Cell Chemistry PDF

**The Chemical Components of a Cell** **All living things are highly organized and diverse, but they all contain the same type of chemicals** **The most common elements in all living cells are:** - C-carbon - H- hydrogen - N-nitrogen - O-oxygen - P-phosphorus - S-sulfur The smal...

**The Chemical Components of a Cell** **All living things are highly organized and diverse, but they all contain the same type of chemicals** **The most common elements in all living cells are:** - C-carbon - H- hydrogen - N-nitrogen - O-oxygen - P-phosphorus - S-sulfur The smallest particle of an element that still retains its distinctive chemical properties is an *atom*. **Atoms are linked together in groups to form *molecules*.** **Atoms and molecules combine via chemical bonds:** - **Covalent bond.** - **Ionic bond.** - **Hydrogen bond.** - **Hydrophobic interaction.** - **Van-der Waals attractions.** **[Water (65-85 % of a cell's weight)]** In each water molecule the two H atoms are linked to the O atom by covalent bonds The two bonds are highly polar because O is strongly attractive for electrons, whereas the H is weakly attractive When a positively charged region of one water molecule approaches a negatively charged region of a second water molecule, the electrical attraction between them can result in a weak bond called hydrogen bond Hydrogen bonds are much weaker than covalent bonds, but the combined effect of many weak bonds can be profound **Properties of water** Water is the universal solvent and facilitates chemical reactions both without and within living systems. e.g. When a salt -- sodium chlorine (Na^+^Cl^-^) is put into water they dissolve. Water is also solvent for larger molecules that contain ionized atoms or are polar molecules: - Water is the only common molecule that can be solid, liquid, or gas according to the environmental temperature. - The temperature of liquid water rises and falls more slowly than that of most other liquids. - Water tends to remain a liquid rather than change to ice or steam. Most substances contract when they solidify but water expends. At 0^0^C frozen water is least dense and at 4^0^C liquid water it is most dense (ice floats on liquid water). Water boils at +100^0^C. High surface tension is characteristic for water. **All these properties are defined by hydrogen bonding between water molecules.** *Water tends to ionize or dissociate, releasing an equal number of hydrogen ions (H+) and hydroxyl ions (OH-).* This reaction is reversible. These same ions can join together to form water. Protons don't stay separately in solutions, they associate with water molecules and form Hydronium ion -- (H~3~0)^+^ **Biologists use the pH scale**; it is logarithmic scale for expressing the acidity or alkalinity of a solution. Namely pH scale indicates the relative concentrations of (H^+^) and (OH^-^) in a solution. The pH scale range is from 0 to 14. The pH of pure water is 7; this is neutral pH. A pH below 7 indicates an acid solution; one above 7 indicates alkaline solution. pH stands for 'potential of hydrogen'. Most organism maintain a pH of about 7; A much higher or lower pH causes illness. Normally, pH stability is possible because organisms have built-in mechanisms to prevent pH changes. A buffer is chemical or a combination of chemicals that can both take up and release hydrogen ions. Carbonic acid (H~2~CO~3~) helps buffer human blood because it is weak acid that does not totally dissociate: **H~2~CO~3~ \ HCO~3~^−^ + H^+^** **^carbonic\ acid\ bicarbonate\ ion\ hydrogen\ ion^** **Buffers** usually **keep the pH within normal** limits despite many biochemical reactions that either release or take up hydrogen or hydroxyl ions. - **Salts** within cells play an important role. They **provide cells with osmosis** -- the net movement of water molecules from the region where their concentration is high to a region where their concentration is low through a partially permeable membrane. - Salts are dissociated in water as ions. - Among various ions, Sodium (Na^+^), Potassium (K^+^) and Calcium (Ca^2+^) are the most important for cells, the rest (Iron, Copper, Zinc, Magnesium, Nickel, Cobalt, Cadmium) also play vital roles for cells. **[Important gases for living cells]** Oxygen is the essential element in the **respiratory processes** of most of the living cells and in combustion processes. Oxygen supports **combustion**, **combines with most elements**, and is a component of hundreds of thousands of organic compounds. It is colorless, odorless and tasteless diatomic gas. It is a very reactive oxidizing agent. Oxygen is sparingly soluble in water. **Nitric oxide** Functions as a gaseous mediator in mammals and other vertebrates, especially in the cardiovascular and nervous systems. **[A cell is formed from carbon compounds]** - If we disregard water, **nearly all the molecules in a cell are based on carbon**. Carbon is outstanding among all the elements in its ability to form large molecules. - Because it is small and has four electrons and four vacancies in its outermost shell, a carbon atom can form four covalent bonds with other atoms. Most important, one carbon atom can join to other carbon atoms through highly stable covalent C-C bonds to form chains and rings and therefore generate large and complex molecules with no obvious upper limit to their size. The small and large carbon compounds made by cells are called ***organic molecules.*** Certain combinations of atoms, such as chemical groups: - methyl (-CH~3~), - hydroxyl (-OH), - carboxyl (-COOH), - carbonyl (-C=O), - phosphate (-PO~3~ ^2-^), - amino (-NH~2~) occur repeatedly in organic molecules. Each of them has distinct chemical and physical properties that influence the behavior of the molecule in which the group occurs. **[Cells contain four major families of small organic molecules]** - The small organic molecules of the cell are carbon-based compounds that have molecular weights in the range 100 to 1000 and contain up to 30 or so carbon atoms. - They are usually found free in solution and have many different fates. - Some are used as monomer subunits to construct the giant polymeric macromolecules---the proteins, nucleic acids, and large polysaccharides---of the cell. - Others act as energy sources and are broken down and transformed into other small molecules in a maze of intracellular metabolic pathways. - Many small molecules have more than one role in the cell---for example, acting both as a potential subunit for a macromolecule and as an energy source. - Small organic molecules are much less abundant than the organic macromolecules, accounting for only about one-tenth of the total mass of organic matter in a cell. As a rough guess, there may be a thousand different kinds of these small molecules in a typical cell. **[Macromolecules of the cell]** - Proteins - Carbohydrates - lipids - Nucleic acids **[Proteins]** - Proteins constitute most of a **cell's dry mass**. - They are not only the cell's building blocks, but they also execute nearly all the cell's functions. - Proteins are the most structurally complex and functionally sophisticated molecules; - Molecular weights range from 6 to several thousand kilodaltons (kDa); **Proteins belong to polymers, so their monomers are amino acids.\ Amino acids are water-soluble organic compounds that possess both a carboxyl and an amino group attached to the same carbon atom, called the α-carbon atom.** **R - may be hydrogen or an organic group, which may be non-polar, basic, acidic, or polar.\ The nature of R group determines the properties of any amino acid.** Through the **formation of peptide bonds**, amino acid joins together to form short chains (peptides) or much longer chains (polypeptides). All protein has an amino group at one end (N-terminus) and a carboxyl group at its another (C-terminus); this gives it a polarity - Proteins are composed of various proportions of about **20** commonly occurring amino acids. - The sequence of these amino acids in the protein polypeptides determines the shape, properties and hence biological role of the protein. - Some amino acids are **not synthesized in sufficient quantities by animal organisms**, so they are called as **essential amino acids.** - **Essential amino acids must be present in the diet.** **Levels of protein structural organization** Each type of polypeptide commonly bends, folds, and twists in a particular way within a protein. Proteins have at least three levels of structure, and some have a fourth level. The primary structure of a protein is the sequence of the amino acids joined together by peptide bond. ***The secondary structure*** of protein comes about when the polypeptide chain takes a **particular orientation in space:** one common arrangement of the chain is the **α helix** or **right-handed coil,** with 3.6 amino acids per turn. Many polypeptide have a secondary structure called a **β sheet** or **pleated sheet**. Hydrogen bonding between the oxygen and nitrogen atoms of different amino acids stabilizes secondary structure of proteins. Very often, secondary structure is considered as a crucial for protein. Really, functional activity of protein molecules depends on spiralization degree and helix parameters. Spiralization of protein molecule is determined by its coiling. ~~Special group of proteins in living cells assist newly synthesized or denatured proteins to fold. They are named as molecular chaperones.~~ ~~There are two classes of so called molecular chaperones: 1. Heat-Shock Proteins and their regulators and 2. Cylindrical Chaperones.~~ ~~The chaperones bind to the protein and prevent improper interactions within the polypeptide chain, so that it assumes the correct folded orientation. This process may require energy in the form of ATP.~~ ~~Heat-Shock Proteins (HSP) occur in both eukaryotes and prokaryotes. They are synthesized by living cells in response to increased temperature or other forms of stress.~~ ~~There are several families of HSPs, named according to their relative molecular mass (in kilodaltons,kDa). HSP100, HSP90, HSP70 and HSP60, tend to predominate in animal cells.~~ **Molecular Chaperones - Simplified Explanation** 1. **What are Molecular Chaperones?** - Special proteins in living cells that help **newly made or damaged (denatured) proteins** fold correctly into their functional shapes. - They prevent incorrect folding by binding to the protein and guiding it, sometimes using energy from **ATP**. 2. **Types of Molecular Chaperones**: - **Heat-Shock Proteins (HSPs)**: - Found in both eukaryotic and prokaryotic cells. - Produced when cells face stress, like high temperature. - Named by their molecular size (e.g., HSP100, HSP90, HSP70, HSP60). - **Cylindrical Chaperones**: - Specialized structures that also assist in protein folding. 3. **Why are Chaperones Important?** - Ensure proteins fold into the correct shape, which is essential for their proper function. - Prevent misfolding ***Tertiary structure*** of polypeptide is maintained by various types of bonding between the R groups: Hydrogen bonds Ionic bonds Covalent bonds (-S-S-) Hydrophobic interactions All these bonds give **stability** to the shape of the protein molecule in tertiary structure. If a particular protein molecule is formed as a **complex of more than one polypeptide** chain, the complete structure is designated as a ***quaternary structure*.** Between polypeptide chains hydrogen and ionic bonds are found. Each polypeptide chain exists with its own primary, secondary and tertiary structures. **[Conjugated proteins]** - **Polypeptides linked with non-protein molecules** are named as a conjugated proteins. They are divided into 3 main groups: **Chromoproteins** - proteins conjugated with a metal‐containing group, such as the haem group of hemoglobin, myoglobulin and cytochrome, which contain iron. - **Glycoproteins** -- contains carbohydrates, that are linked to a protein covalently. Glycoproteins are important components of plasma membranes, in which they extend throughout the lipid bilayer. They are also **constituents of body fluids**, such as mucus, that are involved in **lubrication**. Many of the **hormone receptors** on the surfaces of cells are glycoproteins. - **Lipoproteins** -- are compounds consisting of a **lipid** combined with a **protein**. Lipoproteins are the **main structural materials** of the membranes of cells and cell organelles. They also occur in [blood and lymph]. - ~~**Nucleoproteins** - these group of molecules **[does not belong to conjugated proteins]**, because the nucleic acid of nucleoproteins always act independently and binds to protein only for its function regulation. Two types of nucleoproteins are known: deoxyribonucleoprotein (proteins linked to DNA) and ribonucleoproteins (protein linked to RNA).~~ ~~The proteins that combine with DNA are generally of characteristic types called **histones** and protamines. The resulting nucleoproteins (deoxynucleoproteins) make up the chromosomes of living cells.~~ ~~Histones contain a large proportion of the basic (positively charged) amino acids lysine, arginine, and histidine.~~ ~~They are involved in the condensation and coiling of chromosomes during cell division, and chemical modification of histones is key aspect of suppressing or activating gene activity.~~ **Nucleoproteins - Simplified Explanation** 1. **What are Nucleoproteins?** - A special group of proteins that bind with **nucleic acids (DNA or RNA)** for **function regulation**. - They **do not belong to conjugated proteins** because the nucleic acids (DNA or RNA) act independently. 2. **Types of Nucleoproteins**: - **Deoxyribonucleoproteins**: Proteins linked to DNA (e.g., in chromosomes). - **Ribonucleoproteins**: Proteins linked to RNA. 3. **Deoxyribonucleoproteins (DNA + Protein)**: - The proteins that bind to DNA are mainly **histones** and **protamines**. - These nucleoproteins form the structure of **chromosomes** in cells. 4. **Histones - Key Facts**: - Histones are rich in **basic amino acids** like lysine, arginine, and histidine, which are positively charged. - Functions: - **Condensation and coiling** of chromosomes during cell division. - **Gene regulation**: Chemical modifications of histones (e.g., acetylation or methylation) determine whether genes are **active or suppressed**. **[Carbohydrates]** - One of a group of organic compounds based on the general formula (CH2O) n. Among carbohydrates generally monosaccharides, oligosaccharides and polysaccharides are discussed. - The **simplest carbohydrates are the monosaccharides**, mainly with 5 or 6 carbon atoms (e.g. ribose, deoxyribose, glucose and fructose). Monosaccharide residues link to each other via **glycosidic bonds** forming long chain. Carbohydrates containing **2-9 monosaccharide residues are called oligosaccharides**. Carbohydrates with more than 9 monosaccharide residues are polysaccharides. - Polysaccharides are divided into two basic groups: **structural and nutrient** polysaccharides. - Structural polysaccharides form **extracellular and intracellular supporting structures** (e.g. cellulose, chitin, manna, hyaluronic acid, keratan sulphate and chondroitin sulphate). - **Nutrient polysaccharides** serve as **reserve for monosaccharides** (e.g. starch, glycogen, paramylon, inulin). - By monosaccharide composition, polysaccharides may exist as a **homo- and hetero**. (Monosaccharides are cellulose, starch, glycogen - they are composed from glucose. Hyaluronic acid, keratan sulphate, chondroitin sulphate -- are heterosacharides). Among heterosacharides so called glycosaminoglycans are detached, disaccharides serve as monomers for this kind of polysaccharides (e.g. heparin, hyaluronic acid). Glycosaminoglycans bind proteins and form proteoglycans (proteoglycans are component of cartilage, intercellular substances). Polysaccharides are member of glycoproteins and glycolipids. They are important components of cell membrane. **Lipids** A variety of organic compounds are classified as lipids. Many of these are insoluble in water because they lack any polarized groups. The most familiar lipids are those found in fats and oils. Organisms use these molecules as long-term energy storage compounds. Phospholipids and steroids are also important lipids found in living things (e.g. they are components of plasma membranes). Fats and oils, sometimes called neutral fats, contain two types of unit molecules: fatty acids and glycerol. **Each fatty acid consists of a long hydrocarbon chain with an acidic carboxyl group at one end.** Most of the fatty acids in cells contain 16 to 18 carbon atoms per molecule, although smaller ones are also found **Fatty acids** are either saturated or unsaturated. Saturated fatty acids have no double bonds between the carbon atoms. The carbon chain is saturated, so to speak, with all the hydrogens that can be held. Unsaturated fatty acids have double bonds in the carbon chain wherever the number of hydrogens is less than two per carbon atom. **Glycerol** is a compound with three hydroxyl groups. When fat is formed, the acid portions of three fatty acids react with these groups so that fat and three molecules of water are formed. Since it takes three fatty acid per one glycerol, these molecules are often called triglycerides. Fats and oils are utilized for long-term energy storage because they have mostly hydrogen-carbon bonds, making them a richer supply of chemical energy than carbohydrates, which have many C-OH bonds. Molecule per molecule, animal fat contains over twice as much energy as glycogen. This is because fat droplets are concentrated and don't contain water. **In waxes a very long-chain fatty acid bonds with a very long-chain alcohol.\ Waxes are solid and have a high melting point. They are also waterproof and resistant to degradation.** **Phospholipids** contain a phosphate group, and this accounts for their name. Essentially, phospholipids are constructed as neutral fats are, except that **in place of the third fatty acid there is a phosphate group** or a grouping that contains both phosphate and nitrogen. The group can ionize; therefore, this hydrophilic chain forms what is called the **polar head** of the molecule while the other two hydrophobic chains are the nonpolar tails. When **phospholipid** molecules are placed in **water**, they form a sheet in which the polar heads face outward, and the nonpolar tails face each other. This property of phospholipids contributes to the structure of **membranes**. **Steroids** are lipids that have entirely different structures than neutral fats. Each steroid has a **backbone of four fused carbon rings** and varies primarily according to the type of **functional group attached** to it. **Cholesterol** is the precursor of several other steroids such as certain vertebrate hormones including aldosterone, a hormone that helps regulate the sodium content of the blood, and the sex hormones, which help maintain male and female characteristics. Such different functions are due solely to the attached groups. Cholesterol is also found in animal **cellular membranes**. Lipids - Simplified Summary Overview: Lipids are organic compounds that are mostly insoluble in water due to a lack of polarized groups. They include fats, oils, phospholipids, steroids, and waxes. Fats and Oils: Made of glycerol and fatty acids (called triglycerides when three fatty acids are attached to one glycerol). Fatty acids have: Long hydrocarbon chains with a carboxyl group (-COOH). Saturated: No double bonds, fully \"saturated\" with hydrogen. Unsaturated: Contain double bonds, less hydrogen per carbon atom. Store energy efficiently due to many hydrogen-carbon bonds, holding twice as much energy as **glycogen**. Waxes: Formed from a long-chain fatty acid and a long-chain alcohol. Solid, high melting point, waterproof, and resistant to degradation. Phospholipids: Structure: Similar to fats but with a phosphate group replacing one fatty acid. Polar head (water-attracting) and nonpolar tails (water-repelling). In water, they form membranes with heads facing outward and tails inward. Steroids: Lipids with a backbone of four fused carbon rings. Functions vary based on attached functional groups. Cholesterol: A precursor for hormones like aldosterone (regulates sodium) and sex hormones (controls male and female traits). Found in animal cell membranes, contributing to structure and function. **[Nucleic acids]** Nucleic acids are huge polymers of nucleotides with very specific functions in cells. A nucleotide is a molecule made up of a nitrogen-containing ring compound linked to a five-carbon sugar, which in turn carries one or more phosphate groups. The five-carbon sugar can be ribose or deoxyribose. Nucleotides containing ribose are called ribonucleotides, and those containing deoxyribose are called deoxyribonucleotides The nitrogen-containing rings are generally referred to as bases. These structures are called bases because they have chemically basic characteristics that raise the pH of a solution. Cytosine, thymine and uracil are called pyrimidines; guanine and adenine are called purines. ~~A sugar-base compound that is a nucleotide precursor is called **nucleoside**.~~ ~~Depending on the pentose sugar component, a **nucleoside** may be a ribonucleoside (e.g. adenosine, guanosine, cytidine, and uridine) or a deoxyribonucleoside (e.g. deoxyadenosine, deoxyguanosine, deoxycytidine, deoxythymidine).~~ ~~Nucleoside can be formed by partial hydrolysis of a nucleic acid.~~ ~~Guanosine and Adenosine can be phosphorylated to become guanosine monophosphate (GMP) and adenosine monophosphate (AMP), cyclic guanosine monophosphate(cGMP) and cyclic adenosine monophosphate(cAMP), guanosine diphosphate (GDP) and adenosine diphosphate (ADP), guanosine triphosphate (GTP) and adenosine triphosphate (ATP).~~  **What is a Nucleoside?** - A **nucleoside** is a compound made of: - A **sugar** (pentose, like ribose or deoxyribose). - A **nitrogenous base** (e.g., adenine, guanine, cytosine, thymine, or uracil). - It is a **precursor** to nucleotides (the building blocks of DNA and RNA).  **Types of Nucleosides**: - Based on the sugar type: - **Ribonucleosides**: Contain ribose (e.g., adenosine, guanosine, cytidine, uridine). - **Deoxyribonucleosides**: Contain deoxyribose (e.g., deoxyadenosine, deoxyguanosine, deoxycytidine, deoxythymidine).  **How Are Nucleosides Formed?** - They are created by the **partial hydrolysis** of nucleic acids, where the phosphate group is removed.  **Phosphorylated Forms (Nucleotides)**: - Nucleosides can gain one or more **phosphate groups** to become **nucleotides**, which are key molecules in energy transfer and signalling: - **Monophosphates**: GMP (guanosine monophosphate), AMP (adenosine monophosphate). - **Diphosphates**: GDP (guanosine diphosphate), ADP (adenosine diphosphate). - **Triphosphates**: GTP (guanosine triphosphate), ATP (adenosine triphosphate). - **Cyclic Monophosphates**: cGMP, cAMP (involved in cell signaling). These forms play important roles in various biochemical processes such as energy transfer, synthesis of nucleic acids and proteins, photosynthesis, muscle contraction and intracellular signal transduction. There are two main types of nucleic acids: RNA is based on sugar ribose and contains bases A, G, C and U. DNA is based on sugar deoxyribose and contains bases A, G, C and T. When nucleotides join to form DNA or RNA they occur in a definitive sequence. The nucleotides form a linear molecule called a strand in which the backbone is made up of phosphate-sugar-phosphate-sugar, with the bases projecting to one side of the backbone. Since the nucleotides occur in a definite order, so do the bases. RNA is single stranded, but DNA is double stranded. The two strands of DNA twists about one another in the form of a double helix. The two strands are held together by hydrogen bonds between purine and pyrimidine bases. Thymine (T) in one strand is always paired with adenine (A) in the opposite strand, and a guanine (G) is always paired with cytosine (C). This is called complementary base pairing. DNA two strands run in opposite directions to each other and are therefore anti-parallel, one backbone being 3\' (three prime) and the other 5\' (five prime). This refers to the direction the 3rd and 5th carbon on the sugar molecule is facing. - There are three different classes of RNA, each with specific functions in protein synthesis: messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA). - DNA is the genetic material that stores information regarding its own replication and the order in which amino acids are to be joined together to make a protein. - RNA works in conjunction with DNA to bring about protein synthesis.