chapter 3 - the molecules of cells

carbon

carbon

element that is most used when making molecules

• almost all molecules a cell makes are composed of carbon atoms bonded to one another and to atoms of other elements

• carbon has the ability to form large and complex molecules that build structures and carry out functions

• the carbon atom has 4 electrons in its valence shell that holds 8, meaning it has the ability to form FOUR covalent bonds

organic compounds

carbon-based molecules (that usually contain hydrogen atoms as well)

• its shape usually determines its function

• the atoms attached to the carbon skeleton of an organic compound affects its properties

carbon skeletons

carbon chains that form the backbone of most molecules

• they differ in length and can be straight, branched, or arranged in rings (where each corner represents a carbon and it’s hydrogen)

  • can include double bonds which can differ in number and location

• they can have the same chemical formula (C4H10 for butane and isobutane) but differ in arrangement

  • applies to double bonds as they would have a different 3-D shape due to its location

isomers

compounds with the same formula but different structural arrangements

• add greatly to the diversity of organic molecules and its properties

  *can result from the different spatial arrangements that can occur when four different properties are bonded to a carbon atom

  • important in pharmaceuticals because the two isomers may not be equally effective or could lead to harmful/dangerous effects

hydrocarbons

molecules only consisting of only carbon or hydrogen

• provides much of the world’s energy

  • rare in living organisms but hydrocarbon chains are found in regions of molecules

  • ex. fat contains chains that provide fuel to the body

length in carbon skeletons

carbon skeletons can vary in length in which depends on the amount of carbons (more carbons, the more longer)

double bonds in carbon skeletons

carbon skeletons may have carbon that are double bonded together that vary in location but include the same amount of carbons, but less hydrogen because there are less valence capacity for those carbon atoms that are double bonded

branching in carbon skeletons

carbon skeletons may be branched or not, meaning that carbons may be bonded to the backbone that extended from it in another direction, like branches from the trunk of a tree

rings in carbon skeletons

carbon skeletons may be arranged in to rings which are abbreviated ring structures where each corner of the ring represents a carbon and it’s hydrogens unless stated otherwise

functional groups

groups that affect a molecule’s function by participating in chemical reaction

• these groups are usually polar (the methyl group is not polar and not reactive, meaning its hydrophobic, but affects the shape and function of the molecule), allowing for them to be hydrophilic

  • soluble in water, making it necessary for life

hydroxyl group

[-OH]

• consists of a hydrogen atom bonded to an oxygen atom

  • alcohols are organic compounds that contain hydroxyl groups (ex. ethanol)

carbonyl group

[>C=O]

• consists of a carbon atom double bonded to an oxygen stom

  • can be located within or at the end of a carbon skeleton

  • simple sugars contain carbonyl groups

carboxyl group

[-COOH]

• consists of a carbon atom double bonded to an oxygen atom and also bonded to a hydroxyl group

  • can act as an acid by contributing H+ to solutions (becoming ionized)

    • called carboxylic acids

amino group

[-NH2]

• consists of a nitrogen atom bonded to two hydrogen atoms

  • can act as a based by absorbing H+ from a solution (and becoming ionized)

    • called amines (amino acids — amino group and carboxyl group)

phosphate group

[-OPO32-]

• consists of a phosphorus atom bonded to four oxygen atoms (usually ionized)

  • called organic phosphates and are often involved in energy transfers (energy rich compound —> adenosine triphosphate)

methyl group

[-CH3]

• consists of a carbon bonded to three hydrogen atoms

  • methylated compounds (a component of DNA) affects the expression of genes

four main classes of molecules in all living things

1. carbohydrates

2. lipids

3. protiens

4. nucleic acids

macromolecules

gigantic molecules

• carbohydrates, proteins, and nucleic acids

  • ex. protein molecules can have over 1,000 atoms

polymers

chains formed by joining smaller molecules to make macromolecules (many parts)

• a long molecule consisting of many identical or similar building blocks strung together

monomers

the building blocks of polymers

dehydration reaction

a reaction that removed a molecule of water as two molecules become bonded together (forming polymers with monomers)

• each monomer contributes part of the water molecule that is released during the reaction

  • one monomer loses a hydroxyl group and the other loses a hydrogen atom to form H2O or water

    • new covalent bonds form to link the two monomers to create a polymer

  *this process is the same regardless of the different monomers and the type of polymer the cell is producing

hydrolysis

the breaking of polymers with water molecules into monomers

• the bonds between monomers are broken by the addition of water molecules

  • hydroxyl group attaches to one monomer

  • the hydrogen atom attaches to another

• most organic molecules are in food and are often in the form of polymers (too large and is needed to be digested)

  • ex. lactose-intolerant people are unable to hydrolyze those bonds in sugar lactose because they lack the enzyme, lactase

enzymes

specialized macromolecules that speed up chemical reactions in cells

• is needed for dehydration reaction and hydrolysis

the diversity of polymers

• a cell makes thousands of different macromolecules from a small lost of ingredients (elements)

  • 40-50 components and a few rare others

  • ex. proteins are built from 20 types of amino acids and DNA is made up from only 4 types of monomers called nucleotides

    *the arrangement of monomers in polymers leads to diversity with the variation in the sequence in which monomers are strung together

• variety in polymers leads to the uniqueness of each organism though monomers themselves are universal

  • SMALL MOLECULES COMMON TO ALL ORGANISMS ARE ORDERED INTO LARGE MOLECULES, WHOCH VARY SPECIES TO SPECIES AND INDIVIDUALS WITHIN A SPECIES

carbohydrates

the class of molecules that range from small sugar molecules to large polysaccharides

• 4 jobs

  1. stores energy

  2. provide structure

  3. cellular identity

  4. building block for other acids

• almost all carbohydrates are hydrophilic owning to the many hydroxyl groups attached to sugar monomers

monosaccharides

simple sugars that act as the monomers of carbohydrates

• they can be hooked together through dehydration reactions to form more complex sugars and polysaccharides

  • ex. monosaccharides in honey are glucose and frutose

• has molecular formulas that are multiples of CH2O

  • glucose and fructose are common monosaccharides that both have a molecular formula of C6H12O6 and contains multiple hydroxyl and carbonyl groups (they are isomers with the same formula but different arrangement - the position of carbonyl groups in this case)

    • minor differences give isomers varying properties and in how they react with other molecules

• has between 3-7 carbons

  • 5-carbon sugars are called pentoses

  • 6-carbon sugars are called hexoses

• 5-6 carbon sugars form rings in aqueous solutions versus maintaining their linear skeletons

  • glucose: carbon 1 bonds to the oxygen of oxygen 5, with carbon 6 extending above the ring

disaccharides

formed by cells with monosaccharides undergoing a dehydration reaction

• sucrose is the most common

  • made up of a glucose monomer linked to a fructose monomer

• maltose is another example

  • made up of two glucose monomers linked together

polysaccharides

macromolecules that are polymers of hundreds to thousands of monosaccharides linked together through dehydration reaction

• they can function as storage molecules or as structural compounds

starch

a storage polysaccharide in plants that consists of long chains of glucose monomers

• coils into a helical shape and may be unbranched or branched

• served as carbohydrate “banks” from which plant cells can withdraw glucose for energy or building materials

  *humans and animals have enzymes that can hydrolyze plant starch into glucose (plants include potatoes, rice, wheat, and corn)

glycogen

a storage polysaccaride where animals store glucose

• more branched than starch

• glycogen is stored as granules in the liver and the muscle cells in which hydrolyze the glycogen to release glucose when needed

celluose

the most abundant organic compound which is a major component of the tough walls that enclose plant cells

• polymer of glucose, but its monomers are linked together in a different oriantation

• when arranged parallel to each other, they are joined by hydrogen bonds (forming cable-like microfibrils that combine with other molecules)

  *animals cannot hydrolyze cellulose as it is insoluble but it does not act as a nutrient but contributes to digestive health as a fiber

  • cows and termites has microorganisms that can hydrolyze cellulose and fungi can hydrolyze cellulose as well

chitin

a structural polysaccharide used by insects and crustaceans to build their exoskeletons (a hard case enclosing an animal)

• found in the cell walls of fungi

lipids

a diverse group of molecules that are classified together because they share one trait of not mixing well with water (hydrophobic —> water fearing: due to nonpolar C - H bonds in the hydrocarbon chains)

• not huge macromolecules nor polymers built from similar monomers (different from carbohydrates, proteins, and nucleic acids)

• three types of lipids

  1. fats

  2. phospholipids

  3. steroids

fats

a large lipid made from a glycerol molecule and 3 fatty acid molecules through dehydration reaction

• fats store energy as it is easiest for it to be stored in the form of fat but harder to burn of excess (a reasonable amount is normal and healthy)

  • stored longer term in adipose cells

  • cushions vital organs snd insulates the body

glycerol

consists of 3 carbons, each bearing hydroxyl group

• major component of lipids

fatty acids

consists of a carboxyl group and a hydrocarbon chain (16-18 carbons in length)

• major component of lipids

unsaturated fatty acids

a fatty acid whose hydrocarbon chain contains one or more double bonds

• each carbon atom connected by a double bond has one fewer hydrogen atoms attached to it which causes kinks in the hydrocarbon chain

• unsaturated fats has a lower melting point and is usually more of a liquid as its kinks in its fatty acids allow for less surface area for intermolecular forces to occur

  • fats of plants and fish are generally unsaturated as their kinks make for them to be a liquid at room temperature (called oils)

saturated fatty acids

a fatty acid that had no double bonds in its hydrocarbon chain meaning that it has the maximum number of hydrogen atoms attached to each carbon atom

• its carbons are “saturated” with hydrogen

• saturated fats have a higher melting point as its fatty acids have a larger surface area with no kinks allowing for stronger molecular forces to occur (london dispersion)

  • most animal fats are saturated as the hydrocarbon chains are packed closely together due to a lack of double bonds, making them solid at room temperature, like butter

trans fats

converted unsaturated fatty acids into saturated fatty acids by adding hydrogen by hydrogenation

• partially hydrogenated oils

  *commonly associated with health risks and is banned by the FDA

phospholipids

contains two fatty acids attached to glycerol instead of three where a phosphate group that is negatively charges is attached to glycerol’s third carbon instead

• is a major component of cell membranes (cells couldn’t exist without it)

• the ends of phospholipids have different relationships with water (they form a double-layered sheet in water)

  • hydrophobic tails are in the center which is excluded from the water

  • hydrophilic heads are on the other side of the membrane which is in contact with water

steroids

lipids in which the carbon skeleton contains four fused rings

cholestrol

a common part of animal cell membranes and is a steroid

• also the precursor (substance that precedes and is transformed into another substance —> complex molecules) for making other steroid

  • steroids vary in the chemical groups attached to the rings

• ex. sex hormones

anabolic steroids

synthetic variants of the male hormone, testosterone, that mimics its effects

• anabolic —> anabolism: the building of substances in the body

proteins

a polymer of small building blocks called amino acids

• the most structurally and functionally varied

  • nearly every function in the body depends on proteins

enzymatic proteins

selective acceleration of chemical reactions (enzymes are chemical catalysts)

• ex. digestive enzymes

  *most important role

defensive proteins

protection against disease

• ex. anti-bodies inactive and destroy viruses and bacterias

storage proteins

storage of amino acids and supply amino acids to embryos

• ex. proteins found in eggs and seeds

transport proteins

transportation of substances

• hemoglobin transports oxygen from the lungs to the body and others transports molecules through cell membranes

hormonal proteins

coordination of an organism’s energy

• insulin

receptor proteins

the response of a cell to chemical stimuli

• ex. signaling pathways, receiving and transmitting, into cells

contractive proteins

contraction and movement

• in muscle cells to contract

structural proteins

to support and form structure

• fibers in tendons and ligaments (connective tissues)

shape of proteins

a protein’s shape determines its function

• order of amino acids or 3-D shape

  *proteins are usually just a long chain of amino acids

• two models

  1. ribbon model

  2. space-filling model

     1. globular

     2. fibrous

denaturation

when a protein is altered when it unravels (losing its shape) thus its function is affected and the protein loses its job

• can be due to excessive heath (ex. frying an egg — the yolk)

renaturation

when denatured proteins fold back into its functional shape

• only occurs in the proper environment

prions

proteins that do not fold back correctly

• an accumulation of misfolded proteins are associated with serious and degenerative brain diseases such as alzheimer’s and parkinson’s)

amino acids

monomers of proteins

• has one amino group and a carboxyl group that are both covalently bonded with a central carbon atom

  • other partners bonded to the central carbon atom is a hydrogen atom and a “R”-group

R-groups

determine the amino acid’s function

• radical as it varies from amino acids to amino acid

hydrophilic amino acids

when the amino acid is polar or charged

• meaning the R-groups contain oxygen and nitrogen

  • often ionized forms as if they contain acids or basic groups, they are charged to the pH of the cell

hydrophobic amino acids

when the amino acid is nonpolar

• meaning that the R-groups contain carbon and hydrogen (similar electronegativity)

peptide bonds

covalent linkage resulting of amino acids bonding together in a dehydration reaction that links the carboxyl group of one amino acid to the amino group of another

dipeptide

two amino acids bonded

polypeptide

more than two amino acids bonded together

primary structure

the precise sequence of amino acids in the polypeptide chain which are connected by peptide bonds

secondary structure

segments of the polypeptide chain that then coil or fold into local patterns

• hydrogen bonds between atoms of the polypeptide backbone (oxygen to hydrogen)

• two forms: alpha helix and beta pleated sheet

quaternary structure

more than one polypeptide bonds in a 3-D structure in which subunits are held together by interactions between R-groups

• 4 identical polypeptides (subunits) form a functional protein

gene

a discrete unit of inheritance

• consists of DNA

nucleic acids

polymers

• “nucleic” comes from the location of DNA in cells

nucleotides

monomers of nucleic acids

• each of DNA’s nucleotides has 4 nitrogenous bases

  • adenine, thymine, cytosine, guanine

    *genetic information is written in a four letter alphabet

• each of RNA’s nucleotides has 4 nitrogenous bases

  • A, C, G, and uracil instead of T

polynucleotides

a nucleic acid polymer that is built from its monomers by dehydration reaction

• the sugar of one nucleotide bonds to the phosphate group of the next monomer

  • results is a repeating sugar-phosphate backbone in the polymer (nitrogenous bases are not apart of the backbone)

RNA

ribonucleic acid

• consists of a single polypeptide strand

• assembles polypeptides according to instructions by DNA

• base pairings can occur between the stretches on complementary nucleotides

  • takes on 3-D shapes for specific functions

  • 3 types of RNA are involved in protein synthesis

DNA

deoxyribonucleic acid

• consists of two polypeptide strands that wind around each other forming a double helix

  • the nitrogenous bases protrude from the backbone and pair in the center of the helix with hydrogen bonds (A with T, C with G)

• the genetic material that humans and all other organisms inherit their parents consist of DNA

  • it resides in a cell as one or more long structures called chromosomes (which carries several hundred and more genes)

• provides directions for its own replication (every time a cell divides, it makes an identical copy of its chromosomes)

  • the double helix “unzips” and new complementary strands assemble along the separated strands (thanks to base pairing)

    *these instructions program all of a cell’s activity by directing the synthesis of proeins

base-pairing rules

the two strands are to be complementary (be a predictable counterpart of the other)

gene expression

the flow of genetic information in the building of a protein — also known as protein synthesis

*DNA is transcribed into RNA which is than translated to form the protein

• gene directs the synthesis of an RNA molecule

  • DNA is transmitted into RNA (same pairing rules apply but A with U because it is RNA)

• RNA molecule interacts with the protein building machinery of the cell

  • the information is translated from “nucleic acid language” to “protein language” which is the amino acid sequence of a polypeptide

*main idea: an organism’s genes determine the proteins —> structure and function of the body

lactose tolerance

a mutation as human stop producing the enzyme in early childhood and lactose intolerance is the norm

• mutations are examples of convergent evoltuton

  • a similar adaptation evolving independently in different lineages