Topic 2: Chemical Principles

What is an atom?

smallest chem. unit of matter which can partake in a chemical reaction

What is an element? State some examples.

matter composed of one type of atom

ex: carbon (C), nitrogen (N), oxygen (O), sodium (Na)

What is a molecule?

two or more atoms combined

What are the diff. types of molecules?

• either same type of atom N2

• or different CO2

  • called a compound

Describe what a nucleus is made up of

• every atom has a central located (atomic) nucleus

  • nucleus is made up of

    • protons (+)

    • neutrons (neutral charge)

      • results in nucleus having a net positive charge

      • stable + does NOT participate in chemical reactions

What are electrons?

exist outside of the nucleus in specialized regions of space called orbitals & are (-) charged

What happens when an atom loses an electron?

It will have a net positive charge

What happens when an atom gains an electron?

It will have a negative charge

What is the electron ratio to protons?

equal # of electrons & protons ⇒ a net charge equal to neutral

What are electron shells? What do they correspond to?

• densely packed in nucleus (compared to protons & neutrons), lighter electrons orbit nucleus in “shells”

• (e-) shells correspond to different energy levels

How do chemical bonds form?

Chemical bonds form between atoms through interactions of (e-) in outer shells with one another

What is the goal of every atom?

goal of every atom is to become chemically stable and do so by filling their outermost shell with electrons

How do atoms achieve their goal of filling their outermost shells?

• achieved by filling its outermost shell with electrons

  • 1st = 2e-

  • 2nd = 8e-

  • 3rd = 8e-

    • atoms achieve a full complement of electrons by combining together to form molecules

What is an ion?

When an atom has an overall positive or an overall negative charge it is no longer neutral and is referred to as an ion

What is a cation?

atoms loses an electron, overall (+) charge

ex: NA+

What is an anion?

atom gains an electron, overall (-) charge

ex: Cl-

What are chemical bonds?

Chemical bonds form in between atoms when electrons in their outer shells interact with one another

• Every atom wants to achieve chemical stability and they do this by filling their outermost shell with electrons

• Atoms achieve a full complement of electrons (8) by combining to form molecules

What are 3 kinds of chemical bonds?

ionic, covalent, hydrogen bonds

What is an ionic bond?

results from attraction between ions of opposite charges

What holds ionic bonds?

anions & cations(attractive force) form ionic bonds → neutralize their charges

What forms from an ionic bond?

• attraction holds the ions together to form a compound

  • ex: NaCl

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

    • Cl receives the electron from Na rather than sharing it : Cl becomes Cl- and Na becomes Na

What are covalent bonds?

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

→ strongest bond

Ex: Water is formed as a result of covalent bonds in between Hydrogen & Oxygen

Where are covalent bonds found?

Found in many compounds ⇒ especially those containing carbon

What is formed with covalent bonds?

almost all organic matter formed with carbon

Are covalent bonds strong or weak?

very strong bonds

How many covalent bonds can carbon atoms form?

4 covalent bonds

• ex: methane CH4

What is the difference between ionic & covalent bonds?

depends on conditions (pH, temp.) / covalent bonds are typically stronger ⇒ require more energy to be broken

How do hydrogen bonds occur? State an example

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

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

    • ex: when two hydrogens are bonded to oxygen, the larger oxygen atom tends to pull the electrons closer to itself

Compare the electronegativity of H & C to H & O

• H : C

  • Carbon is not more electron loving than Hydrogen, thus the electrons are equally shared in between the two atoms

• (partial positive)H : O(partial negative)

  • Oxygen is more electron loving than Hydrogen, thus the electrons are not equally shared in between the two atoms and are held more closely to the oxygen nucleus

What do hydrogen bonds result in?

Because the electrons are not equally shared in between the two atoms there is a resulting partial positive charge on the hydrogen atom (d+ )and a partial negative charge (d- )on the electron loving atom (oxygen in this case)

• Unequal sharing leads to:

  • creates a region w/ partial negative charge (O)

  • and partial positive charge (H)

    • ex: H2O

• on the electron loving atom (oxygen in this case)

• regions can now participate in hydrogen bonding

  →displays polarity

What are polar molecules?

Molecules that contain unequal sharing of electrons

Which elements have the most electronegativity?

Oxygen & Nitrogen

→Electron greedy

Highly electronegative!

C & H are non polar covalent bonds

• (lipid) non soluble because of its equal charge and not partial charge

O & H

• polar(unequal charge)

What type of attraction is between oppositely charged regions of different molecules (hydrogen bonds)?

• loose attraction between oppositely charged regions of different molecules

  • partial positive charge on hydrogen atom is attracted to partial negative charge on atoms within other molecules

Are hydrogen bonds stronger than ionic & covalent bonds?

• weaker than ionic & covalent bonds

Covalent bonds → ionic bonds → hydrogen bonds

How do hydrogen bonds form?

These bonds form when Hydrogen is covalently bound to oxygen or another
electron loving molecule such as nitrogen

1 water molecule will be attracted through covalent bonds

4 charges (2 partial negative & 2 partial positive)

What do hydrogen bonds do?

• serves to bridge separate molecules together

  • ex: in H2O the H’s of one molecules are attracted to the O’s of the other molecule

What do hydrogen bonds result in?

Networks of molecules of different molecules

What are organic compounds?

Organic compounds are compounds which contain Carbon

• Carbonic acid, Carbon dioxide, & Carbon monoxide (inorganic - exception)

What are inorganic compounds?

Inorganic compounds are compounds which do not contain Carbon

What kind of compounds do organisms require?

Organisms require a wide variety of inorganic compounds in order to live & reproduce

What is the most inorganic molecules found in living systems?

• Water accounts for approximately for 75% of cell weight

• Since water is used to dissolve materials it is a solvent and because electrons are not shared equally in between the hydrogen and the oxygen atoms, it is a polar solvent

Like dissolves like (polar & polar: yes/polar & non-polar: no)

How is water an excellent solvent?

• Can dissolve many ionic compounds such as NaCl

  • Not covalent because its polar (like dissolves like)

• Ions (Na+, Cl-) remain dissolved in water to form a solution

• This solution forms because the partial + regions within the water molecules surround the (-) ions Cl- & the partial (-) regions within the water molecules surround the positive ions (Na+) holding them in solution

Does water have an equal charge distribution, why or why not? In relation to temperature?

• has an unequal charge distribution

  • each water molecule can form up to four hydrogen bonds with other water molecules → excellent ability to hydrogen bond allows water to form networks of interconnected water molecules which gives water:

    • a high boiling point (100°C)

    • makes water resist rapid changes in temp. (keeps it in liquid state in most of the places found on Earth

      • great temp. buffer because of its strong hydrogen bonds

Can water be easily split into its component ions?

Yes it can be easily split into its component ions H+ & OH-

• This characteristic allows water to play key roles in many chemical reactions

What kind of solvent is water & why?

water ⇒ universal solvent (reach 4 degrees - highest density of water, closer to each other) (polar solvent)

What does water allow due to its unequal charge of distribution?

unequal charge of distribution allows it to dissolve many ionic compounds

What does the (+) region of water do?

• (+) region of water molecules surround (-) ions

  • holds ion in solution

    • ex: NaCl easily dissolves into Na+ & Cl- in water

What does water’s polarity facilitate?

• water’s polarity facilitates the splitting & joining of hydrogen ions H+ & hydroxide ions OH-

  • makes these ions available for chemical reactions

What does the pH scale describe?

• pH scale describes the concentration of $H^+$ ions in a solution

  • measures of acidity

What does a ph of 7 mean? below 7? above 7?

• pH 7 = neutral (pure water)

• pH below 7 = acidic

• pH above 7 = basic or alkaline

What are organic molecules? Why is it so?

any molecule that contains both carbon & hydrogen

• reason: each C atom can participate in 4 covalent bonds, carbon can be used to build an enormous variety of compounds

What are the four major classes of organic molecules?

Carbohydrates, Lipids, Proteins, Nucleic Acids

What is a carbohydrate?

large group of compounds including sugars & starches

What do Carbohydrates contain? State an example of a compound using this ratio

all contain the elements C, H, & O and ratio is C1 H2 O1

• C6 H12 O6

Are carbohydrates polar?

generally polar (so they dissolve in water)

What is carbohydrates used for?

• ready source of energy for cells

• unsaturated = healthy

What is the organ that is given glucose(prioritized) in a fight or flight response?

The brain

Can carbohydrates be insoluble?

Yes and it is dependent on size (smaller-soluble; larger: not soluble)

What are the diff. types of carbohydrates?

monosaccharides

disaccharides

polysaccharides

What are monosaccharides? Example?

• mono = one

  • simple sugars, ex: glucose

  • more stable - least amount of repulsion

What are disaccharides? Example?

• di = two

  • two monosaccharides come together to form a disaccharide

  • ex: glucose + fructose = sucrose (table sugar)

    • covalently bonded together through a dehydration reaction

What are polysaccharides? Solubility? Examples?

• poly = many

  • hundreds of monosaccharides

  • often not soluble in water (too large)

    • ex: glycogen, starch, cellulose (cannot digest)

What are lipids & their importance?

• includes fats, complex lipids (ex: phospholipids) & steroids

• essential to the structure & function of membranes

  • comprises the lipid portion of the phospholipid bilayer

What are lipids used for?

used for energy storage

Are lipids polar or non-polar?

non-polar molecules: hydrophobic ⇒ water hating

• Non-polar (equal sharing) which means no regions of partial (+) or (-) →not attracted to water molecules (polar-unequal sharing)

What are fats made from?

• made from a glycerol backbone +1 or more fatty acids(non-polar; hydrophobic)(function: holds heat in body):

  • monoacylglycerides: glycerol + 1 fatty acid

  • diacylglycerides: glycerol + 2 fatty acids

  • triacylglycerides: glycerol + 3 fatty acids

What can fatty acids be?

• fatty acids can be:

  • saturated ⇒ no double bonds, saturated with hydrogen atoms

    • pack closer together - forms more bonds (more solid)

  • or unsaturated ⇒ at least one double bond, fewer hydrogen atoms

    • has “kinks” therefore influences its fluidity

What makes up a phospholipid?

in complex lipids

contain glycerol, 2 fatty acids, & a phosphate group

Where are phospholipids found?

In membranes of living cells & they are the primary component of prokaryotic & eukaryotic plasma membranes

What makes up a phospholipid?

Included in complex lipids

• glycerol & phosphate group

  • hydrophilic - likes water

• fatty acid tails are non-polar

  • hydrophobic - hates water

  • has two fatty acid tails

    • has permeability to enable certain ions to travel through cell membrane (small non polar material; polar material can’t because of the lack of charges in phospholipid tails(repelled))

What does the fatty acid tails allow the phospholipids to do?

• allows phospholipids to form membranes in water

  • saturated fatty acids tend to form membranes that are more solid

  • unsaturated fatty acids - more fluid

What are biological membranes made from?

are made from a phospholipid bilayer

What are biological membranes?

are semi-fluid (contain a mix of saturated & unsaturated fatty acids)

What are biological membranes function?

• separate the watery inside of the cell from the watery environment

  • one saturated & unsaturated, this is what enables the entrance of certain elements through the cell membrane

What is the difference between steroids & other lipids?

structurally different from other lipids

What are steroids built on?

built on a hydrophobic 4 ring structure

• on exam, portrayed as true or false

Where are steroids found in?

• generally found in eukaryotes (more complex organism) not in prokaryotes(bacteria)

  • ex: Cholesterol ergosterol(thermostability) & vitamin D

What are proteins made up of?

made up of building blocks: amino acids (individual units)

What do proteins contain?

all contain: C, H, O, N (& some have S)

• proteins typically contain: 20 different amino acids

  • have at least one amino -NH2 & one carboxyl (-COOH) group

  • side groups(different on each amino acid) determine properties of amino acid

What are functions of proteins?

• required in all aspects of cell structure & function

  • some are structural

  • but most act as enzymes - increase the rate at which chemical reactions take place in living organisms

What bonds turn amino acids to proteins?

amino acids are joined to make proteins by covalent peptide bonds

What is a chain of amino acids?

protein= polypeptide = chain of amino acids

short chain of amino acids are called peptides

What is the shape & function of protein determined by?

shape & functions of the protein is determined by the sequence of amino acids

How is protein required in all aspects of cell structure & function?

• Structural components of the cell:

  • Membrane channels

• Enzymes

  • Increase the rate of chemical reactions that occur within the cell

What are the 9 amino acids essential for life?

• needs to obtain from other sources

  • histidine, isoleucine, leucine, lysine, methionine (AUG is the starting column), phenylalanine, threonine, tryptophan, and valine

What are types of nucleic acids?

• (double strands)DNA transcribes to RNA then to (single strand) RNA become translated to amino acids (series of amino acids)→ proteins (enzymes or structural)

• DNA = deoxyribonucleic acid

• RNA = ribonucleic acid

What are nucleotides made up of? Describe the 3 building blocks.

• built of building blocks called nucleotides

• each nucleotide has 3 parts

  1. Nitrogenous Base:

     1. Purine → 2 rings = Guanine (G) & Adenine (A)

     2. Pyrimidine →1 ring = Cytosine (C), Thymine (T) or Uracil (U)

        1. Uracil is the change due to evolutionary change to increase genetic stability

  2. Pentose sugar → 5 carbon sugar

     1. ribose or deoxyribose

        1. deoxyribose - no oxygen therefore “dehydrated”

  3. Phosphate group

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

What is DNA made up of?

• nucleotides: A, G, T, & C

• sugar deoxyribose

• double stranded with each strand together by hydrogen bonds

What does DNA do?

stores the genetic info of all cellular organisms (what genes are composed of)

What is the direction of DNA?

forms a double helix

• 5 prime to 3 prime

  • The order of the nucleotide sequence is very specific and forming the genetic instructions for the organism

    • there are viruses that contain DNA

How many base pairs in DNA?

3 billion base pairs in DNA

What is RNA made up of?

• A, G, U, & C

• sugar ribose

• single stranded

  • except in viruses; can be double stranded

What is RNA involved in?

involved in communicating the instructions stored in DNA(transcription)

What is the direction of RNA?

• 3 prime to 5 prime

  • SARS covid 2(viruses that contain RNA)

What is the DNA structure composed of?

• each strand is built from a sugar phosphate backbone

• 2 strands are held together by hydrogen bonds between nitrogenous bases

• forms the double helix

What nitrogenous base pairs are paired in DNA?

• A pairs w/ T

• G pairs w/ C

  • order of bases is specific & forms the genetic instructions for the organisms

    • ex: genes