Post on 21-Jan-2023
The Structure and Function of
Macromolecules
林谷峻Gu-Jiun Lin
國防醫學院 生物及解剖學研究所
National Defense Medical Center
Graduate Institute of Biology and Anatomy
Office: 5358
Phone: 18709
e-mail: lingujiun@mail.ndmctsgh.edu.tw
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Overview:Carbon—The Backbone of
Biological Molecules
What properties make carbon the basis of the life
Although cells are 70–95% water, the rest consists mostly of carbon-
based compounds
Carbon is unparalleled in its ability to form large, complex, and diverse
molecules
Proteins, DNA, carbohydrates, and other molecules that distinguish living
matter are all composed of carbon compounds
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Concept 4.1: Organic chemistry is the study
of carbon compounds (有機化學)1. Organic compounds有機化合物--range from simple molecules to colossal
ones
2. Most organic compounds contain hydrogen atoms in addition to carbon atoms
3. Vitalism (生機說) was the belief in a life force outside the jurisdiction of physical and chemical laws
4. It was thought that organic compounds could only be produced in living organisms
5. Vitalism was disproved when chemists were able to synthesize organic compounds
Carbon can bond to four other atoms or
groups of atoms, making a large variety of
molecules possible.
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Organic Molecules and the Origin of Life on Earth
EXPERIMENT
In 1953, Stanley Miller simulated what were
thought to be environmental conditions on the
lifeless, primordial Earth. As shown in this
recreation, Miller used electrical discharges
(simulated lightning) to trigger reactions in a
primitive “atmosphere” of H2O, H2, NH3
(ammonia), and CH4 (methane)—some of the
gases released by volcanoes.
• Stanley Miller’s classic experiment demonstrated the abiotic synthesis of
organic compounds
• Experiments support the idea that abiotic synthesis of organic compounds,
perhaps near volcanoes, could have been a stage in the origin of life
• Pioneers of organic chemistry helped shift the mainstream of biological
thought from vitalism to mechanism (機械論)
• Mechanism is the view that physical and chemical laws govern all natural
phenomena
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A variety of organic compounds that
play key roles in living cells were
synthesized in Miller’s apparatus.
RESULTS
CONCLUSION
Organic compounds may have been
synthesized abiotically on the early Earth,
setting the stage for the origin of life.
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Concept 4.2: Carbon atoms can form diverse
molecules by bonding to four other atoms
The formation of bonds with carbon : tetravalence 四價a. Organic compounds
The shapes of three simple organic molecular.
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B.Molecular diversity arising from carbon skeleton
variation
1.Hydrocarbons 碳氫化合物
The role of hydrocarbons in fats
1. Hydrocarbons are organic molecules
consisting of only carbon and
hydrogen
2. Many organic molecules, such as
fats, have hydrocarbon components
3. Hydrocarbons can undergo reactions
that release a large amount of energy
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2. Isomers 同分異構物
Three types isomers, compounds with
the same molecular formula but different
structures
• Isomers are compounds with the
same molecular formula but
different structures and properties
– Structural isomers (結構異構物) have different covalent
arrangements of their atoms
– Cis-trans isomers (順式及反式異構物或幾何異構物 )
have the same covalent bonds
but differ in spatial
arrangements
– Enantiomers (鏡像異構物)
are isomers that are mirror
images of each other : D-
(dextro右) form; L-(levo左)
form.
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The pharmacological importance of enantiomers
• Enantiomers are important in the pharmaceutical industry
• Two enantiomers of a drug may have different effects
• Usually only one isomer is biologically active
• Differing effects of enantiomers demonstrate that organisms are sensitive
to even subtle variations in molecules
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Concept 4.3: A few chemical groups are key to
molecular function
A comparison of chemical groups of female (estradiol) and male (testosterone)
A. The chemical groups most important in the processes of life Estradiol and testosterone are both steroids with a common carbon skeleton,
in the form of four fused rings
These sex hormones differ only in the chemical groups attached to the rings
of the carbon skeleton
Distinctive properties of organic molecules depend on the carbon skeleton and
on the chemical groups attached to it
A number of characteristic groups can replace the hydrogens attached to
skeletons of organic molecules
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Functional groups are the parts of molecules involved in chemical reactions官能基
*Polar, hydrophlic極性的,親水性的
1. Hydroxyl group羥基, -OH;alcohol
2. Carbonyl group羰基, >C=O;ketones, aldehydes
3. Carboxyl group羧基, -COOH;carboxylic acids
4. Amino group胺基, -NH2;amines
5. Sulfhydryl硫氫基, -SH;thiol
6. Phosphate group磷酸基, -OPO32-;organic phosphate
7. Methyl group 甲基-CH3, methylated compounds
FUNCTIONAL
GROUP
(may be written HO )
HYDROXYL CARBONYL CARBOXYL
OH C
O O
C
OH
AMINO SULFHYDRYL PHOSPHATE
(may be written HS )N
H
H
SH
O P
O
OH
OH
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B. ATP: An important source of energy for cellular processes
• One phosphate molecule, adenosine triphosphate (ATP), is the primary
energy-transferring molecule in the cell
• ATP consists of an organic molecule called adenosine attached to a string
of three phosphate groups
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You should now be able to:
• Explain how carbon’s electron configuration explains its
ability to form large, complex, diverse organic molecules
• Describe how carbon skeletons may vary and explain how
this variation contributes to the diversity and complexity of
organic molecules
• Distinguish among the three types of isomers: structural,
geometric, and enantiomer
• Name the major functional groups found in organic
molecules; describe the basic structure of each functional
group and outline the chemical properties of the organic
molecules in which they occur
• Explain how ATP functions as the primary energy transfer
molecule in living cells
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Ch5 Biological Macromolecules
and LipidsOverview: The Molecules of Life
All living things are made up of four classes of large biological molecules: carbohydrates, lipids, proteins, and nucleic acids
Macromolecules are large molecules and are complex
Large biological molecules have unique properties that arise from the orderly arrangement of their atoms
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Concept 5.1: Macromolecules are polymers, built from monomers大分子,聚合物,單體
Three of the four classes of life’s organic molecules are polymers 1.
carbohydrates, 2.proteins, and 3. nucleic acids
A. The synthesis and breakdown of polymers Condensation reaction (dehydration reaction) 縮合反應,脫水反應 Hydrolysis 水解
B. The diversity of polymers1. Each cell has thousands of different kinds of macromolecules.2. This diversity comes from various combinations of the 40–50 common
monomers and some others that occur rarely
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Concept 5.2: Carbohydrates serve as fuel and building material 醣類A. Sugars1. Monosaccharides單醣類--(CH2O)n;are the simplest sugars, be used
for fuel, be converted into other organic molecules and are combined into polymersa. Carbonyl group (C=O) and hydroxyl group (-OH) 羰基,羥基b. Aldose and ketose醛醣及酮醣
- glucose and galactose葡萄糖及半乳糖
- fructose 果糖
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B. Polysaccharides 多醣類1. Storage polysaccharides 儲存性多醣a. Starch 澱粉
• α glucose• amylose and amylopectin
直鏈澱粉,分枝澱粉b. Glycogen 肝糖
31Starch and cellulose structure
•Polymers with glucose are helical; Polymers with glucose are straight
2. Structural polysaccharides 結構性多醣a. Cellulose 纖維素
- β glucose
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Cellulose digesting prokaryotes are found
in grazing such as this cow
1014 kg/year
Enzymes that digest starch by hydrolyzing linkages can’t hydrolyze linkages in
cellulose
The cellulose in human food passes through the digestive tract as “insoluble fiber”
Some microbes use enzymes to digest cellulose
Many herbivores, from cows to termites, have symbiotic relationships with these
microbes
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b. Chitin 幾丁質
Chitin, another structural
polysaccharide, is found in
the exoskeleton of
arthropods
Chitin also provides
structural support for the cell
walls of many fungi
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Concept 5.3: Lipids are a diverse group of hydrophobic molecules 脂質,疏水性的A. Fats 脂肪:Lipids are the one class of large biological molecules that
do not consist of polymers; share the common trait of being hydrophobic
1. Triacylglycerol 三醯甘油(or triglyceride 甘油三酸脂)a. Glycerol and fatty acids 甘油及脂肪酸
b. Ester linkage 酯鍵
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B. Phospholipids 磷脂:Cell membranesPhospholipids have only two fatty acids, have a phosphate group instead of a third fatty acid
1. Hydrophobic tail and hydrophilic head 親水性的
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2. Phospholipid bilayer 磷脂雙層
Bilayer structure formed by self-assembly of phospholipids
in an aqueous environment
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C. Steroids 類固醇: Steroids are lipids characterized by a
carbon skeleton consisting of four fused rings
1. Cholesterol (膽固醇), a type of steroid, is a component in animal cell membranes and a precursor from which other steroids are synthesized
2. Sex hormones
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Concept 5.4: Proteins include a diversity of structures, resulting in a wide range of functions
Proteins account for more than 50% of the dry mass of most cells.
Protein functions include structural support, storage, transport, cellular communications, movement, and defense against foreign substances
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•Enzymes酶 are a type of protein that acts as a catalyst催化劑 to speed up chemical reactions
•Enzymes can perform their functions repeatedly, functioning as workhorses that carry out the processes of life
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b. The 20 amino acids of proteins:differ in their properties due to differing side chains, called R groups
- nonpolar, hydrophobic 非極性
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2. Polypeptides (Amino acid polymers)a. Peptide bond 胜肽鍵b. Amino end (N-terminus)
and carboxyl end (C-
terminus)N端及C端
Frederick Sanger
1940~1950 insulin
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The exact match of shape between an antibody and the particular
foreign antigen
•The sequence of amino acids determines a protein’s three-dimensional
structure, and the structure determines its function
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b. Secondary structure次級結構• hydrogen bonds between the
polypeptide backbone• helix or pleated sheet 螺旋或褶板
x
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c. Tertiary structure三級結構• interactions between the side chains of amino acids
*weak interactions: hydrophobic interactions, hydrogen bond,ionic bond
*covalent linkage: disulfide bridges雙硫鍵
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3. What determines protein structure?a. Factors determining conformation: physical and chemical
conditions of the protein’s environment.
b. Denaturation and renaturation 變性及復性
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b. X-ray crystallography is used to determine a protein’s
three-dimensional (3D) structure
NMR:
Nuclear magnetic resonance
Roger Kornberg
1950
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Concept 5.5: Nucleic acids store, transmit, and help express hereditary information
(Central dogma)
A. The roles of nucleic acids• There are two types of nucleic acids
– Deoxyribonucleic acid (DNA)
去氧核糖核酸
– Ribonucleic acid (RNA)
核糖核酸
• DNA provides directions for its own
replication
• DNA directs synthesis of messenger RNA
(mRNA) and, through mRNA, controls
protein synthesis
• The mRNA molecule interacts with the
cell’s protein-synthesizing machinery to
direct production of a polypeptide
• The flow of genetic information can be
summarized as DNA → RNA → protein
• This process is called gene expression (基因表達)
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B. The Components of Nucleic Acids
Nucleotide monomers 核苷酸:are made up of nucleosides核苷and phosphate groupsa. Nitrogenous bases 含氮鹼基• pyrimidines 嘧啶類
*cytosine (C), thymine (T),uracil(U)胞嘧啶,胸腺嘧啶,脲嘧啶
• purines 嘌呤類*adenine (A), guanine (G)腺嘌呤,鳥糞嘌呤
b. Pentose (five-carbon sugar)五碳醣
• ribose 核糖• deoxyribose 去氧核糖c. Phosphate group 磷酸根
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C. Nucleotide polymers: are made up of nucleotides
linked by the–OH group on the 3´ carbon of one nucleotide and
the phosphate on the 5´ carbon on the next.
*Phosphodiester linkage 磷酸二酯鍵
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RNA molecules usually exist as single polynucleotides chains
DNA molecules have two polynucleotides spiraling around an imaginary axis, forming a double helix
In the DNA double helix, the two backbones run in opposite 5→ 3directions from each other, an arrangement referred to as antiparallel逆向平行
One DNA molecule includes many genes
The nitrogenous bases in DNA pair up and form hydrogen bonds: adenine (A) always with thymine (T), and guanine (G) always with cytosine (C)
Called complementary base pairing
Complementary pairing互補can also occur between two RNA molecules or between parts of the same molecule
In RNA, thymine is replaced by uracil (U)
so A and U pair
D. The Structures of DNA and RNA Molecules
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Concept 5.6: Genomics and proteomics have transformed biological inquiry and applications
Once the structure of DNA and its relationship to amino acid sequence was
understood, biologists sought to “decode” genes by learning their base
sequences
The first chemical techniques for DNA sequencing were developed in the
1970s and refined over the next 20 years
It is enlightening to sequence the full complement of DNA in an organism’s
genome
The rapid development of faster and less expensive methods of sequencing
was a side effect of the Human Genome Project
Many genomes have been sequenced, generating reams of data
Bioinformatics uses computer software and other computational tools to deal
with the data resulting from sequencing many genomes
Analyzing large sets of genes or even comparing whole genomes of different
species is called genomics (基因體學)
A similar analysis of large sets of proteins including their sequences is called
proteomics (蛋白質體學)
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MAKE CONNECTIONSContributions of Genomics and Proteomics to Biology
Paleontology Evolution
HippopotamusShort-finned pilot whale
Medical Science Conservation BiologySpeciesInteractions
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DNA and proteins as tape measures of evolution 測量尺1. Sequences of genes and their protein products document the hereditary background
of an organism
2. Linear sequences of DNA molecules are passed from parents to offspring
3. We can extend the concept of “molecular genealogy” to relationships between
species
4. Molecular biology has added a new measure to the toolkit of evolutionary biology
Analyzing polypeptide sequence data
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You should now be able to:
•List and describe the four major classes of molecules
•Describe the formation of a glycosidic linkage and distinguish
between monosaccharides, disaccharides, and polysaccharides
•Distinguish between saturated and unsaturated fats and between
cis and trans fat molecules
•Describe the four levels of protein structure
•Distinguish between the following pairs: pyrimidine and purine,
nucleotide and nucleoside, ribose and deoxyribose, the 5 end and
3 end of a nucleotide
The Ends