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Globular Proteins

Myoglobin/Hemoglobin

Hemeproteins: group of specialized proteins that contain heme

group as a tightly bound prosthetic group.

prosthetic group: is a non-protein compound that is permanently

associated with proteinThe role of heme group is dependent on the environment created

by the three-dimensional structure of the protein.

e.g. heme in cytochrome electron carrier,

enzyme catalase active site

Myoglobin and hemoglobin Oxygen carrier

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First protein structuresdetermined

Oxygen carriers

Hemoglobin transport O2from lungs to tissues

Myoglobin O2 storageprotein

Myoglobin/Hemoglobin

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Mb and Hb subunits structurallysimilar

hemoglobin

8 alpha-helicesContain heme group

Mb monomeric

protein

Hb heterotetramer (2 2)

myoglobin

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Hemoglobin A1c

Under physiologic conditions HbA is slowly

and non-enzymatically glycosylated

The extent of glycosylation is dependenton the plasma level of particular hexoses

The most abundant glycosylated Hb is

HbA1c which has glucose unit that

covalently linked to amino group of N-

terminal valines of the beta chain

In the case of Diabetes mellitus, the

amount of HbA1c will increase

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Hemoglobinopathies

Defined as a family of disorders caused either by production of

structurally abnormal hemoglobin molecule, synthesis of insufficient

quantities of normal hemoglobin or rarely both

Sickle- cell anemia (HbS)

Hemoglobin C disease (HbC)

Thalassemia

Sickle- cell anemia (Hemoglobin S disease HbS)

a glutamate residue is replaced by valine residue in the -chains. This

results in two fewer negative charges for the tetrameric structure.

The substitution of a hydrophobic amino acid for a hydrophilic one makes

the resulting molecule sticky. which causes molecules to stick together

at this point. This causes aggregation to occur in deoxyhemoglobin.

Subsequent to strand formation, several strands can assemble to form aninsoluble fiber, which is what gives sickled cells there shape.

People with sickle cell anemia suffer from repeated crises brought on by

physical exertion.

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Hemoglobinopathies

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Sickle- cell anemia (Hemoglobin S disease HbS)

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Hemoglobin C disease

HbC is a hemoglobin variant having a single substitution in the sixth

position of the -globin chain. In this case lysine is substituted.

Patients have a relatively mild chronic hemolytic anemia and they don't

suffer from infractive crises

Thalassemias

Thalassemia is a hereditary hemolytic disease in which an imbalance in the

synthesis of globin chains occurs Normally the synthesis of -chains and -chains are coordinated so that

each -globin has its -globin

in the thalassemia the synthesis of either - or -globin chain is

defective

-thalassemia: defect in the synthesis of the -globin and there are 4different levels of this type

-thalassemia:-globin is decreased or absent, there are 2 different level

of this type

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Nearly all the reactions of the body are mediated by

enzymes

Enzymes are protein catalysts that increase the rate of

the reactions without being changed in the overall process

Catalysts for biological reactions

Lower the activation energy. It will not affect theequilibrium but decrease the time required to reach the

equilibrium

Increase the rate of reaction

Activity lost if denatured May be simple proteins

May contain cofactors such as metal ions or organic

(vitamins)

Enzymes

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EnzymesNomenclature of enzymes

Enzyme has two names

a. Short Recommended nameb. Systemic name

Recommended name

End in ase,

Identifies a reacting substance

sucrase reacts sucrose

lipase - reacts lipid

Describes function of enzyme

oxidase catalyzes oxidation

hydrolase catalyzes hydrolysislactate dehydrogenase, adenylate cyclase

Common names of digestion enzymes still use which don't provide any

hint as pepsin and trypsin

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Systematic name

The international union of Biochemistry and Molecular Biology (IUBMB)

developed a system for nomenclature in which enzymes are divided into

6 groups and sub classes. These names are unambiguous andinformative but sometimes long and difficult to be of general use.

Class Reactions catalyzed

1. Oxidoreductoases oxidation-reduction

2. Transferases transfer group of atoms

3. Hydrolases hydrolysis

4. Lyases add/remove atoms to/from a double

bond

5. Isomerases rearrange atoms

6. Ligases combine molecules using ATP

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Enzyme Action:

Lock and Key Model

An enzyme binds a substrate in a region

called the active site

Active site is a special pocket or cleft inthe enzyme molecule

The active site contains amino acids

side chains that form a three

dimensional surface complementary tothe substrate

Only certain substrates can fit the

active site

The active site binds to the substrate

and form enzyme-substrate complex that

will dissociate into the enzyme and

product.

Amino acid R groups in the active site

help substrate bind

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Lock and KeyThe active site of the unbound enzyme is complementary in shape tothat of the substrate

E l

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Enzyme Action: Induced Fit Model

Enzyme structure flexible, not rigid

Enzyme and active site adjust shape to bind substrate

Increases range of substrate specificity

Shape changes also improve catalysis during reaction

The enzyme changes

shape upon binding

substrate

The active site has ashape complementary

to that of the

substrate only after

the binding

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Cofactors

-Some enzymes associate with non-protein

cofactor that is needed for enzymatic activity

-These cofactor include metal ions (Zn, Fe) and

organic molecules called coenzymes that often

derivative of vitamins; NAD+, FAD, CoenzymeA..

-Holoenzyme refers to the enzyme with its

cofactor, Apoenzyme refers to the protein

portion of the holoenzyme and it dose not showbiological activity.

- Prosthetic group is a tightly bound enzyme

that dose not dissociate from the enzyme

Location of enzymesMany enzymes are located into specific

organelles in the cell serve to isolate the

reaction substrate or product from each other

and to provide a special environment for a

reaction and to organize these reactions

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Nucleic Acids

Nucleic acids are linear polymers of nucleotides-pyrimidine and purine

bases linked to ribose or deoxyribose sugars (nucleosides) and bound to

phosphate groups. The backbone of the nucleic acid consists ofalternating phosphate and pentose units with a purine or pyrimidine base

attached to each.

The nucleotide has three characteristic components

Nitrogenous base

Pentose sugar

Phosphate

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DNA and RNA

DNA differs from RNA in that it lacks a hydroxyl group at the pentose's

C/ position, and it contains T rather than U.

DNA structure consists of two a-helical DNA strands coiled around the

same axis to form a double helix. The strands are antiparallel-the 5',

3'-internucleotide phosphodiester links run in opposite directions.

RNA exists in three forms.

(1) Ribosomal RNA (rRNA) functions as a framework to bind bothmessenger and transfer RNA. It is comprised of numerous subunits with

the 405 and 605 being the most well known. Ribosomal RNA is also

thought to have other functions; however, these have not been fully

elucidated.(2) Messenger RNA (mRNA) serves as the template for protein synthesis

and specifies a polypeptide's amino acid sequence.

(3) Transfer RNA (tRNA) carries activated amino acids to the ribosomes,

where the amino acids are incorporated into the growing polypeptidechain.

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Nitrogenous BasesNitrogenous base: derivatives of Purines and pyrimidines

DNA and RNA contain the same purine bases and the pyrimidine base

Cytosine But Thymine found only in DNA and Uracil found only in RNA

(A) (G)

(C) (T)(U)

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Pentoses of Nucleotides

D-ribose (in RNA) 2-deoxy-D-ribose (inDNA)

The difference - 2'-OH

vs 2-H This difference affectssecondary structure andstability

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Nucleic Acids

Nucleic acid: are polymers of

Nucleotides linked with 3,5- phosphodiester bonds

Nucleotide residues are all

oriented in the same

direction (5 to 3) giving thepolymer directionality.

The sequence of DNA

molecules is always read in

the 5 to 3 direction

5'

3'

5'

3'

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DNA 1o Structure - Linear array of nucleotides and their sequence

can be determined by different methods.

2o Structure double helix

3o Structure - Super-coiling, stem-loop formation

4o Structure Packaging into chromatin

DNA Secondary structure DNA is double stranded with antiparallel strands

Right hand double helix

Three different helical forms (A, B and Z DNA.

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Bases from two

adjacent DNA

strands canhydrogen bond

Adenine pairs withthymine using two

H-bondsGuanine pairs withcytosine usingthree H-bonds

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Properties of DNA Double Helix

* The two chains are coiled around a common axis

* The chains are paired in an anti-parallel manner

* Distance between the 2 sugar-phosphate

backbones is always the same, give DNA

molecule a regular shape.

* Plane of bases are oriented perpendicular to

backbone* Hydrophilic sugar phosphate backbone winds

around outside of helix

* Noncovalent interactions between upper and

lower surfaces of base-pairs (stacking) formsa closely packed hydrophobic interior.

* Hydrophobic environment makes H-bonding

between bases stronger (no competition with

water)

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DNA supercoiling:

Supercoiling: means the coiling

of the coil. Typical phone cord is coiled like

a DNA helix and the coiled cord

can itself coil in a supercoil

A number of measurable

properties of supercoiling have

been established

DNA 3o Structure Supercoiling

Cruciform structures

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DNA 4o Structure: Chromosome Structure

In chromosomes, DNA is tightly associated with proteins

Human DNAs total length is ~2 meters!

This must be packaged into a nucleus that is about 5 micrometers indiameter

This represents a compression of more than 100,000!

It is made possible by wrapping the DNA around protein spools called

nucleosomes and then packing these in helical filamentsNucleosome Structure

Chromatin, the nucleoprotein complex, consists of histones and

nonhistone chromosomal proteins

% major histone proteins: H1, H2A, H2B, H3 and H4

Histone octamers are major part of the protein spools

Nonhistone proteins are regulators of gene expression

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Nucleosome Structure

High content of Lysine and

arginine (+ve charge)4 major histone (H2A, H2B,H3, H4) proteins for octomer

200 base pair long DNA

strand winds around theoctomer

146 base pair DNA spacerseparates individualnucleosomes

H1 protein involved in higher-order chromatin structure.

Chromatin looks like beads onstring