dec 12.00 – 12.30 Break DR Facilitator
17 12.30 – 14.00 Student Project
14.00 – 15.00 Plenary C Ayu Dewi

9 08.00 – 09.00 Lecture 9. Cell Cycle C Ratnayanti

Wed 09.00 - 10.30 Independent Learning
10.30 – 12.00 SGD
06 12.00 – 12.30 Break DR Facilitator
Dec 12.30 – 14.00 Student Project
17 14.00 – 15.00 Plenary C Ratnayanti

10 08.00 – 09.00 Lecture 10. Signal transduction C Wihandani

Thu 09.00 - 10.30 Independent Learning
10.30 – 12.00 SGD
7 12.00 – 12.30 Break DR Facilitator
Dec 12.30 – 14.00 Student Project
17 14.00 – 15.00 Plenary C Wihandani

11 08.00 – 10.00 PPKN C UPT. PPKB

Fri 12.00 – 13.00 DNA isolation and Clinical C Tianing
application of molecular biology
08 laboratory (Practicum)
Dec
13.00 – 16.00 Student Project - Lecturer
17

Mon
18 10.00-14.00 Assessment Team
Dec
17

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 Study Guide The Cell as Biochemical Machinery

TIME TABLE
CLASS B

Day/
Time Activity Venue Lecturers
date
1 08.00 – 10.00 Student Project DR Facilitator
Fri 10.00 – 12.00 PPKN C UPT. PPKB
13.00 – 14.00 Lecture 1. The Structure of plasma C Adiputra
24 membrane & transport mechanism
Nov of various substances
17 12.00 – 13.00 Break
14.00 – 15.00 SGD
15.00 – 16.00 Plenary C Adiputra

2 09.00 – 10.00 Lecture 2. Organelles and Inclusions C Linawati

Mon 10.00 – 11.30 Independent Learning
11.30 – 12.00 Break
27 12.00 – 13.30 Student Project DR Facilitator
Nov 13.30 – 15.00 SGD
17 15.00 – 16.00 Plenary C Linawati

3 09.00 – 10.00 Lecture 3. Cytoskeleton C Sugiritama

Tue 10.00 – 11.30 Independent Learning
11.30 – 12.00 Break
28 12.00 – 13.30 Student Project DR Facilitator
Nov
13.30 – 15.00 SGD
17
15.00 – 16.00 Plenary C Sugiritama

4 09.00 – 10.00 Lecture 4. Nucleus and chromosome C Arijana

Wed 10.00 – 11.30 Independent Learning
11.30 – 12.00 Break
29 12.00 – 13.30 Student Project DR Facilitator
Nov 13.30 – 15.00 SGD
17 15.00 – 16.00 Plenary C Arijana

5 09.00 – 10.00 Lecture 5. Introduction to molecular C Januartha

Thu biology
10.00 – 11.30 Independent Learning
30 11.30 – 12.00 Break
Nov 12.00 – 13.30 Student Project DR Facilitator
17 13.30 – 15.00 SGD
15.00 – 16.00 Plenary C Januartha

6 08.00 – 10.00 Student Project DR Facilitator

Fri 10.00 – 12.00 PPKN C UPT. PPKB
13.00 – 14.00 Lecture 6. DNA mutation and repair C Wihandani
01 system
Dec 12.00 – 13.00 Break

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 Study Guide The Cell as Biochemical Machinery

17 14.00 – 15.00 SGD

15.00 – 16.00 Plenary C Wihandani

7 09.00 – 10.00 Lecture 7. Gene expression C Surudarma

Mon 10.00 – 11.30 Independent Learning
11.30 – 12.00 Break
04 12.00 – 13.30 Student Project DR Facilitator
Dec 13.30 – 15.00 SGD
17 15.00 – 16.00 Plenary C Surudarma

8 09.00 – 10.00 Lecture 8 Application of molecular C Ayu Dewi

Tue biology techniques in medicine
10.00 – 11.30 Independent Learning
05 11.30 – 12.00 Break
Dec 12.00 – 13.30 Student Project DR Facilitator
17 13.30 – 15.00 SGD
15.00 – 16.00 Plenary C Ayu Dewi

9 09.00 – 10.00 Lecture 9. Cell Cycle C Ratnayanti

Wed 10.00 – 11.30 Independent Learning
11.30 – 12.00 Break
06 12.00 – 13.30 Student Project DR Facilitator
Dec 13.30 – 15.00 SGD
17 15.00 – 16.00 Plenary C Ratnayanti

10 09.00 – 10.00 Lecture 10. Signal transduction C Wihandani

Thu 10.00 – 11.30 Independent Learning
11.30 – 12.00 Break
7 12.00 – 13.30 Student Project DR Facilitator
Dec 13.30 – 15.00 SGD
17 15.00 – 16.00 Plenary C Wihandani

11 08.00 – 10.00 Student Project - Lecturer

Thu 10.00 – 12.00 PPKN C UPT. PPKB
DNA isolation and Clinical C Tianing
08 application of molecular biology
13.00 – 14.00
Dec laboratory (Practicum)
17

12
Mon
19 10.00-14.00 Assessment Team
Dec
17

Notes:
C : Class room ( Lecture Room 4.01, 4th floor)
DR : Discussion Room
SGD : Small Group Discussion (Discussion Room of west wing 2nd floor, room with
partitions no. 2.01, 2.02, 2.03, 2.04, 2.05, 2.06, 2.07, 2.08 and rooms no. 2.22 & 2.23 are
used interchangably between Class A and Class B).

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 Study Guide The Cell as Biochemical Machinery

MEETING

Meeting of the Student Representatives and the facilitators

The meeting between block planners team and the student group representatives
will be held on Friday,8nd December 2017, at 15.00 until 16.00 at Class room. In this
meeting, all of the student group representatives are expected to give suggestions and
inputs or complaints to the team planners for improvement. For this purpose, every student
group must choose one student as their representative to attend the meeting.

PLENARY SESSION

For each learning task, the student is requested to prepare a group report. The
report will be presentedin plenary session. Lecturer in charge will choose the group
randomly. The aim of this presentation is to make similar perception about the topic that
has been given.

ASSESSMENT METHOD

Assessment will be performed on 18th December 2017, 10.00 until 14.00 a.m for
both Regular class and English class. There are 100 questions for the examination that
consist of Multiple Choice Question (MCQ).
The borderline to pass exam is 70. The proportion of examination score are:
Small group discussion : 5%
Paper (student project) : 15%
Final exam (MCQ) : 80%

STUDENT PROJECT

Students have to write a paper with topics that has been given by lecturer. The topic
will be chosen randomly on day 1. Each small group discussion is consist of 2 paper with
different tittle. Therefore, 1 paper will be wrote by 5-7 students.Students can discuss about
content of paper with relevant lecturer. Students can discuss about format of paper
with respective facilitator. Students write a paper as student project and will be presented
in front of the class. The paper and the presentation will be evaluated by respective
facilitator and lecturer.

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 Study Guide The Cell as Biochemical Machinery

Format of the paper :

1. Cover  Tittle
Name
Student Registration Number

Faculty of Medicine, Udayana University 2017

2. Introduction
3. Content
4. Conclusion
5. References (minimal 3 references)
Example :
Journal
Porrini M, Risso PL. 2011. Lymphocyte Lycopene Concentration and DNA Protection from
Oxidative Damage is Increased in Woman. Am J Clin Nutr 11(1):79-84.
Textbook
Abbas AK, Lichtman AH, Pober JS. 2011. Cellular and Molecular Immunology. 4th ed.
Pennysylvania: WB Saunders Co. Pp 1636-1642.
Note.
5-10 pages; 1,5 spasi; Times new roman 12

Topic of Student Project

Regular and English Class

No SG Title Evaluator Date of
D presen
tation
1 A1 The effect of free radical on cell membrane Adiputra
2 A2 Intermediate filament and cancer diagnosis Sugiritama
3 A3 The Role of Microtubule Associated Protein Tau in Sugiritama
Neurological Functions and Diseases
4 A4 Lysosomaldisorders Linawati
5 A5 Ribosomal disorders Linawati
6 A6 Chromosomal aberrations in cancer Arijana
7 A7 The Effect of Free Radical on Nucleus Arijana
8 A8 The Effect of Glucose on Nucleus in tipe II DM Arijana
9 A9 The mutation of DNA Repair system and cancer Wihandani
10 A10 Telomerase and aging Wihandani
11 B1 Dogma central in molecular biology Januartha
12 B2 PCR in diagnosis of infectious diseases Januartha
13 B3 The role of calcium in nerve transmission Wihandani
14 B4 The role of DAG in signal transduction Wihandani
15 B5 The role of CDKs in cell cycle Ratnayanti
16 B6 The role of cyclin in cell cycle Ratnayanti
17 B7 The role of gene promoter in transcription process Surudarma
18 B8 Genetic codes Surudarma
19 B9 Methods for detection of DNA mutation in inherited Ayu Dewi
diseases
20 B10 Gene cloning and therapy Ayu Dewi

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 Study Guide The Cell as Biochemical Machinery

LEARNING PROGRAMS

Lectures

LEC. 1: The Structure of the Plasma Membrane & the Transport

Mechanism of Various Substances

Lecturer : Prof Adiputra

Objective : To understand the structure of plasma membrane
Abstract :

Every eukaryotic cell is covered by plasma membrane, which separates the extracellular
from the intracellular fluid. Plasma membrane is mainly composed of phospholipids bilayer,
protein and lesser amount of polysaccharide and cholesterol.
The functions of plasma membrane are maintaining cell integrity, as a barrier at membrane-
plasma and recognizing antigens.

Phospholipid Bilayer Membrane

Dominant phospholipids component of plasma membrane are phosphatidylcholine,
phosphatidylethanolamine, phosphate-dylserine and sphingomyelin. Other phopolipids e.g
inositol phospholipids, arachidonic acid phospholipids are present in lesser amount, even
though its have important functional value, phospholipids bilayer is said to be amphipathic
because it has hydrophilic, hydrophobic nature. Small uncharged and lipid molecules can
get through plasma membrane, it is called simple diffusion.

Protein Membrane
Protein of plasma membrane consists of integral protein (transmembrane protein/multipass
protein (fluid mosaic model) and peripheral protein. These proteins have role in selective
permeability as facilitated diffusion. Integral protein may function as channel protein, carrier
protein. Channel protein could adjust with the across hydrophilic molecule by forming polar
inner lining channel, which could be gated channel (ligand-gated channels, voltage-gated
channel and G-protein gated ion channel) and ungated channel.

Carbohydrate and Cholesterol Membrane

Polysaccharide molecule on the outer side of plasma membrane is called glycocalyx, can
inform of glycoprotein and glycolipid. It functions in protection.

Lecturer : Prof Adiputra

Objective: to understand the transport mechanism of various substances through
plasma membrane
Abstract :

Cell membrane separates cytoplasm (intacellular fluid) from its environment (extracellular
fluid). Both fluids consist of different substances which are maintained by the existence of
cell membrane. Its structure makes the transport of spesific substances occur to support cell
life.
There are two types of transport mechanism across the cell membrane i.e. passive transport
(diffusion) and active transport. The diffusion itself can be differentiated into simple diffusion
and facilitated diffusion, with its different mechanism. There are too many factors that can
affect diffusion, each of which must be learnt by the students. Active transport can be

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 Study Guide The Cell as Biochemical Machinery

divided inti primary active and with its own character including the substance to be
transported and factors that involve.
Transport across cell membrane can describe many physiologic processes that take place
in different parts of human cells such as intestine epithelium, renalis tubules epithelial,
exocrine glands epithel, gall bladder epithel and membrane of choroideus plexus in the
brain. All will be learnt in this topic.

LEC. 2: Organelles & Inclusion

Lecturer : dr. Ni Made Linawati, M.Si

Objective: to differentiate functionally cytoplasmic organelles from cytoplasmic
inclusions
Abstract :

The cytoplasm contains other organelles, which are better visualized with an
electron microscope that can view components as small as 2 nm. The organelles include
the nucleus, mitochondria, endoplasmic reticulum, Golgi apparatus, lysosomes,
peroxisomes, proteasomes, cytoskeleton, and plasma membrane.
Mitochondria contain a double membrane; with the inner membrane containing many
infolds, referred to as the cristae that contain the machinery for cellular respiration.
Mitochondria contain their own mitochondrial DNA and make proteins.The endoplasmic
reticulum (ER) consists of flattened sheets, sacs, and tubes of membranes throughout the
cytoplasm and is responsible for protein synthesis (rough ER) and lipid metabolism (smooth
ER and rough ER). The Golgi apparatus is a stack of flattened membranous sacs involved
in the modification and transport of molecules made in the endoplasmic reticulum. The
membrane-enclosed Lysosome contains enzymes required for intracellular digestion.
Peroxisomes are membrane-bound organelles in which hydrogen peroxide is generated and
degraded. Proteasomes responsible for proteolysis of malformed and ubiquitin-tagged
protein or antigenic protein have to be cleaved into epitopes.
Cytoplasmic inclusion is not always present in every cell. Glycogen is the polymer of
simple glucose. Blood glucose metabolized within cell to produce ATP or stored in the
glycogen vesicle.Lipid, stored in triacylglycerol form as various sizes of droplets whether as
a single and hugedroplet (lipocytes), or small and multiple consisted of ester cholesterol
(dominantly within cells that synthesized steroid hormones).Lipofuchsin pigmen is residual
bodies that unable to be digested by lysosomes, permanently in nature. The amount
become increasingly in number due to the increasing of life span and often existed in
nervous cell.

LEC. 3: Cytoskeleton

Lecturer : dr. Wayan Sugiritama, M.Kes

Objective : to understand the general structure and function of cytoskeleton in
relation to endocytosis, pinocytosis, and locomotion
Abstract :

The cytoskeleton is a dynamic three-dimensional structure that fills the cytoplasm,

acts as both muscle and skeleton. This structure maintains cell shape, protects the cell,

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 Study Guide The Cell as Biochemical Machinery

enables cellular motion (using structures such as flagella, cilia and lamellipodia), and plays
important roles in both intracellular transport (the movement of vesicles and organelles, for
example) and cellular division.
The long fibers of the cytoskeleton are polymers of subunits. The primary types of
fibers comprising the cytoskeleton are micro(thin) filaments, microtubules, and intermediate
filaments.

Thin filaments are fine, thread-like protein fibers, 6 nm in diameter, composed of two
intertwined chains of G-actin. Thin filaments are most concentrated just beneath the cell
membrane, and are responsible for resisting tension and maintaining cellular shape, forming
cytoplasmatic protuberances (pseudopodia and microvillus), and participation in some cell-
to-cell or cell-to-matrix junctions. Thin filaments are also important for cytokinesis (formation
of the cleavage furrow) and, association with myosin responsible for muscle contraction.
Actin/Myosin interactions also help produce cytoplasmic streaming in most cells.

Microtubules are hollow-like cylindrical structure, 25 nm in diameter. They are

composed of subunits of the protein tubulin--these subunits are termed alpha and beta. .
They have a very dynamic behaviour, binding GTP for polymerization. They are commonly
organized by the Centrosome. Microtubules act as a scaffold to determine cell shape, and
provide a set of "tracks" for cell organelles and vesicles to move on. Microtubules also form
the spindle fibers for separating chromosomes during mitosis (mitotic spindle). When
arranged in geometric patterns inside flagella and cilia, they are used for locomotion
Intermediate filaments are about 10 nm diameter and provide tensile strength for the cell.
These filaments, are more stable (strongly bound) than actin filaments, and heterogeneous
constituents of the cytoskeleton.]Like actin filaments, they function in the maintenance of
cell-shape by bearing tension. Intermediate filaments organize the internal three-
dimensional structure of the cell, anchoring organelles and serving as structural components
of the nuclear lamina and sarcomere. They also participate in some cell-cell and cell-matrix
junctions. Different types of intermediate filaments are: vimentin, keratin, neurofilaments,
lamin, and desmin.

LEC. 4: Nucleus & Chromosomes

Lecturer : dr.I G K Nyoman Ariana, M.Si.Med

Objective : to understand the general functional structure of cell nucleus and
chromosome
Abstract :
The nucleus is the largest organelle of the cell. where the size, shape of the nucleus are
generally constant for particular cell type. The nucleus is usually spherical and is centrally
located in the cell. Each cell usually has a single nucleus, some cells possess several nuclei
(such as osteoclast), where mature red blood cells have extruded nuclei. The nucleus
contains nearly all of DNA (deoxyribonucleic acid) for RNA (ribonucleic acid) synthesis. It
has nucleolus for the essembly of ribosomal subunits.
The nucleus bounded by two lipid membranes, houses three major components:
- Chromatins. The genetic material of the cell
- The nucleolus, the center for ribosomal RNA (r RNA) synthesis
- Nucleoplasm, containing macromolecules and nuclear particles involved in the
maintenance of the cell.

Nuclear envelope is composed of two parallel unit membranes that fuse with each other at
certain regions to form perforation known as nuclear pore.

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LEC. 5: Introduction to Molecular Biology

Lecturer : Dr. dr. Komang Januartha Pinatih, M.Kes

Objective : to understand the principles mechanisms by which genes control general
cell functions
Abstract :

The term genome comes from gene and chromosome. Genome is the entire DNA of
one species. Human Genome Project (HGP) is a project to find out the total DNA ofhuman.
Part of DNA in chromosome which has a special function is called gene. Recently,
only about 5% of genome is identified as gene. According to their location, we identify 2
kinds of DNA i.e. nuclear DNA (n-DNA) and mitochondrial DNA (mt-DNA). Recent
researches have focused on mtDNA because of its special characteristic (small molecule,
prone to get mutation and its maternal inheritance characteristic).
Molecular mechanism of inheritance involves a process known as replication in
which parental DNA is divided into two DNA progenies by semi conservative mechanism.
An error which happens in replication process will repair through DNA repair system.
Central dogma explains how the DNA can act as a messenger molecule which
carries the inheritance characteristic [DNA (replication)  transcription  translation]. Gene
expression requires two processes i.e. transcription and translation. DNA is transcribed into
3 forms of RNA i.e. mRNA, tRNA, dan rRNA which involved in translation process (protein
synthesis). mRNA will acts as a template for protein synthesis. tRNA contains the anticodon
that recognizes the codon in mRNA corresponding to the amino acid it carries and several
rRNA associate with a large number of proteins to form the small and large ribosomal
subunits. Codon is a three-base sequence in mRNA, are arranged to form amino acid which
sequence is inherited from the parental. As we know, there are 4 bases so we have 64
codons (43) consist of 61 generating codons and 3 stop codons. The genetic code stand for
20 amino acids, it means that 1 amino acid can be coded by more than 1 codon. Genetic
code is almost universal for both nDNA inti and mtDNA, wirh several exception: AGA and
AGG encode for arginin in nDNA but act as stop codon in mtDNA, UGA code for stop
codon in nDNA but encode tryptophan in mtDNA.

LEC. 6: DNA mutation and repair system

Lecturer : Dr. dr. Desak Made Wihandani, M Kes.

Objective : to understand DNA mutation and repair system
Abstract :

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LEC. 7: Gene Expression

Lecturer : dr. Wayan Surudarma, M.Si.

Objective : to understand gene expression
Abstract:

Gene expression is the process by which a gene is decoded and its information is used to
produce polypeptide or RNA molecule. A cell uses some of the information encoded by DNA
to manufacture protein. To do this, first the process of transcription copies a particular part
of the DNA sequence of a chromosome into an RNA molecule that complement to one
strand of the DNA double helix. Then the process of translation uses the information copied
into messenger RNA (mRNA) to manufacture a specific protein by aligning and joining the
specified amino acid. Messenger RNA is a template of protein synthesis where sequences
of codon are present. There are 64 codons stand for 20 amino acids. The protein synthesis
is started by initiating codon and will be lasted by stop codon. Many kind of protein are
produced in our body. Each has a specific function.

LEC. 8: Applications Of Molecular Biology In Medicine

Lecturer : Dr. rer. Nat. dr. Ni Nyoman Ayu Dewi, M.Si

Objective : to understand application of molecular biology in medicine
Abstract :
Following the advancement of science and technology, medical science also
reaches its molecular state. Genetic, genomic and proteomic open the way to a new deeper
understanding about processes inside the human body, and provide more accurate
intervention tools when disturbance in body function occur. Scientists believe that all
diseases have genetic component, whether it is inherited or as a body response against
environmental stress. Therefore, genetic plays an important role in prevention, diagnosis
and therapy for infectious and non-infectious diseases.
Molecular medicine is the clinical application of molecular biology for prevention,
diagnosis and treatment of diseases, both infectious and non-infectious. Molecular medicine
can be used to increase the accuracy of diagnostic method, detection of predisposed
genetic disorders, designing new drugs based on molecular information, gene therapy, and
development of DNA-vaccine and also in forensic medicine.
Testing for inherited diseases and susceptibilities will become standard practice as
health care becomes increasingly individualized. Tests that detect specific variations in
genetic material will enable physicians to select treatments that a person can tolerate and
that are the most likely to be effective. Genetics impacts our lives in diverse ways. Genetic
tests serve many purposes. They are widely used to screen newborns for a variety of
disorders. Often this information enables the doctors to minimize the damage caused by the
mutation. In oncology, doctors use gene testing to diagnose cancer, to classify cancer into
subtypes, or to predict a patient’s responsiveness to new treatments.
Much of the excitement today centers on gene expression profiling that use a
technology called microarrays. A DNA microarray is a thin-sized chip that has been spotted
at fixed locations with thousands of single-stranded DNA fragments corresponding to
various genes of interest. A single microarray may contain 10,000 or more spots, each
containing pieces of DNA from a different gene. Fluorescent-labeled probe DNA fragments
are added to ask if there are any places on the microarray where the probe strands can
match and bind. Complete patterns of gene activity can be captured with this technology.

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Genes, which are carried on chromosomes, are the basic physical and
functional units of heredity. Genes are specific sequences of bases that encode instructions
on how to make proteins. Although genes get a lot of attention, it’s the proteins that perform
most life functions and even make up the majority of cellular structures. When genes are
altered so that the encoded proteins are unable to carry out their normal functions, genetic
disorders can result. Gene therapy is a technique for correcting defective genes responsible
for disease development. Researchers may use several approaches for correcting faulty
genes.

LEC. 9: Cell Cycle

Lecturer : dr. I G A Dewi Ratnayanti

Objective : to understand normal and abnormal cell cycle and its clinical implications
Abstract :

The cell cycle is a series of events within the cell that prepare the cell for dividing into two
daughter cells. The cell cycle is divided into two major events: interphase and mitosis.
Interphase period is a longer period of time and take place 95% of cycle, while mitosis, a
shorter period of time and take place 5% of cycle. The capability of the cell to begin and
advance through the cell cycle is governed by the presence and interactions of a group of
related proteins known as cyclin, with specific cyclin dependent kinase (CDKs).
In interphase period, occur replication of genetic material and the cell increases its size.
Interphase is subdivided into three phases: G1 (Gap) phase, when the synthesis of
macromolecule essential for DNA duplication begins; S (synthesis), when the DNA is
duplicated; and G2 phase, when the cell undergoes preparations for mitosis. There are some
cells able to undergo mitosis permanently (e.g., muscle cells, neurons), while temporarily
(e.g., lymphocytes) will return to the cell cycle at a later time. Cell that have left the cell cycle
are said to be in a resting stage, the G0 or the stable phase. Cell division can occur by
mitosis and meiosis. Mitosis is cell division that result in the formation of two daughter cells
whose chromosome number is equal from theparental chromosome number (diploid), while
meiosis will give rise daughter cells whose chromosome number is reduced from the diploid
(2n) to the haploid (1n) number (1/2 from mother chromosome number).
The process of mitosis is divided into five stage: prophase, prometaphase, metaphase,
anaphase, an telophase; while in meiosis consist of two events: meiosis I and meiosis II.
The last stage of cell division is cytokinesis.

LEC. 10: Signal Tranduction

Lecturer : Dr. dr. Desak Wihandani, M.Kes

Objective : Explain applications of molecular biology in medicine
Abstract :to understand the signaling mechanism underlying cell to cell communication &
its clinical or practical implications

Signal transduction pathways allow cells to respond to their environment and to

change their behavior accordingly. Signals are sensed by a receptor and changed in their
form so that they can exert their final effect on the cell.

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Signals take a variety of forms, but for our purposes there only two. The first type are
signals that go into the cell, bind to internal receptors and excert their effects.Steroid
hormones, vitamin D, thyroid hormone, and retinoids are the only members of this class. All
of the intracellular receptors ultimately activate the transcription of regulated genes. The
common feature of signals that enter the cell is that they are small lipophilic molecules that
can across the cell membrane. All the other signals exert their effects by binding to
extracellular receptor and initiating a cascade of signaling events. They work by activating a
phosphorylation cascade and/or the release of second messengers in the cell.
Receptors recognize a signal molecule and transmit the signal by activating a downstream
signaling pathway. Cytosolic receptors are soluble, cytoplasmic proteins (signal must get
inside). The signal grosses the membrane and activates gene transcription.
Transmembrane receptors span a membrane (signal outside, response outside). This signal
activates a channel, an enzyme, or a G-protein cascade.

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Learning Task

LECTURE 1

THE STRUCTURE OF THE PLASMA MEMBRANE & THE TRANSPORT MECHANISM

OF VARIOUS SUBSTANCES

Learning Task
(Fawcett & Gartner; Guyton & Ganong)
1. Describe the structure and function of plasma membrane!
2. Thecomposition of intra-cellular fluid and extra-cellular fluid is different! Why it
happen? How cells regulate it?
3. Describe the mechanism of types of diffusion and example of substances diffused
through cell membrane!
4. Describe the mechanism of type of active transport, and example of substances
actively transported through cell membrane!
5. Describe the difference between the co-transport and counter-transport!
6. Describe the active transport through cellular sheets occurs at many places in the
body!

LECTURE 2

ORGANELLES AND INCLUSIONS

Learning task
(Gartner)
Vignette
A new born baby was died because of deficiency in β-galactosidase enzyme.
1. Please describe the structure of organelle involved in this disorders.
2. Please describe the structure of the organelles that involves in protein syntesize!
3. Please describe the functional structure of the organelle that involve in post
translation modification !
4. Please describe the structure of the organelle that involve in ATP synthesize and in
which part of the organelle the process of ATP occur ?

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LECTURE 3

CYTOSKELETON

Learning task 3
(Fawcett & Gartner; Guyton)

Vignette 1
A woman, 40 years old come to Hospital complains with mass in her right breast.
Anamnesis and physical examination is performed, supported by histopathology and
laboratory test. Finally, the diagnosis is breast cancer but the cancer hasn’t yet disseminate
into other organs (metastasis). In other to follow up the progression of the cancer, mRNA of
keratin 19 in patient’s bloodd is monitored as a biomarker.

Learning Task
1. Keratin 19 is a part of cytoskeleton, which one and what is the function?
(microfilaments, intermediate filaments, or microtubules)
2. Keratin 19 is expressed in mainly epithelial cell as cytoskeleton, what is the logic
keratin 19 can be also used as biomarker for metastasis in breast cancer?

Vignette 2
A man, 48 years old come to Hospital complains headache, vomiting since several months
ago. Anamnesis and physical examination is performed, supported by histopathology and
laboratory test. Using immunohistochemistry staining, it reveals that GFAP expression is
increasing. Finally, the diagnosis is astrocytoma (a type of brain cancer).

Learning Task
1. GFAP is a part of cytoskeleton, which one and what is the function? (microfilaments,
intermediate filaments, or microtubules)
2. What is the logic GFAP expression is increasing in astrocytoma?

rsday
LECTURE 4

NUCLEUS & CHROMOSOMES

Learning task
(Gartner; Strachan & Read)
1. Describe the composition of the nucleus, and its envelope!
2. Describe the nuclear pore, and its role in the cell!
3. Describe the nuclear pore complex !
4. Explain about the chromatin! How many types of chromatin that you know ?
5. Describe about the sex chromatin !

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LECTURE 5

INTRODUCTION TO MOLECULAR BIOLOGY

Researchers from German Cancer Research Centerand Essen University Hospital

Germany unravelled the cause of malignant melanoma. They found an identical mutation in
the gene for telomerase, an enzyme often called “immortality enzyme”. Telomerase protects
the ends of chromosomes from being lost in the process of cell division and, thus, prevents
that the cell ages and dies. The inherited gene mutation leads to the formation of a binding
site for protein factors in the controlling region of the telomerase gene, causing it to become
overactive. As a result, mutated cells overproduce telomerase and hence become virtually
immortal.
(Susanne Horn, Adina Figl, P. SivaramakrishnaRachakonda, Christine Fischer, Antje
Sucker, Andreas Gast, Stephanie Kadel, Iris Moll, Eduardo Nagore, Kari Hemminki, Dirk
Schadendorf and Rajiv Kumar: TERT Promoter Mutations in Familial and Sporadic
Melanoma. Science 2014, DOI: 10.1126/science.1230062).

To have a better understanding on above information, you need to discuss the following
tasks:
1. Definition of chromosome, gene, genome, central dogma in molecular biology, and
mutation.
2. Mechanism of DNA replication.
3. Role of telomerase in DNA replication process.
4. Define about point mutations. Distinguish between transition and transversion.
5. Compare the differences between mutation caused by UV radiation and X-rays. How do
the DNA repair systems fix it?

LECTURE 6

LECTURE 7

GENE EXPRESSION

Learning Task
(Baynes, J.W. and Dominiczak, M.H. Medical Biochemistry)

Thalassemias are common world-wide causes of anemia. Often, however, DNA sequencing
of the exons of the ß-globin genes reveals no abnormal nucleotides, but the ß-globin mRNA
is smaller than expected. The hemoglobin produced is defective.

1. How do you define gene expression?

2. Explain about types of RNAs and their function.
3. Describe major steps of transcription.
4. Describe major steps of translation.
5. Define codon, anticodon, stop codon and start codon.
6. How might genetic mutations lead to such abnormal gene expression as the above
case?

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LECTURE 8

APPLICATIONS OF MOLECULAR BIOLOGY IN MEDICINE

Learning Task
(Gene Therapy and Genetic Counseling)
1. Describe the implications of gene testing regarding to social and ethical issues!
2. What are the advantages of using recombinant vaccine compared with non-
recombinant/conventional one?
3. What is your opinion about reproductive cloning? Is it legal or illegal?

LECTURE 9

CELL CYCLE

Learning task
(Gartner)
1. Describe about the cell cycle!
2. How do you subdivided the interphase in cell cycle!
3. Describe the role of the protein cyclin in continuing the cell cycle process!
4. Describe about the mitosis!
5. Compare the mitosis and meiosis cell division!
6. Describe the clinical correlations of mitosis and the cell cycle!

LECTURE 10

SIGNAL TRANSDUCTION

Vignette:
A 23 year-old man presents to the emergency room complaining severe diarrhea. Base on
the result of the examination, the diagnose of that patient is Cholera. As the doctor known,
cholera is caused by Vibrio Cholera that exert their toxin and bind covalently to the G-
protein receptor.
Learning Task
1. Explain about signals and its classification!
2. Explain about receptors and its classification!
3. Describe G-protein-coupled receptors!
4. Outline the activation of downstream intracellular signaling cascades by
heterotrimetric G-proteins
5. Explain the mechanism of diarrhea caused by V. cholera!
6. Expalin about the role of calcium as a second messenger!

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PRACTICE

Practice 1: Isolation of DNA

Objective : to increase understanding about DNA isolation

Facilitator : Dr. Ni Wayan Tianing, S.Si, M.Kes.

DNA Isolation Procedure from Whole Blood (Genomic DNA Extraction)

1. Add 12 ml blood + 36 ml (3 times blood volume) 1X RBC solution to a 50 ml Falcon

centrifuge tube. Invert the tube 2-3 times during the preparation. Incubate the sample for
at least 10 minutes at room temperature. Do not allow the sample to sit in the RBC lysis
solution for extended periods of time, this can be detrimental to the sample.
2. Centrifuge at room temperature at 1500 rpm for 10 minutes. Remove the supernatant
leaving behind the visible layer of white blood cells pellet. Then repeat step 1 until
virtually all of the red blood cells are gone. Then vortex the pellet to spread the cells into
the remaining drops of supernatant.
3. Add 3 ml of cell lysis solution to the centrifuge tube and right away pipette up and down
to lyse the cells (make sure the solution is homogenous).
4. Add 6 l of RNase A (10 mg/ml) to the centrifuge tube. Mix the solution by inverting it
several times and then incubate in a 37 oC water bath for 15 minutes. This can be run
longer.
5. For protein precipitation, add 2 ml of protein precipitation solution (5 M ammonium
acetate) to the centrifuge tube and then vortex until the solution look milky.
6. Centrifuge at 3000 rpm at 4 oC 15 minutes. The precipitated proteins will from a light
brown pellet. If a protein pellet is not visible, repeat step 5.
7. Then pour the supernatant containing the DNA into a clean 50 ml Falcon tube containing
9 ml of isopropanol, do this at room temperature.
8. Mix the tube by inverting 25-30 times until white DNA pellet becomes visible (make sure
all the pellet becomes visible).
9. Centrifuge at 3000 rpm at 4 oC 15 minutes. The DNA should be visible as a small white
pellet.
10. Pour the supernatant and add 10 ml of 70 % ethanol. Invert several times to wash the
DNA.
11. Spin again and pour off the 70 % ethanol. Then left the DNA air dry. Use a cotton swab
to remove the excess supernatant on the sides of the tube.
12. Rehydrate the DNA in 1-1.5 ml of TE. Placed in 37 oC water bath for 2 hours to get the
DNA in solution. Make sure that it is a homogenous solution.
13. Store at – 20 oC.

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SELF ASSESSMENT

The Structure of the Plasma Membrane & The Transport Mechanism

of Various Substances

1. Describe structure and function of phospholipids membrane; which molecule can diffuse
across the membrane without mediated by protein (channel or carrier protein)?
2. Describe the structure of protein membrane and function of each protein in transport
mechanism and its example!
3. Explain the difference of content and composition between intracellular and extracellular
fluids!
4. Describe the passive transport mechanism through cell membrane!
5. Explain various substances which transported through passive process!
6. Describe factors that determine diffusion process!
7. Explain transport mechanism for molecule that soluble in lipid!
8. Describe sodium channel mechanism!
9. What is voltage gating channel?
10. Explain the difference between primary and secondary transportation with its examples!
11. What is co-transport?

Organelles & Inclusions

Comprehend the structure of the organelles that involve in drug and alkohol detoxication !

Cytoskeletons
1. Mention three types of cytoskeleton!
2. Mentions minimal 1 examples and its function of each type in cytoskeleton!

3.

Identify the structures labeled of an axoneme and explain the role of each cytoplasmic
component in the generation of axoneme movement.

Nucleus & Chromosomes

1. Describe all of the protein that found at nucleoplasm!
2. Describe the definition and function of nucleoplasmic ring and nuclear basket!
3. Describe the nucleosome! Mention the proteins that arranged them!
4. Describe chromatin assembly factor!
5. Describe the function of nuclear pores!
6. Describe the X-machvation (lionization)!
7. Describe the differences between chromosome 1 and 2!

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8. Describe the differences between chromosome X and Y!

9. Describe monosomy and trisomy!
10. Describe poliploidi, aneuploidi!

Introduction to Molecular Biology

1. Describe about replication mechanism, and enzymes that are involved!
2. Describe how to detect mutation in the gene.
3. Describe about mutation, and its clinical implication
4. Describe about DNA repair system!

Gene Expression
1. In When considering the initiation of transcription one often finds consensus sequences
located in the region of the DNA where RNA polymerase(s) bind. Which are common
consensus
A. CAAT
B. TATA
C. TTTTAAAA
D. both B and C
E. both A and B
2. Which of the following occurs when RNA polymerase attaches to the promoter DNA?
A. elongation of the growing RNA molecule
B. initiation of a new polypeptide chain
C. initiation of a new RNA molecule
D. termination of the RNA molecule
E. addition of nucleotides to the DNA template
3. When examining the genetic code it is apparent that
A. there can be more than one amino acid for a particular codon.
B. AUG is a terminating codon
C. there can be more than one codon for a particular amino acid
D. the code is ambiguous in that the same codon can code for two or more amino acids
E. there are 44 stop codons because there are only 20 amino acids.

4. A short segment of an mRNA molecule is shown below. The polypeptide it codes for is
also shown:

5’-AUGGUGCUGAAG : methionine-valine-leucine-lysine

Assume that a mutation in the DNA occurs so that the fourth base (counting from the 5’
end) of the messenger RNA now reads A rather than G. What sequence of amino acids
will the mRNA now code for?
A. methionine-valine-leucine-lysine
B. methionine-lysine-leucine-lysine
C. methionine-leucine-leucine-lysine
D. methionine-valine-methionine-lysine
E. methionine-methionine-leucine-lysine
5. Which of the following takes place during translation?
A. the conversion of genetic information from DNA nucleotides into RNA nucleotides
B. conversion of genetic information from the language of proteins to the language of
enzymes
C. the conversion of genetic information from the language of nucleic acids to the
language of proteins
D. DNA replication
E. the addition of nucleotides to a DNA template

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6. During the process of translation, which translation site on the ribosome is filled by the
iniatortRNA molecule
A. A
B. B
C. P
D. O
E. E
7. Which of the following statements is true regarding gene expression?
A. The 3' end of mRNA corresponds to the carboxyl terminus of the protein
B. The first step is the association of mRNA with an intact ribosome
C. Involves proof-reading of the mRNA
D. Prokaryotic RNA usually undergoes nuclear processing
E. Polypeptides are synthesized by addition of amino acids to the amino terminus
8. Which of the following best describes the relationship between genes and proteins
A. one gene: one enzyme
B. one gene: two polypeptides
C. one gene: one polypeptide
D. one gene: one protein
E. none of the above describe the relationship
9. To describe the genetic code as degenerate indicates that
A. mRNA is rapidly degraded
B. The code is not universal among organisms
C. Some amino acids have more than one codon
D. Frameshift mutations are tolerated
E. Stop codons may have corresponding tRNA molecules
10. A peptide has the sequence NH2-phe-pro-lys-gly-phe-pro-COOH. What is the sequence
in DNA that codes for this peptide?
A. 3' UUU-CCC-AAA-GGG-UUU-CCC
B. 3' AUG-AAA-GGG-TTT-CCC-AAA-GGG
C. 3' AAA-GGG-TTT-CCC-AAA-GGG
D. 5' GGG-AAA-TTT-AAA-CCC-ACT-GGG
E. 5' ACT-TAC-CAT-AAA-CAT-TAC-UGA

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Signal Transduction
1. Explain the character of ligand/signaling molecules!
2. Explain structure and function of each receptor type!
3. Describe various second messengers forming process!
4. Describe about phosphorylation protein kinase in the cytoplasm!
5. Describe cell signaling mechanism until gene expression occurs!
6. Describe the mechanism of action of drugs-receptors until biology’s responses occur!

Cell Cycle
1. Cell cycle consists of several phases. Describe the events that occur during every
phase!
2. Describe the type of cell division and its differences!
3. Describe the phases in mitosis and the events that occur during every phases!

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 Study Guide The Cell as Biochemical Machinery

REFERENCES

Used in the Block The Cell as Biochemical Machinery

Student Standard References:

1. Gartner LP, Hiatt JL : Concise Histology, Philadelphia, W.B. Saunders, 2011, pp 8-

73(H2)
2. Guyton AC, Hall JE : A Textbook of Medical Physiology, 11th ed., 2006, pp.1-51; 829
901 (PS1)
3. Baynes, J.W. and Dominiczak, M.H. Medical Biochemistry second edition.Elsevier
London. 2005:p. 641 (B𝟏)
4. Robbins SL, Kumar V : Basic Pathology, London, Saunders, 7th ed, 2003, pp.3-31 (BP)
5. Strachan T & Read AP; Human Molecular Genetics, John Wiley & Sons (Asia) PTELTD
(HMG)
6. Trevor AJ, Katzung BG, and MastersSB :Pharmacology Examination & Broad Review,
7th ed, 2005, pp. 10-19(PH)
7. Goodman SR : Medical Cell Biology, 2nd ed, pp. 195-202 (CB)
8. Gene Therapy and Genetic Counseling

Additional recommended reading:

9. Fawcett DW, Jensh RP : Bloom & Fawcett’s Concise Histology, 2nd ed, London, Arnold,
2002, pp 1- 27(H1)
10. Ganong, WF: Review of Medical Physiology, 20thed, New York, Lange Medical
Books/McGraw-Hill, 2001, pp 1-48 (PS2)
11. Murray RK, Granner DK, Mayes PA : Harper, s Illustrated Biochemistry,26th ed, New
York, Lange Medical Books / McGraw-Hill, 2003 , 314 – 373; 74-102 (B2)
12. Alberts B, Johnson A, Lewis J : Molecular Biology of THE CELL, 4TH ed , New York,
Garland Science, 2002, pp 1010 – 1021 (MB2)

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 Study Guide The Cell as Biochemical Machinery

Paper Assessment Form

Block The Cell as Biochemical Machinery

Name : ...........................................
Student Reg. Number : ...........................................
Facilitator : ...........................................
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Supervisor’s (Facilitator) scoring with 60% qualification :]

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Paper Assessment Form

Block The Cell as Biochemical Machinery

Name : ...........................................
Student Reg. Number : ...........................................
Facilitator : ...........................................
Title : ...........................................

Evaluator’sscoring (presentation) with 40% qualification : :

No Item Assessment Range Score (%) Score

1. Ability to find the literature 0-20
2. Communication/Attitude 0-30
3 Quality of material 0-40
4 Student’s interest and 0-10
motivation
TOTAL 100

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 Study Guide The Cell as Biochemical Machinery

Department of Medical Education (DME), 2017 32