mbio 1220 chemical principles, lecture 2

cations

atoms carrying a positive charge

anions

atoms carrying a negative charge

three types of chemical bonds found in living systems

covalent

ionic

hydrogen

covalent bonds

• very strong bonds

• formed when two atoms come together and share electrons within their outer shell

• water is formed as a result of covalent bonds between H and O

ionic bonds

• form as a result of the attractive force between ions of opposite charge (cation or ion)

• weaker than covalent bonds

• attractive force holds the two atoms together in the bond

example of ionic bonds

NaCl

• Na requires the loss of an electron to achieve stability and Cl requires and electron to achieve stability

• Cl received electron from Na rather than sharing

• Cl- and Na+

Hydrogen bonds

• hydrogen covalently bound to oxygen or another electron loving molecule such as nitrogen

• atom bound to hydrogen is ‘electron loving’ so it holds the shared electrons closer to its nucleus than hydrogen

• UNEQUAL SHARING OF ELECTRONS ARE POLAR MOLECULES

• partial positive on hydrogen, partial negative on electron loving atom

• weakest of the bonds

• result in networks of molecules of different molecules

H:C

carbon is not more electron loving than hydrogen, electrons shared equally between two atoms.

non-polar covalent bonds

δ+ H—-:O δ-

oxygen more electron loving than hydrogen, electrons not being shared equally. held more closely to the oxygen atom

polar covalent bond

organisms require a wide variety of __________ in order to live and reproduce

inorganic compounds

whats the most important inorganic molecule found in living systems?

water H2O

• 75% of cell weight

• water is used to dissolve materials, it is a solvent.

• because electrons are not shared equally it is POLAR SOLVENT

3 exceptions to inorganic molecules

carbon dioxide

carbon monoxide

carboxylic acid

why is water an excellent solvent?

• dissolve many ionic compounds like NaCl

• ions Na+, Cl- remain dissolved in the water and from a solution

• solution forms due to partial positive regions within the water molecules surround the negative ions cl-. partial negative regions within the water molecule surround the positive ions na+ holding them in solution

• forms sodium chloride crystal

how to break down a sodium chloride crystal?

adding heat

mechanically break it apart

water molecule can from four hydrogen bonds with other molecules

• hydrogen bonds allow water to from networks of interconnected water molecules which gives water a very high BP

• high BP 100 degrees C keeps water in liquid state in most places on Earth

• solid, 4 H bonds (freezing/melting) liquid, 3.4 H bonds (boiling/evaporating) gas

why is water a great temperature buffer?

because of its strong hydrogen bonds

water can easily split into its component ions ____

H+ and OH-

• plays key role in many chemical rxns

four major classes or organic compounds found in living things

1. carbohydrates

2. proteins

3. lipids

4. nucleic acids

carbohydrates

• energy source immediately utilizable by cells

• polar covalent compounds - dissolve easily in water (only if they are small enough)

• contain the elements C, H, O (CnH2nOn)

three major groups of carbohydrates

1. monosaccharides

2. disaccharides

3. polysaccharides

monosaccharides

• one sugar

• glucose, fructose

disaccharide

• two monosaccharides form a disaccharide

• glucose + fructose = sucrose

polysaccharides

• hundreds of monosaccharides come together

• often too large to be water soluble

• starch, cellulose (plants use to cage themselves, dietary fiber — clears u out)

glycogen is a storage method

lipids

• fats, complex lipids (phospholipids), and steroids

• essential to the structure and function of membranes (phospholipid bilayer)

• used as means of energy storage

• molecules are non-polar therefore don’t interact well with water HYDROPHOBIC

• fat stores 2x more energy than sugar, we store as fat because its better for us but we still store some as sugar i.e in liver

lipids - Fats

• composed of a glycerol molecule plus one to three fatty acids

  1. monoglycerides

  2. diglycerides

  3. triglycerides (stored in adipose tissue)

lipids - fatty acids

• saturated or unsaturated

• complex lipids include phospholipid which are found in the membrane of living cells — primary component of prokaryotic and eukaryotic plasma membrane

saturates fatty acid

no double bonds

saturated with H atoms

unsaturated fatty acids

has at least one double bonds

fewer H atoms

less saturated because double bond takes space for a H

more fluid at given temp.

heavy group placements

cis - both on same side

trans - on opposite sides (favourable)

steroids

structurally distinct from other lipids

• four ring structure

• found mainly in eukaryotes

• ex. cholesterol and vitamin D

proteins

composed of individual units of amino acids

• individual AA are joined by peptide bonds which are covalent bonds

• AA sequence important for determining shape of protein

• proteins required in all aspects of cell structure and function — membrane channels

• ex. hair — different textures come from AA

amino acids

• all amino acids and thus proteins are composed of C, O, H, N (some have S)

• 20 known

• side group -r determines chemical properties of AA

• NH2 and COOCH (n and c terminus)

peptide

short chain of amino acids

polypeptide

long chain of amino acids

(proteins)

enzyme

increase the rate of chemical reactions that occur within the cell

nucleic acids

• made of nucleotides

each nucleotide has three components

1. nitrogenous base

2. pentose sugar

3. phosphate group

1. nitrogenous base

• purines: contain 2 rings

  • two types: Adenine (A), Guanine (G)

silver is very pure and makes nice rings Ag double rings

• pyrimidines: contain 1 ring

  • three types: Cytosine (C), Thymine (T) DNA option, Uracil (U) RNA option

2. pentose sugar

• five carbon sugar

• two types: ribose and deoxyribose

3. phosphate group

phosphate group is attached to the nucleotide and serves as the site of attachment for the next nucleotide

enzyme specificity

two types of nucleic acid

deoxyribonucleic acid DNA and ribonucleic acid RNA

deoxyribonucleic acid (DNA)

always the genome

• composed of deoxyribose sugar

• double stranded, each strand held by h-bonds (virus can be single stranded)

• DNA is what genes composed of

  • “recipe book“

• order of nucleotide sequence is very specific and forming the genetic instructors for the organisms

• made of nucleotides A, C, T, G

ribonucleic acid (RNA)

• composed of ribose sugar

• single stranded (virus can have double stranded RNA)

• involved in communicating the instructions of DNA

• made of nucleotides A, C, U,G