Macromolecules Biology

Proper&es  of  Macromolecules  

Lecture  2  

Overview  

Proper&es  of  Carbon    

Structure  and  Func&onal  groups    

Isomers    

Polymers    

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

Biomolecules  range  in  size  and  complexity  

CO2 Carbon Dioxide

CH4N2O Urea

C6H12O6 Glucose

Large molecule Phospholipid

Macromolecules DNA

Supramolecular Complex Ribosome

Life  exists  even  in  harsh  environments  

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  

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  

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  

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

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

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  

example:

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

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  

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  

Func&onal  Groups  Carbonyl  Group:  Aldehydes  and  

Ketones  

Simple  sugars  can  be  aldehydes  or  ketones  

Ketone

Aldehyde

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  

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  

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  

Func&onal  Groups  

Amino  Group  

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

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  

Func&onal  Groups  

Phosphate  Group  

Nucleic  acids  (building  blocks  of  DNA  and  RNA)  

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

Func&onal  Groups  Phosphate  Group  

Adenosine  Triphosphate  

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

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  

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:

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:

Review  Func&onal  groups  

OH

C O

CO

OH

NH

H

P O-

O

O

O-

SH

Sulfhydryl

Amino

Hydroxyl group

Carbonyl

Carboxyl

Phosphate

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  

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:

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

•  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

•  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  

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

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

Synthesis  and  Decomposi&on  Reac&ons  

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  

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)