Đại phân tử sinh học & liên kết hóa học yếu pps

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DAI PHAN TU SINH HOC & LIEN KET HOA HOC YEU

œ Các mức độ tổ chức của sinh vật os Cac dai phan tu sinh hoc :

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PHAN LOAI SINH GIOI Animals Plants Fungi Ciliates Euglena Microsporidia EUKARYOTA Slime molds | Diplomonads (Giardia lamblia) E coli Sulfolobus EUBACTERIA | ARCHAEA B subtilus Thermococcus Thermotoga i | Methanobacterium : Halococcus Flavobacteria Green sulfur Halobacterium bacteria Borrelia ee s rs burgdorferi J

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CAC MUC DO TO CHUC CUA SINH VAT The inorganic precursors: (18-64 daltons) Carbon dioxide, Water, Ammonia, Nitrogen(Ng), Nitrate(NOg~) Carbon dioxide ‡ Metabolites: (50-250 daltons) Pyruvate, Citrate, Succinate, Glyceraldehyde-3-phosphate, _—": 9 Fructose-1,6-bisphosphate, H / - 3-Phosphoglyceric acid y Pyruvate | Building blocks: H (100-350 daltons) ÖH 9 Amino acids, Nucleotides,

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KiCH THUGC NGUYEN TU DEN SINH VAT DA BAO ¥ > % ị s 3 ` ` + ; “at "ú,ú: Aya ~~ ` L 5 ae 5 oa số" c ® _ Pm b oie - ~ ’ ae ee 2 a 4 ˆ BN s ‹ - 7 - si Ò L4 s J 4 ` ị / 7 `» › - i ‘ ẹ ° _ ` ¬ i ` A 4 Nanometers Micrometers Millimeters Meters Small Assemblies molecules pacro-

Atoms molecules Cells Multicellular organisms

Glucose Ribosome Bacterium C elegans Newborn human

: Red blood

C-C bond Hemoglobin | Mitochondrion all Bumblebee

1079m 103m 108m 10m 108m 10°° m 104m 103m 102m 101m 10° m

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TE BAO PROKARYOTE & EUKARYOTE

(a) Prokaryotic cell (b) Eukaryotic cell = Periplasmic space and cell wall

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CAC DAI PHAN TU SINH HOC

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DUONG CH;OH CH;OH CH;OH CH;OH O O HO O O HO ⁄4 OH i 7 OH HO JI | i 7 OH OH H IP + OH H > On H YP O OH H H H HO H H H H H OH H OH H OH H OH

Galactose Glucose Lactose

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LIPIDS G—0—G—H | O i CH, —O— P—O— CH,CH,—N+*+-CH, | om So i iF 22772 Se aR Re Ne as SS 2 Phosphatidylcholine CH, 3 GLYCEROLIPIDS WITH OTHER HEAD GROUPS: O + —O—P—O— CH,CH,— NH, | oF Phosphatidylethanolamine O —O—P—O— CH, | o- H—C—OH O —O—P—O— CHy O COO —O—P—O—CH,—CH | |+ O- Diphosphatidylglycerol (Cardiolipin) om NH, Phosphatidylserine - : it | oO ok HO OH || H —O—P—O—CH,— CH —CH, —O—P—O | | | O- OH OH O- Phosphatidylglycerol Phosphatidylinositol

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LIPIDS

Number

of Carbons Common Name Systematic Name Symbol Structure

Saturated fatty acids

12 Lauric acid Dodecanoic acid 12:0 CHs(CHo) ;gCOOH 14 Myristic acid Tetradecanoic acid 14:0 CHs(CH›)¡sCOOH 16 Palmitic acid Hexadecanoic acid 16:0 CHs(CHo) ;4,COOH 18 Stearic acid Octadecanoic acid 18:0 CH;s(CHs)¡¿COOH 20 Arachidic acid Eicosanoic acid 20:0 CHs(CHo»);gCOOH 22 Behenic acid Docosanoic acid 22:0 CHs(CHo») 9 COOH 24 Lignoceric acid Tetracosanoic acid 24:0 CHs(CHo).0 COOH Unsaturated fatty acids (all double bonds are cis)

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LIPID VA MANG SINH HOC ~ Hydrophilic head group Hydrophobic > fatty acyl tails Glycerophospholipid tu xxx xxx x24 Phospholipid bilayer Water-seeking Cholesterol head group

Fatty acid chains

-atty chains

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CAC AMINO ACID THONG DUNG HYDROPHOBIC AMINO ACIDS G00" G00" — GOO” Foo” GOO” mẽ GOO” HN TH "HSN CTH THạN—C—H “HSN CTH "HN CTH HN TH “NCH "HN CTH CH; we — 2 ge CH; CH; GMa HạC CHạ CH, JH CHa C=CH CH OH

Alanine Valine Isoleucine Leucine Methionine Phenylalanine Tyrosine Tryptophan (Ala or A) (Val or V) (Ile or 1) (Leu or L) (Met or M) (Phe or F) (Tyr or Y) (Trp or W)

1 Acidic amino acids Polar amino acids with uncharged R groups Basic amino acids COO” COO- + —f '— + —f + —f—— COO” COO” COO" H2N ữ H HạN ĩ H HạN—C—H CH CH H—C—OH ` ` "` (ˆ L7 COO” OH CH CH, | CH, | CH, | Aspartate Serine Threonine số CH, CH, C—NH (Asp or D) (Ser or S) (Thr or T) | | | N CH (He Ge Ld COO~ COO~ COO~ ihe là HH *HạN—C—H THẠN—Ệ—H “HN CH NH‡ c= NH CH, CH, CH, | | NH, | CH, C CH; : Pa istidi Ñ

Lysine Arginine Histidine — H NO No |

(Lys or K) (Arg or R) (His or H) COO - ZN

HạN O

Glutamate Asparagine Glutamine

SPECIAL AMINO ACIDS (Glu or E) (Asn or N) (Gin or Q)

COO™ COO COO-

a HạN——C—H Fi HạN—C—H | | -H A FIGURE 2-13 The 20 common amino acids used to - - N SỰ có oy a | | *HzN CH, build proteins The side chain (R group; red) determines the CH, H | characteristic properties of each amino acid and is the basis bu HạC CH, for grouping amino acids into three main categories: hydrophobic,

- - - hydrophilic, and special Shown are the ionized forms that exist at

Cysteine Glycine Proline T\ - Tự TC cay - -

(Cys or C) (Gly or G) (Pro or P) the pH (<7) of the cytosol In parentheses are the three-letter and

one-letter abbreviations for each amino acid

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(a) Primary structure

Amino end H O Ro H O Ha H oO Re Carboxyl end Hl | H | | HY so "GAC BAC CAU TRÚC CUA POLYPEPTIDE ro HA og ott Hạ ff H fyi ho H ff H ty Mo Ry 5 (b) Secondary structure

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CAC BAC CAU TRUC CUA CHYMOTRYPSIN

(a) Chymotrypsin primary structure

H,N-CGVPAIOPVL | pSGL[SR]IVNGEggpEAVPGSWPWQ.,VSLODKTGFH yyGGSLINEN.,WVV TAAHCGV ¢9 PTSDVVVAGE-7)FDOGSSSEKI p OKLKIA

KVFKogNSKYNSLTIN j 99 NDITLLKLST , }pAASFSQTVSA } 99 VCLPSASDDF 3pAAGTTCVT TG, 4p WGLTRY[TN]AN) 59LPSDRLOQQASL | 69PLLSNTNCK Ky 79 YWGTKIKDAM) gol CAGASGVSS 99 CMGDSGGPLV 99g CKKNGAWTLYV ,, GIVSWGSSTC5o9STSTPGVYA Roo VT ALVNWVQQ,,4,3TLAAN-COOH

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CAU TRUC CUA TO NHEN lo VN CAE cd

(a) Spider web (b) Radial strand | ` ©

(c) Ordered f-sheets surrounded (d) B-sheets impart strength and

by disordered o-helices and o-helices impart flexibility

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MOT SO PROTEIN

Protein M, Number of Residues per Chain Subunit Organization

Insulin (bovine) 5,733 21 (A) ap

30 (B)

Cytochrome c (equine) 12,500 104 ay

Ribonuclease A (bovine pancreas) 12,640 124 ay

Lysozyme (egg white) 13,930 129 ay Myoglobin (horse) 16,980 153 ay Chymotrypsin (bovine pancreas) 22,600 13 (a) apy 132 (B) 97 (y) Hemoglobin (human) 64,500 141 (a) Qo Bo 146 (B) Serum albumin (human) 68,500 550 đi Hexokinase (yeast) 96,000 200 a4 y-Globulin (horse) 149,900 214 (a) œsBs 446 (8)

Glutamate dehydrogenase (liver) 332,694 500 a

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CAC CHUC NANG CUA PROTEIN

(a) (MOLECULAR STRUCTURE Primary (sequence) Cấu trúc bậc 1

Secondary (local folding) Cấu trúc bậc 2

Tertiary (long-range folding) Cấu trúc bậc 3

Quaternary (multimeric organization) Cấu trúc bậc 4 << Supramolecular (large-scale assemblies) Phức hợp đại phân tử (b) e | — GD

Diéu hoa ) Regulation | Signaling Os Tin hiéu té bao

Structure FUNCTION Transport

° ? Cấu trúc | Movement Oo Catalysis 4 | I) Vận chuyên

= @¢

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MOT SO BASE BAT THUONG S O Hw Ho \ ` > ( an N ¬ N wi se hb se 4-Thiouridine (S*U) Enosine () Đ CH; | | ( an N Ise Ribothymidine (T)

FIGURE 11.26 © Unusual bases of RNA—

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DNA C in phosphate ester chain Cand N in bases Sugar—phosphate backbone Sugar—phosphate backbone A nucleotide monophosphate unit (a)

Figure 7-9 Two representations of the DNA double helix [Part b from C Yanofsky, "Gene Structure and Protein Structure." © 1967 by Scientific American, Inc All rights reserved]

(a) BDNA (b) ADNA (c) ZDNA

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'mRNA has a sequence of bases that represent protein

HN size range 500-10,000 bases ÔN,

tRNA is a small RNA with extensive secondary structure: size range 74 - 95 bases 5'

Amino acid stem

Darm swe arm RNA

Anticodon arm

2D projection has 2 perpendicular duplexes

Backbone follows L-shaped structure R I C a NH Ke Amino acid 6

» TwC arm Amino acid stem

major rRNAs have extensive

secondary structure and D arm

associate with proteins

to form the ribosome: Anticodon ar

size range 1500-1900 (small rRNA) ©witualext www.©@FIEO com Anticodon

and 2900-4700 (large rRNA)

— Number of Percentage of

Sedimentation Nucleotide Total Cell

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TÍNH ON DINH CUA PHAN TU DNA & RNA RNA: A C U G oO © oO oO | li | oO I etc etc, To | ~O | oO om oO- œ

A nucleophile such as OH™ can absiract the H of the 2'-OH, generating 2'-O7 which attacks the 5* P of the phosphodiester bridge: A C & G oO O o. || “PL -| “PL etc elc, ie) | 90 oT so A U G O O o | o le o | ee etc | “oO | “oO oO7 œ A L G rế O oO he oO

On, I mn On | etc

etc, xe) a’ | Oo oO œ _* ), backbone cleaved 9 A A C oO O—P—- oO Ọ | O~ o.| etc etc, | “oO œ

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CAC LIEN KET HOA HOC YEU

Strength Distance

Force (kJ /mol) (am) Description

Van der Waals interactions 0.4—4.0 0.2 Strength depends on the relative size of the atoms or molecules and the distance between them The size factor determines the area of contact between two molecules: The greater the area, the stronger the interaction

Hydrogen bonds 12-30 0 Oo Relative strength is proportional to the polarity of the H bond donor and H bond acceptor More polar atoms form stronger H bonds

Strength also depends on the relative polarity of the interacting charged species Some ionic interactions are also H bonds:

—NH;` OOC—

Hydrophobic interactions <40 — Force is a complex phenomenon determined by the degree to which the structure of water is disordered as discrete

hydrophobic molecules or molecular regions coalesce 9 or Ionic interactions 20 0 Noncovalent interactions Covalent bonds A A f 1 ¢ ` Electrostatic van der Hydrogen Waals bonds

Thermal Hydrolysis of ATP

energy phosphoanhydride bond C-C C=C

| | |

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LIEN KET VAN DER WAALS

& LIEN KET HYDRO => — Covalent van der Waals radius radius (0.062 nm) (0.14 nm) ồ— ð+ Anồ— ồ— ð+ - Aồ— D — LỊ sec š A ——— D —H ee+eane *, A ì _— Hydrogen bond (a) (b) Twat el O—H -: O—H ng :O—H —H :- : bot hice

sors H—O? H—O: =O O—CH,

Water-water Methanol-water Methylamine-water Nonpolar substance Highly ordered water molecules Unaggregated state:

Water population highly ordered Lower entropy; energetically unfavorable Hydrophobic aggregation Waters released into bulk solution Aggregated state:

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CAU TRUC DNA BO GENE 6 PROKARYOTE & EUKARYOTE

Chromosomal

Bacterium segment

OO na OC ee 20 kb

eee eee ee eee eee ớ

Gene Gene Gene Gene Gene Gene Gene Gene Gene Gene Gene Gene Gene Yeast

im "Am a LTD ee ee | 20 kb

ii =m eee Se eee ee eee eee ee eee K.ưưƯ”ÊIẬ i

Gene Gene Gene Gene Gene Gene Gene Gene Gene Gene Gene

Drosophila

= " = _ = FF 8 ee | a = a ee a Fe i i | 200 kb >3 = — Ga ee | ww : | pail es ae aa ae eo @Wa W á ái Á ii |

Gene Gene Gene Gene Gene Gene Gene Gene Human

’ a ee ff Pee m.pưẽ m7 sw PF ere Flt Ff re Ff 200 kb

a í ã“@ ã & & & ii @G@ moa & áâ = @ ti 8 w ai: & as & aiaa 6 =

Gene Gene Gene

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NHIEM SAC THE E COLI fog TƯ, ẹ el 2 is is a i 7 4 vi rg oe is aes 1 ~ sae —= a ages supercoiled region Figure 6.3

An electron micrograph of an £ coli chromosome showing

the multiple loops emerging from a central region

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MOT DAC TINH VAT LY CUA DNA BO GENE — > ' — lo Relative absorbance (260 nm) 1.0 70 80 90 100 Temperature (°C)

FIGURE 12.17 © Heat denaturation of DNA from various sources, so-called melting curves The midpoint of the melting curve is defined

as the melting temperature, T,, (From Marmur; J.,

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MOT DAC TINH VAT LY CUA DNA BO GENE

FIGURE 12.20 © These cot curves show the

rates of reassociation of denatured DNA from various sources and illustrate how the rate of

reassociation is inversely proportional to genome complexity The DNA sources are as follows: poly A+ poly U, a synthetic DNA

duplex of poly A and poly U polynucleotide chains; mouse satellite DNA, a fraction of mouse DNA in which the same sequence is repeated many thousands of times; MS-2 dsRNA, the double-stranded form of RNA found during replication of MS-2, a simple bac-

teriophage; T4 DNA, the DNA of a more com-

plex bacteriophage; F coli DNA, bacterial DNA; calf DNA (nonrepetitive fraction), mammalian DNA (calf) from which the highly repetitive DNA fraction (satellite DNA) has been

removed Arrows indicate the genome size (in

bp) of the various DNAs (From Britten, R J, and

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CAU TRUC BO GENE EUKARYOTE Nucleus Interphase ` chromosome Mitochondrion ca Simple- S sequence

ene DNA tư

Single families Pel, ry

copy gene Mobile

WIRLASY COCYVAWH wor Mobile™

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(a) DI NHIEM SAC CHAT - BAT HOAT NST X Random X-chromosome inactivation Mosaic

Figure 10-30 X inactivation produces the coat pattern of a

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500 genes

BO GENE Ở MỘT SỐ Extracellular (parasitic)

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cAU HOI PHAN 3

1 Vai trò của các đại phân tử sinh hoc (protein, lipid, polysaccharide, nucleic

acid) trong hệ thống sống

Đặc tính chung của các đại phân tử sinh học

Các bậc cấu trúc của protein —- Ý nghĩa của từng bậc cấu trúc ? Ví dụ về các phức hợp đại phân tử sinh học

Khác biệt về cấu trúc giữa DNA và RNA > khác biệt về tính chất hóa học Vai trò của từng loại liên kết yếu trong hệ thống sống

Những khác biệt giữa liên kết cộng hóa trị và liên kết hóa học yếu ?

Những khác biệt về bộ gene giữa prokaryote và eukaryote