Organic Molecules
What two functional groups make up an amino acid?
Amino acids make up your proteins carboxyl and amino
What two functional groups does an amino acid contain?
An amino group (-NH 2) and a carboxyl group (-COOH). These groups are joined to a single (aliphatic) carbon. In organic chemistry, the carbon directly attached to a carboxyl group is the alpha (α) position, so the amino acids in proteins are all alpha‐amino acids.
How does taking an antacid (such as tums) neutralize stomach acid?
An antacid neutralizes. This means it doesn't allow the digestive process to occur in the stomach. When you take things that are acidic and add things that are basic, their pH is neutralizes. So, an antacid works by introducing something with a high pH into your stomach and mixes to balance out the stomach acid which has a low pH, typically around 2. Chemistry dictates the actual chemical reactions that go on, but the bottom line is the acid is neutralized
What is the abbreviation of hydrogen ions and hydroxide ions?
H+ and OH-
What is the concentration of H+ ions to OH- ions in an base/alkaline solution?
H+ ions < less than OH-
What is the concentration of H+ ions to OH- ions in an acidic solution?
H+> more than OH-
Carbon usually bonds with?
H.O.N - hydrogen, oxygen, nitrogen -The valences of carbon and its most frequent partners (hydrogen, oxygen, and nitrogen) are the "building code" that governs the architecture of living molecules
What are structural isomers?
Have different covalent arrangements of their atoms
What are isomers?
Iso + Mer = similar + unit = similar unit Compounds with the SAME molecular formula, but different structures and properties C4H10 = C4H10 <- same molecular formula, but could have different structure
What is an enantiomer?
Isomers that are mirror image of each other, right hand left hand. However, they are not the same.. The mirror image changes how molecules can interact with each other - Very useful -Enantiomers are important in the pharmaceutical industry, Two enantiomers of a drug may have different effects -Usually only one isomer is biologically active because it has the right shape to adapt into your body -Differing effects of enantiomers demonstrate that organisms are sensitive to even subtle variations in molecules *Has to have the right shape to bond with a receptor. MUST fit together in order to get a signal.
An organic chemical compound is said to be "saturated" when
It does not contain any double or triple covalent bonds Saturated organic molecules include only single covalent bonds
What causes acid precipitation?
Various pollutants that are in water, comes most from the air Burning coal creates the most acid rain. When we burn coal, it releases the most sulfur type compounds. It goes into the atmosphere and attaches with water to create sulfuric acid.
Molecular Formula only tells about...
how many atoms there are in each elements, doesn't tell you anything about its actual structure.. Ex C4H2 Only tells you there is 4 Carbons, 2 Hyrdogens
pH of human blood and MOST biological fluids
human blood = pH7 .. other biological fluids around 6-8 (around neutral)
What is the concentration of H+ ions to OH- ions in a solution that has a pH of 7?
pH7 is neutral, that means it is H+ = OH-
Name the seven function groups that can be added to a carbon chain.
- Hydroxyl group - Carbonyl group - Carboxyl group - Amino group - Sulfhydryl group - Phosphate group - Methyl group
Structural Polysaccharides
-Cellulose is a major component of the tough wall of plant cells -Like starch, Cellulose is a polymer of glucose, but the glycosidic linkages differ -The difference is based on two ring forms for glucose: alpha () and beta () Polymers with alpha glucose are helical Polymers with beta glucose are straight -In straight structures, H atoms on one strand can bond with OH groups on other strands (Parallel cellulose molecules held together this way are grouped into microfibrils, which form strong building materials for plants)
All inorganic compounds have...
-Doesn't need carbon.. could have it but doesn't need it Ex: carbon monoxide CO, C02 carbon dioxide <- both missing hydrogen - Does not have a carbon change - No macromolecules Ex: H20, HCl, S04, NaCl, NaOH <-- very small amount of atoms, doesn't have carbon
Diversity of Polymers
-Each cell has thousands of different kinds of macromolecules -An immense variety of polymers can be built from a small set of monomers
Why are electron configurations important in a carbon atom?
-Electron configuration is the key to an atom's characteristics -Electron configuration determines the kinds and number of bonds an atom will form with other atoms -Electron configuration of carbon gives it covalent compatibility with many different elements -This ability makes large, complex molecules possible
Carbon chains
-Form the skeletons of most organic molecules -Vary in length and shape
What is glycogen?
-Glycogen is a storage polysaccharide in animals -Glycogen is a multibranched polysaccharide of glucose that serves as a form of energy storage in animals and fungi -Humans and other vertebrates store glycogen mainly in liver and muscle cells
What is a hydrocarbon?
-Hydrocarbons are chemical compounds that are formed from only hydrogen atoms and carbon atoms. -Store a large amount of energy Ex: calories, fat have energy Ex: Ethane, propane, Butane.. they are all flammable and has a lot of energy - Many fats have hydrocarbon in it Ex: Alkanes - *saturated hydrocarbons, only single bonds Alkenes - *unsaturated hydrocarbons, include a double bond Alkynes - *unsaturated hydrocarbons, include a triple bond H H H H | | | | H- C-C-C-C - H | | | | H H H H
What do characteristics of molecules depend on?
-It depends on the carbon skeleton, length, number of bonds, branching AND molecular components attached to it -A number of characteristic groups can replace the hydrogens attached to skeletons of organic molecules.. this makes it no longer a hydrocarbon
Distinct characteristics of carbon
-It is the backbone of life -Carbon is unparalleled in its ability to form large, complex, and diverse molecules -Proteins, DNA, carbohydrates, lipids and other molecules that distinguish living matter are all composed of carbon compounds -Most organic compounds contain a carbon chain of two or more (100's) of carbons bonded together the exception is methane gas.
What is organic chemistry? and Inorganic chemistry?
-Organic means- things were either alive or once a live -It is the study of compounds that contain carbon -Range from simple molecules to colossal ones -
All organic compounds have...
-Presence of Carbon & Hydrogen Ex CH4 methane .. has carbon AND hydrogen - In organic molecules, carbons bond together to form a CARBON CHAIN .. C-C-C-C-C-C They have a carbon backbone, skeleton - Able to bond macromolecules due to carbon chains Ex: Cn, Hn, On, Pn, Sn (CHONPS) <-- all of these have an n in them ... meaning it contains varies of numbers (n) of carbon
What is the difference between a saturated and unsaturated fat?
-Saturated fatty acids have no double bonds between carbons -Unsaturated fatty acids have at least one double bond
What are we looking at when we build an organic molecule?
-Varying the length of carbon chain by adding more atoms to it will change the characteristics of the actual molecule, because it changed its shape, structure and chemical properties.. - Add branches, changes its structure and properties - Taking hydrogen away in order to create a double bond, double bond change the shape of molecules and makes it bend, once again changing its structure - The ring structure, has completely different functioning characteristics than something that is linear..changing its structure
What is a buffer? How can it help a solution maintain pH? If the buffer was removed from your blood what would be the likely outcome?
A buffer is a substance that minimizes and resist changes in pH. It works like a sponge to ABSORB hydrogen ions, causing no change in a pH. It DOES NOT neutralize a solution, but only absorbs by attaching the ions to its own structure so that the hydrogen ions are no longer a free ion. This causes no change in the pH. Our blood would become extremely susceptible to pH changes, which is NOT good because it has to stay around H 7.35- 7.45 A buffer must be in a solution ahead of time. Cannot be added after because the solution would've already been changed.
What does it mean to be a hydrophilic or a hydrophobic substance?
A hydrophobic substance is one that has an affinity for water Hydrophobic substance is one that does not have an affinity for water
What is the difference between a molecule and compound?
A molecule like H2 has the same elements but not a compound because it doesn't contain a DIFFERENT element bonded to it. 02 is a molecule, not compound H20 is a molecule AND compound because it has 2 different element, Hydrogen + Oxygen
What is a polymer?
A polymer is a long molecule consisting of many similar building blocks called monomers .. it is strong together to make a long chain Carbohydrates •Proteins •Nucleic acids are all polymers
How is strong acid created?
A strong acid is one which is virtually 100% ionized in solution. It gives up all of the hydrogen ions. A strong acid can dissociate COMPLETELY. When an acid dissolves in water, a proton (hydrogen ion) is transferred to a water molecule to produce a hydroxonium ion and a negative ion depending on what acid you are starting from. These reactions are all reversible, but in some cases, the acid is so good at giving away hydrogen ions that we can think of the reaction as being one-way. The acid is virtually 100% ionised. For example, when hydrogen chloride dissolves in water to make hydrochloric acid, so little of the reverse reaction happens At any one time, virtually 100% of the hydrogen chloride will have reacted to produce hydroxonium ions and chloride ions. Hydrogen chloride is described as a strong acid Other common strong acids include sulphuric acid and nitric acid.
How is a weak acid created?
A weak acid is one which doesn't ionize fully when it is dissolved in water. It only gives a couple of hydrogen ions. Ethanoic acid is a typical weak acid. It reacts with water to produce hydroxonium ions and ethanoate ions, but the back reaction is more successful than the forward one. The ions react very easily to reform the acid and the water. Most organic acids are weak. Hydrogen fluoride (dissolving in water to produce hydrofluoric acid) is a weak inorganic acid
If a substance has a pH of 2, is it acidic or basic?
Acidic (digestive stomach juice, lemon juice)
What is an acid, base and salt?
Acids: Donates (increases) H+ hydrogen ions to a solution Base: Donates hydroxide ions to a solution by reducing H+ This is the biggest difference between an acid and base. Ex: pH 0 = Pure hydrogen ions, no hydroxide ions pH 14= Pure hydroxide ions, no hydrogen ions Salts: When solution is neutralized, it forms equal weights of acid and base *The amount of acid needed is the amount that would give one mole of protons (H+) and the amount of base needed is the amount that would give one mole of (OH-) Because salts are formed from neutralization reactions with equivalent concentrations of weights of acids and bases: N parts of acid will always neutralize N parts of base.
What is the normal pH of the blood?
pH 7.35 to 7.45 .. body fluids are typically 6-8, around neutral
What makes one organic carbon chain different from another?
Functional groups- small groups of atoms with specific chemical properties. One biological molecule can contain many functional groups
What pH does most living organisms like?
pH of 6 to 8
Name four ways in which a hydrocarbon can be changed from one type to another?
By either varying the length of the compound, branching, forming double bonds or formation of a ring
Can more than one functional group be added to a carbon chain?
Can add several, or varying the length. Yes. Ex: Glycine
What two functional groups does a carbohydrate such as glucose contain?
Glucose contains the Carbonyl Functional Group. It is an aldehyde, thus it has the structure: R-C=O Also contains Hydroxyl group
What is the functional properties on the Sulfhydryl group?
Can be written as -SH or HS- Sulfur attached to hydrogen -Two sulfhydryl groups can react, forming a covalent bond. This "cross-linking" helps stabilize protein structure. -Cross-linking of cysteines in hair proteins maintains the curliness or straightness of hair. Straight hair can be "permanently" curled by shaping it around curlers and then breaking and re-forming the cross-linking bonds.
What are the major functional groups in organic molecules?
Carbohydrates Proteins Lipids- Fats, oils, waxes Nucleic Acids - DNA, RNA
Name the four classifications of organic compounds.
Carbohydrates are sugars such as glucose, sucrose and starch. Lipids are fats and usually do not like water, so they form part of the cell membrane to act as barriers to a watery environment. Proteins have a variety of functions and are typically large molecules. They act as structural components, are significant in cell-to-cell communication, and speed up or catalyze reactions within the cells. Nucleic acids carry the genetic material to make new organisms. Two types of nucleic acids exist in organisms: DNA and RNA.
What elements are found in carbohydrates?
Carbohydrates include sugars and the polymers of sugars carbon, hydrogen and oxygen.
What is the functional properties on the Carboxyl group?
Carboxyl goup can act as an acid.. can make organic acid, or weak acid COOH - carboxyl - Hydrogen can dissociate as a hydrogen ion and breaks off .. cannot break off completely, making it a weak acid, not a strong one -Acts as an acid; can donate an H+ because the covalent bond between oxygen and hydrogen is so polar -Found in cells in the ionized form with a charge of 1- and called a carboxylate ion. EX: Acetic acid aka vinegar/ organic acids
Organic acids like acetic acid (vinegar) and citric acid are composed of a carbon chain with a _________ functional group added.
Carboxyl group added (these groups make organic acid and weak acids)
What is a cistrans isomers
Cis-trans isomers have the same covalent bonds but differ in spatial arrangements Cis- the x's are on the same side trans- x's are on the opposite side, diagonally across
With acid, the lower the number, the stronger the acidity because it can dissociate completely
Ex: Two glasses of water, both at a neutral pH of 7 We pour equal amounts of hydrochloric acid and acidic acid into each glass of water. Hydrochloric acid = pH 0 Acidic acid = pH 2 Will they both have the same amount of pH after these acids are added? NO Which one has more acid? Hydrochloric Why? It is at the lower 0 end of the pH scale, meaning it is more acidic Which one will give up more hydrogen ions? hydrochloric, because it can dissociate completely
Why is pH so important?
It effects the structures of macromolecules in our bodies, such as proteins, fat lipids, DNA, sugars .. Acids and bases alter the structures of our macromolecules, taking away its functions Ex: If we change a shape of a molecule, it changes its functions/ could even lose it... Proteins are very sensitive to pH changes
A carbonyl groups has been added to the beginning of a carbon chain. What classification of organic molecule is it now?
It is a keytone group
Why is carbon so easy to bond with?
It is missing 4 electrons in its valence shell. This makes it able to create a covalent bond easily with four other atoms, or more carbons in order to form a carbon chain. Ex: Carbon bonds with another carbon C-C, each of these carbons are able to bond with 4 other atoms, making it 8 atoms altogether. You can add more in order to make it even bigger. -Carbon has the ability to form complex and large macromolecules
A carbonyl groups has been added to the end of a carbon chain. What classification of organic molecule is it now?
It is now an aldehyde group.
How is acid precipitation?
It refers to an acid rain, fog, or snow that has a pH lower than 5.6
What does the pH scale do?
It tells us of the amount of hydrogen ions concentration of a solution Acid- 0 to 6 Neutral/equal H+ and OH- = 7 (water) Base/ Alkaline solution 8-14
What is the functional properties on the Meythl group?
Methylated compounds -Addition of a methyl group to DNA, or to molecules bound to DNA, affects the expression of genes. -Arrangement of methyl groups in male and female sex hormones affects their shape and function.
What is a function group?
Molecules attached to the carbon chain that give it a specific function.. changes its characteristics.. changes it so that it's no longer a hydrocarbon
Why is hydrolysis?
Polymers are disassembled to monomers by hydrolysis, a reaction that is essentially the reverse of the dehydration reaction
Name the three types of carbohydrates, explain their structures and give examples of each.
Monosaccharides •Disaccharides •Polysacchariedes Monosaccharides -The simplest carbohydrates/ single sugars -Molecular formulas that are usually multiples of CH2O Glucose is the most common monosaccharide -Monosaccharides are classified by location of the carbonyl group and by number of carbons in the carbon skeleton (keytone) Disacchardies -Formed when two sugars are joined together and a molecule of water is removed. For example, milk sugar (lactose) is made from glucose and galactose whereas cane sugar (sucrose) is made from glucose and fructose -A disaccharide is formed when a dehydration reaction joins two monosaccharides - This covalent bond is called a glycosidic linkage Polysacchariedes -Polysaccharides, the polymers of sugars, have storage and structural roles -The structure and function of a polysaccharide are determined by its sugar monomers and the positions of glycosidic linkages -Polymeric carbohydrate molecules composed of long chains of monosaccharide units bound together by glycosidic linkages. They range in structure from linear to highly branched.
What is the functional properties on the amino group?
NH2, or NH3 (same thing) If added to carbon change, it will make an amino acid .. we have 20 different ones -Acts as a base; can pick up an H+ from the surrounding solution (water, in living organisms) -Found in cells in the ionized form with a charge of 1
Is Na a molecule or compound? What about H2 or H20?
Na is neither. It is just an individual atom. H2 is a molecule because it has 2 atoms bonded together H20 is a molecule AND compound
What is the difference between inorganic and organic compounds?
Organic compounds have carbon and hydrogen, inorganic compound does not. Organic compounds can build macromolecules, inorganic compounds cannot. Organic molecules bond together to form a carbon chain, inorganic molecules do not form a carbon chain.
What is an acidophiles?
Organisms that like/love to grow in an acidic environment Ex: Mold, pH 4
What is the functional properties on the Phosphate group?
Phosphate will always be attached to oxygen Organic phosphates -Contributes negative charge to the molecule of which it is a part (2- when at the end of a molecule, as at left; 1- when located internally in a chain of phosphates). This makes it POLAR -Molecules containing phosphate groups have the potential to react with water, releasing energy.
What is the buffer in our system?
Sodium bicarbonate system or bicarbonate system Our blood has bicarbonate in it If the pH in our system is too low/acidic .. the kidneys will conserve and hold on to bicarbonate. It will increase the bicarbonate so that it can attach all of the hydrogen ions in our body. If our body is too alkaline or high in pH, the bicarbonate can release some so that our pH can go down a bit.
What is an organic acid?
Something made by a living thing -- Vinegar is made by a bacteria, lemon juice comes from organic acid, vitamin c, etc.. These acids have a -COOH group Organic acids essentially contain hydrogen and carbon with another elements. Organic acids are weak acids and partially dissociate in water.
What is a buffer?
Something that all living systems have in them, very important A substance that minimizes/resist changes in pH, aka resist changes in concentrations of H+ and OH- of a solution Buffers are similar to sponges - They will absorb the hydrogen ions of a substance .. It takes it and attaches it to a molecule, causing the pH NOT to change, it doesn't neutralize, it only absorbs the ions. It attaches it to its own structure so that they hydrogen ions are no longer a free ion.
What is storage Polysaccharides
Starch, a storage polysaccharide of plants, consists entirely of glucose monomers
What is the functional properties on the carbonyl group?
Take away hydrogen, to double bond into a oxygen. >C=O Depends on where it is.. it will form a different compond: Keytone- (within a carbon skeleton) middle of chain Aldehydes- carbonyl group is at the end of the carbon skeleton - A ketone and an aldehyde may be structural isomers with different properties -Ketone and aldehyde groups are also found in sugars, giving rise to two major groups of sugars: ketoses (containing ketone groups) and aldoses (containing aldehyde groups).
How do Cis-trans isomers differ from each other in structure?
The cis isomers have molecules, or x's on the same side the trans isomers have molecules or x's on the opposite side, diagonal from each other
The difference between organic and inorganic acid -
The process of disassociation. Strong acid - dissociate completely Weak acid- doesn't dissociate completely, doesn't give up all of their hydrogen ions. Doesn't change pH much - Organic acids contain carbon, and inorganic acids don't contain carbon - Generally organic acids are weaker acids than inorganic acids -Most of the organic acids are unable to dissolve (insoluble) in water, soluble in organic solvents -Inorganic acids are generally well soluble in water and non soluble in organic solvents
What are hydrogen ions aka acid?
They are protons
What happens when you mix an acid and a base?
They neutralize each other by forming water and a salt. Involves the combination of hydrogen ions (H+) and hydroxide ions (OH-) to generate water. Neutralization of strong acid and strong base has a pH of 7. The neutralization of a strong acid and weak base will have a pH of less than 7 The resulting pH when a strong base neutralizes a weak acid will be greater than 7
How does stomach produce acid?
They pump hydrogen protons into gastric juice in order to make it acidic
What is pH of urine? Does it vary?
Typically at pH of 6, slightly acidic.. varies depending the type of acidic food we eat
Stomach Acid pH
pH2 , sometimes even almost down to 0
What is the functional properties on the hydroxyl group?
Written with -OH, or HO- "OH! Alcohol turns you into a HO!" Usually associated with alcohOL groups Example: Ethanol -Is POLAR as a result of the electrons spending more time near the electronegative oxygen atom -Can form hydrogen bonds with water molecules, helping dissolve organic compounds such as sugars
Does our body regulate our own pH?
YES. Only our body can regulate our own pH.. nothing else. We have homeostasis to do it.. Most things in nature that are alkaline are poisonous.. therefore, we cannot truly purchase REAL alkaline ingredients. Alkaline things tends to taste bitter
Unsaturated organic molecules include
at least one double or triple covalent bond
How do monomers form larger molecules?
by condensation reactions called dehydration reactions
pH of black coffee, rain water?
pH 5-6
