Biochemistry 1

Fall semester 2019/2020

Lecturer: Assist. Prof. Dr. Altijana Hromic-Jahjefendic

Laboratory assistant: MSc Jasmin Sutkovic

Contact Information

Office: A F1.7

ahromic@ius.edu.ba

Office hours:

Monday 08:00-11:00

Thursday 13:00-15:00

General information

Syllabus

2 quizes (5% each) – FIRST QUIZ 29.10.2019 !!!!

Lab tutorials (20%)

Mid term exam (30%)

Last semester week: review of all lectures and preparing for

final exam

BOOK

- -”Principles of Biochemistry”, Moran- Horton-Scrimgeour-Perry, 2012 Pearson, 5th edition

- -”Biochemistry” Voet &Voet, 4th edition, 2011

- b-ok.org

What is Biochemistry?

History and Development

How to study Biochemistry?

Biochemistry

Definition:

The science concerned with the chemical basis of life.

The science concerned with the various molecules that

occur in living cells and organisms and with their chemical

reaction.

Anything more than a superficial comprehension of life in

all its diverse manifestation -demands a knowledge of

biochemistry.

Aim: to describe and explain, in molecular terms, all chemical

processes of living cells

Structure-function

Metabolism and Regulation

Disease development and treatment

Significance:be essential to all life sciences as the common

knowledge

Genetics; Cell biology; Molecular biology

Physiology and Immunology

Pharmacology and Pharmacy

Toxicology; Pathology; Microbiology

Zoology and Botany

Students who acquire a sound knowledge of biochemistry

will be in a strong position to deal with two central concerns

of the health sciences:

(1) the understanding and maintenance of health

(2) the understanding and effective treatment of disease:

▪Causes of cancers

▪Molecular lesions causing various genetic diseases

▪Rational design of new drugs

What is the purpose of biochemistry?

Structure and function of cellular components

proteins, carbohydrates, lipids, nucleic acids and other biomolecules

Metabolism and Regulation

Gene expression and modulation

The cell

Life is based on a morphological unit known as the cell

Two basic types of cells are found in nature: Prokaryotes

and eukaryotes

Eukaryotes (Greek: eu, good or true + karyon, kernel or

nut) have a membrane-enclosed nucleus containing their DNA.

They can form multicellular organisms.

Prokaryotes (Greek: pro, before) lack this organelle.

Prokaryotes are unicellular (bacteria).

Prokaryotes

First described by Antoni van Leeuwenhoek in 1683

Simple anatomy

1-10 μm

Three basic shapes:

Spheroidal (cocci)

Rodlike (bacilli)

Helically coiled (spirilla)

Bounded by a 70 Å plasma membrane and a 30 to 250 Å

cell wall

Eukaryotes

10- 100 μm, i.e. 103 to 106 times the volume of a

prokaryotic cell

it is not the size, however, but the high degree of complexity

of eukaryotic cells that makes the difference

• Cell membrane & cell wall Cell membrane

• Nucleoid region contains the DNA Nucleus

• Contain ribosomes (no membrane) Cytoplasm with organelles

Characteristic Biomembranes and Organelles

Plasma Membrane-Cell’s defining boundary. Providing a

barrier and containing transport and signaling systems.

Nucleus –Cell’s information center. Double membrane

surrounding the chromosomes and the nucleolus. The place

where almost all DNA replication and RNA synthesis occur.

Mitochondria-the power generators Mitochondria (Greek:

mitos-thread; chondros-granule). Functions in energy production

through metabolism.Contains its own DNA.

Characteristic Biomembranes and Organelles

Rough endoplasmic reticulum (RER). Covered with

ribosomes (causing the "rough" appearance) which are in the

process of synthesizing proteins for secretion or localization

in membranes.

•Ribosomes- Protein and RNA complex responsible for protein

synthesis

Smooth endoplasmic reticulum (SER) - A site for synthesis

and metabolism of lipids.

Golgi apparatus -process and package the macromolecules. Vesicles carry materials from the RER to the Golgi apparatus. Vesicles move between the stacks while the proteins are "processed" to a mature form.

Lysosomes-contain digestive enzyme. Is responsible for degrading proteins and membranes in the cell.

Cytoplasm - enclosed by the plasma membrane, liquid portion called cytosol and it houses the membranous organelles.

Biomolecules

biomolecules are building blocks of cells.

Animal and plant cells contain approximately 10,000 kinds of

biomolecules.

Water constitutes 50-95% of cells content by weight.

Ions like Na+, K+ and Ca2+may account for another 1%.

Almost all other kinds of biomolecules are organic (C, H, N,

O, P, S).

Organic compounds are compounds composed primarily of a

carbon skeleton.

Carbon

Carbon is more abundant in living organisms than it is in the

rest of the universe.

What makes Carbon Special?

ability of Carbon atoms to bond together to form long chains

and rings.

Biomolecules are compounds of carbon with a

variety of functional groups

Biochemistry - the lowest level of

complexity

Major building blocks are:

1. Proteins (Greek: proteios, of first importance)

2. Nucleic acids

3. Polysaccharides (Greek: sakcharon, sugar)

4. Lipids (Greek: lipos, fat)

The first three categories are complex polymers made of

smaller building blocks: amino acids, nucleotides and

monosaccharides

The information for the generation of such complex structures is encoded in

nucleic acids.

The flow of this information is regulated in a complex fashion.

The entire process is fueled by metabolic processes that generate energy from

organic energy sources and use this energy to synthesize complex molecules.

Metabolism Metabolism has been traditionally divided into two major

categories:

Catabolism - break down of nutrients and cell constituents to produce energy (ATP) and/or reuse for biosynthesis

Anabolism - biosynthetic pathways to generate the biomolecules required; the energy for biosynthesis is derived mostly from catabolic reactions (i.e. ATP).

Thus catabolism and anabolism are linked by the reciprocal interconversion of the „energy currency“ ATP.

Polymers and Monomers

Each of these types of molecules are polymers that are

assembled from single units called monomers.

Each type of macromolecule is an assemblage of a different

type of monomer.

How do monomers form polymers?

In condensation

reactions (also called

dehydration synthesis), a

molecule of water is

removed from two

monomers as they are

connected together.

Chemical composition of a healthy

person (65 kg)

Constituent Percent (%) Weight (kg)

Water 61.6 40

Protein 17.0 11

Lipid 13.8 9

Carbohydrate 1.5 1

Minerals 6.1 4

The beginning of biochemistry

biochemical processes are ubiquitous among living

organisms, it was the study of one particular process which

led to the discovery of biochemical principles:

ALCOHOLIC FERMENTATION

Fermentation was discovered at the start of the neolithic age around 10000 years

ago with the start of settlements and agriculture (confirmed for 6000 years).

Transformation of a juice of crushed grapes to a gift of euphoria.

Fermentation is also accompanied by the emergence of bubbles, production of heat

and the occurrence of a fine, cloudy suspension that eventually settles to the bottom

of the fermentation vats („yeast“)

The Vital Force - Aristotle Aristotle’s teleology:

Every living thing has a natural end or goal toward which it tends. The acorn’s natural tendency, for example, is to become an oak tree and a warrior’s natural goal is to become a hero.

Applying this teleological view to fermentation, grape juice can be regarded as an immature form of wine, and the process of fermentation is then the maturation of grape juice to wine (its final destiny).

What causes this inherent tendency?

In Aristotle’s view these maturation processes are under the control of inner driving forces, called vital force, lat. vis visa. Although the vital force is undefined in material terms, it is a real part of the organism endowing it with life. Indeed, the basic distinction between the animate and inorganic world is the very existence of the vital force (vitalism).

Alchemists identify alcohol as the product of fermentation

In Greek chemistry the world was made up of four fundamental substances: Earth, Air, Fire and Water. In addition to these physical elements, philosphocial considerations have led to the proposal of a fifth element, called quinta essentia or quintessence which reflects the vital force in animate things. This essence was thought to have a volatile character and hence alchemists in the Middle Ages have attempted to capture it using distillation. By the end of the 12th century distillation had become efficient enough to recover the vapors released from various heated substances. It became apparent that the distillation of grape juice and for example wine produced different vapors, in the latter case this vapor could be condensed to a burning liquid (aqua ardens). Hence it became clear that fermentation was not just a maturation but the formation of an entirely different new substance. We now know that this „spirit“ of wine or other alcoholic fermentation products is ethanol.

Antoine Lavoisier (1734-1794) One of the founders of modern

chemistry

Lavoisier’s two fundamental laws:

1. Substances undergoing a reaction

combine (or break apart) in specific

quantitative amounts - the law of

combining ratios.

2. The amount of matter present at the

beginning of a reaction is equal to

the amount of matter present at the

end - the law of the

conservation of mass.

2H2 + O2 -> 2H2O

2 + 1 -> 2 (combining ratio)

4H + 2O -> 4H + 2O (conservation of matter)

A unifying approach to the organic and

inorganic world Lavoisier proposed: fermentation was a chemical reaction in which

the sugar of the starting grape juice was converted into the ethanol of the finished wine.

In his experiments, he used sugar (instead of the grape juice), water and a small amount of yeast taken from a previous fermentation.

Comparison of the carbon present in the sugar and in the products (ethanol and carbon dioxide) revealed the conservation of mass, i.e. established that the laws of the inorganic world are applicable to the organic world as well.

By the end of the 18th century the inorganic and organic world were reunited in obeying the same rules.

The question of what caused the chemical transformation was unsolved.

The role of yeast in fermentation

Liebig’s theory:

The vibrational impact of decomposing yeast leads to the

disruption of the sugar atoms

-> Yielding ethanol and carbon dioxide as products.

This view was widely accepted among contemporary

chemists.

Opposing views: Theodor Schwann (1810-1882) & Charles Cagniard-Latour

(1777-1859):

• Yeast is a living organism

• Decomposition of sugar to ethanol and carbon dioxide is directly linked to the growth of yeast

• The „force“ that drives fermentation derives from a living organism as a result of its growth

ideas were rejected by most chemists at that time as an unwarranted intrusion of biology into the higher domain of chemistry. Basically, the idea of yeast as a living organism was totally dismissed

Pasteur on fermentation

A series of unsuccessful fermentations in the wine industry in

1856, prompted Pasteur to investigate the differences in the

sediments obtained from a normal and an unsuccessful

fermentation mixture

normal: yeast unsuccessful: bacteria

Seeding experiments

• Support for Schwann’s

and Cagniard-Latour’ s

that fermentation was

connected

with a living organism

Fermentation outside the living cell Eventually the stage was set for the final synthesis:

The Buchner brothers, a microbiologist and a chemist, developed a procedure to obtain a cell-free yeast extract by using a hydraulic press to generate a cell extract.

To preserve this extract they added 40% sucrose to it and observed bubbles some minutes later. This process sometimes continued for days and they could demonstrate that ca. 3% ethanol was produced during this fermentation.

This led to the demise of Pasteur’s concept of „higher and lesser“ processes and to the general acceptance of the idea of biological catalysis.

„The enzyme theory of life“

The discovery of zymase

Buchners called the active ferment isolated from yeast cells,

marked the beginning of biochemistry as an exact science

which „predicted that all cellular reactions would be

found to be controlled by specific enzymes“.

Although the Buchners believed that zymase was a single

entity, later on chemical events known as „metabolic

pathways“ were discovered

The discovery of the first amino acids

Liebig noticed that acid treatment resulted in the release of

smaller compounds which he could identify and obtain exact

formulars for: leucine, C6H13O2N and tyrosine

C9H11O3N (Greek: tyros, cheese)

Leucine and tyrosine were not the first amino acids

discovered!

A substance that was found to crystallize from extracts of

asparagus (especially when grown in the dark) was called

asparagine and turned out to be an amino acid

The polypeptide chain The current list of 20 amino

acids was eventually completed in 1935.

Franz Hofmeister and Emil Fischer had proposed the first clear theory of protein structure

they proposed that the protein is a chain of amino acids joined together by bonds between the regularly repeating amino and carboxyl groups.

The resulting chain, or polymer of linked amino acids, was termed a polypeptide chain.

Later on many experiments and discoveries regarding

proteins/enzymes

Structure determinations

Enzyme catalysis etc.

History and development of

Biochemistry

1903, Neuberg(German): “Biochemistry”

“Chemistry of Life”

Life possesses the properties of replication, catalysis and

mutability

Biochemistry is the study of life on the molecular level

Two important breaktroughts

(1) Discovery of the role of enzymes as catalysts

(2) Identification of nucleic acids as information

molecules

One gene one protein theory

DNA > RNA > Protein

Historic events

In 1937, Krebs for the discovery of the Citric Acid

Cycle-won the Nobel Prize in Physiology or

Medicine in 1953

In 1953, Watson & Crick for the discovery of the

“DNA Double Helix” -won the Nobel Prize in

Physiology or Medicine in 1962

Historic events In 1956. Sanger for the determination of insulin sequence-

won the Nobel Prize in Physiology or Medicine.

In 1980.Sanger & Gilbert for Sequencing of DNA-won the Nobel Prize in Chemistry.

In1993.KaryB. Mullis for invention of PCR method -won the Nobel Prize in Chemistry.

In 2016.-The Nobel Prize in Chemistry 2016 was awarded to Jean-Pierre Sauvage, Sir J. Fraser Stoddart and Bernard L. Feringa for their design and production of molecular machines. They have developed molecules with controllable movements, which can perform a task when energy is added

Historic events

The Nobel Prize in Chemistry 2018 was divided:

-one half awarded to Frances H. Arnold "for the directed

evolution of enzymes“

-the other half jointly to George P. Smith and Sir Gregory P.

Winter "for the phage display of peptides and

antibodies."

Historic events

Human Genome Project

Completed in 2003

Most complex project in the modern science

Summary

The cell

Eukaryotes vs Prokaryotes

Monomers vs polymers

Metabolism

Historic development of biochemistry