Biological Macromolecules

Structure and Function of Carbohydrates, Nucleic Acids,

Proteins, Lipids

Cells as chemical reactors Living organisms obey the laws of

chemistry and physics Can think of cells as complex chemical reactors in

which many different chemical reactions are proceeding at the same time

All cells more similar then different if looked at on the inside! Strip away the exterior and we see that all cells need

to accomplish similar tasks and in a broad sense they use the same mechanisms (chemical reactions)

Reflects a singular origin of all extant living things!

Similarities among all types of cells

All cells use nucleic acids (DNA) to store information RNA viruses, but not true cells

(incapable of autonomous replication) All cells use proteins as catalysts (enzymes) for

chemical reactions A few examples of RNA based enzymes, which may reflect

primordial use of RNA All cells use lipids for membrane components

Different types of lipids in different types of cells All cells use carbohydrates for cell walls (if present),

recognition, and energy generation All cells use nucleic acids (RNA) to access

stored information

Macromolecules

Large Molecules Macromolecules are formed when

monomers are linked together to form longer chains called polymers.

The same process of making and breaking polymers is found in all living organisms.

Consider some generic monomers with OH groups on their ends. These monomers can be linked together by a process called

dehydration synthesis (also called a condensation reaction) in which a covalent bond is formed between the two monomers while a water molecule is also formed from the OH groups.

This reaction is catalyzed by a polymerase enzyme. This same type of condensation reaction can occur to form many

kinds of polymers, from proteins to carbohydrates, nucleic acids to triglycerides.

Condensation Reaction

Hydrolysis Reactions

Polymers of all sorts can be broken apart by hydrolysis reactions. In hydrolysis the addition of a water molecule (with the help of a hydrolase enzyme) breaks the covalent bond holding the monomers together.

Macromolecules

Biotechnology often concerned with the manipulation of cells through the manipulation of the macromolecules contained within those cells

DNA Proteins Lipids & Carbohydrates (indirectly)

Biologically important macromolecules are “polymers” of smaller subunits

Created through condensation reactions

Carbohydrates : simple sugars

Lipids : CH2 units

Proteins : amino acids

Nucleic acids : nucleotides

Macromolecule Subunit

Where do the subunits come from? All cells need a source of the atomic components of the

subunits (C, O, H, N, P, and a few other trace elements )

Some cells can synthesize all of the subunits given these atomic components and an energy source

Some cells can obtain these subunits from external sources Some cells can convert other compounds into these subunits

We will discuss further in section on metabolism and cell growth

Carbohydrates All have general formula CnH2nOn (hydrates

(H2O) of carbon)

A variety of functions in the cell Large cross-linked carbohydrates make up the

rigid cell wall of plants, bacteria, and insects In animal cells carbohydrates on the exterior

surface of the cell serve a recognition and identification function

A central function is energy storage and energy production !

Carbohydrates

Carbohydrates are always composed of carbon, hydrogen and oxygen molecules

Monosaccharides typically have five or six carbon atoms.

Monosaccharides can, such as the ribose and deoxyribose of RNA and DNA, can serve very important functions in cells.

Carbohydrates

Condensation reactions form covalent bonds between monosaccharides, called glycosidic linkages.

Monosaccharides are the monomers for the larger polysaccharides.

Polysaccharides play various roles, from energy storage (starch, glycogen) to structure (cellulose).

Carbohydrates

Cell structure: Cellulose, LPS, chitin

Cellulose in plant cell walls Lipopolysaccharides (LPS)

in bacterial cell wall

Chitin in exoskeleton

Carbohydrate Structure

Monosaccharides may also form part of other biologically important molecules

Carbohydrate Structure

Complex carbohydrates built from simple sugars Most often five (pentose) or six (hexose) carbon

sugars Numerous –OH (hydroxy) groups can form many

types of “cross links” Can result in very complex and highl;y cross

linked structures ( cellulose, chitin, starch, etc.)

Carbohydrate StructureA Few Examples

Triose (3 carbon) Glyceraldehyde

Pentose (5 carbon) Ribose

Carbohydrate StructureExample of two hexoses

Glucose Galactose

What’s the difference? Both are C6H12O6 They are isomers of one another! Same formula, but different structure (3D-shape).

Carbohydrate Structure

Monosacharides can be joined to one another to form disaccharides, trisaccharides, ……..polysaccharides

Saccharide is a term derived from the Latin for sugar (origin = "sweet sand")

Carbohydrates classified according to the number of saccharide units they contain. A monosaccharide contains a single carbohydrate, over

200 different monosaccharides are known. A disaccharide gives two carbohydrate units on

hydrolysis. An oligosaccharide gives a "few" carbohydrate units on

hydrolysis, usually 3 to 10. A polysaccharide gives many carbohydrates on

hydrolysis, examples are starch and cellulose.

Carbohydrate Structure

Ring (cyclic) form

Pentoses and hexoses are capable of forming ring (cyclic) structures. An equilibrium exists between the ring and open form.

Linear form

Carbohydrate Structure

Monosaccharides can link to form disaccharides

Glucose Fructose Sucrose+

Complex Carbohydrates

CelluloseMost abundant carbohydrate on the planet!

Component of plant cell walls Indigestible by animals

β 1-4 bonds

Starch Energy storage molecule in plants Can be digested by animals

α 1-6 bonds

Cellulose Cellulose is a linear

polysaccharide in which some 1500 glucose rings link together. It is the chief constituent of cell walls in plants.

Human digestion cannot break down cellulose for use as a food, animals such as cattle and termites rely on the energy content of cellulose. They have protozoa and bacteria with the necessary enzymes in their digestive systems. Only animals capable of breaking down cellulose are tunicates.

Starches Starches are carbohydrates in which

300 to 1000 glucose units join together. It is a polysaccharide used to store energy for later use. Starch forms in grains with an insoluble outer layer which remain in the cell where it is formed until the energy is needed. Then it can be broken down into soluble glucose units. Starches are smaller than cellulose units, and can be more readily used for energy. In animals, the equivalent of starch is glycogen, which can be stored in the muscles or in the liver for later use.

α-1,6 bonds

Complex Carbohydrates

Glycogen Branched chain polymer of glucose Animal energy reserve Found primarily in liver and muscle

α 1-4 & α 1-6 bonds

Glycogen

polysaccharides can be linked to other molecules to form glyco-proteins and glyco-lipids

GlycoproteinsSome examples

Polysaccharide component of antibodies has major effect on antibody function

Polysaccharides attached to proteins on surface of red blood cells (RBC) determine blood type (A,B,O)

Polysaccharides are attached to proteins in the Golgi apparatus through a process of post-translational modification

Different types of cells do different post-tranlational modifications More about this later

Glycolipids Polysaccharides can also be attached to lipid molecules

•An outer-membrane constituent of gram negative bacteria, LPS, which includes O-antigen, a core polysaccharide and a Lipid A, coats the cell surface and works to exclude large hydrophobic compounds such as bile salts and antibiotics from invading the cell. O-antigen are long hydrophilic carbohydrate chains (up to 50 sugars long) that extend out from the outer membrane while Lipid A (and fatty acids) anchors the LPS to the outer membrane.

Glycolipids

Polysaccharides (blue) are also used in animal cells to link surface proteins and lipid anchors to the membrane.

Lipids

Lipids Fatty acids (Polymers of CH2 units) Glycerol Triglycerides Other subunits (phosphate, choline, etc) may be attached

to yield “phospholipids” Charged phosphate groups will create a polar molecule with a

hydrophobic (nonpolar) end and a hydrophillic (polar) end

Lipids

Lipids constitute a very diverse group of molecules that all share the property of being hydrophobic.

Fats and oils are lipids generally associated with energy storage. Fatty acids, which make up fats and oils, can be saturated or

unsaturated, depending on the absence or presence of double bonded carbon atoms.

Other types of lipids are used for a other purposes, including pigmentation (chlorophyll, carotenoids), repelling water (cutin, suberin, waxes) and signaling (cholesterol and its derivatives).

Lipids

Lipids are joined together by ester linkages. Triglyceride is composed of 3 fatty acid and 1

glycerol molecule Fatty acids attach to Glycerol by covalent ester

bond Long hydrocarbon chain of each fatty acid makes

the triglyceride molecule nonpolar and hydrophobic

Lipids

Lipids

Phospholipids

Lipids

Function Energy Storage

Triglycerides Cell membranes and cell compartments Bi-layer structure

Outer or plasma membrane Nuclear membrane Internal structures

Er, Golgi, Vesicles, etc.

Phospholipid bilayer

Hydrophillic heads

Hydrophobic tails

Steroids

Proteins Proteins serve many essential roles in the cell

Polymers of amino acids 20 naturally occurring amino acids

A few modified amino acids are used The large number of amino acids allows huge diversity

in amino acid sequence

N = # of amino acids in a protein N20 = # of possible combinations

Proteins

Proteins consist of one or more polymers called polypeptides, which are made by linking amino acids together with peptide linkages.

Peptide linkages are formed through condensation reactions.

All proteins are made from the same 20 amino acids. Different amino acids have different chemical properties.

Proteins

Protein’s primary structure largely determines its secondary, tertiary (and quaternary) structure.

Proteins subjected to extreme conditions (large changes in pH, high temperatures, etc.) often denature.

Proteins act as enzymes, and catalyze very specific chemical reactions.

Protein FunctionSome examples

Structure- form structural components of the cell including: Cytoskeleton / nuclear matrix / tissue matrix

Lamins, collagen, keratin…….

Movement - Coordinate internal and external movement of cells, organells, tissues, and molecules. Muscle contraction, chromosome separation, flagella………

Micro-tubueles, actin, myosin

Transport-regulate transport of molecules into and out of the cell / nucleus / organelles.

Channels, receptors, dynin, kinesin

Communication-serve as communication molecules between different organelles, cells, tissues, organs, organisms. Hormones

Protein FunctionSome examples

Chemical Catalyst – serves to make possible all of the chemical reactions that occur within the cell. Enzymes (thousands of different enzymes)

Defense-recognize self and non-self, able to destroy foreign entities (bacteria, viruses, tissues). Antibodies, cellular immune factors

Regulatory-regulates cell proliferation, cell growth, gene expression, and many other aspects of cell and organism life cycle. Checkpoint proteins, cyclins, transcription factors

Protein Structure Polymers of 20 amino acids

All amino acids have a Common “core”

Amino end (N end) Acid end (C end, carboxy

end) Linked by peptide bond 20 different side chains

Properties of amino acids amino acids: acidic basic hydrophobic

Amino acids all have The same basic structure

Chemical properties of the amino acids yield properties of the protein!

Properties of amino acids

Protein Structure The 3-D shape and properties of the protein

determine its function.

Shape and properties of protein determined by interactions between individual amino acid components.

Four “levels” of protein structure Primary (Io), secondary (IIo), tertiary (IIIo), and

quaternary (IVo) (sometimes).

Levels of Protein Structure I0 (primary) structure

Linear order of amino acids in a protein:

1 A A S X D X S L V E V H X X V F I V P P X I L Q A V V S I A 31 T T R X D D X D S A A A S I P M V P G W V L K Q V X G S Q A 61 G S F L A I V M G G G D L E V I L I X L A G Y Q E S S I X A 91 S R S L A A S M X T T A I P S D L W G N X A X S N A A F S S 121 X E F S S X A G S V P L G F T F X E A G A K E X V I K G Q I 151 T X Q A X A F S L A X L X K L I S A M X N A X F P A G D X X 181 X X V A D I X D S H G I L X X V N Y T D A X I K M G I I F G 211 S G V N A A Y W C D S T X I A D A A D A G X X G G A G X M X 241 V C C X Q D S F R K A F P S L P Q I X Y X X T L N X X S P X 271 A X K T F E K N S X A K N X G Q S L R D V L M X Y K X X G Q 301 X H X X X A X D F X A A N V E N S S Y P A K I Q K L P H F D 331 L R X X X D L F X G D Q G I A X K T X M K X V V R R X L F L 361 I A A Y A F R L V V C X I X A I C Q K K G Y S S G H I A A X 391 G S X R D Y S G F S X N S A T X N X N I Y G W P Q S A X X S 421 K P I X I T P A I D G E G A A X X V I X S I A S S Q X X X A 451 X X S A X X A

Single letter code for amino acids, also a three letter code. Refer to your genetic code handout.

Levels of Protein StructurePrimary Structure

Amino acids combine to form a chain

Each acid is linked by a peptide bond

Io structure by itself does not provide a lot of information.

Protein Structure II0 (secondary) structure

Based on local interactions between amino acids Common repeating structures found in proteins. Two

types: alpha-helix and beta-pleated sheet. In an alpha-helix the polypeptide main chain makes up

the central structure, and the side chains extend out and away from the helix.

The CO group of one amino acid (n) is hydrogen bonded to the NH group of the amino acid four residues away (n +4).

Can predict regions of secondary structure

Ribbon Diagram

α-helical regions

Beta sheet Two types parallel

and anti-parallel

Beta Sheet ribbon diagram

antiparallel parallel

Protein Structure III0 (tertiary structure)

Complete 3-D structure of protein (single polypeptide)

Chymotrypsin with inhibitor

hexokinase

Protein Structure IV0 (quaternary)

structure Not all proteins have

IV0 structure Only if they are made

of multiple polypeptide chains

Nucleic Acid

DNA is transmitted from generation to generation with high fidelity, and therefore represents a partial picture of the history of life.

Nucleic Acid Two types of nucleic acids:

DNA RNA

DNA stores the genetic information of organisms; RNA is used to transfer that information into the amino acid sequences of proteins.

DNA and RNA are polymers composed of subunits called nucleotides. Nucleotides consist of a five-carbon sugar, a phosphate group and a nitrogenous base. Five nitrogenous bases found in nucleotides:

the purines adenine (A) guanine (G)

the pyrimidines cytosine (C) thymine (T) (DNA only) uracil (U) (RNA only)

Nucleic Acids DNA –deoxyribonucleic acid

Polymer of deoxyribonucleotide triphosphate (dNTP) 4 types of dNTP (ATP, CTP, TTP, GTP) All made of a base + sugar + triphosphate

RNA –ribonucleic acid Polymer of ribonucleotide triphosphates (NTP) 4 types of NTP (ATP, CTP, UTP, GTP) All made of a base + sugar + triphosphate

So what’s the difference? The sugar (ribose vs. deoxyribose) and one base (UTP vs.

TTP)

Function

Nucleic Acids Information Storage

DNA / mRNA Information transfer / Recognition

rRNA / tRNA / snRNA Regulatory

microRNA ?

DNAInformation for all proteins stored in DNAin the form of chromosomes or plasmids. Chromosomes (both circular and linear) consist of two strands of DNA wrapped together in a left handed helix.

The strands of the helix are held together by hydrogen bonds between the individual bases. The “outside” of the helix consists of sugar and phosphate groups, giving the DNAmolecule a negative charge.

Complimentary Base Pairs

A-T Base pairing G-C Base Pairing

DNA Structure The DNA helix is “anti-parallel”

Each strand of the helix

has a 5’ (5 prime) end and

a 3’ (3 prime) end.

DNA Structure

Strand 1

(Watson strand)

Strand 2 (Crick strand)

5 ‘ end

3 ‘ end

3’ end

5’end

DNA Structure

1 atgatgagtg gcacaggaaa cgtttcctcg atgctccaca gctatagcgc caacatacag 61 cacaacgatg gctctccgga cttggattta ctagaatcag aattactgga tattgctctg 121 ctcaactctg ggtcctctct gcaagaccct ggtttattga gtctgaacca agagaaaatg 181 ataacagcag gtactactac accaggtaag gaagatgaag gggagctcag ggatgacatc 241 gcatctttgc aaggattgct tgatcgacac gttcaatttg gcagaaagct acctctgagg 301 acgccatacg cgaatccact ggattttatc aacattaacc cgcagtccct tccattgtct 361 ctagaaatta ttgggttgcc gaaggtttct agggtggaaa ctcagatgaa gctgagtttt 421 cggattagaa acgcacatgc aagaaaaaac ttctttattc atctgccctc tgattgtata

Because of the base pairing rules, if we know one strand we also know what the other strand is. Convention is to right from 5’ to 3’ with 5’ on the left.

Chromosomes and Plasmids

Chromosomes are composed of DNA and proteins. Proteins (histone & histone like proteins) serve a

structural role to compact the chromosome. Chromosomes can be circular, or linear.

Both types contain an antiparallel double helix! Genes are regions within a chromosome.

Like words within a sentence.

For an animation of the organization of a human chromosome see: http://www.dnalc.org/ddnalc/resources/chr11a.html

RNA Almost all single stranded (exception is

RNAi). In some RNA molecules (tRNA) many of the

bases are modified (i.e. psudouridine). Has capacity for enzymatic function. One school of thought holds that early

organisms were based on RNA instead of DNA (RNA world).

RNA

Several different “types” which reflect different functions mRNA (messenger RNA) tRNA (transfer RNA) rRNA (ribosomal RNA) snRNA (small nuclear RNA) RNAi (RNA interference)

RNA function

mRNA – transfers information from DNA to ribosome (site where proteins are made)

tRNA – “decodes” genetic code in mRNA, inserts correct A.A. in response to genetic code.

rRNA-structural component of ribosome snRNA-involved in processing of mRNA RNAi-double stranded RNA, may be component of

antiviral defense mechanism.

RNA

A - hairpin loop B- internal loop C- bulge loop

D- multibranched loop E- stem

F- pseudoknot

Complex secondary structures can form in linear molecule

mRNA

Produced by RNA polymerase as product of transcription

Provides a copy of gene sequence (ORF) for use in translation (protein synthesis).

Transcriptional regulation is major regulatory point Processing of RNA transcripts occurs in eukaryotes

Splicing, capping, poly A addition In prokaryotes coupled transcription and translation can

occur