Week 1: Chemistry of life - Reactions in living systems

Question 1

define catabolic and anabolic

Answer 1

Catabolic:
- release energy
- breakdown of food and other molecucules to release energy
- negative enthalpy and are exothermic (heat lost to surrounding)

Anabolic:
- uses up energy
- builds larger molecules from smaller ones
- positive enthalpy and are endothermic (takes up heat from surroundings.

Question 2

4 types of chemical reactions required for life

Answer 2

1. synthesis = A + B –> A-B
2. decomposition = A-B –> A + B
3. Single replacement = A-B + C –> A-C + B
4. Double replacement = A-B + C-D –> A-c + B-D

Question 3

why do biological systems never destroy covalent bonds but make up another?

Answer 3

• according to law of conservation of energy: energy cannot be created nor destroyed, only converted between different forms. Due to the high energy yeilding nature of covalent bonds, when one bond is broken a lot of energy is release as heat energy. If biological systems break covalent bonds constantly - releasing a lot of heat - the cells will become damaged and proteins wills tart to denature.
  - therefore, when a covalent bond is broken another one is made to ensure no damage to the system.

Question 4

what is hydrolysis?

Answer 4

• breaking a large compound into 2 smaller products via the addition of a water molecule.
• hydrolysis can break bonds (i.e. covalent bonds) which releases energy.
• bonds between phosphate molecules in ATP are broken via hydrolysis.

Question 5

What is ATP

Answer 5

• primary, high energy yeilding, short-term energy currency.
• ## continually sysntheised in cells for energy requiring processes.

Question 6

what is the metabolic process that cells undergo to make and use ATP

Answer 6

• glucose (obtained by food and drinks) cannot be broken down immediately for energy. :. ATP is formed
• formation of ATP via aerobic (Cellular) respiration: C6H12O6 + 6O2 → 6CO2 + 6H2O
• during this process, when covalent bonds of glucose are broken, electron transport chain takes place where electrons are grabbed to synthesise ATP before the conversion into the products (CO2 and H2O).

Question 7

what are covalent bonds

Answer 7

• covalent bonds are high energy bonds between elements which make up biological molecules
• allow atoms to become stable through shared electrons
• single covalent bond = 1 shared electron
• double covalent bond = 2 shared electrons
• food high in fat

Question 8

Weak non-covalent bonds

Answer 8

• dipole-dipole interactions and hydrogen bonds
• low energy bonds
• many events in cells rely on the associaition and dissociation of these weak non-covalent bonds (e.g. antibiodies/antigen binding)
• important for protein structure –> bonds between amino acids.
  –> provides proteins with shape and function

Question 9

2 resons why weak non-covalent bonds are essential to biological life.

Answer 9

1. structural stability for proteins
2. molecular recognition and binding

Question 10

in cellular respiration, what is the importance of electronegativity

Answer 10

oxygen is essential in cellular respiration as electrons are in lower energy levels, hence allowing the energy to be released easier due to the electronegatovoty of oxygen.
electrons move from glucose via electron transport chain towards oxygen, passing to lower and lower energy states and releasing energy at each step.
this energ released is used to synthesise the third phosphate bond on ADP –> forming ATP.

during this process, protons are transported out of the miktochondria –> creates an electrochemical (conc.) gradient [more protons outside mitochondria and more hydroxide ions inside] –> creates a seperation of charge across membrane (voltage gradient)

Question 11

what is derived from breaking of covalent bonds to make ATP?

Answer 11

electrons are derived when covalent bonds are broken to make ATP

Question 12

why is an atom’s electronegativity important in the aerobic (oxidative) respiration?

Answer 12

• more electronegative elements allow electrons to be in lower energy levels. –> energy released in the form of ATP
• oxygen = very electronegative while the electrons in glucose = higher energy state.
• therefore, by introducing oxygen to these electrons, they can be transfered to a more electronegatove atom (oxygen) via electron trasnport chain. –> make H2O and CO2 –> producing ATP

Question 13

role of water and its ionising products in living systems

Answer 13

• water and its ionising products (H+ and OH-) influence structure, self-assembly and properties of cellular components.
• water is polar :. polar groups are hydrophillic and water soluble forming H-bonds
• non-soluble compounds (e.g. gases) interfere with water-water interactions as they cluster togther and for an energetically unfavourable presence. typically hydrophobic and insoluble in water.

Question 14

what is an amphipathic molecule.

Answer 14

• contain both polar and non-polar domains.
• e.g phospholipids.
• when dissolved in water –> 2 mains have conflicted tendencies –> causes micelles, bilayer sheets and liposomes to form in aqueous environments.

Question 15

why do we carry oxygen on proteins (haemoglobin) in our blood?

Answer 15

• Oxygen is insoluble in water (non-polar) and interfere with water-water interactions by clustering together and providing an energetically unfavourable presence.
• therefore, proteins (i.e. haemoglobin) used to carry oxygen through blood (an aqueous environment)
• haemoglobin = quaternary protein structure and forms H-bonds with water molecules –> hence, movement throught he blood. also has enough non-polar components :. interact with non-polar molecules.
  –> this allows Oxygen to attach to haemoglobin and be carried through blood.

Question 16

why are hydrophobic interactions important for biological life?

Answer 16

• hydrophobic interactions = forces that hold non-polar regions of molecules togther.
• these interactions within lipids and proteins determin the structure of biological membranes.
• examples:
  1. the hydrophobic interactions between the non-polar amino acids stabalise the 3D folding patterns of proteins. :. structure of protein determined by hydrophobic interactions of amino acids with water. –> resulting in the different shapes/structures of proteins and their corresponding fucntions
  2. Integrity of Cell membrane –> phospholipid bilayer resulsts in the hydrophobic interaction between the lipid tails of the phospholipid which allows for the fluidity of the membrane, and regulates the movements of molecules in and out of the cell.

Question 17

what role does saliva play in maintianing oral health?

Answer 17

• helps build and maintain soft and hard oral tissue.
• helps prevent dental caries.
• washes away food and other debris from teeth and gums
• nuetralises/dilutes sugary foods and acids (pH buffering)
• keeps surface of teeth strong –> provides high level of calcium, flouride and phosphate ions to tooth surface.

Question 18

what is pH? what is the mathematical formula?

Answer 18

• a measurement of the concentration of H+ (hydrogen ions) and H3O+ (hydronium).
• measure of acidity/basicity
• each uni decrease in pH = ten-fold increase in hydronium/hydrogen ion conc.
  FORMULAR : pH = - log [H3O+] or pH = −log [H+]

Question 19

What is the normal range and optimal range of pH in saliva?

Answer 19

Normal range = 6.2-7.6

Optimal range = 6.7-7.4

Question 20

how does saliva act as a pH buffer?

Answer 20

• when acidic food/drinks is consumed, pH of saliva decreases.
• decreased pH can cause caries or affect enamel composition (reacts with calcium phosphate which makes up enamel.
• chewing increases saliva production –> :. acidic compounds/sugars composed are washed away from oral cavity –> restoring pH back to normal range.
• saliva contains pH buffers (salivary amylase) –> allows pH of mouth to stabalise around normal range.

Question 21

how do pH buffers in saliva indicate oral health of individuals?

Answer 21

the buffering ability of the salivary buffers determine how the pH is regulated within the oral biome/environment while the oral environment changed due to the consumption of food/drinks, and bacteria in the mouth.
therefore, saliva is important for the health and integrity of the hard and soft oral tissues.

Question 22

what pH denotes acidity and basicity?

Answer 22

acidity = pH below 7
basicity = pH above 7
neutral = pH 7

Question 23

3 general causes for lowering pH in the mouth

Answer 23

1. food
2. drinks
3. bacteria

• foods and drinks consumed can lower pH in the mouth. carbohydrates (especially starch) –> metabolised by bacteria in the mouth –> produces acids (as a biproduct)
• food/drinks can also be acidic in nature (e.g. orange juice, soft drinks) - immediately introduces acids to the oral environment.

Question 24

what are the 3 major biological buffering systems in saliva?

Answer 24

1. carbonic acid/bicarbonate (most significant)
- in saliva, carbonic acid/bicarbonate buffering system has a weak acid (carbonic acid) and its conjugate base (bicarbonate ion). –> at low pH, bicarbonate ions react with excess H+ to remove it from environment –> neutralising acidic compounds.

**2. phosphate ions **

3. proteins/enzymes
- amino acid histidine has a pKa 6.

Question 25

the basic universal law of acid-base pairs to maintain pH range

Answer 25

to maintain a pH range, the buffer must contain a weak conjugate acid-base pair: weak acid and its conjugate base OR a weak base and its conjugate acid.

Question 26

why do biological buffers only work efficiently if their pKa is between 6 and 7?

Answer 26

in a living cell, pH is maintians between 7.2-7.4 and pH of saliva is normally 6.2-7.6. therefore, role of buffers are to

Question 27

what is pKa?

Answer 27

the point at which an acid is 50% dissociated and describes the acidity of a particular molecule.
- measures strength of acid by how tightly a proton is held.

Question 28

what is a type of catabolic reaction

Answer 28

• hydrolysis = chemical breakdown by the addition of a water molecule.

Question 29

type of anabolic reaction

Answer 29

• dehydration synthesis = water molecule removed as larger molecules are formed.

Question 30

type of anabolic reaction

Answer 30

• dehydration synthesis = water molecule removed as larger molecules are formed.

Question 31

example of dehydration synthesis reaction.

Answer 31

when 2 amino acids join together, forming a peptide bond, peptide bond is when:
- the carboxyl group (COOH) of one amino acid bins with the amino group (NHH) of another amino acid.
done via dehydration synthesis –> thr amino group loose a hydrogen atom and the carboxyl group loses and oxygen and hydrogen :. releasing H2O molecule.

Question 32

how does a weak acid (e.g. carbonic acid) act as a buffer when an acid or base is present in the environment.

Answer 32

• in an aqueous environment (saliva), weak acids (e.g. carbonic acid) partially ionise. H2CO3 ↔ H+ + HCO3-
• If pH rises = increase in Hydroxide ions (OH-) and decrease in H+ ions. –> carbonic acid (H2CO3) will split into H+ + HCO3- (bicarbonate) –> provides more H+ into environment –> decrease pH
• if pH drops = increase in H+ and decrease in OH –> bicarbonate ions (HCO3-) will bind to the excess H+, forming carbonic acid (H2CO3) –> decreasing H+ from environment –> increasing pH
• continues supply of acids (H+) and bases (OH-) will deplete the buffer –> exhaust buffering system –> pH begins to fall or rise significantly.

Question 33

what factors determine how effective buffering system of saliva is?

Answer 33

• amount og saliva produced
• buffering capacity of saliva (makeup of saliva)

Question 34

how does concentration of bicarbonate (HCO3-) imapct buffering capacity of saliva?

Answer 34

• more saliva = more bicarbonate = individual has a good buffering system.

Question 35

what is an acid and a base

Answer 35

• acid = can donate a H+ ion
• base = can take up a H+ ion

Question 36

how do proteins buffer pH chanes?

Answer 36

accepting or donating protons –> increasing or decreasing the pH of an environment.

Question 37

what are electrolytes and non-electrolytes
- give examples and explain acids and bases.

Answer 37

ELECTROLYTES:
compounds that produce ions in an aqueous environment - AKA salts.
- acids are electrolytes that can release H+ due to ionisation.
- bases are electrolytes that produce OH- upon ionisation.
- strong electrolytes = fully ionise
- weak electrolytes = dissolve to produce a mix of ions and molecules.

NON-ELECTROLYTES:
usually covalent compounds, may dissolve in water but does not produce ions - e.g. glucose

Question 38

hydronium ions.

Answer 38

H3O+
- hydrogen ion bonded to molecule of water (H+ + H20 –> H3O+)
- associated with acidity of aqueous solutions.

Question 39

strong acids and weak acids

Answer 39

• strong acids = ionise completely in water, have a higher Ka
• weak acids = partially ionise in water (producing a mix of ions and molecules in equilibrium); have a lower Ka

Question 40

how does carbonic anhydrase maintain a neutral pH in the mouth?

Answer 40

• carbonic anhydrase is an enzyme in the saliva.
• secreted by serous acinar cells of parotid and submandibular major salivary glands.
• mops up hydronium ions when conc. carbonic acid is too high.
• convertes bicarbonate ions and hydrogen ions back into carbonic acid, which can then further break down into CO2 and water This equilibrium reaction enables the removal of excess hydrogen ions, thus maintaining a neutral pH in the mouth.

Question 41

what is a pellicle?

Answer 41

a bacterial growth in the form of a sheet on the durface of liquid medium
e.g. salivary glycoproteins that coat the surface of teeth and oral epithelium