BIOLOGY

1: BIOLOGICAL MOLECULES & INTRODUCTION TO THE CELL

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Some suggested textbooks

Biology, 4th Ed, Neil A Campbell

Biology 1
Biological Molecules & Introduc3on to the Cell
Fundamental Concepts

Biology, 2nd Ed, Bruce R Knox Human Physiology: from cells to systems, 7th Ed, Lauralee Sherwood

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2010-09

Biologically important elements

Carbon is the central element of organic chemistry. In its elemental form it possesses six electrons over two levels (2, then 4) Because of its ability to form four covalent bonds per atom it is well suited to serving as a building block for simple or complex molecular structures Carbon atoms act as an important backbone structure in biological molecules including: carbohydrates, lipids, proteins, and nucleic acids

Biologically important elements

Other important elements found in organic chemistry include: hydrogen, oxygen, and nitrogen Water (H2O), is cri3cally important to life. Water acts as a solvent into which biological ions/molecules can dissolve, diuse, and interact with one another Dissolved inorganic ions (e.g. Na+, Cl-, K+, Ca++ etc) are important for establishing a solu3ons osmo3c pressure, for maintaining protein structure, and for driving cellular processes

Monomers & polymers

Carbohydrates
Carbohydrates are composed of carbon, oxygen and hydrogen Carbohydrates act as an energy source for cells whereby oxida3on of their chemical bonds liberates energy. This energy is ul3mately used to generate ATP (adenosine triphosphate) - the most common energy molecule used in cells Monosaccharides are the basic form of carbohydrates. Humans can u3lise three types of monosaccharide for energy: glucose, fructose or galactose Disaccharides are present in our food & drink; these include: sucrose (glucose + fructose), lactose (glucose + galactose), and maltose (glucose + glucose), though they cannot be absorbed as disaccharides Polysaccharides are long chain carbohydrates; these are found in foods such as rice or potatoes (starch)

(Frank Boumphrey. Ring Structure of Glucose. 1 May 2009) (Frank Boumphrey. Glycogen bonds. 20 May 2009)

Monomers are the basic building block molecules that can be bound covalently to other monomers to build a polymer Examples of monomers are: simple sugars (monosaccharides), individual amino acids, or individual nucleic acids. Each of these can be chemically bonded to other monomers of the same type to produce a more complex biological molecule (polymer) The chemical bonds formed between biological monomers commonly require a dehydra3on reac3on

(Frank Boumphrey. Structure of Common disaccharides. 20 May 2009)

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BIOLOGY 1: BIOLOGICAL MOLECULES & INTRODUCTION TO THE CELL

Lipids
Lipids are typically hydrophobic molecules that are large and contain a rich store of C-H bonds compared to carbohydrates, hence a greater amount of energy can be liberated from their metabolism
Triglyceride molecule

Phospholipids
(Bryan Derksen, Vishnu2011. Phospholipid structure. 20 Nov 2009)

Lipids can serve structurally to make up cellular membranes or even as signalling molecules The backbone of a lipid molecule is built by glycerol Glycerol is chemically bonded to free fa]y acids - long chains of carbon & hydrogen

Saturated fatty acid

Unsaturated fatty acid

Fa]y acids can be saturated (no C=C) or unsaturated (C=C)

(Mariana Ruiz Villarreal, Phospholipids aqueous solution structures. 6 Nov 2007)

Phospholipids possess a phosphate group bound to the glycerol backbone which creates a hydrophilic head The fa]y acid tails are hydrophobic Phospholipids are therefore ideal for forming into bilayers since the hydrophilic parts align with water, and the fa]y acid tails associate with one another crea3ng a hydrophobic compartment Phospholipid bilayers are used as the basis of cell membranes, intracellular compartments, and vesicles

Amino acids & protein

Polypeptide/protein structure
Protein structure is oben described in terms of primary, secondary, ter3ary or quarternary structure Ter3ary structure is the overall 3D structure of the whole polypep3de Quarternary structure involves the overall 3D structure of a protein that is formed by mul3ple polypep3de chains (e.g. haemoglobin) Secondary and ter3ary protein structure is dependent on environmental factors such as temperature, pH, osmolality. Proteins denature in subop3mal environmental condi3ons

Amino acids are the monomeric structures used to build polypep3des or proteins. They can also be used as a source of energy 20 amino acids exist in humans, each with the same basic chemical structure that varies only at its R group Amino acids are chemically bound together via pep3de bonds (COO- + NH2) to form polypep3des/proteins
(Dan Cojocari. Amino Acids. Jan 2010)

Proteins serve many func3ons including ac3ng as: structural proteins, receptors, signalling molecules, enzymes

Deoxyribonucleic acid (DNA)

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Deoxyribonucleic acid (DNA)

(Frank Boumphrey. A Strand of DNA showing basic structure. 1 July 2009)

DNA forms into a ladder-like structure whereby bases pair up (via hydrogen bonding), and the backbone forms into a double-helix structure The length of one human cells DNA is >3 billion base pairs - over 1.8 metres long

DNA acts as the hereditary gene3c Each nucleo3de contains a base (A, T, G, C), a sugar, and a phosphate group informa3on storage molecule of cells The cell uses DNA to produce RNA, then protein The DNA backbone is formed by a covalent bond between the sugar of one nucleo3de and the phosphate of the next

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BIOLOGY 1: BIOLOGICAL MOLECULES & INTRODUCTION TO THE CELL

The eukaryote cell

Eukaryote cells are complex cells containing mul3ple organelles. These contrast with prokaryote cells (bacterial) which have a rela3vely simple architecture The major organelles of the eukaryote cell are: the nucleus, ribosomes, endoplasmic re3culum, golgi apparatus and mitochondria
(Mariana Ruiz Villarreal. Animal cell structure. April 2006)

The prokaryote cell

Prokaryo3c cells are bacterial cells The DNA is housed within the cytoplasm Ribosomes are present in the cytoplasm A agellum, if present, allows the bacterium to move about in aqueous environments The bacterial cell wall primarily prevents the cell from burs3ng due to external osmo3c pressure

In contrast, the prokaryote cells only contain gene3c material (no nucleus) and ribosomes macroscopically.

(Mariana Ruiz Villarreal. Average prokaryote cell. 2 March 2008)

Cell membrane
(Mariana Ruiz Villarreal, Dhatfield. The cell membrane. 16 June 2008)

The cell membrane is mainly composed of phospholipids and proteins The cell membrane serves to create a barrier between the cytoplasm and the external environment. It is important for allowing regula3on of the cells internal environment - e.g. the dieren3al ionic concentra3ons either side of the cell membrane Proteins embedded in the membrane func3on as structural proteins, receptors, channels, and pumps

Nucleus
This contains a cells DNA The walls of the nucleus are formed by a double-membrane structure called the nuclear envelope. Pores exist in the envelope that allow communica3on between the nucleus and the cytoplasm. A dark staining region within the nucleus is oben visible, this is called the nucleolus - a highly ac3ve area where ribosomal RNA is produced. Euchroma3n, light staining regions of gene3c material, are highly ac3ve gene transcrip3on areas. Heterochroma3n, dark staining regions of gene3c material, are less ac3ve sites of transcrip3on.

(Mariana Ruiz Villarreal A diagram of a human cell nucleous. 27 April 2006)

Histones
Histones are proteins present in the nucleus DNA wraps around histones forming a nucleosome This ac3on of wrapping DNA allows ordering of the DNA molecule and inac3va3on of gene3c material within the nucleosome

Ribosomes
Ribosomes are organelles composed of two-subunits containing rRNA and protein Ribosomes interact with mRNA and tRNA-amino acid molecules in the cytoplasm to generate polypep3des The ribosome builds a polypep3de by reading the mRNA molecules codon sequence and bonding the coded amino acids together Ribosomes can be found either a]ached to the cells endoplasmic re3culum or free within the cytoplasm Bacteria possess 70S ribosomes, whereas eukaryote cells possess 80S ribosomes

(Frank Boumphrey. Illustration of tRNA building. 4 July 2009)

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BIOLOGY 1: BIOLOGICAL MOLECULES & INTRODUCTION TO THE CELL

Endoplasmic reticulum (ER)

The ER forms a network of membranous sacs throughout the cell. Within these sacs a number of cellular processes occur:
Conforma3onal folding of proteins Biosynthesis of complex molecules (steroids, cholesterol, lipids) Storage of Ca++ ions (muscle)

Golgi apparatus
The golgi apparatus is made up of a small network of parallel membranous sacs The golgi receives vesicles transported from other areas of the cell, such as the ER or the membrane Proteins are oben sent to the golgi body to be modied before being sent to a nal cellular des3na3on Each golgi apparatus has a cis and a trans side.
The cis side receives vesicles The trans side sends out modied products to specic des3na3ons

The golgi also acts as a quality control sta3on for cellular proteins

Mitochondria
Mitochondria act as the sites for cellular respira3on and energy produc3on Mitochondria are responsible for genera3ng the majority of the cells ATP; this is via aerobic respira3on The mitochondrion has an inner membrane that contains many oxida3ve enzymes involved in cellular respira3on (Krebs cycle and electron transport chain) The intermembrane space is used to generate a H+ ion gradient so that ATP can be generated The newly formed ATP can then diuse out of the mitochondrion to other areas of the cell to be used to drive cellular processes

Cytoskeleton
Cytoskeletal proteins can serve to provide the cell, or en3re 3ssues, with a matrix to maintain their shape
(Frank Boumphrey. Construction of Microtubules. 24 June 2009)

Intracellular structural proteins consist of:

Microtubules (e.g. axonal transport) Intermediate laments (e.g. hair & nails) Microlaments (e.g. thin laments in muscle bres)

(Mariana Ruiz Villarreal . Diagram of a human mitochondrion. 2 May 2006)

(Y. Tambe. Microfilament of mouse embryo fibroblasts. 19 Oct 2005.)

Receptors
Receptors are proteins which bind signalling molecules and ac3vate a specic cellular response Receptors are found:
On the cell membrane (hydrophilic signals) Or in the cytoplasm or nucleus (lipid-soluble signals, or signals generated from within the cell)

Signalling molecules
Hormones are signalling molecules produced by a specic 3ssue and carried in the bloodstream to aect distant target cells Paracrine agents act within local 3ssues, whilst autocrine agents act only on the secre3ng cell
(Nrets. Synapse. 29 Sep 2006.)

All receptors possess several important biochemical characteris3cs:

(XcepticZP. Insulin and glucose metabolism. 10 Apr 2007)

Anity & specicity Satura3on kine3cs Desensi3sa3on Up or down regula3on

Neurotransmi]ers are released from neurons at a synapse to aect a single cell

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BIOLOGY 1: BIOLOGICAL MOLECULES & INTRODUCTION TO THE CELL

Intracellular signalling
Membrane-bound receptors respond to hydrophilic signalling molecules. These cannot diuse across the membrane Membrane-bound receptors oben produce a cellular response by ac3ng through a cascade of intracellular chemical messengers (2nd messengers) In this example: a signal binds to the receptor, this ac3vates adenylate cyclase via a G protein, which catalyses the produc3on of cyclic AMP - a cellular signalling molecule

Steroid hormones
Steroid hormones are lipid soluble and therefore can diuse across the cell membrane The receptors for steroid hormones are located either in the cytoplasm or in the nucleus Binding of the steroid hormone to its receptor typically results in changes in gene expression within the cell - this tends to be a slower response than that of membrane receptors

(David S. Goodsell. G protein signal transduction. 2004.)

Homeostasis
The process of maintaining a constant internal environment via -ve feedback For a func3oning homeosta3c process to occur there must be:
A controlled physiological variable (s3mulus) Receptors that detect changes in the controlled variable An integra3ng centre that compares the receptor info with a desired set point Eerent pathways that allow the integra3ng centre to communicate with the eectors Eectors that, when s3mulated, act to restore the controlled variable towards its normal value

Homeostasis example
Body temperature (controlled variable) is normally maintained between 36.5-37.2C Receptors/integra3ng centre are found in the hypothalamus. These detect the temperature of the hypothalamic blood supply Major eectors include: skeletal muscle (shivering), cutaneous/ peripheral blood vessels (constric3on/dilata3on), sweat glands (swea3ng) Eerent pathways are predominantly neural

(Mikael Hggstrm. Calcium regulation. 15 Nov 2009.)

Note: Receptor and integra3ng centre are oben found in the same anatomical loca3on Eerent pathways act either neurally (fast eector response), or hormonally (slower eector response)

Topics covered
Important biological elements and molecules, their basic structure, and their func3on within living organisms Characteris3cs of prokaryote and eukaryote cells, including the func3on of the eukaryote cells major organelles Signalling molecules, receptors and 2nd messenger systems Homeostasis

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