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2: Chemistry and Biochemistry - Biology

2: Chemistry and Biochemistry - Biology



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  • 2.1: Atoms, Isotopes, Ions, and Molecules - The Building Blocks
    At its most fundamental level, life is made up of matter. Matter is any substance that occupies space and has mass. Elements are unique forms of matter with specific chemical and physical properties that cannot be broken down into smaller substances by ordinary chemical reactions. There are 118 elements, but only 92 occur naturally. The remaining elements are synthesized in laboratories and are unstable.
  • 2.2: Water
    The polarity of the water molecule and its resulting hydrogen bonding make water a unique substance with special properties that are intimately tied to the processes of life. Life originally evolved in a watery environment, and most of an organism’s cellular chemistry and metabolism occur inside the watery contents of the cell’s cytoplasm. Understanding the characteristics of water helps to elucidate its importance in maintaining life.
  • 2.3: Carbon and Organic Molecules
    Cells are made of many complex molecules called macromolecules, such as proteins, nucleic acids (RNA and DNA), carbohydrates, and lipids. The macromolecules are a subset of organic molecules (any carbon-containing liquid, solid, or gas) that are especially important for life. The fundamental component for all of these macromolecules is carbon.
  • 2.4: Carbohydrates
    The most abundant biomolecules on earth are carbohydrates. From a chemical viewpoint, carbohydrates are primarily a combination of carbon and water, and many of them have the empirical formula (CH2O)n, where n is the number of repeated units. This view represents these molecules simply as “hydrated” carbon atom chains in which water molecules attach to each carbon atom, leading to the term “carbohydrates.”
  • 2.5: Lipids
    Although they are composed primarily of carbon and hydrogen, lipid molecules may also contain oxygen, nitrogen, sulfur, and phosphorous. Lipids serve numerous and diverse purposes in the structure and functions of organisms. They can be a source of nutrients, a storage form for carbon, energy-storage molecules, or structural components of membranes and hormones. Lipids comprise a broad class of many chemically distinct compounds, the most common of which are discussed in this section.
  • 2.6: Proteins
    Amino acids are capable of bonding together in essentially any number, yielding molecules of essentially any size that possess a wide array of physical and chemical properties and perform numerous functions vital to all organisms. The molecules derived from amino acids can function as structural components of cells and subcellular entities, as sources of nutrients, as atom- and energy-storage reservoirs, and as functional species such as hormones, enzymes, receptors, and transport molecules.
  • 2.7: Nucleic Acids
    Nucleic acids are the most important macromolecules for the continuity of life. They carry the genetic blueprint of a cell and carry instructions for the functioning of the cell.

Peptides: Chemistry and Biology, 2nd Edition

Norbert Sewald studied Chemistry at the Technical University of Munich, Germany, where he also obtained his PhD degree. After postdoctoral work with J. E. Baldwin in Oxford, UK, he became an Assitant Professor at Leipzig University. Since 1999 he is full Professor at the University of Bielefeld where he holds the chair in Organic and Bioorganic Chemistry. His main scientific interest is in peptide chemistry, bioactive peptides., and their application in biochemistry and medical sciences. He has authored more than 120 publications and together with Hans-Dieter Jakubke, has written the book Peptides from A - Z, also published by Wiley-VCH.

Hans-Dieter Jakubke studied Chemistry at the Martin-Luther-University Halle-Wittenberg, Germany. After finishing his PhD and postdoctoral work with Josef Rudinger in Prague (Czeck Republic), he was appointed Assistant Professor at the Department of Biochemistry in Halle, and Full Professor of Biochemistry at the University of Leipzig in 1977. He was director of the Department of Biochemistry from 1993-1997 and member of the Council of the European Peptide Society from 1990-1994. He authored several textbooks and encyclopedias on various aspects of chemistry and biochemistry including peptide research.


About the Author

GERHARD MICHAL, PhD, has retired from research at Boehringer Mannheim GmbH (now Roche Diagnostics). He is internationally acclaimed for developing the "Biochemical Pathways" wall chart. The first edition, which was published some forty years ago, has been continuously updated and is used in many biochemistry laboratories around the world.

DIETMAR SCHOMBURG, PhD, is a Full Professor and Head of the Department of Bioinformatics and Biochemistry at the Technische Universität Carolo-Wilhelmina in Braunschweig. His research interests include protein structure and function, structural biochemistry, bioinformatics, and enzyme information/metabolic networks. Dr. Schomburg has been widely praised for establishing BRENDA, the principal source of enzyme function and property data.


Summary

SARS-CoV-2 (previously 2019-nCoV or Wuhan coronavirus) caused an unprecedented fast-spreading worldwide pandemic. Although currently with a rather low mortality rate, the virus spread rapidly over the world using the modern world’s traffic highways. The coronavirus (CoV) family members were responsible for several deadly outbreaks and epidemics during the last decade. Not only governments but also the scientific community reacted promptly to the outbreak, and information is shared quickly. For example, the genetic fingerprint was shared, and the 3D structure of key proteins was rapidly solved, which can be used for the discovery of potential treatments. An overview is given on the current knowledge of the spread, disease course, and molecular biology of SARS-CoV-2. We discuss potential treatment developments in the context of recent outbreaks, drug repurposing, and development timelines.


Degree programs

We offer undergraduate degrees in biochemistry and chemistry, with programs leading to teacher certification, American Chemistry Society certification, and preparation for medically-related professional programs . As of Fall 2018, we now offer a NEW track in environmental chemistry, which allows you to study the role of chemical species in natural places such as water, air and soil. A chemistry minor also is available to TWU undergraduate students.

Our flexible master of science degree in chemistry is custom- designed by a faculty committee to suit your individual career goals. As a graduate student in our program, you will have the opportunity to choose from a broad range of research focuses, attend advanced courses, and participate in seminars and research.


The Bachelor of Science in Chemistry and Biology prepares students for careers that involve applications of both subjects, including the pharmaceutical and biotechnology industries, as well as further graduate study in biochemistry, molecular biology, and chemical biology. The interdepartmental major program also provides a strong foundation for the study of clinical and research careers in medicine and related health professions.

The curriculum provides strong foundations in both Chemistry and Biology, with flexibility in elective subjects that enables students to tailor their major program to their specific interests within the broad interface of Biology and Chemistry. The requirements listed below are effective for the 2019-2020 Academic Year. The prior degree requirements are available here if you have questions about the different requirements please contact Jennifer Weisman (Academic Administrator).

Required Lecture Subjects

  • 5.03 Principles of Inorganic Chemistry I
  • 5.07 or 7.05 Introduction to Biological Chemistry or General Biochemistry
  • 5.08 Fundamentals of Chemical Biology
  • 5.12 Organic Chemistry I
  • 5.13 Organic Chemistry II
  • 5.601 Thermodynamics I
  • 5.611 Introduction to Spectroscopy
  • 7.03 Genetics
  • 7.06 Cell Biology

Restricted Electives

Select 30 units of the following:

  • 5.04 Principles of Inorganic Chemistry II
  • Module 6 (5.363) Organic Structure Determination
  • Module 7 (5.371) Continuous Flow Chemistry: Sustainable Conversion of Reclaimed Vegetable Oil into Biodiesel
  • Module 8 (5.372) Chemistry of Renewable Energy
  • Module 9 (5.373) Dinitrogen Cleavage
  • Module 10 (5.381) Quantum Dots
  • Module 11 (5.382) Time-and Frequency- resolved Spectroscopy of Photosynthesis
  • Module 12 (5.383) Fast-flow Peptide Protein Synthesis
  • 5.39 Research and Communication in Chemistry
  • 5.43 Advanced Organic Chemistry
  • 5.602 Thermodynamics II and Kinetics
  • 5.612 Electronic Structures of Molecules
  • 5.62 Physical Chemistry
  • 7.093 Modern Biostatistics
  • 7.094 Modern Computational Biology
  • 7.19 Communication in Experimental Biology
  • 7.20 Human Physiology
  • 7.21 Microbial Physiology
  • 7.23 Immunology
  • 7.26 Molecular Basis of Infectious Disease
  • 7.27 Principles of Human Disease and Aging
  • 7.28 Molecular Biology
  • 7.29 Cellular and Molecular Neurobiology
  • 7.30 Fundamentals of Ecology
  • 7.31 Current Topics in Mammalian Biology: Medical Implications
  • 7.32 Systems Biology*
  • 7.33 Evolutionary Biology: Concepts, Models, & Computation
  • 7.371 Biological & Engineering Principles Underlying Novel Biotherapeutics
  • 7.45 The Hallmarks of Cancer
  • 7.46 Building with Cells
  • 7.49 Developmental Neurobiology

*Subject has prerequisites that are outside the program.

Departmental Laboratory Requirement

  • Module 1 (5.351) Fundamentals of Spectroscopy
  • Module 2 (5.352) Synthesis of Coordination Compounds and Kinetics (CI-M)
  • Module 3 (5.353) Macromolecular Prodrugs
  • 7.002 Fundamentals of Experimental Molecular Biology

Select one of the following options:

Option 1
5.361 Recombinant DNA Technology
5.362 Cancer Drug Efficacy (CI-M)

Option 2
7.003 Molecular Biology Laboratory (CI-M)

Chemistry & Biology Major Roadmaps

Roadmap for Lab Option 1

First Year – Fall

First Year – Spring

Sophomore – Fall

  • 5.13 Organic Chemistry II
  • 5.351 (Lab Module 1)*
  • 5.352 (Lab Module 2)*
  • 5.353 (Lab Module 3)*

Sophomore – Spring

  • 5.03 Principles of Inorganic Chemistry
  • 7.05 General Biochemistry
  • 7.002 Fundamentals in Experimental Microbiology*

Junior – Fall

Junior – Spring

  • 7.06 Cell Biology
  • 5.08/7.08 Fundamentals of Chemical Biology
  • 5.361 (Lab Module 4)
  • 5.362 (Lab Module 5)

Senior – Fall

Senior – Spring

*Alternative path: 7.002 in Sophomore – Fall & 5.351, 5.352, and 5.353 in Sophomore – Spring

Roadmap for Lab Option 2

First Year – Fall

First Year– Spring

Sophomore – Fall

  • 5.13 Organic Chemistry II
  • 5.351 (Lab Module 1)*
  • 5.352 (Lab Module 2)*
  • 5.353 (Lab Module 3)*

Sophomore – Spring

  • 5.03 Principles of Inorganic Chemistry
  • 7.05 General Biochemistry
  • 7.002 Fundamentals in Experimental Microbiology*

Junior – Fall

Junior – Spring

  • 7.06 Cell Biology
  • 5.08/7.08 Fundamentals of Chemical Biology
  • Restricted Elective Subject(s)

Senior – Fall

Senior – Spring

*Alternative path: 7.002 in Sophomore – Fall & 5.351, 5.352, and 5.353 in Sophomore – Spring

** 7.003 may be taken anytime during the Junior or Senior year after 7.002 and 5.07/7.05 have been completed

Roadmap for Lab Option 1 - 1st Term Sophomore Start

First Year – Fall

First Year – Spring

Sophomore – Fall

  • 5.12 Organic Chemistry I
  • 5.351 (Lab Module 1)*
  • 5.352 (Lab Module 2)*
  • 5.353 (Lab Module 3)*

Sophomore – Spring

  • 5.03 Principles of Inorganic Chemistry
  • 7.05 General Biochemistry
  • 7.002 Fundamentals in Experimental Microbiology*

Junior – Fall

Junior – Spring

  • 7.06 Cell Biology
  • 5.361 (Lab Module 4)
  • 5.362 (Lab Module 5)
  • Restricted Elective Subject(s)

Senior – Fall

Senior – Spring

*Alternative path: 7.002 in Sophomore – Fall & 5.351, 5.352, and 5.353 in Sophomore – Spring

Roadmap for Lab Option 2 - 1st Term Sophomore Start

First Year – Fall

First Year– Spring

Sophomore – Fall

  • 5.12 Organic Chemistry I
  • 5.351 (Lab Module 1)*
  • 5.352 (Lab Module 2)*
  • 5.353 (Lab Module 3)*

Sophomore – Spring

  • 5.03 Principles of Inorganic Chemistry
  • 7.05 General Biochemistry
  • 7.002 Fundamentals in Experimental Microbiology*

Junior – Fall

Junior – Spring

  • 7.06 Cell Biology
  • 5.08/7.08 Fundamentals of Chemical Biology
  • Restricted Elective Subject(s)

Senior – Fall

Senior – Spring

*Alternative path: 7.002 in Sophomore – Fall & 5.351, 5.352, and 5.353 in Sophomore – Spring

** 7.003 may be taken anytime during the Junior or Senior year after 7.002 and 5.07/7.05 have been completed


College of Letters and Science

Graduate Degrees

The Department of Chemistry and Biochemistry offers the Master of Science (M.S.) and Doctor of Philosophy (Ph.D.) degrees in Chemistry, and the Master of Science (M.S.) and Doctor of Philosophy (Ph.D.) degrees in Biochemistry, Molecular and Structural Biology.

Biochemistry, Molecular and Structural Biology

Master’s Degree

Initial academic advising is handled by the appropriate faculty area advisor. Students continue to consult with this advisor each quarter until completion of their course requirements. During this period, students also choose a Research Director to supervise their thesis research. The Graduate Studies Committee, consisting of the graduate advisor and other key faculty, reviews each student’s progress quarterly. Notification in writing is given to students who are performing at a very high level and to those who are not making adequate progress. The faculty graduate advisor, faculty area advisors, and Director of Graduate Student Affairs are available for personal consultation.

Areas of Study

Biochemistry and Molecular Biology.

Foreign Language Requirement

Course Requirements

Thirty-eight units of coursework are required. At least 20 of the 38 units must be at the graduate level (courses numbered 200 and above), while the remaining units may be upper division undergraduate courses (courses numbered from 100 to 199). Required courses include Chemistry and Biochemistry 269A-269B-269C-269D-269E (10 units) Chemistry and Biochemistry 258 during the first quarter of the second year Chemistry and Biochemistry 268 during the first three quarters and three laboratory rotations (Chemistry and Biochemistry 596) during the first year. After completion of Chemistry and Biochemistry 269A-269B-269C-269D-269E, at least four additional units of graduate level courses are required. Additional lecture courses are chosen from a list of approved graduate courses available from the schedule of classes. Up to 24 units of Chemistry and Biochemistry 596 or 598 may be applied toward the total course requirement up to eight units may be applied toward the graduate course requirement. Up to four units of graduate-level seminar courses may be applied to the graduate course requirement. Substitutions may be made with the consent of the faculty graduate adviser.

Teaching Experience

Not Required. Students who serve as teaching assistants must enroll in and receive a grade of S for Chemistry and Biochemistry 375 for each quarter they teach in order to continue teaching.

Field Experience

Comprehensive Examination Plan

In exceptional cases, a comprehensive examination is administered in lieu of a thesis. This written examination is administered and graded by a faculty committee selected by the faculty graduate adviser and is graded pass or fail. For students who fail, recommendation for or against a second examination is made by the faculty graduate advisor.

Thesis Plan

Every master’s degree thesis plan requires the completion of an approved thesis that demonstrates the student’s ability to perform original, independent research.

The thesis plan is the preferred method of attaining the M.S. degree in Biochemistry, Molecular and Structural Biology. Preference in admissions is given to students who have already identified a research adviser under whose direction the thesis research is conducted. By the sixth week of the first term in residence, a master’s committee is appointed for each student consisting of the student’s faculty research adviser and two additional faculty members chosen by the faculty graduate adviser. This committee has the responsibility for approving or disapproving the master’s thesis. By the end of the first term, the student is required to submit a brief written research proposal for approval by the master’s committee. Students have five academic quarters after the submission of proposal to complete the degree.

Time-to-Degree

From admission to completion of courses: Three academic quarters (one calendar year).

From admission to award of degree: Three to six academic quarters (one to two calendar years).

Doctoral Degree

Initial academic advising is handled by the Biochemistry, Molecular and Structural Biology program faculty adviser. Students continue to consult with this adviser each quarter until completion of their course requirements. During this period, students also choose a research director to supervise their dissertation research. The Graduate Studies Committee, consisting of the faculty and staff graduate advisers, reviews each student’s progress quarterly. Notification in writing is given to students who are performing at a very high level and to those who are not making adequate progress. The faculty graduate adviser, faculty area advisers, and Director of Graduate Student Services are available for personal consultation.

Minimum Progress. At the end of the first and second year, the overall progress of each student is evaluated by the Biochemistry Faculty Committee. They assess student progress by evaluating each student’s performance in their courses, written examinations, teaching, and research. The committee may recommend that students (1) proceed to the oral examination, (2) be redirected to the M.S. program, or (3) be recommended for termination.

Major Fields or Subdisciplines

Biochemistry, Molecular and Structural Biology

Foreign Language Requirement

Course Requirements

Candidates typically complete at a minimum the coursework indicated below. Required coursework must be completed prior to advancement to candidacy. Substitutions may be made with the consent of the faculty graduate adviser. Some of the course requirements listed below can be met on the basis of courses taken prior to entry into the graduate program with consent of the faculty adviser.

(1) Required background material: one year organic chemistry, one course in physical chemistry or biophysical chemistry, one year of biochemistry, some coursework in the life sciences, and some biochemistry laboratory experience.

(2) Chemistry and Biochemistry 269A-269B-269C-269D-269E (10 units) should be taken in the first year.

(3) Sixteen units of additional upper division or graduate-level courses, including four to six units of seminar courses or the equivalent. Courses are chosen in consultation with the graduate adviser. The courses are to be chosen with the following goals in mind: (a) in addition to the in-depth training in the student’s areas of specialization, the selected courses should provide broad training in the multiple areas of biochemistry, molecular and structural biology and (b) in addition to a didactic lecture component, there should be a significant discussion component. Two seminar courses should be included in the selected courses to ensure that the student gains training in the critical evaluation of scientific literature.

(4) Chemistry and Biochemistry 258 during the first quarter of the second year.

(5) Chemistry and Biochemistry 268 during the first three quarters of the first year.

(6) Three laboratory rotations (Chemistry and Biochemistry 596) during the first year.

Teaching Experience

One year of teaching experience (three quarters) is generally required. Students who serve as teaching assistants must enroll in Chemistry and Biochemistry 375 for each quarter that they teach. Students must receive a satisfactory grade (‘S’) in order to continue teaching in the program.

Written and Oral Qualifying Examinations

Academic Senate regulations require all doctoral students to complete and pass University written and oral qualifying examinations prior to doctoral advancement to candidacy. Also, under Senate regulations the University oral qualifying examination is open only to the student and appointed members of the doctoral committee. In addition to University requirements, some graduate programs have other pre-candidacy examination requirements. What follows in this section is how students are required to fulfill all of these requirements for this doctoral program.

The written examination requirement is coupled to the graduate student seminar (Chemistry and Biochemistry 258). Chemistry and Biochemistry 258 requires a presentation of the student’s proposed dissertation research. After completing this oral presentation, the student prepares a written dissertation research proposal. The proposal includes information about the background and significance of the area of research, the specific aims to be addressed and experiments proposed. The written qualifying component of the Ph.D. program is fulfilled after the student satisfactorily completes this proposal. A written proposal that is deemed unsatisfactory may be revised once.

The University Oral Qualifying Examination consists of an original research proposal in an area related to the student’s dissertation research. The specific topic of the exam is chosen in consultation with the student’s Ph.D. adviser. The exam is prepared by the student without assistance from the research adviser. The proposal is presented orally to the committee, and the committee questions the candidate on the proposal, general knowledge of the area, and dissertation research progress. The proposal represents independent work and offers the doctoral committee the opportunity to judge the student’s ability to think creatively and to formulate significant ideas for research.

All students are required to take the University Oral Qualifying Examination by June 30 of their second year. The committee’s decision to advance a student to candidacy, to allow the student to repeat all or part of the oral, or to disqualify the student, is based on the student’s overall record at UCLA as reflected in coursework and examinations, and the student’s research ability and productivity.

Advancement to Candidacy

Students are advanced to candidacy upon successful completion of the written and oral qualifying examinations. The Candidate in Philosophy (C.Phil.) degree is awarded for the quarter in which students are advanced to candidacy.

Doctoral Dissertation

Every doctoral degree program requires the completion of an approved dissertation that demonstrates the student’s ability to perform original, independent research and constitutes a distinct contribution to knowledge in the principal field of study.

Final Oral Examination (Defense of the Dissertation)

Required for all students in the program.

Time-to-Degree

The following are normal times to complete the requirements of the program:

From admission to completion of written qualifying examinations (see above for definition/description of these for each major): three to five academic quarters (one to one and two-thirds calendar years).

From admission to advancement to candidacy: six academic quarters (two calendar years).

From admission to award of degree: 12 to 18 academic quarters (four to six calendar years).

Termination of Graduate Study and Appeal of Termination

University Policy

A student who fails to meet the above requirements may be recommended for termination of graduate study. A graduate student may be disqualified from continuing in the graduate program for a variety of reasons. The most common is failure to maintain the minimum cumulative grade point average (3.00) required by the Academic Senate to remain in good standing (some programs require a higher grade point average). Other examples include failure of examinations, lack of timely progress toward the degree and poor performance in core courses. Probationary students (those with cumulative grade point averages below 3.00) are subject to immediate dismissal upon the recommendation of their department. University guidelines governing termination of graduate students, including the appeal procedure, are outlined in Standards and Procedures for Graduate Study at UCLA.

Special Departmental or Program Policy

A student may be recommended for termination by the Graduate Study Committee or the Biochemistry Faculty Committee. A student may appeal a recommendation for termination to the departmental chair.

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2 Chemistry

Chemistry comprises several distinct subdisciplines, namely, physical, inorganic and organic chemistry. In some ways it's a broader field than chemistry, since it's concerned with the structure and behavior of matter and the types of reactions compounds can undergo. The dividing line between biochemistry and chemistry is a little fuzzy, but in general, chemists are interested in designing useful new materials, finding more efficient ways to synthesize existing materials, or understanding why substances have the property that they do, while biochemists use chemistry to understand why and how certain processes take place in living organisms.


Soil Biology and Biochemistry

SCOPE
The scope of Soil Biology & Biochemistry publishes scientific research articles of international significance which describe and explain fundamental biological and biochemical features and processes occurring in soil systems.

The emphasis is on original research which substantively advances or directs our understanding of the mechanistic basis of how soils function. Articles may involve applications of basic knowledge to applied issues if they provide distinct insight into the role of soil biology and biochemistry in regulating soil functions. Some examples of major topics include:

  • The ecology of all soil organisms (including viruses)
  • How soil biology interacts with soil physical and chemical properties and processes to regulate belowground functions
  • Relationships and functional interactions between soil biota and plants
  • The effects of soil organisms on ecosystem dynamics across spatial and temporal scales

SBB also emphasizes the application of molecular, microscopic, and analytical techniques and modelling approaches to understand, explain and visualise soil functioning. Technique-focused papers must involve a particularly high degree of novelty or significance.

In addition, the journal publishes state-of-the-art reviews that consider contemporary research and synthesise knowledge to provide enhanced understanding of biotic roles in soil system functioning.

Benefits to authors
We also provide many author benefits, such as free PDFs, a liberal copyright policy, special discounts on Elsevier publications and much more. Please click here for more information on our author services .

Please see our Guide for Authors for information on article submission. If you require any further information or help, please visit our Support Center


Chemistry, Biochemistry, and Biology of 1-3 Beta Glucans and Related Polysaccharides

Chemistry, Biochemistry, and Biology of 1-3 Beta Glucans and Related Polysaccharides presents a comprehensive, systematic and authoritative survey of information about a family of chemically related, but functionally diverse, naturally occurring polysaccharides--the (1-3)-glucans. International contributors describe the chemical and physicochemical properties of these glucans and their derivatives and the molecular biological and structural aspects of the enzymes involved in their formation and breakdown. A detailed analysis of their physiological roles in the various biological situations in which they are found will be provided. Additionally, evolutionary relationships among the family of these glucans will be described.

Chemistry, Biochemistry, and Biology of 1-3 Beta Glucans and Related Polysaccharides presents a comprehensive, systematic and authoritative survey of information about a family of chemically related, but functionally diverse, naturally occurring polysaccharides--the (1-3)-glucans. International contributors describe the chemical and physicochemical properties of these glucans and their derivatives and the molecular biological and structural aspects of the enzymes involved in their formation and breakdown. A detailed analysis of their physiological roles in the various biological situations in which they are found will be provided. Additionally, evolutionary relationships among the family of these glucans will be described.