Nursing Notes 1st year - Biochemistry PDF

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CHEM123 – WEEK 1 - 2Content:Biochemistry of the CellCellsEukaryotic cell Structure and FunctionFunctional GroupsBIOCHEMISTRY OF THE CELLThe living matter is composed of mainly six elements: carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur. These elements together constitute about 90% of th...

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CHEM123 – WEEK 1 - 2 Content: Biochemistry of the Cell Cells Eukaryotic cell Structure and Function

monosaccharides, amino acids, fatty acids, purine, and pyrimidine nucleotides, peptides, hormones, vitamins and coenzymes. Compounds Found in Living Things Carbohydrat e

CHO

Monomer: monosacch aride

Lipid

CHO

Protein

CHON

Nucleic Acid

CHONP (S)

Monomer: Function: 1 glycerol Long-term 3 fatty acids energy STORAGE Monomer: Function: Amino acid Structure; Builds and repairs tissues Monomer: Function: Nucleotide Genetic code (DNA) or Immediate energy (ATP

Functional Groups

BIOCHEMISTRY OF THE CELL The living matter is composed of mainly six elements: carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur. These elements together constitute about 90% of the dry weight of the human body.

Water Water account for about 70-75% of the weight of the cell. Other cellular constituents are either dissolved or suspended in water.

Function: main source of energy

Carbohydrates Organic Compound Organic compounds accounts for 25-30% of the cell weight They are nucleic acids, proteins, polysaccharides (carbohydrates) and lipids. Proteins accounts 10-20% of the weight of the cell. Nucleic acids account 7-10% of the cell weight.

Include sugars and starches, contain carbon, hydrogen, and oxygen Classified according to size as monosaccharides (one), disaccharides (two), or polysaccharides (many) Provide a ready, easily used source of food energy for cells.

Lipids

Polysaccharides usually account for 2-5% of the cell weight

Large and diverse group of organic compounds

About 3% of cell weight is due to lipids. Lipids content may be higher in adipocytes or fat cells.

Most lipid are insoluble in water but readily dissolve in other lipids or organic solvents.

Proteins may account more of cell weight in cells like erythrocytes.

Most abundant lipids in the body triglycerides, phospholipids and steroids.

Other low molecular weight organic compounds may account for 4% of cell weight. They are

Triglycerides – represent the body’s most abundant and concentrated source of usable energy. When oxidized, they yield large

Janella Ericka D. Doblada – BSN 1 B-12

are

amounts of energy. They are stored chiefly in fat deposits beneath the skin and around the body organs.

They do not only increase the speed of chemical reactions, they also determine just which reactions are possible at a particular time.

Phospholipids – has a hydrophilic (water loving) and hydrophobic (water fearing) region. It is present in cell membranes and allow cells to be selective about what may enter or leave

Without enzymes, biochemical reactions would occur far too slowly to sustain life.

Steroids – cholesterol, the single most important steroid molecule, is the raw material used to form vitamin D, some hormones, and bile salts.

Enzymes are very specific in their activities, each controlling only one (or small group) chemical reaction(s) and acting only on specific molecules.

Proteins Proteins accounts for over 50% of organic matter in the body, and they have the most varied functions of the organic molecules. The building blocks of proteins are small molecules called amino acids. Amino acids are joined together in the chains to form large, complex protein molecules. Fibrous/Structural proteins – strand-like proteins that appear most often in body structure. They are very important in binding structures together and for providing strength in certain body tissues. Globular/Function Proteins – they are mobile, generally spherical molecules that play crucial roles in virtually all biological processes. Some help provide immunity, others help growth and development, and some are biological catalysts (enzymes).

Nucleic Acids The role of nucleic acids is fundamental; they make up the genes, which provide the basic blueprint of life. Not only do they determine what type of organism you will be, but they also direct ones growth and development – and they do this largely by dictating protein. There are two major kinds: the deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).

Enzymes Functional proteins that act as biological catalysts. A catalyst is a substance that increases the rate of a chemical reaction without becoming part of the product or being changed itself.

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DNA – it is the genetic material found within the cell nucleus. It has two roles. One is to replicate

itself before a cell divides, thus ensuring that the genetic information in every body cell is identical. Second is it provides instructions for building every protein in the body.

CELL Human cell contains subcellular structures like nucleus, mitochondria, lysosomes, and peroxisomes etc.

RNA – considered as a molecular slave of DNA. It is because RNA carries out orders for protein synthesis issued by DNA.

Cell is the universal functional unit of all forms of life.

The major complex biomolecules of cells

Human body contains wide variety of cells that differ in structure and function.

Biomolecule

Protein

Building Block (repeating unit) Amino acids

Deoxyribonucleic Deoxyriboacid (DNA) nucleotides

Major Function

Fundamental basis of structure and function Respect of hereditary information

Ribonucleic acid Ribonucleo(RNA) tides

Polysaccharide (glycogen)

Lipid

Essentially required for protein biosynthesis Monosaccha- Storage form ride of energy to meet short term demand Fatty acids, Storage form glycerol of energy to meet long term demand; structural components of membranes

Inorganic Compounds Inorganic compounds account for the rest of the cell weight They are cations like sodium, potassium, calcium, magnesium, copper, iron, and anions like chloride, phosphate, bicarbonate, sulfate, iodide and fluoride. Janella Ericka D. Doblada – BSN 1 B-12

All higher living organisms including humans are made up of cells.

EUKARYOTIC FUNCTION

CELL

STRUCTURE

AND

In eukaryotes, cells aggregate to form tissues or organs and these are further organized to form whole organism. In humans, eukaryotic cells exist in large number of sizes and shapes to perform variety of function

Cell Membrane The outermost structure of the cell It separates the cells from its surrounding It is a lipid bi-layer. It also consists of proteins and small amounts of carbohydrates.

Cytoplasm Is the cellular material outside the nucleus and inside the plasma membrane. The three major elements: cytosol, organelles, and inclusions

It is semi permeable, meaning only selected compounds are allowed to pass through from outside. The selective permeability is responsible for the maintenance of internal environment of the cell. The modification of the cell membrane results in information of specialized structures like axon of nerves, microvilli of intestinal epithelium and tail of spermatids.

Nucleus

Cytosol

Control center of the cell

It is a semitransparent fluid that suspends the other elements

It contains genetic material (DNA) that is like a blueprint that contains all the instructions needed for building the whole body.

Dissolved in the cytosol, which is largely water, are nutrients and a variety of other solutes.

Nucleus is the information center of eukaryotic cell. More than 90% of the cellular DNA is present in the nucleus. It is mainly concentrated in the form of chromosomes.

Janella Ericka D. Doblada – BSN 1 B-12

Organelles

Lysosomes

They are metabolic machinery of the cell.

They are small vesicles present in cytoplasm

Each type of organelle is specialized to carry out specific functions for the cell as a whole.

Lysosomes are called suicidal bags of the cell (they destroy dead or old cells)

Inclusions Not functional units, but instead are chemical substances that may or may not be present, depending on the specific cell type. Most inclusions are stored nutrients or cell products.

Functions: They are rich hydrolytic enzymes.

Functions of the Cytoplasm It is the site of most cellular activities Numerous enzymes, proteins and many other solutes are found in the cytosol.

Mitochondria Generally, mitochondria are ellipsoidal in shape.

Functions: Powerhouse of the cell. It is responsible for the production of energy in the form of ATP. In highly metabolically active cells, mitochondria are more numerous and larger. Janella Ericka D. Doblada – BSN 1 B-12

The lysosomal enzymes digest the molecules brought into the cell by phagocytosis. Macrophages are rich in lysosomes Medical Importance of Lysosomes: Disease, shock or cell death causes rupture of lysosomes and release of enzymes In some disease like arthritis and muscular dystrophy, lysosomal enzymes are released to cause uncontrolled destruction of surrounding tissues. Lysosomal proteases cathepsins are involved in spreading of cancer (metastasis).

Peroxisomes

Endoplasmic Reticulum

Are also small vesicles surrounded by a membrane. They are also called as microbodies.

It is a system of fluid filled tubules or canals that coil and twist through the cytoplasm.

Functions:

Rough Endoplasmic Reticulum (RER)

They contain enzymes of H2O2 metabolism

The rough ER is studded with ribosomes

The enzymes of H2O2 catabolism present in peroxisomes are peroxidase are catalase.

The proteins made in the ribosomes migrate into the tubules of the rough ER where they fold into their functional three-dimensional shapes and then are dispatched to other areas of the cell.

Ribosomes They are tiny, dark bodies made of protein and ribosomal RNA Ribosomes are actual sites synthesis in the cell.

of

protein

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It serves as a mini circulatory system for the cell because it provides a network of channels for carrying substances from one part of the cell to another.

Smooth Endoplasmic Reticulum

Cytoskeleton

The smooth ER function in lipid metabolism (cholesterol and fat synthesis and breakdown) and detoxification of drugs and pesticides.

These are filament like structures made up of proteins present in cytoplasm.

Golgi Apparatus The golgi bodies are well developed in cells, which are involved in secretion. Material produced in the cell for export is processed by golgi body and is packaged as vesicles and is pinched off. Golgi apparatus helps in the information of other organelles like lysosomes and peroxisomes.

Functions: They act as the cell’s bones and muscles by furnishing and internal framework that determines cell shape, supports other organelles, and provides machinery for intracellular transport and various types of cell movements.

Cell Death Cells are not immortal, and they have finite lifespan. Cell division and cell death are two opposite processes required to maintain constant tissue volume (tissue homeostasis) Types of Cell Death:

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Necrosis “cell murder”. Cell undergo necrotic death if cell membrane is damaged or due to decreased oxygen supply and if energy (ATP) production is blocked. Apoptosis It is a genetically programmed cell death. Individual cells or group of cells undergo this type of death. Aged cells in the body are removed by apoptosis. Atrophy

Examples:

This type of cell death occurs in the absence of essential survival factors. Survival factors required by the cell are produced by other cells. Absence of nerve growth factor leads to atrophy of nerves.

FUNCTIONAL GROUPS

Alkane Alkene Alkyne

Replace the underlined part to the general name

Alkyl

Table: Root word used for writing trivial or common names No. of carbon atoms 1. 2. 3. 4. 5.

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Root word Form Acet Propion Butyr Valer

CHEM123 – WEEK 3

recognication (glycoproteins)

Contents:

processes

Carbohydrates Classification

Chirality

Most simple carbohydrates have empirical formula CnH2nOn which can be written as Cn(H2nO)n. This became the basis of the term carbohydrate (hydrate of carbon).

Simple Chiral Molecules Fischer Projection Formula Dextrorotatory and Levorotatory Compounds

A carbohydrate is a polyhydroxy aldehyde or polyhydroxy ketone or a compound that yield polyhydroxy aldehydes or polyhydroxy ketones upon hydrolysis.

CARBOHYDRATES Occurrence and Functions Carbohydrates are the most abundant class of bioorganic molecules on planet earth (75% by mass of dry plant materials). Plants produce photosynthesis:

carbohydrates

by

chlorophyll

CO2 + H2 O + energy ---→ carbohydrates + O2 Plant enzymes

Usage 1. Structural Plant: Cell wall – cellulose Plant and animal: Forms part of structural framework of DNA and RNA Links to lipids for structural components of cell membrane (glycolipids). 2. Provides energy – oxidation of carbohydrates 3. Energy reserves – plant: starch animal: glycogen 4. Provides carbon for synthesis of other biomolecules 5. Links to proteins for various functions of cell-cell and cell-molecule Janella Ericka D. Doblada – BSN 1 B-12

A monosaccharide is a carbohydrate that contains a single polyhydroxy aldehyde or polyhydroxy ketone unit. They cannot be broken down to simpler units by hydrolysis reaction. Naturally occurring monosaccharides have 3 to 7 carbon atoms with 5 to 6 which are especially common. Examples: fructose, glucose, galactose

An oligosaccharide is a carbohydrate that contains 2-10 monosaccharide units covalently bonded to each other. Disaccharides are the most common type of oligosaccharides Examples: sucrose, lactose

Both monosaccharides and disaccharides are white, crystalline, water-soluble solids.

Within the human body, oligosaccharides are often found in association with proteins and lipids that have both structural and regulatory functions. Free oligosaccharides other than disaccharides, are seldom found in biological systems.

Superimposable mirror images Images that coincide at all points when the images are laid upon each other. Non-superimposable mirror images Images where not all points coincide when the images are laid upon each other.

A polysaccharide is a carbohydrate that contains many monosaccharide units covalently bonded to each other. They often contain thousands of monosaccharide units. Examples: starch, glycogen

CHIRALITY Monosaccharides are the simplest type of carbohydrate where their structures exhibit “handedness” since most monosaccharide molecules exist in two forms: a “left-handed” form and a “right-handed” form.

Mirror Images Molecular handedness is best described by mirror images. Objects can be divided into two classes on the basis of their mirror images: objects with superimposable mirror images and objects with non-superimposable mirror images.

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Not all molecules possess handedness. Only those molecules where a carbon atom is attached to four different groups show handedness. Such a carbon atom is called a chiral center.

A molecule containing a chiral center is called a chiral molecule shows molecular handedness. A molecule with no chiral center is an achiral molecule. The simplest chiral monosaccharide is glyceraldehyde.

Monosaccharides may contain more than one chiral centers:

Biological significance of handedness SIMPLE CHIRAL MOLECULES

Left-handed and right-handed molecules may elicit different responses within the body. Sometimes they have the same response but one form’s response if many times greater than the other form or one form may be biologically active but the other form may be not.

STEREOISOMERISM: Diastereomers

Enantiomers

and

The left-handed and right-handed forms of chiral molecule are isomers. But they are not the same as the constitutional isomers. Constitutional isomers have the same molecular formula but different in structural formula and are very prevalent in organic molecules. Left handed and right handed forms of chiral molecules have the same molecular and structural formulas, they just differ in orientations of atoms in space. Since left handed and right handed forms of a chiral molecule are the same molecules, they are known as stereoisomers. Stereoisomers are isomers that have the same molecular and structural formula but differ in the orientation of atoms in space. By contrast, atoms are connected to each other in different ways in constitutional isomers. Janella Ericka D. Doblada – BSN 1 B-12

FISCHER PROJECTION FORMULA Originated by Hermann Emil Fischer A Fischer projection formula is a twodimensional structural notation for showing the spatial arrangement of groups about a chiral center in molecules.

Structural features of stereoisomerism: 1. The presence of a chiral center 2. The presence of “structural rigidity” Stereoisomerism

Enantiomers

Diastereomers

(Mirror images)

(Non-mirror images)

Enantiomers and Diastereomers

Classifying Enantiomers and Diastereomers

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Properties of Enantiomers Constitutional isomers differ in most chemical and physical properties. For example constitutional isomers may have different boiling and melting point can have different chemical reactions with the same substance.

Ordinary light can be converted to planepolarized light by passing it through a polarizer, an instrument with lenses or filters containing special types of crystals. When plane-polarized light is passed through a solution of a single enantiomer, it will either be rotated clockwise (to the right) or counterclockwise (to the left) depending on the enantiomer. The two enantiomeric pairs will rotate the planepolarized light the same number of degrees but in opposite direction. A polarimeter is used to measure the degree of rotation.

Diastereomers also differ in most chemical and physical properties. They also have different melting and boiling points. On the other hand, nearly all the properties of all the enantiomers are the same, for example, they have identical melting and boiling points. Enantiomers differ only in properties in two areas. 1. Their interaction with plane polarized, polarized light; and 2. Their interaction with other substances.

Dextrorotatory compound is a chiral compound that rotates plane-polarized light in clockwise direction or to the right (“dextro” for right).

Interaction of Enantiomers with Planepolarized light

Levorotatory compound is a chiral compound that rotates plane-polarized light in a counterclockwise direction or to the left (“levo” for left)

Ordinary light (unpolarized) vibrate in all planes at right angles to their direction of travel while polarized light vibrate only in one plane at right...