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Chemistry > Option B - Human biochemistry > Flashcards

Option B - Human biochemistry Flashcards

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1
Q

Outline how respiration makes energy out of glucose

A
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2
Q

How is a bomb calorimeter used to measure the energy value of food samples?

A
  1. The food is burned to completion in the bomb
  2. The heat released as it burns is measured by the temperature rise in a known mass of pure water
  3. The specific heat capacity of the water is used to calculate how much energy was used to increase the temperature with the following formula:

Q = cm∆T

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3
Q

Draw the general formula of 2-amino acids

A
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4
Q

What defines an amino acid?

A

Its R group

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5
Q

What is a buffer?

A

A solution which resists changes in pH on the addition of a small amount of acid or alkali

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6
Q

What are the three major chemical properties of amino acids?

A
  1. Form zwitterions
  2. Work as buffers
  3. Have isoelectric points
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7
Q

Describe how amino acids form zwitterions

A
  • Internal acid-base reaction
  • The acidic –COOH transfers a proton to the basic –NH2 group in the same amino acid
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8
Q

Describe the ionic properties of amino acids

A
  • Crystalline compounds
  • High melting points, usually over 200°C
  • Much greater solubility in water than in non-polar solvents
  • Move in an electric field
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9
Q

Describe the amphoteric properties of amino acids

A
  • Contain both an acid and a basic group
  • Are able to react with both bases and acids
  • In zwitterion form
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10
Q

Why is the buffering nature of amino acids important?

A
  • Due to the zwitterion ion and amphoteric nature of amino acids
  • Help in maintain constancy of the pH in body cells
  • Proteins are extremely sensitive to change in pH
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11
Q

What is meant by the isoelectric point of an amino acid and what are its properties?

A

An intermediate at which the amino acid is electrically neutral

  • Amino acids won’t move in an electric field
  • The molecules have minimum mutual repulsion → least soluble
  • Different amino acids have different isoelectric points
  • If the R group contains an acidic or a basic compound, the pKa and pKb of these groups will affect the charge as pH changes
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12
Q

What is the relationship between pH and the charge on amino acids?

A
  • pH determines the net charge that the amino acid carries
  • Positively charged at low pH
  • Negatively charged at high pH
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13
Q

How are amino acids condensed together?

A
  • Condensation rection in which a molecule of water is eliminatend and a new bond is formed between the acids
  • Called a peptide bond
  • Two acids are a dipeptide, three acids a tripeptide, and eventually a polypeptide is formed
  • The acid group (—COOH) of one acid and the amino group (—NH2) of the other join together
  • After the condensation there are free functional groups on both ends to the peptide can undergo further condensation
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14
Q

What is the primary structure of a protein?

A

The number and sequence of amino acids in its polypeptide chain

(e. g. Asn-Cys-Val-…)
- The covalent backbone of the molecule
- Dictates the entire structure and function of the protein
- The alteration of just one amino acid can completely change the function of the protein

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15
Q

What is the secondary structure of proteins?

A
  • Either α-helix or β-pleated sheet
  • Folding of the polypeptide chain as a result of hydrogen bonding
  • Bonds can form between the –C=O group of one peptide and the –N–H group of another
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16
Q

What is the α-helix secondary structure of proteins?

A
  • Regular coiled configuration of the polypeptide chain
  • Hygrogen bonds between two peptide bonds four amino acid units apart
  • This twists the chain into a tightly coiled helix (spiral staircase)
  • Flexible and elastic because the intra-chain hydrogen bonds easily break and reform when stretched
  • E.g. keratins = structural proteins in hair, skin, and nails
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17
Q

What is the β-pleated sheet secondary structure of proteins?

A
  • Side by side polypeptides bonded together
  • Not tightly coiled
  • Arranged in pleated sheets that are cross-linked by inter-chain hydrogen bonds
  • Flexible but inelastic
  • Found in webs of spiders and silkworms and the beaks and claws of birds
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18
Q

What is the tertiary structure of proteins?

A
  • Further twisting, folding, and coiling of the polypeptide chain
  • A result of interactions between the R groups (side chains)
  • Very specific compact three-dimensional structure (conformation)
  • The most stable arrangement of the protein
  • Takes into account all the possible interaction between the side chains
  • Intra-molecular forces as they occur within one chain
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19
Q

What is meant by an enzyme’s conformation?

A

Its very specific compact three-dimensional structure.

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20
Q

Why is the tertiary structure of proteins important?

A
  • Important in globular proteins (enzymes and proteins)
  • Water soluble
  • Specific structure necessary for the enzymes
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21
Q

What kind of interactions define and maintain the conformation of a protein?

A
  1. Hydrophobic interactions
    - between non-polar side chains (e.g. van der Waals’)
  2. Hydrogen bonding
    - between polar side chains
  3. Ionic bonding
    - between side chains carrying a charge
  4. Disulfide bridges
    - between the sulfur atoms
    - covalent bonds and the strongest of the interactions
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22
Q

What is the quaternary structure of a protein?

A
  • The association between different polypeptides
  • E.g. collagen: a triple helix of three polypeptide chains, with inter-chain hydrogen bonds in between → stable rope-like structure that is resistant to stretching
  • E.g. haemoglobin: four polypeptide chains, two α and two β, bound together tightly around an iron
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23
Q

What needs to be done to proteins before they can be analysed?

A

They need to be split into their amino acids. The peptide bonds are broken through hydrolysis (reverse condensation)

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24
Q

What are the two ways of analysing proteins?

A
  1. Chromatography
  2. Electrophoresis
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25
Q

How is chromatography used to analyse proteins?

A
  1. A small sample of the amino acid mixture is spotted near the bottom of some chromatographic paper
  2. This position (the origin) is clearly marked in pencil
  3. The paper is put in a chromatographic tank containing a small volume of some solvent, ensuring that the spot is above the level of the solvent
  4. The solvent rises by capillary action and passes over the spot
  5. Amino acids in the spot will distribute themselves to different extents because they move up the paper in different speeds and become spread out
  6. When the solvent reaches the top of the paper its final position is marked (solvent front)
  7. The paper is removed and developed by sparying with ninhydrin
  8. The ninhydrin makes the amino acids purple and visible and they can be distinguished as separate spots up the length of the paper
    - The position of each amino acid can be expressed as an Rf value (retention factor): (distance moved by amino acid)/(distance moved by solvent)
    - If some amino acids are not separated, the paper can be rotated 90° and the procedure can be repeated with another solvent, this way the rest will spread too
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26
Q

How is electrophoresis used to analyse proteins?

A
  • Based on the movement of charged particles in an electric field
  • Amino acids carry different charges and can be separated by this means when placed in a buffered solution
    1. A polyacrylamide gel is used and the amino acid mixture is placed in wells in the centre of the gel
    2. An electric field is applied.
    3. Depeding on the pH of the buffer used, different amino acids will move at different rates towards the oppositely charged electrodes
    4. At their isoelectric point, amino acids will not move as they carry no net charge
    5. When the separation is complete they can be detected by a stain or under UV light and identified from their position using data tables
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27
Q

What are the major functions of proteins in the body?

A
  1. Structural proteins
  2. Enzymes
  3. Hormones
  4. Immunoproteins
  5. Transport proteins
  6. Energy source
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28
Q

What are examples of structural proteins?

A
  1. Keratin
    - Protective covering in hair and finger nails
  2. Collagen
    - Connective tissue in skin and tendons
  3. Myosin
    - Contractile action in muscles to bring about movement
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29
Q

What is an example of a storage molecule?

A

Casein

  • Fod substance in milk
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30
Q

What do carbohydrates consist of?

A

Carbon, hydrogen, and oxygen

(H and O are always in the same ratio, 2:1)

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31
Q

What are carbohydrates used for in the human body?

A
  1. Energy source (glucose and fructose)
  2. Energy reserves (glycogen)
  3. Precursors for other biologically important molecules
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32
Q

What are the structural features of monosaccharides?

A
  • Contain a carbonyl group (C=O)
  • At least two –OH groups
  • Have the empirical formula CH2O
  • Ring structures are either α or β
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33
Q

What are the two most common isomers of C6H12O6?

A

Glucose and fructose

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34
Q

Draw the straight-chain structural formulas of glucose and fructose

A
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35
Q

Draw the ring structural formulas of glucose and fructose

A
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36
Q

Draw the structural formulas of α-glucose and β-glucose

A

In α the –OH group at C1 is below the plane of the ring

In β the –OH group at C1 is above the plane of the ring

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37
Q

What is a glycosidic link?

A

The link between monosaccharides. Lies between the C1 and C4 of the separate molecules

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38
Q

How can disaccharides be hydrolysed into two monosaccharides?

A

By acid hydrolysis or enzyme-catalysed reaction

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39
Q

How are lactose, maltose, and sucrose condensed from monosaccharides?

A

Lactose = β-glucose + β-galactose

Maltose = α-glucose + α-glucose

Sucrose = α-glucose + β-fructose

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40
Q

How are starch, glycogen, and cellulose condensed from monomers?

A

Starch = α-glucose monomers condensed together

Glycogen = α-glucose monomers

Cellulose = β-glucose monomers

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41
Q

What is starch?

A
  • A polymer of α-glucose, used as the main storage carbohydrate in plants
  • A mixture of two separate polysaccharides: amylose and amylopectin
  • Amylose is a straight-chain polymer with 1-4 α-glucose linkages
  • Amylopectin is a branched polymer with both 1-4 and 1-6 α-glucose linkages
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42
Q

What is glycogen?

A
  • A polymer of α-glucose
  • The main storage carbohydrate in animals, found in the liver and muscles
  • Structure very similar to amylopectin
  • Much more 1-6 branches
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43
Q

What is cellulose?

A
  • A polymer of β-glucose
  • Structural material in plant cell walls
  • A linear polymer with 1-4 links known as β-glycosidic links
  • The cellulose chain forms an uncoiled linear structure
  • This enables the hydroxyl groups to form hydrogen bonds with the hydroxyls of other cellulose molecules lying parallel
  • Forms cables, known as microfibrils, of parallel chains that give it its rigid structure
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44
Q

Compare the structural properties of starch and cellulose

A
  • Both are polymers of glucose units
  • Starch has two forms: amylose and amylopectin
  • Cellulose has one structure
  • Starch has α-1,4 and α-1,6 linkages
  • Cellulose has β-1,4 linkages
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45
Q

Why cannot humans digest cellulose?

A

The β-1,4 linkages between the monomers can be hydrolysed by the enzyme cellulase, which is absent in most animals

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46
Q

What is dietary fibre?

A

Mainly plant material that is not hydrolysed by enzymes secreted by the human digestive tract but may be digested by microflora in the gut.

e.g. cellulose, hemicellulose, lignin, and pectin

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47
Q

Why is dietary fibre imporant in diet?

A
  • Beneficial to the health of the large intestine
  • The cellulose fibrils abrade the wall of the digestive tract and stimulate the lining to produce mucus
  • This helps in the smooth passage of undigested food through the gut
  • Helps to reduce conditions such as constipation, hemorrhoids, and irritable bowel syndrome
  • May be helpful in preventing the development of colorectal cancer
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48
Q

What are the three types of lipids found in the human body?

A
  1. Triglycerides (fats and oils)
  2. Phospholipids (lecithin)
  3. Steroids (cholesterol)
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49
Q

What is the difference between LDL and HDL?

A
  • Considered as bad cholesterol and good cholesterol, respectively
  • LDL (low density lipoprotein) gets stuck on the walls of the arteries

HDL (high density lipoprotein) protects against heart attach by carrying cholesterol away from the arteries

  • LDL main sources are saturated fats and trans fats
  • HDL main source is unsaturated fats
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50
Q

What is the composition of saturated fats in naturally occurring fats?

A
  • Contain a mixture of saturated, mono-unsaturated, and poly-unsaturated fatty acids
  • Are classified according to the predominant type of unsaturation present
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51
Q

What is the difference between saturated and unsaturated fatty acids?

A
  • Saturated fatty acids contain all single carbon–carbon bonds
  • Unsaturated fatty acids contain one or more double carbon–carbon bond in the hydrocarbon chain
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52
Q

What is a triglyceride?

A

An ester formed by condensation reaction between a glycerol and three fatty acids

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53
Q

What is glycerol?

A

A molecule of three carbon atoms, each of which bears an alcohol group

54
Q

What is a fatty acid?

A

A long chain carboxylic acid, R–COOH

55
Q

What defines the properties of triglycerides?

A
  1. The length of their hydrocarbon chain
    - Usually an even number between 14 and 22 carbons
  2. The number and position of carbon–carbon double bonds (affects its melting point)
    - No double bonds → saturated
    - One double bond → mono-unsaturated
    - Several double bonds → polyunsaturated
56
Q

What are saturated fatty acids and what are their properties?

A
  • All carbon–carbon bonds are single, 109.5° bond angles in between
  • This allows the molecules to pack closely together
  • This leads to strong van der Waals’ between them
  • As a result, they have high melting points and are solids at room temperature
  • Known as fats and are derived mostly from animals
  • E.g. butter and lard
57
Q

What are unsaturated fatty acids and what are their properties?

A
  • Contain one or more carbon–carbon double bonds with 120° angles
  • The angles cause kinks in the chains that make it harder for the molecules to pack closely together
  • Weaker intermolecular forces
  • Lower melting points, liquids at room temperature
  • Known as oils and are found mostly in plants and fish
  • E.g. corn oil and cod liver oil
58
Q

What are essential fatty acids?

A

Fatty acids that the body is unable to produce and must be obtained in the diet:

  1. linoleic acid (omega-6-fatty acid)
  2. linoleic acid (omega-3-fatty acid)
59
Q

Where can essential fatty acids be obtained from?

A
  • Omega-3 → green leaves
  • Omega-6 → seeds and vegetable oils
60
Q

Why are essential fatty acids essential?

A
  • They are involved in lowering blood pressure
  • Play a role in lowering LDL cholesterol
  • Essential in many other metabolic processes
61
Q

What is iodine number?

A

The number of moles of I2 reacting with one mole of fat/oil indicates the number of double bonds present in the fat/oil molecule

(the unsaturated bonds undergo addition reactions)

62
Q

What are trans fats?

A
  • Fats produced industrially by adding hydrogen to decerase the degreee of unsaturation
  • As a result has a higher melting point and solids at room temperature
  • Have a longer shelf life
  • e.g. margarines and fatty acids
63
Q

What are the health effects of trans fats?

A
  • Raise the level of LDL cholesterol
  • Reduce the blood levels of HDL cholesterol
64
Q

How are fats digested?

A
  • Insoluble molecules so cannot be transported in the blood
  • Broken down to fatty acids and glycerol
  • Hydrolysis with the help of lipases (enzymes)
  • The slowest molecules to be broken down (takes hours)
65
Q

Why do lipids have a higher energy value than carbohydrates?

A
  • Lipids are less oxidised than carbohydrates and so can effectively undergo more oxidation, thus release more energy per unit mass
  • A gram of lipid releases almost twice as much energy as a gram of carbohydrate
66
Q

Describe phospholipids

A
  • Derived from fatty acids and glycerol (two fatty acids and one glycerol)
  • Also one phosphate group condensed
  • e.g. lecithin
  • Hydrophilic head and two hydrophobic tails
  • Spontaenously form a phospholipid bilayer → maximises the interactions between polar groups and water, while creating a non-polar, interior
  • Basis of membrane structure
67
Q

What are steroids?

A
  • Lipids with a structure consisting of four fused rings (backbone)
  • e.g. cholesterol
68
Q

What are the important roles of lipids in the body?

A
  1. Energy storage
  2. Insulation and protection of organs
  3. Steroid hormones
  4. Structural component of cell membrane
  5. Omega-3 poly-unsaturated fatty acids reduce the risk of heart disease
  6. Poly-unsaturated fats may lower levels of LDL cholesterol
69
Q

What are the negative effects of lipids in the body?

A
  • Increased risk of heart disease from LDL and trans fatty acids
  • Obesity
70
Q

What is the difference between micronutrients and macronutrients?

A

Micronutrients are substances required in very small amounts (mg or µg) and that mainly function as a co-factor of enzymes (<0.005% of body weight)

Examples include vitamins and (FADEKCB) and trace minerals (Fe, Cu, F, Zn, I, Se, Mn, Mo, Cr, Co, B)

Macronutrients are chemical substances that are required in relatively large amounts (>0.005% body weight)

Examples include proteins, fats, carbohydrates, and minerals (Na, Mg, K, Ca, P, S, Cl)

71
Q

What are vitamins?

A

Organic micronutrients

72
Q

What are the differences between water- and fat-soluble vitamins?

A
  • Water-solubles are transported directly in the blood and excesses are filtered out by the kidney and excreted (C and B)
  • Fat-solubles are slower to be absorbed and excesses tend to be stored in fat tissues where they can produce side-effects (F,A,D,E,K)
  • Differences in their structure determine the solubility differences
  • Water-solubles have polar bonds and the ability to form hydrogen bonds with water
  • Fat-solubles are mostly non-polar molecules with long hydrocarbon chains or rings
73
Q

What is vitamin A (retinol)?

A
  • A fat soluble vitamin
  • Hydrocarbon chain and ring are non-polar and influence the solubility more than the one polar –OH group
  • Involved in the visual cycle in the eye and particularly important for vision in the dark
74
Q

What is vitamin C (ascorbic acid)?

A
  • A water soluble vitamin
  • Several –OH groups enable hydrogen bonds with water
  • Cofactor in some enzymic reactions
  • Important in tissue regeneration following injuries
  • Helps give resistance to some diseases
75
Q

What is vitamin D (calciferol)?

A
  • A fat soluble vitamin
  • Predominantly a hydrocarbon molecule with four non-polar rings and only one –OH group
  • Chemically similar to cholesterol
  • Stimulates the uptake of calcium ions by cells and so is important in the health of bones and teeth
76
Q

What are examples of micronutrient deficiencies?

A
  1. Iron → anemia
  2. Iodine → goitre
  3. Vitamin A → xerophtalmia, night blindness
  4. Vitamin B3 → pellagra
  5. Vitamin B1 → beriberi
  6. Vitamin C → scurvy
  7. Vitamin D → rickets
77
Q

What are examples of macronutrient deficiencies?

A
  1. Proteins → marasmus and kwashiorkor
78
Q

What are the causes of malnutrition?

A
  1. Lack of distribution of global resources
  2. Depletion of nutrients in the soil and water cultures through soil erosion
  3. Lack of education about, or understanding of, the importance of a balanced diet
  4. Over-processing of food for transport and storage
  5. The use of chemical treatments such as herbicides in food production
79
Q

What aer the solutions for malnutrition?

A
  1. Providing food rations that are composed of fresh and vitamin- and mineral-rich foods
  2. Adding nutrients missing in commonly consumed food
  3. Genetic modification of food
  4. Providing nutritional supplements
  5. Providing selenium supplements to people eating foord grown in selenium-poor soil
80
Q

What are hormones?

A

Chemical messengers that stimulate different actions around the body

81
Q

Where do hormones come from?

A

They are secreted directly into the blood by the endocrine system (endocrine glands)

82
Q

What is anti-diuretic hormone (ADH)

A
  • A short peptide
  • Produced in the pituitary gland
  • Target cells are kidney tubules
  • Increases uptake of water, so raises the concentration of urine; important in the control of osmotic potential of the blood
83
Q

What is thyroxine?

A
  • A modified amino acid containing iodine
  • Secreted by thyroid gland
  • Target cells include all cells
  • Regulate the basal metabolic rate, growth, and development
84
Q

What is aldosterone?

A
  • A steroid
  • Produced in the adrenal cortex
  • Target cells are kidney cells
  • Increases uptake of Na+ by the kidneys and is important in the control of Na+ and K+ ratios in fluids; raises blood pressure
85
Q

What is adrenaline (epinephrine)?

A
  • A modified amino acid
  • Produced in the adrenal medulla
  • Target cells are many parts of the body including muscles, brain, circulatory, and digestive systems
  • Raises blood glucose level, increases rate and force of heartbeat, and increases blood supply to heart and skeletal muscles
86
Q

What is insulin?

A
  • A protein
  • Produced by the pancreas
  • Target cells are all cells, especially liver cells
  • Decreases blood glucose level by increasing uptake and utilisation by cells; increases glucose to glycogen conversion in the liver
87
Q

What are estrogen (estradiol) and progesterone?

A
  • Steroids
  • Produced in the ovaries
  • Target cells are many parts of the body; especially the uterus lining during pregnancy
  • Develop secondary female characteristics, control mestrual cycle, growth and development of the placenta and fetus
88
Q

What is testosterone?

A
  • A steroid
  • Produced in the testes
  • Targets many parts of the body
  • Develop male secondary sexual characteristics
89
Q

Compare the structures of cholesterol and the sex hormones

A
  • Common steroid backbone
  • The different side chains and functional groups give the different properties
  • Progesterone differs from testosterone only by having a ketone group instead of an alcohol
  • Estrogen has an aromatic ring (benzene) and two alcohol groups
90
Q

How do oral contraceptives function?

A
  • Work by preventing ovulation
  • Contain a mixture of progesterone and estrogen
  • Act to suppress the secretion of FSH and LH
  • Stimulate the hormonal conditions of pregnancy
  • Taken every day for three weeks and then stopped for one week
  • Also morning after pills, which contain higher concentrations to prevent fertilisation from occurring after unprotected intercourse
91
Q

Outline the medical use of steroids

A
  • Female hormones used in medications prescribed to women at menopause to alleviate some of the unpleasant symptoms → HRT (hormone replacement therapy)
  • Male hormones used in treatment of disorders of the testes and breast cancer or medically help to gain weight after debilitating diseases
92
Q

Outline the abuse of steroids

A
  • Anabolic steroids have been used by athletes to build up muscle and increase endurance
  • Can cause many changes in secondary sexual characteristics: changes in hair distribution, sexual desire, and fertility
  • Hormones are toxic to the liver
  • Increased risk of liver cancer
93
Q

What are anabolic steroids?

A

Male hormones that promote tissue growth of especially of muscles

94
Q

Describe the characteristics of enzymes

A
  • Proteins, typically containing several hundred amino acids
  • Well-defined tertiary structure → globular proteins
  • Soluble in water
  • Structure determined by the interactions between all its R groups and is essential for its function
  • Some enzymes are made of more than one polypeptide and so have a quaternary structure
  • Some require the binding of non-protein molecules (co-factors) for activity
95
Q

What are co-factors?

A

Organic or inorganic molecules that aid enzymes in their action

e.g. vitamins, metal ions

96
Q

How does an enzyme function?

A
  • Increase the rate of a chemical reaction without undergoing chemical change itself
  • The enzyme lowers the activation energy of the reaction → enables the reaction to occur more quickly at the same temperature
  • Forms a temporary binding to the substrate (enzyme substrate complex) that occurs at the active site
  • Interactions such as hydrophobic interactions, dipole-dipole attractions, hydrogen bonds, and ionic attractions form between the active site and the substrate
  • The binding puts a strain on the substrate molecule and its bonds
  • The enzyme facilitates the breaking and the forming of bonds
  • Once the substrate has reacted, the product no longer fits in the active site and so detaches
  • The enzyme is released unchanged and is able to catalyse further reactions
97
Q

What is meant by the induced fit model of enzyme action?

A
  • Instead of being a rigid active site, the site changes it shape when a substrate binds to it
  • The active site undergoes conformational changes, shaping itself to allow a better fit
  • Think of a hand and glove
98
Q

What can be deduced from the substrate concentration–rate of reaction graph?

A
  1. At low substrate concentration, the rate of the reaction is proportional to the substrate concentration; enzyme is available to bind to the substrate
  2. As the substrate concentration is increased, the rate decreases and is no longer proportional; some of the enzyme has its active sites occupied by substrate and is not available
  3. At high substrate concentration, the rate is constant and independent of the substrate concentration; the enzyme is saturated with the substrate and is working at full speed
99
Q

What is meant by the maximum velocity of enzyme activity?

A
  • The maximum velocity of the enzyme under the conditions of the experiment
  • Varies greatly between enzymes
  • Affected by pH and temperature
100
Q

What is the Michaelis constant, Km?

A
  • The substrate concentration at which the reaction rate is equal to one half of its maximum value
  • The substrate concentration when the rate is Vmax/2
  • Varies with pH and temperature
  • The value gives information about the affinity of the enzyme for its substrate
  • A low value of Km means that the reaction is going quickly even at low substrate concentration
  • A high value means that the enzyme has a lower affinity for its substrate
101
Q

What are factors that affect enzyme activity?

A

Conditions that affect the enzyme’s shape and binding ability

  1. Temperature
  2. pH
  3. Presence of heavy-metal ions
102
Q

How does temperature affect enzyme activity?

A
  • Rate of a reaction is increased y a rise in temperature due to the increase in the average kinetic energy of the particles (more collisions)
  • Only true up to a certain temperature (≈40°C)
  • After this the enzyme becomes denatured
  • Lowering temperature deactivates an enzyme but it is reversible as it does not change the tertiary structure
103
Q

What is the effect of pH on enzyme activity?

A
  • Represents changes in the hydrogen ion concentration
  • Alters the ionic charge in the amino acids
  • Alters the attractive forces stabilising the molecule, hence its shape and ability to bind a substrate
  • The specific effect depends on the pKa and pKb of the R groups
  • Different for each enzyme
  • Usually there is a clear optimum value
  • Changing pH is one way of controlling enzymatic activity
104
Q

How do heavy-metal ions affect enzyme activity?

A
  • When metals are present as positive ions they react with sulfydryl groups (–SH)
  • Form a covalent bond with the sulfur atom displacing a hydrogen ion
  • Disrupts the folding of the protein, which may change the shape of the active site and its ability to bind susbtrates
  • A form of non-competitive inhibition
  • This is why lead, copper, mercury, and silver are poisonous
105
Q

What are the two types of inhibitors?

A
  1. Competitive inhibitors (bind to the active site)
  2. Non-competitive inhibitors (bind away from the active site)
106
Q

What are competitive inhibitors?

A
  • Chemicals chemically similar to the substrate that compete with the substrate for the binding position
  • Block the active site and make it unavailable to the substrate
  • Increasing concentration of substrate reduces the effect of inhibition
  • Vmax is not altered as there is a substrate concentration where full activity of the enzyme can be achieved
  • Km is increased
107
Q

What are non-competitive inhibitors?

A
  • Chemicals that bind reversibly away from the active site
  • Cause a conformational change in the protein change that alters the active site, inhibiting its ability to bind to substrates
  • Increasing the substrate concentration will not reduce the effect of inhibition
  • Vmax is reduced and cannot be restored
  • Km is unchanged because the uninhibited enzymes are perfectly functional
108
Q

Compare the curves of competitive and non-competitive inhibition to an uninhibited reaction

A
109
Q

Compare inorganic catalysts and biological catalysts (enzymes)

A

Enzyme VS inorganic catalyst

1. Structure:

All are proteins VS varied structure

2. Mode of action:

Both lower the activation energy

3. Effect on equilibrium constant:

No effect on either one

4. Specifity:

Highly specific VS much less specific

5. Saturation:

Reach a maximum reaction rate VS do not show reactant saturation

6. Phase:

Homogenous catalysts VS homo- and heterogenous

7. Speed:

Very fast VS pretty slow

8. Regulation by chemicals:

Regulated by inhibitors and activators VS not regulated

9. Sensitivity to temperature and pH:

Sensitive VS not sensitive

110
Q

What are nucleic acids?

A

Polymers made up of nucleotides

111
Q

What are the parts of a nucleotide?

A
  1. A phosphate group PO4-3
  2. A pentose sugar C5H10O5
  3. An organic nitrogenous base (A,G,C,T,U)
112
Q

What are the required functions of a DNA molecule in order for it to carry out its function?

A
  1. Must be a very stable molecule, able to retain its precise chemical structure in cell conditions
  2. It must contain some code that stores genetic information
  3. It must be able to replicate
113
Q

What are purines and which bases are classified as purines?

A
  • Large bases that contain two fused rings
  • Adenine and guanine
114
Q

What are pyrimidines and which bases are classified as pyrimidines?

A
  • Smaller bases that contain a single ring
  • Cytosine, thymine, and uracil
115
Q

How is a nucleotide formed?

A
  • The pentose, phosphate, and base are condensed together
  • The base always condenses to the C1 of the sugar
  • The phosphate condenses to the C5 of the sugar
116
Q

What is the structural difference between DNA and RNA?

A
  • RNA has ribose as its pentose sugar; DNA has deoxyribose
  • Deoxyribose lacks an oxygen atom on C2
  • RNA has uracil instead of thymine as one of its bases
  • RNA is a single-strand nucleic acid; DNA is a double-strand acid
117
Q

How are polynucleotides (strand of nucleotides) formed?

A
  • The phosphates and sugars condense forming covalent bonds (phosphodiester links)
  • The phosphate links to either the C5 or to the –OH group at the C3 of the sugar
118
Q

How are adenine and thymine (or uracil) bonded together?

A

By two hydrogen bonds:

119
Q

How are guanine and cytosine bonded together?

A

By three hydrogen bonds:

120
Q

Describe the structure of DNA

A
  • Double helical structure
  • Two strands held together by hydrgen bonds
  • Sugar-phosphates are on the outside and bases on the inside
  • Anti-parallel, run in opposite directions (3’ → 5’ and 5’ → 3’)
121
Q

How does DNA achieve high stability?

A

Achieved by the fact that it maximises hydrophobic interaction between the stacked bases in the middle of the molecule, while allowing polar and charged groups in the sugar-phosphate backbone to interact with the aqueous solution

122
Q

Where does the genetic code of DNA come from?

A

The sequence of bases in the polynucleotide strand (infinite variety is possible)

123
Q

What are the main functions of DNA?

A
  1. Contains the inherited genetic material
  2. Directs mRNA synthesis (transcription)
  3. Directs protein synthesis (translation) through mRNA using codons
124
Q

What are the stages in DNA profiling?

A
  1. DNA is extracted from the source (blood, semen, hair, saliva)
  2. The DNA is cut into small pieces using restriction enzymes
  3. Short tandem repeats (STRs) are produced from the pieces of DNA. STRs are unique for every individual
  4. Polymerase chain reaction (PCR) is used to amplify the unique regions of DNA by making multiple copies
  5. The DNA fragments are separated and detected using gel electrophoresis. Due to its phosphate groups, DNA carries a negative charge and moves to the positive terminal.
  6. The distance travelled depends on the size of the DNA fragments: shorter fragments move further than longer fragments
  7. The sheet used is treated with radiation (32P) and exposed using X-ray film
  8. An autoradiogram is produced, showing the positions of the fragments as dark bands. The pattern of these bands is the DNA profile
125
Q

What are the applications of DNA profiling?

A
  1. To identify victims whose bodies are not recovered from the scene of an accident or crime.
  2. In forensic cases to identify the suspect.
  3. To confirm biological relationships between individuals. (determining paternity or family relationships)
  4. To determine relationships between populations (evolution, migration, ecology)
126
Q

What is respiration?

A

The process of chemical breakdown of energy-rich molecules in cells with the release of energy. Takes place in all living cells all the time

127
Q

Compare aerobic and anaerobic respiration in terms of oxidation and reduction, and energy released

A

In aerobic respiration, glucose is converted into pyruvate, which, in the presence of oxygen, changes to carbon dioxide and water. Glucose undergoes oxidation and oxygen undergoes reduction. Lots of energy released

In anaerobic respiration, pyruvate is converted to lactate in humans, and to ethanol and carbon dioxide in yeast. Little energy released

128
Q

What are cytochromes?

A
  • Electron transport carriers
  • Proteins that are embedded in a membrane
  • Become successively reduced and then re-oxidised as they accept and pass on the electrons
  • Are organised in sequence correspoinding to their electrode potentials
  • Electrons flow down an electrochemical gradient
  • Contain a non-protein component called a prosthetic group (a ring containing Fe)
  • The iron changes its oxidation state from +2 to +3 when oxidised
129
Q

Why is cyanide poisonous?

A
  • It acts at the end of the electron transport chain
  • Inhibits the enzyme cytochrome oxidase and blocks the whole chain
  • Prevents aerobic respiration from occurring
130
Q

How does haemoglobin carry oxygen?

A
  • Uptake of oxygen is not accompanied by a change in the oxidation number
  • The oxygen is bound in molecular form, O2, in the structure in a complex way that involves a conformational shift of the protein
  • Molecules are called oxygenated
  • Each oxygenated haemoglobin carries four molecules of oxygen

Chemistry (13 decks)

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