Macromolecules Biology

37
Proper&es of Macromolecules Lecture 2

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Biology

Transcript of Macromolecules Biology

Page 1: Macromolecules Biology

Proper&es  of  Macromolecules  

Lecture  2  

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Overview  

Proper&es  of  Carbon    

Structure  and  Func&onal  groups    

Isomers    

Polymers    

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Carbon:  The  Backbone  of  Life  •  Living organisms consist mostly of carbon-based

compounds

•  Carbon is unparalleled in its ability to form large, complex, and diverse molecules

•  Proteins, DNA, carbohydrates, lipids, and other molecules that distinguish living matter are all composed of carbon compounds

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Biomolecules  range  in  size  and  complexity  

CO2 Carbon Dioxide

CH4N2O Urea

C6H12O6 Glucose

Large molecule Phospholipid

Macromolecules DNA

Supramolecular Complex Ribosome

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Life  exists  even  in  harsh  environments  

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Proper&es  of  Carbon  •  Contain  carbon  (C  backbone)  Why  is  carbon  so  special?  

•  Most  contain  H  and  O,  but  may  contain  other  elements      N  =  Nitrogen                  P  =  Phosphorus      S  =  Sulfur  

à  Carbon  can  form  4  covalent  bonds  –  bonds  with  up  to  4  separate  atoms  –  can  bond  with  other  C  atoms  

à   long  chains  of  carbon  atoms  

à   can  combine  with  many  other  kinds  of  atoms  

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Tetravalence  in  Carbon  Can  form  4  single  bonds  

C  

H  

H   H  

H  

Methane  

…  1  double  bond  and  2  single  bonds  

C  O  

H  

Formaldehyde  

H  

…  2  double  bonds  

C  O   O  

Carbon  dioxide  

…  1  triple  bond    &  1  single  

C  H   N  

Hydrogen  Cyanide  

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Distinctive properties of an organic molecule depends on:

1. Carbon skeleton 2. Functional

groups –  molecular components

attached to the carbon skeleton

–  responsible for characteristic chemical reactions of the molecule

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Together,  these  two  characteris&cs  give  organic  molecules  dis&nc&ve  physical  and  chemical  proper&es  and  creates  diversity  among  organic  molecules  

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Carbon Skeletons •  Made up of chains or rings •  Skeletons differ in:

–  length (number of carbons) –  branching –  number and position of double bonds

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•  In molecules with multiple carbons, each carbon bonded to four other atoms has a tetrahedral shape

•  When two carbon atoms are joined by a double bond, the molecule has a flat shape

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Hydrocarbons  •  Hydrocarbons:  Organic  

compounds  composed  only  of  carbon  and  hydrogen    (no  func&onal  groups)  

•  Covalent,  non-­‐polar  bonds  between  C  &  H  

•  Hydrocarbons  are  largely  hydrophobic  

Nucleus

Fat droplets

(b) A fat molecule (a) Part of a human adipose cell

10 µm

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Func&onal  Groups  •  Replacing  H  with  func&onal  groups  changes  

the  characteris7cs  of  the  molecule    

•  Most  func&onal  groups  form  ionic  or  hydrogen  bonds  with  other  molecules  

•  Gives  hydrophilic  proper&es  (water  soluble)    

*Some  func&onal  groups  are  non-­‐polar  and  may  cause  molecule  to  be  hydrophobic  

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example:

These subtle variations in molecular architecture influence development of anatomical and physiological differences

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Func&onal  Groups  Hydroxyl  Group  

•  R-­‐OH  or  HO-­‐R  (‘R’  =>  remainder  of  molecule)  

•  Hydroxyl  groups  are  polar  because  electronega&ve  oxygen    

•  Organic  compounds  having  only  hydroxyl  groups  are  called  alcohols  (ethanol,  methanol,  etc.)  

•  Sugars  owe  their  solubility  in  water  to  the  presence  of  hydroxyl  groups  

 

Glucose  molecule  (red=O,  light  gray=  H)  Ethanol  

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Func&onal  Groups  Carbonyl  Group:  

Aldehydes  and  Ketones  •  R-­‐C=O  •  Polar  carbonyl  groups,  such  as  aldehydes  and  ketones  a`ract  

covalent  electrons  

•  Aldehydes  contain  the  carbonyl  group  bonded  to  the  end  of  the  carbon  skeleton  

•  Ketones  have  the  carbonyl  group  bonded  within  the  carbon  skeleton  

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Func&onal  Groups  Carbonyl  Group:  Aldehydes  and  

Ketones  

Simple  sugars  can  be  aldehydes  or  ketones  

Ketone

Aldehyde

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Func&onal  Groups  Carboxyl  Group  

•  R-­‐COOH  •  Carboxyl  groups  are  weakly  acidic;  in  cells,  this  func&onal  group  is  found  in  the  ionized  form  COO-­‐  

•  An  important  part  of  amino  acids:  

All  amino  acids  contain  a  carboxyl  group  which  can  donate  a  hydrogen  

aka.  Carboxylic  acid  

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Carboxyl Group… examples

•  Other compounds that contain this functional group include:

•  Formic acid a simple organic molecule released by formicine ants (which account for about 10% of the planet’s ants) as a defense mechanism

•  Acetic acid, gives vinegar its sour taste

Formic  acid  Ace&c  acid  

h`p://www.youtube.com/watch?v=Sp8b1vVnQSY  

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Func&onal  Groups  Amino  Group  

•  R-­‐NH2  

•  Amino  groups  are  weakly  basic;  under  cellular  condi&ons  this  func&onal  group  is  found  in  the  ionized  form  NH3

+  

•  Also  an  important  part  of  amino  acids:  

All  amino  acids  contain  an  amino  group  which  can  accept  a  hydrogen  

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Func&onal  Groups  

Amino  Group  

•  Nitrogenous  bases  in  DNA  and  RNA  contain  many  amino  groups…  

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Func&onal  Groups  Phosphate  Group  

•  R-­‐PO4H2  

•  Phosphate  groups  are  weakly  acidic;  in  cells,  this  func&onal  group  contributes  a  nega&ve  charge  to  the  molecule  

•  Phosphate  groups  are  cons&tuents  of:  

Phospholipids  

•  Phosphate  group  contributes  to  the  polarity  of  the  head  region  

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Func&onal  Groups  

Phosphate  Group  

Nucleic  acids  (building  blocks  of  DNA  and  RNA)  

=>  hence,  sugar-­‐phosphate  backbone  due  to  alterna&ng  sugar  and  phosphate  

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Func&onal  Groups  Phosphate  Group  

Adenosine  Triphosphate  

•  Phosphate  groups  create  instability  in  the  molecule  which  is  responsible  for  its  high  energy  state  

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Func&onal  Groups  Sulhydryl  Group  

•  R-­‐SH  •  Helps  stabilize  protein  structure    

When  two  sulhydryl  groups  (func&onal  group  of  amino  acid  cysteine)  within  a  protein  are  facing  each  other,  they  oien  form  a  disulfide  bridge  

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STRUCTURE

CHEMICAL GROUP Hydroxyl

NAME OF COMPOUND

EXAMPLE

Ethanol

Alcohols (Their specific names usually end in -ol.)

(may be written HO—)

Carbonyl

Ketones if the carbonyl group is within a carbon skeleton

Aldehydes if the carbonyl group is at the end of the carbon skeleton

Carboxyl

Acetic acid Acetone

Propanal

Carboxylic acids, or organic acids

FUNCTIONAL PROPERTIES

• Is polar as a result of the electrons spending more time near the electronegative oxygen atom. • Can form hydrogen bonds with water molecules, helping dissolve organic compounds such as sugars.

• A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal. • Ketone and aldehyde groups are also found in sugars, giving rise to two major groups of sugars: ketoses (containing ketone groups) and aldoses (containing aldehyde groups).

• Found in cells in the ionized form with a charge of 1- and called a carboxylate ion.

Nonionized Ionized

• Acts as an acid; can donate an H+ because the covalent bond between oxygen and hydrogen is so polar:

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Amino Sulfhydryl Phosphate Methyl

Methylated compounds Organic phosphates

(may be written HS—)

Thiols Amines

Glycine Cysteine

• Acts as a base; can pick up an H+ from the surrounding solution (water, in living organisms):

Nonionized Ionized

• Found in cells in the ionized form with a charge of 1+.

• Two sulfhydryl groups can react, forming a covalent bond. This “cross-linking” helps stabilize protein structure. • Cross-linking of cysteines in hair proteins maintains the curliness or straightness of hair. Straight hair can be “permanently” curled by shaping it around curlers and then breaking and re-forming the cross-linking bonds.

• Contributes negative charge to the molecule of which it is a part (2– when at the end of a molecule, as above; 1– when located internally in a chain of phosphates). • Molecules containing phosphate groups have the potential to react with water, releasing energy.

• Arrangement of methyl groups in male and female sex hormones affects their shape and function.

• Addition of a methyl group to DNA, or to molecules bound to DNA, affects the expression of genes.

Glycerol phosphate 5-Methyl cytidine

STRUCTURE

CHEMICAL GROUP Hydroxyl

NAME OF COMPOUND

EXAMPLE

Ethanol

Alcohols (Their specific names usually end in -ol.)

(may be written HO—)

Carbonyl

Ketones if the carbonyl group is within a carbon skeleton

Aldehydes if the carbonyl group is at the end of the carbon skeleton

Carboxyl

Acetic acid Acetone

Propanal

Carboxylic acids, or organic acids

FUNCTIONAL PROPERTIES

• Is polar as a result of the electrons spending more time near the electronegative oxygen atom. • Can form hydrogen bonds with water molecules, helping dissolve organic compounds such as sugars.

• A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal. • Ketone and aldehyde groups are also found in sugars, giving rise to two major groups of sugars: ketoses (containing ketone groups) and aldoses (containing aldehyde groups).

• Found in cells in the ionized form with a charge of 1- and called a carboxylate ion.

Nonionized Ionized

• Acts as an acid; can donate an H+ because the covalent bond between oxygen and hydrogen is so polar:

STRUCTURE

CHEMICAL GROUP Hydroxyl

NAME OF COMPOUND

EXAMPLE

Ethanol

Alcohols (Their specific names usually end in -ol.)

(may be written HO—)

Carbonyl

Ketones if the carbonyl group is within a carbon skeleton

Aldehydes if the carbonyl group is at the end of the carbon skeleton

Carboxyl

Acetic acid Acetone

Propanal

Carboxylic acids, or organic acids

FUNCTIONAL PROPERTIES

• Is polar as a result of the electrons spending more time near the electronegative oxygen atom. • Can form hydrogen bonds with water molecules, helping dissolve organic compounds such as sugars.

• A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal. • Ketone and aldehyde groups are also found in sugars, giving rise to two major groups of sugars: ketoses (containing ketone groups) and aldoses (containing aldehyde groups).

• Found in cells in the ionized form with a charge of 1- and called a carboxylate ion.

Nonionized Ionized

• Acts as an acid; can donate an H+ because the covalent bond between oxygen and hydrogen is so polar:

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Review  Func&onal  groups  

OH

C O

CO

OH

NH

H

P O-

O

O

O-

SH

Sulfhydryl

Amino

Hydroxyl group

Carbonyl

Carboxyl

Phosphate

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1)  Structural  Isomers  •  Structural isomers have different covalent arrangements of

their atoms

à Isomers  are  compounds  with  the  same  molecular  formula  (i.e.  the  same  numbers  and  types  of  atoms)  but  different  structures  and  proper&es.  

à Three  important  kinds  for  Biology:  

Isomers  

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2)  Geometric  Isomers  

•  Geometric isomers have the same covalent arrangements but differ in spatial arrangements (arrangement around a double bond)

•  Double bonds are rigid and do not allow the joined atoms to rotate freely

•  As a result, two isomers are always possible if different groups are attached around a double bond

cis  isomer trans  isomer:

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Example:  Rhodopsin  

11-cis retinal

All-trans retinal

photon

•  The visual pigment rhodopsin in the human eye rotates around a double bond when hit by light at the back of the retina

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•  Enantiomers are isomers that are mirror images of each other •  Usually consists of a carbon (i.e. asymmetric carbon) attached

to 4 different functional groups

3)  Enan&omers  

•  Cells will recognize one enantiomer (i.e. biologically active) but not the other

L  isomer D  isomer

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•  Two enantiomers of a drug may have different effects

•  This demonstrates that organisms are sensitive to even subtle variations in molecules

L-Dopa (effective against Parkinson’s disease)

D-Dopa (biologically

Inactive)

Ex: L-Dopa

Example:  Drug  Enan&omers  

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Macromolecules  

•  Macromolecules are large molecules composed of thousands of covalently connected atoms

à small organic molecules are joined together to form larger molecules (aka polymers)

•  The architecture of a macromolecule helps explain how that molecule works

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Hydrolysis  adds  a  water  molecule,  breaking  a  bond

Short  polymer Unlinked  monomer

Dehydra&on  removes  a  water  molecule,  forming  a  new  bond

Longer  polymer

Monomers  form  larger  molecules  by  condensa&on  reac&ons  (dehydra&on  reac&ons)  

Synthesis  

Requires: energy and catalyst

Breakdown  Polymers  are  disassembled  to  monomers  by  hydrolysis  (the  reverse)  

Occurs passively, but cells use a catalyst

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Synthesis  and  Decomposi&on  Reac&ons  

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4 Main Classes of Biomolecules

1.  Carbohydrates

2.  Lipids

3.  Proteins

4.  Nucleic Acids

Polymer? Monomer

NO

SOME MONOSACCHARIDE

ALL AMINO ACID

ALL NUCLEOTIDES

NA  

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Lecture  3:  Learning  Objec&ves  -  Describe the importance of carbon in living organisms -  List and describe the two properties of Organic Compounds -  Know the structure, functions and give an example for the

main functional groups (hydroxyl, carbonyl, carboxyl, amino, sulphydryl, and phosphate)

-  Know the difference between structural isomers, geometric isomers and enantiomers

-  Understand dehydration and hydrolysis reactions -  Name the four classes of Macromolecules

Next  Lecture:    Carbohydrates  (ch.  3)