BIOL 313: INTRODUCTION TO BIOCHEMISTRY

Dr. Nadeem Asad

Lecture Objectives

Applications and meaning of Biochemistry Appreciate the basic molecular themes of life The ultrastructure of the cell and it being the

fundamental unit of living organisms Difference between prokaryotic and eukaryotic

cells Difference between plant and animal cells Understanding of small molecules and

macromolecules in the human body

What is Biochemistry?

Biochemistry and molecular biology are the scientific disciplines that aim to understand life in molecular terms

Traditionally, Biochemistry is the study of the metabolism of food and small molecules

In the 21st century, the distinction between Biochemistry and Molecular Biology is blurred and increasingly both are being merged and taught as one discipline

4 billion years ago, life forms started appearing on Earth; simple microorganisms came into being that harnessed energy from sunlight or simple molecules to synthesize more complex biomolecules essential to life

Biochemistry is therefore a study of how inanimate chemical structures and reactions through interaction facilitate essential processes in living organisms which ensure their survival and propagation

Three areas to study: Structural and Functional Biochemistry: Chemical structures and 3D

arrangements of molecules Informational Biochemistry: Language for storing biological data and for

transmitting that data in cells and organisms Bioenergetics: The flow of energy in living organisms and how it is

transferred from one process to another

Applications of Biochemistry

Medicine (clinical)-diagnose and monitor a wide range of infectious and autoimmune diseases, cancer and neurodegenerative disorders

Designer drugs- producing new generation antibiotics, more efficacious chemotherapy agents and vaccines

Agriculture-producing insecticides and herbicides Transgenic crops Genetically modified food and organisms Industry-enzyme catalysis, synthesis, detoxification Understanding metabolic disorders

Fundamental cellular living processes RESPIRATION--the breakdown of nutrients to yield (or give off)

chemical energythere are 2 types1) aerobic respiration- uses oxygen2) anaerobic respiration- doesn't use oxygen

REGULATION--the process where a living thing controls and coordinates its various activities.in animals--1) nervous system uses nerve cells2) endocrine system uses hormonesin plants--some parts produce hormones like auxins and gibberellins

REPRODUCTION--the process by which living things produce new living things of the same kindthere are 2 types1) asexual reproduction--involves one parent and the offspring are identical to the parent2) sexual reproduction--involves two parents and the offspring is a combination of both parents

Fundamental cellular living processes II

EXCRETION--the process by which living things remove waste products produced by cellular activities

GROWTH--the process by which living things increase in size or cell number

NUTRITION--the process by which living things take in material from their environment for growth and repair; there are 2 types1) autotrophic nutrition--where a living thing can synthesize its own food2) heterotrophic nutrition--where a living thing must ingest (take in) its food

Fundamental cellular living processes III

TRANSPORT--the process by which usable materials are taken into the living thing (ABSORPTION) and distributed throughout the living organism (CIRCULATION)

SYNTHESIS--the process by which smaller, simple substances are combined chemically to form larger, more complex substances

When we refer to all of the life functions of an organism, we are referring to its METABOLISM--the total of all the life functions required to sustain life (to stay alive)

R + R + R + E + G + N + T + S =METABOLISM An organism's external (outside) environment is always changing.

By keeping the controlling and regulating it’s metabolic activities, an organism can maintain a stable internal (inside) environment. This is called HOMEOSTASIS.

HOMEOSTASIS--the process by which an organism's metabolic activities are in a state of balancee.g. body temperature, blood sugar levels, hormone levels

The Living Cell

The cell-is the structural and functional unit of all known living organisms-smallest unit of an organism often referred to as the “building brick” of life All organisms consist of one or more cells

(viruses included)

History of the cell

1632-1723 Antonie van Leeuwenhoek- first to observe bacteria and protozoa

1665 Robert Hook- first to coin the term “cell” 1839 Theodor Schwann and Mathias Jakob Schleiden-

former is the founder of modern histology as he defined the cell as the basic unit of animal structure, the latter was a co-founder with Theodor of the cell theory

1855 Rudolf Virchow- pioneer of pathological processes, explained that diseases arose in individual cells not organs or tissues in general

1953 Watson and Crick put forward their first structure of DNA being a double stranded helix, the cornerstone of genetics, cell biology and molecular biology among other disciplines

General Classification of the Cell 1. Eukaryotic cell - having a true nucleus -compartmentalized membrane bound organelles with specific metabolic activities

2. Prokaryotic cell -no defined nucleus -single celled -no membrane bound organelles

Diagram of a Prokaryotic Cell

Diagram of a Eukaryotic Cell

Differences between prokaryotic and eukaryotic cells

Plant and Animal Cells

Differences between plant and animal cells

Animal Cell

Plant Cell

Cell wallAbsent Present (formed

of cellulose)

ShapeRound (irregular shape) Rectangular

(fixed shape)

Vacuole

One or more small vacuoles (much smaller than plant cells).

One, large central vacuole taking up 90% of cell volume.

CentriolesPresent in all animal cells Only present in

lower plant forms.

Chloroplast

Animal cells don't have chloroplasts. Plant cells have chloroplasts because they make their own food.

Cytoplasm Present PresentEndoplasmic

Reticulum (Smooth and Rough)

Present Present

Ribosomes Present PresentMitochondria Present Present

Plastids Absent PresentGolgi Apparatus Present Present

Plasma MembraneOnly cell membrane Cell wall and a

cell membraneMicrotubules/

MicrofilamentsPresent Present

FlagellaMay be found in some cells May be found in

some cells

LysosomesLysosomes occur in cytoplasm. Lysosomes

usually not evident.

Nucleus Present PresentCilia Present It is very rare.

Plasmodesmata are intercellular junctions between plant cells that enable the transportation of materials between cells.A tight junction is a watertight seal between two adjacent animal cells, which prevents materials from leaking out of cells.Desmosomes connect adjacent cells when cadherins in the plasma membrane connect to intermediate filaments.Similar to plasmodesmata, gap junctions are channels between adjacent cells that allow for the transport of ions, nutrients, and other substances.

Source: Boundless. “Intercellular Junctions.” Boundless Biology. Boundless, 03 Jul. 2014. Retrieved 02 Feb. 2015 from https://www.boundless.com/biology/textbooks/boundless-biology-textbook/cell-structure-4/connections-between-cells-and-cellular-activities-63/intercellular-junctions-325-11462/

Functions of Animal Cell Organelles I

1. Cytoplasm/cytosol - Viscous aqueous environment (NOT free flowing) - Contains small molecules, nutrients, salts, soluble proteins - 20-30% of cytosol is protein – Very concentrated - Highly organized environment - A major site of cellular metabolism (e.g. glycolysis) - Contains cytoskeleton 2. Cytoskeleton - 3-dimensional matrix made of protein fibers - Functions to give cells shape, allows cells to move, guides internal organelle

movement. 3. Nucleus - Site of most DNA and RNA synthesis - Storage of genetic information - Bound by a double membrane - Largest organelle in eukaryotic cells

Functions of Animal Cell Organelles I

1. Cytoplasm/cytosol - Viscous aqueous environment (NOT free flowing) - Contains small molecules, nutrients, salts, soluble proteins - 20-30% of cytosol is protein – Very concentrated - Highly organized environment - A major site of cellular metabolism (e.g. glycolysis) - Contains cytoskeleton 2. Cytoskeleton - 3-dimensional matrix made of protein fibers - Functions to give cells shape, allows cells to move, guides internal organelle

movement. 3. Nucleus - Site of most DNA and RNA synthesis - Storage of genetic information - Bound by a double membrane - Largest organelle in eukaryotic cells

FtsZ was the first protein of the prokaryotic cytoskeleton to be identified. Like tubulin, FtsZ forms filaments but these filaments do not group into tubules. During cell division, FtsZ is the first protein to move to the division site, and is essential for recruiting other proteins that synthesize the new cell wall between the dividing cells

MreB and ParMProkaryotic actin-like proteins, such as MreB, are involved in the maintenance of cell shape. Some plasmids encode a partitioning system that involves an actin-like protein ParM. Filaments of ParM exhibit dynamic instability, and may partition plasmid DNA into the dividing daughter cells by a mechanism analogous to that used by microtubules during eukaryotic mitosis.CrescentinThe bacterium Caulobacter crescentus contains a third protein, crescentin, that is related to the intermediate filaments of eukaryotic cells. Crescentin is also involved in maintaining cell shape, such as helical and vibrioid forms of bacteria, but the mechanism by which it does this is currently unclear.

Functions of Animal Cell Organelles I

1. Cytoplasm/cytosol - Viscous aqueous environment (NOT free flowing) - Contains small molecules, nutrients, salts, soluble proteins - 20-30% of cytosol is protein – Very concentrated - Highly organized environment - A major site of cellular metabolism (e.g. glycolysis) - Contains cytoskeleton 2. Cytoskeleton - 3-dimensional matrix made of protein fibers - Functions to give cells shape, allows cells to move, guides internal organelle

movement. 3. Nucleus - Site of most DNA and RNA synthesis - Storage of genetic information - Bound by a double membrane - Largest organelle in eukaryotic cells

Functions of Animal Cell Organelles II

4. Endoplasmic Reticulum (ER) -  Network of interconnected, closed, membrane-bounded vesicles -  Attached to cell and nuclear membrane -  Used for manufacturing, modification and transport of cellular

materials -  Two types: * Smooth ER = site of lipid synthesis * Rough ER = site of protein synthesis via ribosomes -  Ribosomes are made up of RNA and proteins not bound by a

membrane 5. Lysosomes -  Internal sacs bound by a single membrane -  Responsible for degrading cell components that have become

obsolete for the cell or organism. -  Internal pH ~5 (very acidic) -  Compartmentalization ESSENTIAL! Sequesters this biological activity

from the rest of the cell. -  Enzymes in lysosomes degrade polymers into their individual building

blocks.

Functions of Animal Cell Organelles III

6. Golgi Apparatus -  Flattened vesicles of lipid/protein/sugar -  Usually found near smooth ER and nucleus -  Involved in protein and fat processing and trafficking to other organelles

(e.g. lysosomes, plasma membranes) – Distribution and shipping department for cell materials.

7. Mitochondria -  Have double membrane (inner and outer) -  Place where most oxidative energy production occurs = “powerhouse”

of the cell -  Form ATP – Convert oxygen and nutrients to energy -  Small, typically the size of a bacterium -  Contain a circular DNA molecule like that of bacteria (own genome) -  Because of the double membrane, size and presence of own genome,

mitochondria are believed to be descendents of a bacteria that was engulfed by a larger cell billions of years ago = endosymbiotic hypothesis.

-  A cell can have over 1000 mitochondria! Depends on need for energy---muscle cells have a lot of mitochondria.

Underlying simplicity of the living cell

LIVING SYSTEMS APPEAR COMPLEX BUT THERE IS AN UNDERLYING SIMPLICITY AND ELEGANCE:

- Most biological compounds are made of only SIX elements: C, H, O, N, P, S

- Only 31 chemical elements occur naturally in plants and animals

- All organisms have similar biochemical pathways.

- All organisms use the - Limited number of molecular building blocks make up larger macromolecules

4 major classes of biomolecules that make up macromolecules

1. Carbohydrates: e.g. glucose, fructose, sucrose - mainly used as sources of cellular energy

Lipids: commonly known as fats -  organic compounds that are not very water soluble -  used as sources of cellular energy -  components of cell membranes

Amino Acids: -  20 natural amino acids in total -  Used as building blocks for proteins

Nucleotides: -  5 in total -  Used as building blocks for DNA and RNA precursors

OTHER: -  Vitamins: organic compounds necessary for proper growth and

development -  Heme: Organometallic compound containing iron; important for

transporting oxygen in your blood stream.

Monomers to polymers

Starch and Cellulose: polymers of glucose molecules that differ only by how the glucose monomers are linked.

- Proteins/polypeptides: amino acid monomers linked together

- DNA:deoxyribonucleic acid o Heteropolymer of monomeric

nucleotideso Storage of genetic information

- RNA: ribonucleic acido Heteropolymer of monomeric

nucleotideso Involved in the TRANSFER

of the genetic information encoded by DNA

Monomers to polymers

Facts about biomacromolecules

Biomacromolecules: -  self-assemble into cellular structures and

complexes. -  recognize and interact with one another in

specific ways to perform essential cellular functions (e.g. membranes are complexes of

lipids and proteins) -  Interactions are weak and reversible -  Molecules have three dimensions and

shapes! Much of biochemistry relies on this fact.

EVOLUTIONARY FOUNDATION

Reading List

Lehninger “Principles of. Biochemistry”. Fourth Edition. David L. Nelson and Michael M. Cox.

“Biochemistry and Molecular Biology”. Fifth Edition. Despo Papachristodoulou, Alison Snape, William H. Elliott, and Daphne C. Elliott

“Life: The Science of Biology. Ninth Edition by David E Sadava et al.