biochemistry

Question 1

What are the common atoms used to synthesize biomolecules?

Answer 1

carbon, hydrogen, nitrogen, phosphorous, sulphur, oxygen.

Question 2

What are covalent bonds?

Answer 2

they are atoms that share their outer shell electrons.

Question 3

What are non-covalent bonds?

Answer 3

• connections that do not involve electron sharing.
• hydrogen bonds, van der walls forces, ionic bonds, hydrophobic interactions.

Question 4

can covalent bonds be polar or non-polar?

Answer 4

Yes.

Question 5

What is a polar bond?

Answer 5

unequal sharing of electrons.
they create negative and positive dipoles. the atom that hogs the electron has a (-) and the atom that bonds weakly to the electron is (+).

Question 6

What is a non-polar bond?

Answer 6

equal sharing of electrons.

Question 7

what determines if a bond is polar or not?

Answer 7

-electronegativity, is the affinity an atom has for electrons.
- if the difference between electronegativities of the atoms forming the bond is greater than 0.5 then the bond will be polar.

Question 8

How can water dissolve neutral polar molecules?

Answer 8

It is a polar molecule and forms hydrogen bonds allowing it to dissolve other polar molecules.

Question 9

How does water dissolve ionic molecules?

Answer 9

ionic solvents dissolve in polar solvents due to the different charges, the positively charged cation is attracted to the negative oxygen and the negatively charged cation is attracted to the positively charged hydrogen.

Question 10

what happens to hydrophobic molecules in water?

Answer 10

• they tend to hide or turn away from water because they are not attracted to the polar molecule.
• hydrophobic molecules are generally non-polar meaning they have equal sharing of electrons and therefore are not looking to lose or gain electrons.
• does not have affinity for the water.

Question 11

what does amphipathic mean?

Answer 11

has both hydrophilic and hydrophobic qualities.

Question 12

what are van der walls forces?

Answer 12

• Van der Waals forces include attraction and repulsions between atoms, molecules, and surfaces, as well as other intermolecular forces. They differ from covalent and ionic bonding in that they are caused by correlations in the fluctuating polarizations of nearby particles (a consequence of quantum dynamics).
• transient electrostatic interactions between permanent or induced dipoles.
• attractive at an optimal van der waals radius.

Question 13

What are the 3 Van der Waal forces?

Answer 13

1. dipole-dipole. strongest
2. dipole-induced-dipole.
3. induced dipole- induced dipole. weakest.

Question 14

What are dipole-dipole interactions?

Answer 14

Dipole-dipole forces is a type of Van Der Waals force. When two polar molecules interact, opposite partial charges attract, similarly to ionic bonding, but generally weaker, because of the smaller charge magnitude.

Question 15

what are dipole-induced-dipole interactions?

Answer 15

dipole-induced dipole bonds are those electric bonds that exist between a molecule with a permanent dipole moment and a molecule in which a temporary dipole moment has been induced (by the other molecule).

Question 16

What are induced-dipole-induced-dipole interactions?

Answer 16

there exists the attractive force between polar and nonpolar molecules, which are held between cation and anion and this interaction is known as induced dipole-induced dipole interaction or London forces.

Question 17

what are hydrophobic interactions?

Answer 17

• exclusion of non-polar substances from water.
• non-polar molecules form aggregates as opposed to bonding with water.

Question 18

what are ionic interactions?

Answer 18

• attractions between oppositely charged molecules. aka electrostatic interactions.
• when they occur between amino acid side chains they are referred to as salt bridges.

Question 19

What are the different functional groups in organic molecules.

Answer 19

• based on their polarities they form varying types of covalent bonding types*
  1. hydroxyl.
  2. sulfhydryl
  3. carbonyl (ketone /aldehyde).
  4. carboxyl.
  5. phosphoryl.
  6. ester.
  7. amino.
  8. amido.
  9. methyl.
  10. thioester.
  11. ether.
  12. anhydride.
  13. mixed anhydride.
  14. phosphoanhydride.

Question 20

what is a hydroxyl group?

Answer 20

a functional group with the chemical formula −OH and composed of one oxygen atom covalently bonded to one hydrogen atom.

Question 21

what is a sulfhydryl group?

Answer 21

A sulfhydryl group (also called “thiol group”) consists of a sulfur atom with two lone pairs, bonded to hydrogen. The sulfhydryl group is ubiquitous in our body and mostly found in the oxidized form as disulfide linkages. The disulfide linkages contribute to the tertiary and quaternary structures of proteins

Question 22

what is a carbonyl group?

Answer 22

A carbonyl group is a chemically organic functional group composed of a carbon atom double-bonded to an oxygen atom –> [C=O] The simplest carbonyl groups are aldehydes and ketones usually attached to another carbon compound. These structures can be found in many aromatic compounds contributing to smell and taste.

Question 23

what is a carboxyl group?

Answer 23

The functional group of a carboxylic acid, characterized by a carbonyl group bonded to a hydroxyl group. ‘Carboxyl’ can be thought of as a contraction of carbonyl hydroxyl.

Question 24

what is an ester?

Answer 24

The basic structure of an ester consists of a carbon single bonded to carbon, double bonded to oxygen, and single bonded to oxygen.

Question 25

what is a phosphoryl group?

Answer 25

A functional group is characterized by a phosphorus atom bonded to four oxygen atoms.

Question 26

what is an amino group?

Answer 26

An amino group is a nitrogen atom bonded to two hydrogen atoms.

Question 27

What is an amido group?

Answer 27

a carbonyl functional group that is linked to both an amine and a hydrocarbon group

Question 28

what is a methyl group?

Answer 28

an alkyl derived from methane, containing one carbon atom bonded to three hydrogen atoms,

Question 29

What is ether?

Answer 29

consists of an oxygen atom with an R group single-bonded to each side.

Question 30

what is a thioester?

Answer 30

a very labile ester‐bond between the COOH‐group of fatty acid and a ‐SH‐group of a cysteine residue in the polypeptide chain (S‐Acylation).

Question 31

what is an anhydride bond?

Answer 31

A functional group is characterized by two acyl groups joined by an oxygen atom.

Question 32

what is a mixed anhydride group?

Answer 32

when the anhydride is derived from two different carboxylic acids) it is called a mixed anhydride. could be a mix of phosphorous and carboxyl groups joined by hydrogen.

Question 33

What is a phosphoanhydride?

Answer 33

Phosphoanhydride groups are found between phosphate groups in ATP, and attack on this functional group by water or other electron-rich species is important in driving chemical reactions forward in the cell. Disulphide linkages can be formed from two thiol groups under reducing conditions.

Question 34

what are the 4 main biomolecules and their bond types?

Answer 34

1. monosaccharides; glycosidic bonds. 2. fatty acids; ester bonds 3. amino acids; peptide bonds. 4. nucleic acids; phosphodiester bonds.

Question 35

What are oxidoreductases?

Answer 35

EC class 1. - they catalyze the transfer of electrons from a donor (reductant) to an acceptor (oxidant). - can be either an oxidase or dehydrogenase. - Oxidases are generally involved when molecular oxygen functions as an acceptor of hydrogen or electrons. - dehydrogenases work by oxidizing a substrate by transferring hydrogen to an acceptor that is either NAD/NADP or a flavin enzyme. Peroxidases, hydroxylases, oxygenases, and reductases also belong to oxidoreductases. Peroxidases are placed in peroxisomes and could catalyze the reduction of hydrogen peroxide. Hydroxylases give hydroxyl groups to their substrates. Oxygenases could incorporate oxygen from molecular oxygen into organic substrates. In most cases, reductases can act like oxidases, but catalyze reductions.

Question 36

What are transferases?

Answer 36

- Transferases are a class of enzymes that transfer specific functional groups from one molecule (donor) to another (acceptor). - kinase; transfer of a phosphate. - polymerase; transfer monomer to a polymer especially in DNA and RNA.

Question 37

What are hydrolases?

Answer 37

- Transferases are a class of enzymes that transfer specific functional groups from one molecule (donor) to another (acceptor). - phosphatase; cleavage of phosphate using water (ATPase). - protease.

Question 38

what is a lyase?

Answer 38

lyase enzymes catalyze reactions in which a molecule breaks to form two different molecules without reacting with water or oxidation. 1. In addition; add one molecule to another commonly across a double or triple bond. hydratase adds water to get rid of the double bond. 2. elimination; remove atoms in a molecule to form a double bond. - decarboxylase. remove carboxyl group. - dehydratase- remove water to form a double bond. 3. condensation; joins two molecules forming a new c-c bond (synthase).

Question 39

what is an isomerase?

Answer 39

- rearrangement of bonds within a molecule. - mutase. transfer groups intramolecularly. - epimerases; interconvert the groups around an asymmetrical carbon in a molecule that has more than one asymmetrical carbon. - racemases; interconvert the groups around an asymmetrical carbon in a molecule that only has one asymmetric carbon.

Question 40

What is a ligase?

Answer 40

- formation of a covalent bond between two large molecules. - ligases catalyze various reactions that join 2 molecules with the use of ATP. - x- ligases or x- synthetases; x refers to the molecules being joined or the molecule being created.

Question 41

what is the difference between hydration, hydrolysis, hydratase and hydrolase?

Answer 41

hydration; a molecule combines with water. (hydrolase). hydrolysis; hydrolysis reaction is the cleavage of chemical bonds by the addition of water or a base that supplies the hydroxyl ion ( OH−). A chemical bond is cleaved, and two new bonds are formed, each one having either the hydrogen component (H) or the hydroxyl component (OH) of the water molecule. (hydratase) hydratase; Hydratases add the hydroxyl group at the unsaturated functional group. hydrolase; Hydrolase is a class of enzymes that commonly perform as biochemical catalysts that use water to break a chemical bond,

Question 42

what is the difference between dehydration, dehydratase and dehydrogenase?

Answer 42

dehydration; In chemistry, a dehydration reaction is a chemical reaction that involves the loss of water from the reacting molecule or ion. dehydratase; is a group of lyase enzymes that form double and triple bonds in a substrate through the removal of water. dehydrogenase; an enzyme that catalyzes the removal of hydrogen atoms from a particular molecule, particularly in the electron transport chain reactions of cell respiration in conjunction with the coenzymes NAD and FAD.