Bio notes 1

8/8/2019 Bio notes 1

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Nucleic Acids / DNA / RNA

At the core of each cell are molecules that store the blueprint of life,

deoxyribonucleic acid (DNA). DNA is composed of four types ofmolecules known as nucleic acids or nucleotides. The four

nucleotides are: adenine (A), guanine (G), cytosine (C), and thymine(T). These molecules are further classified into two families. Adenine

(A) and guanine (G) are known as purine and cytosine (C) andthymine (T) are known as pyrimidine. During DNA synthesis,

nucleotides are converted into nucleic acids to so that they can be

linked to form strands of DNA. The assembled strand of DNA takes

on the structure of a double helix.

The chemical structures of the four nucleotides are planar due to the

delocalized electrons in the five- and six-membered rings, each

having a thickness of 3.4 angstroms. When the nucleotides form the

double helix structure, A-T and G-C are joined together by a

hydrogen bond to form a base pair. The base pairs are then joinedtogether by sugar bonds to form the helix. X-ray data shows that

there are 10 base pairs per turn of the helix.

The helical model of DNA also explains the theory of genetic

replication. James Watson once described it as the "pretty molecule"

because the method of replication is so self evident in this structure.During replication, the hydrogen bonds between nucleotides break

and allow each single strand of DNA to serve as a template forreplication of the other half. The two identical copies of newly

synthesized of DNA are then distributed to two new daughter cells.Because during each cycle of replication half of the old DNA is

preserved, DNA replication is said to be semi-conservative.

Although DNA contains the genetic blueprint of life, it requires the

assistance of ribonucleic acid (RNA) to be functional. RNA also

consists of strands of nucleic acids joined together by sugar-

phosphate bonds. Unlike DNA, RNA substitutes the nucleotidethymine (T) with uracil (U) and exists as single strands. After DNA

is converted into strands of RNA, the messenger RNA (mRNA) issent to the ribosome to direct the synthesis of proteins.

The two strands of DNA are held

together by hydrogen bonds betweenadjacent complementary nucleotides.

Amino Acids

Amino acids are the subunits of proteins. Each protein is formed by a chain of amino acids linked together

through peptide bonds. The chain of amino acids takes on different shapes to form different proteins. The

various shapes allow proteins to take on different characteristics in cells. Each amino acid is composed of a

constant (always remain the same) group and a variable amine group as shown below:


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There are 20 common amino acids that are responsible for forming proteins. They can be classified into 4main families based on their chemical characteristics: acidic, basic, uncharged polar, and nonpolar.

Picture showing the 3 different amino acids exhibiting different properties.

How Proteins are Made From DNA

Now that you know what amino acids and proteins are, you might ask what the relationship is between DNA

and amino acids and proteins. While they seem to be unrelated entities, DNA actually plays a crucial role in

protein production. When a cell wants to manufacture a certain protein, it has to go find the recipe for that

protein. The recipe is stored in the form of DNA. Combinations of three nucleotides correspond to different

amino acids. For example, CCT codes for proline and CGT codes for arginine. This way, during protein

synthesis, DNA turns into the instruction for making a protein. For the details of protein synthesis, please

visit Protein Synthesis page.

Amino Acid Codon Table. This is commonly used to identify the DNA sequence for each amino acid.


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Proteins

Proteins consist of strands of amino acids folded into a specific shape. The different protein structures can beclassified by four levels of folding, each successive one being constructed from the preceding one.

Primary Structure - The very basic strand of amino acids is the

called the primary structure.

Secondary Structure - The hydrogen-bond interaction amongstrands of amino acids gives rise to the first level of folding, alpha-

helices and beta-sheets.

Tertiary - Interaction between alpha-helices and beta-sheets

comprise the second level of folding, protein domains. These proteindomains are then strung together through third level folding to form

small globular proteins. The combination of second and third levelfolding yields tertiary structure.

Quaternary Structure - In order to achieve enhanced function,small globular proteins often come together to form protein

aggregates. This fourth level of protein structure is called thequaternary structure. A famous example of quaternary structure is

hemoglobin.


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Lipids

Lipids serve a diverse array of functions inside the cell, ranging from

being energy sources to constructing the cell membrane. Lipids aremade of fatty acid molecules (e.g. palmitic acid, shown below) that

consist two distinct regions: a long hydrophobic hydrocarbon chain

and a hydrophilic carboxylic acid group.

Fatty acids are a valuable food source. Each molecule of fatty acid

can be converted into twice the number ofATP molecules asglucose.

The most important function of fatty acid is its ability to combine to

form uniform bilayers of lipid (to prevent the hydrophobic region

from being exposed). These lipid bilayers are used to form theimpermeable cell membrane and helped to define the first cell (see

From Molecules to the First Cell). The hydrophobic property of lipidmembrane also allows the cell to facilitate transport of molecules.

Sugars

Sugars provide the energy resource for cells. The simplest form of sugar, glucose, features a 6-carbon ring

and has the chemical composition of C6H12O2 (shown below).

Glucose is the principal food source for cells. Even larger sugars, called polysaccharides, are digested into

glucose before being converted into ATP. The chemical reaction for converting glucose into energy is as

follows:

C6H12O2 + 6O2 -> 6CO2 + 6H2O + energy (in the form of ATP and NAHD)

Sugar is also used as a form of energy storage in cells. In animal cells, polysaccharides (long repeating

structure containing glucose) in the form of glycogen are used to store energy. Plant cells use starch to store

energy.


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Properties of Water

Life would not have existed on earth without water. Water molecules are composed of one oxygen atom andtwo hydrogen atoms. Together, the hydrogen and oxygen molecules form a shape that resembles the head of

Mickey Mouse.

While water molecules seem to be simple compounds, their properties have profound impact on life.

Because of the arrangement of hydrogen and oxygen atoms, water molecules have polarized charges (oneend is positive and the other end is negative). Due to their polarized nature, 2 adjacent water molecules can

form a linkage via a hydrogen bond.

The polarized nature of water causes other molecules to be either hydrophilic (like water) or hydrophobic(afraid of water). This property allows certain molecules to dissolve in water while preventing others from

entering the cell. For example, hydrophobic interaction can hold molecules together.

Osmosis

Another important property of water is its ability to facilitate the transfer of molecules through osmosis.

When 2 aqueous solutions are separated by a membrane that only allows the passage of water molecules,

water will move from the less concentrated to the more concentrated side (Shown in the diagram below).

Hydrophobic interactions can hold molecules together: 2 or more hydrophobic groups surrounded by water

will tend to coalesce since they thereby cause less disruption to the hydrogen-bonded structure of water

(Shown in the diagram below. Red hexagons represent hydrophobic material and blue dots represent water

molecules.).


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Cell Membrane

While the plant cell has a rigid cell wall, an animal cell membrane is a flexible lipid bilayer. The lipidmolecules (mostly phospholipids) that make up the membrane have a polar, hydrophilic head and two

hydrophobic hydrocarbon tails. When the lipids are immersed in an aqueous solution the lipidsspontaneously bury the tails together and leave the hydrophilic heads exposed. Thus this is a handy

membrane to use, because it can automatically fix itself when torn. There are three different major classes oflipid molecules - phospholipids, cholesterol, and glycolipids. Different membranes have different ratios of

the three lipids.

What makes the membrane truly special is the presence of different proteins on the surface that are used forvarious functions such as cell surface receptors, enzymes, surface antigens, and transporters. Many of the

membrane-associated proteins have hydrophilic and hydrophobic regions. The hydrophilic regions are used

to help anchor the protein inside of the cell membrane. Some proteins extend across the lipid bilayer, others

cross the bilayer several times

Diagram of the cell membrane. The proteins are embedded inside of the cell membrane. The lipid

content of the membrane allows the cell membrane to automatically repair itself when it is torn.

Membrane Transport of SmallMolecules

Because of the hydrophobic interior of the lipid bilayer, polar molecules cannot enter the cell. However,cells devised means of transferring small polar molecules. Transport proteins, each specialized for a certain

molecule, can transport polar molecules across the membrane. There are several types of membranetransport proteins. Uniports simply move solutes from one side to another. Cotransport systems work by

simultaneously sending two solutes across the lipid bilayer. There are two types of cotransport systems -symport, in which the solutes are sent in the same direction, or antiport, in which they are sent in opposite

directions. These transport proteins work passively, meaning that the cell doesn't have to expend energysending the solute in or out. This is dependent on the solute moving in its natural direction - i.e. moving

from more concentrated solution to less concentrated, or from positive to negative.

Some specific examples of transport membranes are channel proteins, which allow solutes to cross if they

are the correct size and charge. Carrier proteins bind to the solute and lead it through the bilayer. These are

examples of passive transport. To move a solute against their natural direction - for example higher

concentration to lower concentration, energy (ATP) is needed to pump the solute in or out.

An example of active transport is the sodium-potassium pump, which in conjunction with the potassium leakchannel, allows the cell the control it's membrane potential. The sodium-potassium-ATPase, which uses the

energy of ATP hydrolysis, pump pumps sodium out and potassium in, which creates a high concentration of


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potassium inside the cell, and a low concentration outside. The reverse applies to the sodium. The potassiumleak channel allows the potassium to leak out (so to even out the concentrations), which gives the cell and

negative charge on the inside.

Diagram comparing uniport, symport, and antiport.

Membrane Transport ofMacromolecules

Most cells use exocytosis and endocytosis to secrete and ingest macromolecules, respectively. In exocytosis

the contents of special vesicles are released when the vesicle fuses with the cell membrane. In endocytosis

the membrane depresses and pinches off, enclosing the molecule. Two different sizes are formed -

pinocytotic (small) and phagocytic (large).

In receptor-mediated endocytosis, coated pits and vesicles bind to specific receptors on the cell surface,

allowing the cell to select what molecules to take and what to reject.

Membrane Receptors

The cell membrane is pocketed with receptors and antigens. Molecules targeted toward that specific cell will

bind with the cell surface receptor, which binds the signaling molecule and sends a signal that alters thebehavior of the target cell. Antigens are used to tell the cell whether foreign materials are present. If anyforeign materials are detected the immune system will mobilize its killer T-cells to destroy the foreign cell.


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Cell Wall

The plant cell wall is a remarkable structure. It provides the most

significant difference between plant cells and other eukaryoticcells. The cell wall is rigid (up to many micrometers in thickness)

and gives plant cells a very defined shape. While most cells have aouter membrane, none is comparable in strength to the plant cell

wall. The cell wall is the reason for the difference between plantand animal cell functions. Because the plant has evolved this rigid

structure, they have lost the opportunity to develop nervous

systems, immune systems, and most importantly, mobility.

The cell wall is composed of cellulose fiber, polysaccharides, and

proteins. In new cells the cell wall is thin and not very rigid. This

allows the young cell to grow. This first cell wall of these growingcells is called the primary cell wall. When the cell is fully grown, it

may retain its primary wall, sometimes thickening it, or it may

deposit new layers of a different material, called the secondary cell

wall.

On the whole, each cell's cell wall interacts with its neighbors to

form a tightly bound plant structure. Despite the rigidity of the cell

wall, chemical signals and cellular excretions are allowed to pass

between cells.

Diagram of a cell wall. The different layers of cell wall are

shown. The cell wall is composed of cellulose, polysaccharides,

and proteins.

Picture ofLily Parenchyma cell. The cell wall which provides a

rigid structure is in green.


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Chloroplast

The chloroplast, basically, is the organelle responsible for

photosynthesis. Structurally it is very similar to the

mitochondrion. It contains a permeable outer membrane, a less

permeable inner membrane, a intermembrane space, and an

inner section called the stroma. However, the chloroplast is

larger than the mitochondria. It needs to have the larger size

because its membrane is not folded into cristae. Also the inner

membrane is not used for the electron transport chain. Instead

it contains the light-absorbing system, the electron transport

chain, and ATP synthetase in a third membrane that forms a

series of flattened discs, called the thylakoids.

Endoplasmic Reticulum

The endoplasmic reticulum (ER) is repsonible for the production

of the protein and lipid components of most of the cell's organelles.

The ER contains a great amount of folds - but the membrane forms

a single sheet enclosing a single closed sac. This internal space is

called the ER lumen. The ER is additionally responsible formoving proteins and other carbohydrates to the Golgi apparatus, to

theplasma membrane, to the lysosomes, or wherever else needed.

There are two types of ER - rough, which is coated with

ribosomes, and smooth, which isn't. Rough ER is the site ofproteinsynthesis. The smooth ER is where the vesicles carrying newlysynthesized proteins (from the rough ER) are budded off.

[Diagram of a plant chloroplast. Notice the bi-layer

[Electron Micrograph of a plant cell'sendoplasmic reticulum. Copyright Daniel

Kunkel]


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Golgi Apparatus

The Golgi complex is composed of numerous sets of smooth

cisternae, which are coated with lipid membranes. Each disc-

shaped cisternae forms a structure that resembles a stack of plates,

called a Golgi stack. The Golgi complex contains a great number

of vesicles. These vesicles are used to send molecules to the

cellular membrane, where they are excreted. There are also larger

secretory vesicles, which are used for selective excretion.

The Golgi is principally responsible for directing molecular trafficin the cell - nearly all molecules pass through the Golgi complex at

some point in their existence. The sorting is mediated by thevesicles. When proteins bind with their appropriate receptor on the

vesicle, they are encoated in the vesicle and transported away.

LysosomesThe lysosome is a membranous bag which contains hydrolytic enzymes

that are used to digest macromolecules. The lysosome contains over 40

enzymes, some of which are the proteases, nucleases, and

phopholipases. These enzymes optimally work at a pH of 5 (acidic), so

should these enzymes leak out they would cause minimal damage to the

cytoplasm. These enzymes, called hydrolases, are made in the ERand

transported to the lysosome by the Golgi complex, using a vesicle.

Should certain hydrolases be missing from the cells, serious illness canoccur because of a buildup of molecules which cannot be digested by

the lysosome. These extra molecules can interfere with normal cell

functions, causing problems.

[Electron Micrograph of the Golgi

complex. Notice the foldings that

form the cisternae. Copyright Daniel Kunkel]

[The lysosome is a membrane

bound structure that contains

hydrolytic enzymes for

digesting macromolecules.]


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Cytoskeleton

Eukaryotic cells have a wide variety of distinct shapes and internal organizations. Cells are capable of

changing their shape, moving organelles, and in many cases, move from place to place. This requires a

network a protein filaments placed in the cytoplasm known as the cytoskeleton.

The two most important protein filaments are called the actin filaments and the microtubules. The actin is

responsbile for contraction (like in muscles) and the microtubules are for structural strength.

Ribosomes

The ribosome is plays a key role is the synthesis of protein. When

the polypeptide chain is growing it must be kept aligned with themRNA molecule so that each codon still hooks up with the tRNA

molecule. After the addition of one amino acid the chain is moveddown three codons. This is done using a large complex composed

of protein and RNA, called the ribosome.

Ribosomes consist of one large unit and one small unit. Half of the

eukaryotic ribosomal weight comes from RNA. The ribosomecontains a groove that guides the polypeptide chain and another

groove that holds the mRNA molecule.

Vacuole

The vacuole is used only in plant cells. It is responsible for

maintaining the shape and structure of the cell. Plant cells don't

increase in size by expanding the cytosplasm, rather they increase

the size of their vacuoles. The vacuole is a large vesicle which is

also used to store nutrients, metabolites, and waste products. Thepressure applied by the vacuole, called turgor, is necessary to

maintain the size of the cell. If turgor is lost the cell becomesflaccid. The vacuole typically is 50% of the volume of the cell, yet

it can take up to 95% of the cell!

[Electron Micrograph of ribosomes.

The ribosomes operate in chains

when translating a mRNA

[Electron Micrograph of plantvacuoles. The vacuoles help to

provide structural support for theplant cells.]


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Nucleus

The nucleus is the cellular control center and exists only in eukaryotes. The nucleus contains the geneticinformation for the cell, in the form ofDNA and RNA. The genetic information is surrounded by a two-

layer nuclear envelope and it is generally found at the center of the cell. The nucleus is responsible forcommunicating with other organelles in the cytoplasm (the gel-like space surrounding the nucleus).

Messages from inside the nucleus travel through pores on the nuclear envelope to enter the cytoplasm.

Inside the nucleus, called the nucleoplasm, DNA is bound by histone proteins and organized into chromatin.During replication, the chromatins are condensed to form highly organized structures called chromosomes.

Besides the genetic information, most nuclei also contain one or more spherical-shaped organelles called thenucleoli. The nucleolus is where ribosomes are assembled.

Nucleic Acids / DNA / RNA

At the core of each cell are molecules that store the blueprint of life,deoxyribonucleic acid (DNA). DNA is composed of four types of

molecules known as nucleic acids or nucleotides. The fournucleotides are: adenine (A), guanine (G), cytosine (C), and thymine

(T). These molecules are further classified into two families. Adenine

(A) and guanine (G) are known as purine and cytosine (C) and

thymine (T) are known as pyrimidine. During DNA synthesis,

nucleotides are converted into nucleic acids to so that they can be

linked to form strands of DNA. The assembled strand of DNA takes

on the structure of a double helix.

The chemical structures of the four nucleotides are planar due to the

delocalized electrons in the five- and six-membered rings, each

having a thickness of 3.4 angstroms. When the nucleotides form the

double helix structure, A-T and G-C are joined together by ahydrogen bond to form a base pair. The base pairs are then joined

together by sugar bonds to form the helix. X-ray data shows thatthere are 10 base pairs per turn of the helix.

The helical model of DNA also explains the theory of genetic

replication. James Watson once described it as the "pretty molecule"

because the method of replication is so self evident in this structure.

During replication, the hydrogen bonds between nucleotides break

and allow each single strand of DNA to serve as a template for

replication of the other half. The two identical copies of newly

synthesized of DNA are then distributed to two new daughter cells.Because during each cycle of replication half of the old DNA is

preserved, DNA replication is said to be semi-conservative.

Although DNA contains the genetic blueprint of life, it requires theassistance of ribonucleic acid (RNA) to be functional. RNA also

consists of strands of nucleic acids joined together by sugar-phosphate bonds. Unlike DNA, RNA substitutes the nucleotide

thymine (T) with uracil (U) and exists as single strands. After DNAis converted into strands of RNA, the messenger RNA (mRNA) is

sent to the ribosome to direct the synthesis of proteins.

Historical Fact: The structure of DNA was

not resolved until the early 1950's whenJames Watson and Francis Crick assembledall of the previously known information

about DNA to construct a model of DNA.

Their result was published as a letter to the

prominent scientific journal Nature and was

later recognized by the Nobel Foundation.

The two strands of DNA are held

together by hydrogen bonds between

adjacent complementary nucleotides.


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Chromosome

A cell's genetic information, in the form of DNA, is stored in the nucleus. The space inside the nucleus is

limited and has to contain billions of nucleotides that compose the cell's DNA. Therefore, the DNA has to be

highly organized. There are several levels to the DNA

packaging.

At the finest level, the nucleotides are organized in theform of linear strands of double helices. As you zoom

out, the DNA strand is wrapped around histones, a form

of DNA binding proteins. Each unit of DNA wrapped

around a histone molecule is called a nucleosome. The

nucleosomes are linked together by the long strand of

DNA.

To further condense the DNA material, nucleosomes are

compacted together to form chromatin fibers. Thechromatin fibers then fold together into large looped

domain. During the mitotic cycle, the looped domains areorganized into distinct structures called the chromosomes.

Chromosomes are also used as a way of referring to the

genetic basis of an organism as eitherdiploidorhaploid.Many eukaryotic cells have two sets of the chromosomes

and are called diploid. Other cells that only contain oneset of the chromosomes are called haploid.

The chromosome also plays an important role in celldeath-related aging phenomena. At the tips of

chromosomes are segments called telomeres. As a cell's

DNA is damaged, the telomeres are shortened. Once thetelomeres have been reduced to a level, the cell decidesthat it can no longer repair itself and initiates apoptosis,

the cellular death process. Today, much research effortshave been devoted to elucidating the specific mechanisms

by which telomeres cause cell death.

Diagram showing the different levels of DNA

packaging. Notice the DNA starts out as single

strand double helices and continues to be

condensed until it reaches the chromosomal

level.

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Bio notes 1