Biochemistry I

Instructor: Dr. Fan Jiang(江凡 )

Class schedule: Monday 1:30--3:05 pm Wednesday 3:20--4:55 pm

Place: Biology Building 214

Teaching assistant:

Requirement: Write in English with correct grammar. Expressions made of only keywords piled together are

NOT acceptable. Leave no chance for guessing.

Course Organization(a metaphor to a play)

Static part (静态部分 ):

Dynamic part (动态部分 ):

To introduce characters, roles, scenes, backgrounds, settings, …etc (structure and function)

To present dialogues, actions, stories, and drama (interesting and exciting)

Rationale for this organization

1. Natural for systematic studies and learning (as opposed to casual understanding).

2. Pedagogic purposes (teaching purposes): easy to add and delete.

3. Organization of our textbook (Lehninger’s is very detailed and well illustrated, good for reading and self-learning. Stryer’s more advanced but less detailed. Zubay’s may be in the middle).

4. Our traditional organization.

Goals of Studying Biochemistry

1. To introduce the language of biochemistry, with careful explanations of the meaning, origin, and significance of terms.

2. To provide a balanced understanding of the physical, chemical, and biological context in which each biomolecule, reaction, and pathway operates.

3. To project a clear and repeated emphasis on major themes, especially those relating to evolution, thermodynamics, regulation, and the relationship between structure and function.

4. To explain and to place in context the most important techniques that have brought us to our current understanding of biochemistry (key experiments)

5. To sustain the student’s interest by developing topics in a logical and stepwise manner; taking every opportunity to point out connections between processes; identifying gaps in our knowledge that promise to challenge future generations of scientists; supplying the historical context of selected major discoveries, when such context is useful; and highlighting the implications of biochemical advances for society (preparing you for research and discovery and other adventures you may undertake in the future).

Chapter 0 Introduction

1. The main features of the living matters

1.1 structurally complicated and highly organized

1.2 metabolize--extract, transform, and use nutrients and energy from their environment

1.3 respond (adapt and survive) by finding energy and raw materials through interacting with their surroundings

1.4 self replicate and self assembly (reproduce and perpetuate)

1.5 evolve and diversify

The origin of the universe

(a) microscopiccomplexity

(b) energy comsumption,food chain

(c) reproduction

Garden of Eden (diversity and unity)

2. What is Biochemistry?

The study of the molecular basis of life or understanding life phenomena in chemical terms.

It is the combination of biology and chemistry or the application of chemical principles to understanding biology.

3. What are the questions for biochemists to answer?

3.1 What are the biomolecules (composition and structure)?

3.2 How do biomolecules act and interact (conferring the remarkable features of living organisms)?

3.3 How are the biomolecules synthesized (biosynthesis)?

3.4 How is energy generated and consumed (energy metabolism, its source and fate)?

3.5 How are the myriad of biochemical reactions regulated (the coordination problem, the network of control)?

3.6 What is the carrier of genetic information and how is it expressed and transmitted (information pathway)? (preserved faithfully)

3.7 How do cells and organisms grow, differentiate, and reproduce?

3.8 What is the molecular basis of evolution?

3.9 What makes living organisms so diversified? (advantages, purposes and natural tendencies)

3.10 How do we make use of life and knowledge about life for the benefits of human being (biotechnology, quality of life, societal welfare)?

4. A Brief History of Biochemistry over the last 200 years (milestones)

1780s Antoine Lavoisier (French): Combustion of a candle is similar to the respiration of animals, as both need O2. For the first time a physiological process was explained with reference to a nonliving mechanism.

1810s-1830s A major substance from animals and plants was identified, composing of C, H, O, and N. The term “Protein”, meaning the most important thing, was first used in 1838.

1850s-1890s Carbohydrates, lipids, and nucleic acids were recognized. The term “biochemistry” was formed in the 1870s.

1890s Eduard Buchner (German): Cell free yeast extract can ferment sugar to alcohol! Enzymes can function when removed from the living cells! Rejected the vitalism theory!

1920s-1930s James Sumner: Enzymes are proteins.

1940s-1950s Avery and Hershey: DNA carries the genetic information.

1950s Franklin, and Watson and Crick: DNA is a double helix.

1960s Nirenberg: Genetic codes deciphered.

1980s Cech: RNA has catalytic activity (Ribosome).

5. Modern Biochemical Science

5.1 It has become the common language of biology: concepts and approaches5.2 It has learned much about the chemical mechanisms of many central processes of life.5.3 It has revealed the remarkable chemical unity under the biological diversity.

5.3.1 Living organisms (e.g., E.coli and human beings) are very much alike at the microscopic and chemical level.

5.3.2 The building blocks for the macromolecules are the same.

5.3.3 The flow of genetic information is the same (from DNA to RNA to protein).

5.4 It has profoundly influenced medicine (and agriculture)

5.4.1 Molecular lesions causing various genetic diseases have been revealed (e.g., sickle-cell anemia; cystic fibrosis).

5.4.2 Clinical diagnostics has been greatly enriched.

5.4.3 Production of valuable proteins by genetic engineering is made possible.

5.4.4 Rational design of new drugs

5.4.5 Generation of crops and domestic animals with new (genetic makeup) features.

5.5 It has pioneered and developed some of the crucial concepts and techniques to tackle the most challenging and fundamental problems in biology and medicine.

5.5.1 Mechanism of cell differentiation and development

5.5.2 Causes of cancers

5.5.3 Molecular basis of memory, thinking, and other functions of the brain.

6. How to Study

6.1 Examine the critical experiments leading to major discoveries

6.2 Understand the major themes in biochemistry. For example, what are the properties and functions of noncovalent interactions, allosteric regulation, and etc.

6.3 Get a sense of developing and evolving concepts and knowledge. That is what we are learning today may be modified or corrected tomorrow (e.g., concept of enzyme).

Chapter 1 Cell Structure

1. The cell doctrine (accepted in the 1850s)

1.1 All living organisms are made up of cells, the smallest unit of living matters.

(It is both the structural and functional unit. The human body contains at least 1014 cells.)

1.2 Cells are capable of self-reproduction.

2. Most cells are microscopic in size

2.1 animal and plant cells: 10-30 microns in diameter (micro-meter, 10-6 meter); bacteria: 1-2 microns long; mycoplasma: 300nm (nanometer, 10-9 m).

2.2 The requirement of optimal surface area to volume ratio probably limits the cell sizes.

2.2.1 Most cells distribute oxygen and nutrient molecules throughout the cell volume through diffusion. The rate of diffusion in acqueous systems limit the extent of the volume accessible. The larger surface area to volume ratio (smaller spherical cells) facilitate the accessibility. Highly convoluted (folded) surfaces facilitate the accessibility (fig. 2-3). An exception is cytoplasmic streaming (energy facilitated distribution).

(a) In cells of the intestinal mucosa, the plasma membrane facing the intestinal lumen is folded into microvilli, increasing the area for absorption of nutrients.

A dividing E. coli 大肠杆菌

Dividing Saccharomyces cerevisiae (baker’s yeast) cells

3. Evolution and Structure of Prokaryotic Cells (the best-studied prokaryotic cell is Escherichia coli)

3.1 It is surrounded by a cell envelop, consisting of (I) Outer membrane (gram-negative bacteria only): permeable to small molecules such as sugars and amino acids; (ii) Inner plasma membrane: a selective barrier, made of many proteins (about 200 kinds) floating in a lipid 脂 bilayer such as receptors and transporters; (iii) Periplasmic space: between the plasma and outer membranes; (iv) Cell Wall: a peptidoglycan layer.

3.2 It has a noncompartmentalized cytoplasm 细胞质 (the part between the plasma membrane and nucleoid), containing the following components:

3.2.1 Ribosomes 核糖体 : the largest particles in the cytoplasm, the protein synthesis machine; smaller but structurally and functionally similar to those of eukaryotic 真核 cells.

3.2.2 Proteins (including enzymes), metabolites, cofactors, and inorganic ions.

3.2.3 Plasmids 细胞质粒 : small circular DNA molecules, often confer resistance to toxins and antibiotics; they replicate independently, and are used as vectors in genetic engineering.

3.3 Nucleoid 核质体（染色体团） : the area where the highly packed single circular chromosomal DNA locates, without the surrounding membrane, but believed to be attached to the membrane.

3.4 It has one or more long flagella 鞭毛 extending from the surface: a complex rotary motor that propels the cell (swim).

4. Major Structural Features of Eukaryotic 真核的 Cells

4.1 Eukaryotic organisms include algae 藻类 , protozoa 原生动物 , fungi 真菌 , plants, and animals.

4.2 An extended intracellular membrane system compartmentalizes 分隔 the cytoplasm 细胞质 of an eukaryotic cell, forming various organelles 细胞器 . They are

a nucleus 细胞核an endoplasmic reticulum 内质网 (ER) systema Golgi apparatus 高尔基体many mitochondria 线粒体lysosomes 溶酶体 (or vacuoles 液泡 in plants)peroxisomes 过氧化物酶体 , and chloroplasts 叶绿

体 (in plants)

4.3 Nucleus

4.3.1 It is the place where genetic information carrier (DNA) is stored.

4.3.2 It is surrounded by an nuclear envelop consisting of double membranes with specialized complex pores facilitating the material passage. The outer layer is continuous with the ER membrane system.

4.3.3 DNA is condensed 螺旋 (compressed) about 10 million fold (in the linear dimension) in a human chromosome 染色体 (becoming the visible rods 杆状 before cell divides).

4.3.4 DNA wraps around histone 组蛋白 proteins to form nucleosomes, which further pack into chromatin fibers, … (other levels of packaging)…, and eventually in chromatin 染色质 .

4.3.5 The dense area (under EM) in a nucleus is called the nucleolus 核仁 , where rRNA is actively synthesized and assembled with proteins into ribosome 核糖体 subunits (particles).

Nuclear pores

nucleolus

4.4 Endoplasmic Reticulum (ER) 内质网

4.4.1 It is a netlike continuous membrane system consisting of tubes and flattened sacs 囊 (cisternae) extending through the cytoplasm 细胞质 (like a labyrinth 迷宫 ), forming an enclosed lumen 腔 .

4.4.2 The ribosomes 核糖体 that synthesize proteins for secretion 分泌 or specific targeting are attached to the cytoplasmic surface of ER, forming the rough ER (RER) structure.

4.4.3 Smooth ER (often tubular) is usually the site for lipid synthesis and abundant in some specialized cells functioning in detoxification (liver), and the site for Ca2+ storage (skeletal muscle).

4.4.4 Smooth ER often generates transport vesicles 泡囊 that fuse with other membrane systems in the cell (usually the Golgi apparatus for specific targeting).

4.5 Golgi Apparatus

4.5.1 It consists of a stack of flattened membrane cisternae 内质网液泡 surrounded by many small vesicles.

4.5.2 It is structurally and functionally asymmetric, with the cis side neighboring the ER and the trans side facing the plasma membrane.

4.5.3 Proteins and lipids move through the Golgi apparatus, entering from the cis side and exiting from the trans side. During this process, they are extensively modified, e.g., glycosylated 糖基化 , sulfated 硫酸化 , phosphorylated 磷酸化 , etc.

4.5.4 The small vesicles serve as transportation tools.

4.5.5 The newly synthesized proteins are “addressed” for their destinations such as various organelles, plasma membranes, and secretion to extracelluar matrix. (sorting and targeting)

4.5.6 It is the place that supplies new cell walls and membranes after cell division in plants (so it is usually more extended, named as dictyosome高尔基体 ).

4.6 Mitochondria 线粒体

4.6.1 It is surrounded by two membranes, a smooth outer membrane and an infolded inner membrane (forming many cristae 突起 ).

4.6.2 The space surrounded by the inner membrane, called matrix, is gel 凝胶 like and contains hundreds of enzymes catalyzing the energy yielding 灵活的 reactions.

4.6.3 The energy carrier (ATP) is generated on the inner membrane (ATP synthase 合酶 , a H+ pump)

4.6.4 It contains its own DNA, RNA, ribosomes核糖体 (in the matrix)! It duplicates itself when cell divides.

4.7 Lysosomes 溶酶体

4.7.1 They are small spherical vesicles surrounded by a single membrane, and are generated from the Golgi apparatus.

4.7.2 They do not have any structural characteristics and are identified by staining for specific enzymes (usually acid phosphatase 磷酸酶 ).

4.7.3 It contains all kinds of acidic hydrolytic 水解 enzymes capable of digesting 消化 all four major biomolecules (proteins, nucleic acids, carbohydrates, and lipids 脂 )

4.7.4 It functions as the recycling center of a cell (hydrolyzes biomolecules collected through endocytosis 内吞作用 , phagocytosis 吞噬作用 , or autophagy 自吞噬 )

4.7.5 Vacuoles 液泡 in plant cells play similar recycling roles.

4.8 Peroxisomes 过氧化物酶体

4.8.1 They are morphologically 形态上 similar to lysosomes 溶酶体 , also being single-membrane surrounded particles 微粒 .

4.8.2 They are specialized in carrying out oxidative reactions using molecular oxygen (O2), generating damaging free radicals and hydrogen peroxide 过氧化氢 (H2O2), which are appropriately destroyed by catalases过氧化氢酶 .

4.8.3 In germinating 培养 plant cells, the glyoxylate 乙醛酸 cycle, converting 转变 the stored fats into carbohydrates, occurs in the peroxisomes 过氧化物酶体 (thus also named as glyoxysomes 乙醛酸循环体 ).

Communication across membranes

4.9 Chloroplasts 叶绿体

4.9.1 They are structurally and functionally similar to mitochondria 线粒体 , also surrounded by two membranes and transforming energy (from sunlight to chemical energy).

4.9.2 But the inner membrane does not form infoldings, instead, there is a third membrane system forming a set of flattened disclike sacs 囊 , named thylakoids 类囊体 .

4.9.3 Many thylakoids are piled up to form a granum 叶绿体基粒 (grana).

4.9.4 The space between the inner membrane and the thylakoid membrane, named as the stroma 基质 , is very similar to the matrix in mitochondria 线粒体 , containing various enzymes involved in photosynthesis 光合作用 .

4.9.5 Chloroplasts 叶绿体 , like mitochondria 线粒体 , contain their own DNA, RNA, and ribosomes 核糖体 in the stroma.

4.10 The endosymbiont 内共生体 hypothesis 假说4.10.1 Mitochondria 线粒体 and chloroplasts evolv

ed 进化 from aerobic 需氧的 and photosynthetic bacteria that took up endosymbiotic 内共生 residence (by engulfing) in early eukaryotic 真核的 cells more than a billion years ago.

4.10.2 The main evidence supporting this hypothesis:

4.10.2.1 similarity in sizes

4.10.2.2 striking similarity in some enzymes involved in oxidative phosphorylation 磷酸化作用

4.10.2.3 similarity in ribosomes (both in size and antibiotic 抗生素 sensitivity).

4.10.2.4 extensive 广泛的 similarity in DNA sequences.

4.10.3 There is no obvious evolutionary advantage for the modern mitochondria 线粒体 and chloroplasts 叶绿体 to still keep their own genetic system, which is costly to maintain. Therefore, the host system is used in endosymbiont 内共生 existence.

4.10.4 The organelle’s 细胞器 genetic systems are probably an evolutionary dead end. It is because the organelles did not have the chance (or the need, if that matters) to complete the transfer of their genes into the eukaryotic 真核 nucleus.

4.11 The cytoskeleton 细胞骨架 system

4.11.1 A dynamic (changing as needed) network of protein filaments extends throughout the cytoplasm 细胞质 of an eukaryotic 真核 cell.

4.11.2 It controls cell shapes, motility 游动性 , intracellular organization, and cell division 分裂 .

4.11.3 This structure was discovered in the 1970s using high-voltage electron microscopes, before which it was believed that the cytosol 细胞质溶胶 was an unorganized mixture of biomolecules.

4.11.4 These protein filaments can be divided into three groups: actin 肌动蛋白 filaments or formerly microfilaments(~7 nm in diameter), microtubules 微管 (~25 nm), and intermediate filaments(~10 nm).

4.11.5 The actin filament contains two chains of globular 球形的 actin molecules twisted one another in a helical 螺旋状的 manner. The actin monomers 单体 assemble and disassemble. Many proteins(e.g., fodrin 胞衬蛋白 , fil-amin 细丝蛋白、肌动蛋白 )can specifically bind to actin to org-anize its structure(crosslinking, severing, capping)and to affect its function.Cytochalasins 细胞分裂抑制素 (fungi 真菌 alkaloids 生物碱 )blocks actin polymerization 聚合作用 and inhibits cytokinesis 细胞分裂 , phagocytosis 吞噬作用 , amoe-boid 变形虫状的 movement, but not chromatid 染色单体 segregation 分离 (microtubules 微管 ).

4.11.5 (cont’d) Actin filaments act as tracks for cytoplasmic streaming, with many organelles and vesicles 小泡 moving towards one direction. Actin filaments are rich and important in skeletal muscles, intestinal microvilli 微绒毛 , etc. Actin is the most abundant protein in most eukaryotic 真核 cells.

4.11.6 A microtubule is a hollow cylinder (of ~200 nm to 25 nm in length) consisting of 13 rows of tubulin 微管蛋白 dimers 二聚体 (fig.).

4.11.6.1 Microtubules usually radiate out from a microtubule organizing center (two centrioles 中心粒 in animal cells) and serve as tracks for intracellular movements.

4.11.6.2 Colchicine, a poisonous plant alkaloid (inhibitor), causes mitotic spindle to disappear and blocks cell mitosis at the metaphase stage (blocking polymerization).

4.11.6.3 Microtubules and associated proteins are responsible for the motion of cilia (e.g., on trachea and oviduct) and eukaryotic flagella (sperm tail, some protists such as trypanosomes).

4.11.7 Intermediate filaments (IF) are strong, ropelike 绳状的 polymers of fibrous proteins that resist stretch and play a structural or tension-bearing role.

4.11.7.1 They were thought to be derived from already identified cytoskeleton 细胞骨架 elements like microtubules and actin filaments.

4.11.7.2 Different IF proteins (e.g., vimentin 波形蛋白 in endothelial 内皮 cells, desmin 结蛋

白 in muscle cells,keratins in certain epidermal cells of vertebrates) are found in different cell types.

4.11.7.3 IF made of keratins are the main components of hair, nails, and horns.

Different organizations

ATP hydrolysis and cycles of conformational changes

A gallery of structurally and functionally differentiated cells

Secretorycell of thePancreas胰腺

Portion of a skeletal muscle cell

Collenchyma cells of a plant stem 茎

Human sperm cells

Mature human erythrocytes

Human embryo at the two-cell stage

In animal cells

Water-tightseal

Reinforced byCytoskeletons细胞骨架Flow of ions and electricalCurrents 电流

In plants, passage formetabolites andproteins

5. A rough analogy between the structure and function of the cell and the human society

5.1 Nucleus: the highest administrative section of the society where the blueprint of the society is kept.5.2 Mitochondria and chloroplasts: the power plant.5.3 Golgi Apparatus: the post office5.4 Cytoskeleton system: the highways (transportation)5.5 Lysosomes: the recycling center5.6 ER: the training and education center5.7 Plasma membrane: the border line5.8 Like the human society, the cytoplasm is crowded, highly organized, and dynamic.

6. Viruses are parasites of cells

6.1 Viruses are supramolecular complexes that can replicate themselves in appropriate host cells.

6.1.1 Viruses usually consist of a nucleic acid molecule surrounded by a protective protein shell, and in some cases, also a membrane envelop.

6.1.2 Viruses exist as nonliving particles (virions) with specific structures and compositions when present outside their host cells

6.2 Hundreds of different viruses have been discovered and, according to their host range, are usually classified as bacteria viruses (bacteriophage, or phage), animal viruses, and plant viruses.

6.3 Some viruses cause diseases to their hosts.

6.4 Biochemists have learned much about how genetic information is duplicated and expressed by studying viruses due to their simplicity.

6.5 Viruses are very likely evolved after cells appeared. Most viruses probably evolved from plasmids (or transposons, introns, …etc).

A gallery of viruses

Turnip yellow mosaic virus (spherical), tobacco mosaicvirus (long cylinder), and bacteriophage T4 (spidery legs)

HIV leaving an infected T lymphocyte of

the immune system

Filamentous phage fd

Molecular surface model of the canine parvovirus

Human poliovirus (type 2), a picornavirus

Bacteriophage X174

7. Biochemical studies of cells

7.1 Representative homogeneous viruses, cells, tissues, and organisms are usually studied for understanding the chemical basis of life.

7.2 Various parts of the cell are separated after being carefully broken. Usually differential and isopycnic centrifugations are used.

7.3 Individual biomolecules can be further purified and studied using modern physical and chemical methods.

7.4 What is true in vitro may not be true in vivo! Deducing what might be happening in a living organism from observations of in vitro studies has to be practiced with great caution!