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IB Chem: HL Human Biochemistry

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Mirza Ma

on 11 January 2014

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Transcript of IB Chem: HL Human Biochemistry

Chem Option B: Human Biochemistry
Nucleic Acids

B.1.1 Calculate the energy value of a food from enthalpy of combustion data
Micro- & Macro-
Specific heat capacity of water = 4.18 J g–1 K–1.

∆T = (29.0 – 20.5) / 8.5(°C);
energy (released by dry bread) = 600 × 4.18 × 8.5 = 21318 / 2.1 × 104 (J);
energy (released by 100 g of dried bread) = 21318 × 50 = 1065900 / 1.1 × 106 (J);
energy released = = 1.1 × 103 (kJ per 100 g);
The combustion of 2.00 g of dried bread in a food calorimeter raised the temperature of 600 cm3 water from 20.5 °C to 29.0 °C. Calculate the energy content of bread in kJ per 100 g.
B.2.1 Draw the general formula of 2-amino acids.
B.2.2 Describe the characteristic properties of 2-amino acids. Include (isoelectric point, formation of a zwitterion and buffer action).
B.2.3 Describe the condensation reaction of 2-amino acids to form polypeptides.
B.2.4 Describe and explain the primary, secondary (α-helix and β-pleated sheets), tertiary and quaternary structure of proteins.
B.2.5 Explain how proteins can be analysed by chromatography and electrophoresis.
B.2.6 List the major functions of proteins in the body.
B.3.1 Describe the structural features of monosaccharides.
B.3.2 Draw the straight-chain and ring structural formulas of glucose and fructose.
B.3.3 Describe the condensation of monosaccharides to form disaccharides and polysaccharides.
B.3.4 List the major functions of
in the human body.
B.3.5 Compare the structural properties of starch & cellulose, + explain Y humans can digest starch but not cellulose.
B.3.6 State
what is meant by the term dietary fibre
B.3.7 Describe the importance of a diet high in dietary fibre.
Include energy source (glucose), energy reserves (glycogen) and precursors for other biologically important molecules.
pretty much sums it all up...
Condensation Reaction- Reaction between 2

), formed when an amine group of 1

of another
form a

, releasing H­­2O.

- molecule composed of 2
- chain of
that, when folded, form proteins
· R groups of
have different
points (pH where charge is 0)
· Similar size molecules can be separated using charge in individual
· Proteins placed in

, +tive R-groups <=> -tive pole of the magnet, & -tive R groups <=> to the +tive pole
· Movement stops when charge reaches 0 (
point is reached)
· Also works with a
pH gradient
are treated with a locating reagent to colorize them. A small amount of the mixture is placed at the origin.
Stationary Phase- does not move (paper)
Mobile Phase- travels taking some sample with it (solvent)
Movement of peptide fragments determined by size.

Rf= distance traveled by amino acid
distance traveled by solvent

Specific amino acids have characteristic Rf values.
Proteins carry out many important functions in the body
=> providing structure
acting as enzymes (biological catalysts)
immunoproteins (as antibodies in poviding protection)
transportation protens
+ energy soource if carbs/fats unavailable.
structural proteins
(e.g. collagen),
(e.g. insulin),
proteins (e.g. hemoglobin) and as an
Monosaccharides contain a carbonyl group (C=O) & at least two –OH groups, and have the empirical formula CH2O.
electrophoresis simulation
6C = hexoses
5C = pentoses
4C = tetrose
3C = triose
Straight chain- carb structure when dry (powder)

Ring- carb structure when wet (in aqueous solution)
Alpha- When the –OH on the rightmost carbon (C1 in glucose, C2 in fructose) is below the plane of the ring

Beta- When the-OH on the rightmost carbon is in line with/above the plane of the ring

Condensation- combining 2+ monosaccharides to form disaccharides/polysaccharides. Usually involves the loss of a water molecule
B-glucose + B-galactose

a-glucose + a-glucose

a-glucose + a-gructose

found in milk

product from starch digestion

cane sugar; the most common form of sugar added to food
Monosaccharide units
Occurence in the body


Examples include:
• disaccharides - lactose, maltose & sucrose
• polysaccharides - starch (polymer of
), glycogen (polymer of
) & cellulose (polymer of
Use of Carbs in the body:
to other important biological molecules



Why can starch be digested but cellulose not?
Starch is composed of
, bringing Oxygen atom opposite the CH2OH group (where human enzymes can digest them). Cellulose is composed of
, bringing Oxygen atom alongside CH2OH where it can
only be digested by cellulase
(found in fungi, bacteria, and protests)
Dietary fibre are substances which cannot be digested by the body.

Examples include cellulose, hemicellulose, lignin and pectin
High fiber diets prevent conditions like Diverticulosis
Irritable bowel syndrome
Chron’s disease.
Dietary fiber aids in digestion
B.4.1 Compare the composition of the 3 types of lipids found in the human body.
B.4.2 Outline the difference between HDL and LDL cholesterol and outline its importance.
B.4.9 Describe the important roles of lipids in the body and the negative effects that they can have on health.
B.4.3 Describe the difference in structure between saturated & unsaturated fatty acids.
B.4.6 Describe the condensation of glycerol and three fatty acid molecules to make a triglyceride.
B.4.7 Describe the enzyme-catalysed hydrolysis of triglycerides during digestion.
B.4.4 Compare the structures of the 2 essential fatty acids linoleic (omega–6 fatty acid) and linolenic (omega–3 fatty acid) & state their importance.
B.4.8 Explain the higher energy value of fats as compared to carbohydrates
LDL cholesterol (Bad cholesterol)- Since the proportion of

, the lipids
cannot move as easily
. It is harder to transport, and
tends to clot
to arterial walls = "atherosclerosis" (increase risk of heart attack/stroke)
HDL cholesterol (Gd cholesterol)- High Density Lipoprotein. Since the proportion of
, the lipid can
move more easily
around the bloodstream. Easier to transport &
doesn't clot as much
The longer a fat is, the more van der walls forces and the higher the melting point
Omega- fatty acids= the no. represents how many C's from the end of the chain there are until the 1st = bond is located. e.g. omega-3 has a = bond 3 carbons away from the end.

Convert so that it is in the molecular formula:
C17H31COOH à C18H32O2
Determine the number of double bonds.
A saturated fat with 18 carbons should have 36 hydrogens. This compound has 32. Therefore, the 4 missing hydrogens suggests 2 double bond
Set up a molar ratio.
For every 1 mole of C17H31COOH, you’ll need 4 moles of iodine. However, since iodine only comes in the I2 form… The ratio of C17H31COOH to I2 will be 1:2
Set up a mass ratio.
Molar mass C17H31COOH = 280 g mol-1 & Molar mass I2 = 254 g mol-1 x 2 mol. Ratio will be 280 g to 508 g
Find the amount of Iodine needed to react with 100g of the fatty acid
Iodine Number = mass of I2 needed to satisfy a particular reaction. Used to identify the number of C=C in a particular unsaturated fat.
B.4.5 Define the term iodine number & calculate the no. of C=C = bonds in an unsaturated fat/oil using addition reactions.
Using an Iodine Number
: Example: Linoleic acid has the formula C18H22O2. What is the iodine number of this acid?
ANSWER: 181 g. iodine number is 181.
B.6.1 Outline the production & function of hormones in the body.
B.6.4 Outline the use and abuse of steroids.
B.6.2 Compare the structures of cholesterol and the sex hormones.
B.6.3 Describe the mode of action of oral contraceptives.
B.7.1 Describe the characteristics of biological catalysts (enzymes)
B.7.3 Describe the relationship between substrate concentration and enzyme activity
B.7.4 Determine V max and the value of the Michaelis constant (Km) by graphical means and explain its significance.
B.7.5 Describe the mechanism of enzyme action, including enzyme substrate complex, active site and induced fit model.
B.7.7 State and explain the effects of heavy metal ions, temperature changes & pH changes on enzyme activity.
Nucleic Acids
B.8.1 Describe the structure of nucleotides and their condensation polymers (nucleic acids or polynucleotides).
B.8.2 Distinguish between the structures of DNA and RNA.
B.8.3 Explain the double helical structure of DNA.
B.8.5 Outline the steps involved in DNA profiling and state its use.
both contain 18-C chains

Linoleic acid
contains 2C = bonds in which the closest = bond to the end of the methyl group is 6C atoms away

Linolenic acid
contains 3 C = bonds with the closest one to the end of the methyl group is 3 C atoms away
Examples include triglycerides (fats and oils), phospholipid (lecithin) and steroids (cholesterol).
2 molecules link together with the elimination of a small molecules (like water). Esters are formed from the condensation reaction of an organic acid & an alcohol in which the ester group connects the 2 molecules together.
Enzymes are protein molecules that are able to catalyse a biological reaction.
Micronutrients are substances required in very small amounts (mg or µg) and that mainly function as a co-factor of enzymes (<0.005% body weight). Examples include vitamins and trace minerals (Fe, Cu, F, Zn, I, Se, Mn, Mo, Cr, Co and B).
Macronutrients are substances that are required in relatively large amounts (>0.005% body weight). used to provide energy to body + build & maintain structure. Examples include proteins, fats, carbohydrates and minerals (Na, Mg, K, Ca, P, S and Cl).
B.5.1 Outline the difference between micronutrients & macronutrients.
Examples include:
• water-soluble—vitamins B and C
• fat-soluble—vitamins A, D, E and K.

Vitamins with long hydrocarbon groups

= fat-soluble
Vitamins with polar OH groups
= water-soluble
B.5.2 Compare the structures of retinol (Vitamin A), calciferol (vitamin D), and ascorbic acid (Vitamin C).
B.5.4 Discuss the causes and effects of nutrient deficiencies in different countries and suggest solutions.
Hormones are chemical messangers that are produced in one area and are sent to another. Hormones perform a variety of functions, such as negative feedback (a high level of a hormone will inhibit its own production).
Ascorbic Acid
- water soluble
- cofactor in some enzymic reactions
- important in tissue regeneration following injury
- helps give resistance to some diseases
- several -OH groups enable H bonds to form with water
- fat soluble
- mostly hydrocarbon molecule with 4 non-polar rings and only 1 -OH group
- chemically similar to cholesterol
- stimulates calcium ion uptake by cells => important in health of teeth + bones
- fat soluble
- hydrocarbon chain & ring non-polar & influence solubility more than the 1 -OH group
- involved in the visual cycle in the eye & particularly important for vision @ low light intensity
Vitamin C
Vitamin D
Vitamin A
Micronutrient deficiencies include:
• iron - essential to hemoglobin. lack=>anemia (fatigue, poor endurance, lowered immunity)
• iodine - needed for hormone thyroxine synthesis regulating metabolic rate. lack => goitre
• retinol (vitamin A) - healthy skin, good eyesight, protection against toxins as antioidant. deficiency => xerophthalmia (night blindness)
• niacin (vitamin B3) => pellagra: dermatitis/diarrhoea/dementia
• thiamin (vitamin B1) => beriberi: weight loss/fatigue/swelling
• ascorbic acid (vitamin C) => scurvy: bleeding gums/dark spots on skin
• calciferol (vitamin D) => rickets: softened & deformed bones
• selenium => Kashin-Beck disease: atrophy & degeneration of cartilage

- lack of distribution of global resources
- low nutrients in soil & water cultures by soil erosion
- lack of education of importance of balanced diet
- over-processing of food for transport and storage
- use of chemical treatments like herbicides in food production

Solutions include:
- providing staple foods with micronutrients
- providing nutritional supplements
- improve nutrient content by genetic modification
- labelling of foods with content info
- education regarding balanced diet and choices
Macronutrient deficiencies include:
• protein - marasmus in infants (failure to gain weight => weight loss & emanciation) and kwashiorkor young childrenwhose diet is ^ in starch but low in protein.
B.5.3 Deduce whether a vitamin is water- or fact-soluble from its structure.
Water-soluble vitamins
are transported directly into
& excess
filtered by kidneys
Polar bonds
and ability to form H bonds with water.

Fat-soluble vitamins

slower to be absorbed
tend to be
stored in fat tissues
where they can produce serious side-effects.
Mostly non-polar
molecules with long hydrocarbon chains/rings.
- produced in endocrine glands (have no duct so secrete hormone directly into the blood)
- circulate through body bringing about responses only in cells with receptors for them = 'target cells'.
modified amino acids/fatty acids
book version of Human Biochem
Androgens = male sex hormones

Estrogens = female sex hormones

Pregestins = present in male+female

All have similar
polycyclic structure
to cholesterol however the
functional groups
on the sex hormones are different and these give rise to
different functions
Steroids are a family of polycyclic ring structured chemicals with a common carbon molecular framework.

The pill mimics pregnancy. The pill is a combination of progesterone and estrogen that work to inhibit release of FSH (follicle stimulating hormone) & LH (luteinizing hormone). This results in the ovaries not being stimulated, thus not releasing an egg. This prevents ovulation because the body thinks it is pregnant.
Most effective contraception is the oral conception which prevents ovulation - the release of an unfertilized ovum.
Steroids stimulate muscle growth & muscle mass. This is beneficial for cancer patients as it helps them recover their body weight.

Athletes have been known to abuse these drugs => improve their performance since they promote muscle build up.
In men, after taking large doses of anabolic steroids, effects of aging are observed: impotence/balness/urinating problems/smaller testes

In women, steroids affect 2ndary sex characteristics, build up of muscles and growth of facial hair.

Both sexes can develop violent tempers, ^ aggressive behaviour and ^ risk of diseases like liver tumours, ^ blood pressure & <3 attacks.

=> Anabolic steroids forbidden @ international athletic competitions. Competitors are given random urine tests to detect steroids/banned drugs and winners often require undergoing compulsory urine tests for such substances.
Hydrolysis of fats during digestion involves splitting the fats into their carboxylic acids & glycerol catalysed by the enzyme lipase
Fats have fewer oxygen atoms than carbohydrate molecules of corresponding molar masses, that is, these are less oxidized and thus more oxidation can take place. Therefore, more energy is released from the oxidation of fats compared with carbohydrates.
- contain stored energy => broken down => released in respiration.
adipose tissue
" =>protects organs like kidneys in fat under skin & insulates body
- lipids less oxidized than carbs so undergo ^ oxidation => ^ energy/unit mass when used as respiratory substrate
- sex hormones: testosterone/estrogen <= lipids in form of steroids. Bile acids, (aid digestion), are also steroid based
- phospholipids: major membrane components binding cells <= selective transport of metabolites across cell.
- help absorb fat-soluble vitamins e.g. A,D,E,K

Bad: Mostly to do with
of lipids
- insolubility (partly) => energy not so readily available as more reactions involved in breakdown.
- low solubility => deposition in walls of main blood vessels => "atherosclerosis" ~ ^ blood pressure => <3 disease
- adipose tissue => too rich lipid diet => OBESITY
- globular proteins (have many AAs)
- tertiary structure
- soluble in water
- exist in cell cytoplasm
- cofactors: have to have non-protein molecules binding to it in order to activate e.g. vitamins.

‘Induced fit’ model = active site not rigid as it can change its shape slightly => better fit for substrate. Weak interactions e.g. H bonds & ionic interactions => ES complex => decomposes => product & free enz. can be recycled. So when bound, catalytic action of enz. converts substrate to product of reaction.
Heavy Metal Ions
Competitive inhibition
The enzyme if a biological catalyst. The active site where the substrate binds provides an alternative pathways for the reaction that has a lower activation energy
the shape of active site is fixed so that only a particular substrate can fit, and hence react.
The active site does not necessarily have a fixed and rigid shape, but can change its shape to allow for a better fit between substrate and enzyme. This increase the surface area between the substrate and enzyme.
Induced fit model
^ temp = ^ rate of reactivity
(^ collisions freq. between enz & substrate molecules which have ^ than activation energy)

! beyond certain temp => change conformation of protein => disrupting bonds+forces responsible for tertiary structure

Too high = DENATURE (irreversible - shape change) Enzyme no longer able to bind to substrate @ active site => CATALYTIC activity diminished

Too low = DEACTIVATION (reversible - shape unchanged)
= changes in H ion concentration => affects equilibrium positions of ionization reactions

R groups of amino acids in enz structure <= change in ionic charge alters attractive forces stabilizing molecule => its shape + ability to bind to substrate

specific effect <= pKa & pKb values of R groups esp. @ active site

different enz have different values for optimum pH <= A way to control their activity

Extremes of pH => Denature enzyme
Occurs through
competitive inhibitors.
competitive inhibitor
has a chemical & structural similarity to the substrate &
with the substrate for the

@ active site
of the enzyme (it resembles the substrate in shape but
cannot react
). The rate of the reaction
slows down
<= active site is
by the
competitive inhibitor
, => active site
less accessible
to the substrate.
When a competitive inhibitor is added to an enzyme, Km will ^ <= more substrate needed to reach Vmax as reaction is slower <= active sites being occupied by the inhibitor.
non-C inhibitors bind to enzyme @ allosteric site => enzyme's active site to change shape => substrate can't bind => v the rate of reaction/enzyme activity decreasing Vmax.
When a non-competitive inhibitor is added to an enz. Km will remain unchanged <= non.C inhibitor doesn't bind to enz. on the active site => doesn't affect the way the substrate interacts with it. Even though the shape of the active site has changed, and Vmax has v, the Km is still based on 1/2 of the new Vmax.
Pb/Cu/mercury/silver => POISONOUS <= effect on enzymes

When they are +ve ions in body they react with sulfhydryl groups, -SH, in side chains of cysteine residues in the proteins => COVALENT BOND with S atom, displacing H atom. => distrupts folding of protein => change active site => ability to bind to substrate

B.7.6 Compare competitive inhibition & non-competitive inhibition.
Competitive inhibition
B.7.2 Compare inorganic catalysts & biological catalysts (enzymes)
@ low [substrate] rate of reaction is proportional to [substrate]; enzyme available to bind to substrate

as [substrate] ^ => rate decreases and is no longer proportional to the [substrate]: some enzymes are occupied by substrates

@ ^ [substrate] rate is constant independent of [substrate] because the enzymes are saturated
Michaelis - menten equation = mathematical expression describing kinetics of saturation effect.
- maximum velocity
- the Michaelis constant
Example: enzyme catalase => FAST. turnover rate of up to 100 000 molecules of its substrate H2O2 per second
units of rate
varies from enzyme to enzyme & with temp + pressure
rate of enzyme = turnover no. = no. of molecules of substrate that can be processed into products per enzyme molecule per unit of time
- [substrate] @ which reaction rate = 1/2 of Vmax
- [S] = Km when rate = Vmax/2
- units of concentration
- varies with pH & temp.
- Km => info abt affinity of enz. for its substrate (inverse relationship)
- low Km = quick reaction even @ low [substrate]
- ^ Km = enz. has low affinity for substrate
Nucleotides are the monomers => nucleic acids. They are made up of a nitrogenous organic base, 5-C sugar (a pentose sugar), and 1 or more phosphate groups. In DNA, the 5-C sugar molecule = deoxyribose. In RNA => ribose.
2 fused rings
single ring
- 2 polynucleotides (anti parallel) double stranded
- stable
- A=T C≡G
- deoxyribose sugar
- always in nucleus

- single stranded
- 3 forms in human cells: tRNA/mRNA/rRNA
- less stable and more short lived in cell
- A=U C≡G
- ribose sugar
- can cross membrane nucleus<=>cytoplasm
DNA profiling = breaking down of DNA to produce a characteristic "fingerprint" that belongs to only a certain person. The type of technique used depends on the sample & the amount of it available for analysis.
1. Extract the DNA from blood/sample (saliva, hair, semen) parent
2. DNA is cut => specific sequence of base fragments using restriction enzymes => act like scissors cutting DNA
3. DNA fragments separated by gel electrophoresis so DNA is -vely charged, & moves towards +tive anode. Shorter fragments move farther + faster than longer fragments => sample seperated by size. DNA then soaked up by an ultra thin nylon sheet.
4. Stained with a fluorescent dye/developed onto x-ray film so pattern which is the 'fingerprint' becomes visible.
5. Compare the the DNA profiles to look for similarities & differences.
B.8.4 Describe the role of DNA as the repository of genetic information, & explain its role in protein synthesis.
2 polynucleotide strands (anti-parallel - run in opposite directions) coiled around same axis => double helix with sugar phosphate backbone outside & nitrogenous bases inside.
- Stable molecule: able to retain its chemical structure in cell conditions <= H bonds between complementary base pairs A=T C≡G + hydrophobic interactions between stacked bases in interior of helix

- contain 'code' that stares genetic information <= sequence of bases is code

- be able to replicate + produce exact copy of itself <= base pairing between complementary strands provides replication of code.
Polynucleotides form by the
condensation reactions
where Ph groups react with ribose sugar molecules @
phophodiester links
between the sugar molecules. The backbone of the polynucleotide strand is an
alternating sequence of sugars and Ph groups
When cells divide during growth the genetic information has to be replicated intact. This genetic info. is condensed & stored in chromosomes, in nucleus. In humans, there are 23 pairs of chromosomes. DNA is unzipped as H bonds are broken, sugar base units will be be picked up from the aqueous solution => complementary new strand, identical to original.
Test Yourslef
The process of chemical breakdown of energy-rich molecules in cells with the release of energy. It takes place in all living cells all the time.
B.9.1 Compare aerobic & anaerobic respiration of glucose in terms of oxidation/reduction & energy released.
B.9.2 Outline the role of copper ions in electron transport and iron ions in oxygen transport.
DNA is the genetic material that an individual inherits from its parents. It directs mRNA synthesis transcription) and, through mRNA, directs protein synthesis (translation) using a triplet code.
In aerobic respiration, glucose => pyruvate, with presence of oxygen,
=> CO2 + H2O
. Overall, glucose undergoes
& oxygen undergoes
. Reactants are reduced and re-oxidized but oxygen acts as the
terminal electron acceptor

In anaerobic respiration, coenzyme must be
as without oxygen no further energy can be released. So, pyruvate => to
in human cells, but in plants/micro-organisms (yeast), pyruvate =>
ethanol & carbon dioxide
. This
but enables cell to
continue Glycolysis => small yield of energy
IRON in Oxygen Transport
CYTOCHROME (oxidase)
During last stage of aerobic respiration, H atoms are split into H ions: H+ and e-

Important in makin [gradient] => to convert released energy into chemical form as ATP

Terminal electron carrier = cytochrome oxidase which has Cu and Fe.
Many of the e- transport carriers are known as
which have a
non-protein component
called a
prosthetic group
(porphyrin ring with Fe ion known as
heme structure
). Iron changes ox. state from +2 to +3 as cytochrome is oxidized.
Pass through chain which has e- transport carriers (proteins in membrane) which become successively reduced & then re-oxidized as they accept & pass on e-. e- flow down electrochemical gradient as proteins are in sequence of electrode potential
is a carrier of molecular
. It has
4 polypeptides
each with a
heme group
allowing it to carry
4 oxygen
, the
does not change ox. state but rather the oxygen is bound in molecular form, O2, which involves a
conformational shift of the protein
. => "
" not oxidized. Binding of
coenzymes - organic molecules required by certain enzymes to carry out catalysis.
Cofactors are often classified as inorganic substances that are required for, or increase the rate of, catalysis.
- Enzymes catalyze / speed up biological reactions by providing an alternative pathway for the reaction with a lower activation energy.

- Enzymes must be highly specific for a particular reaction. This depends on their particular shape (i.e. secondary, tertiary, and quaternary structure)
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