Molecular Biology IB SL

Distinguish between DNA and RNA

DNA
1. more stable
2. double stranded form (helix)
3. stores the genetic blueprint for cells
4. Ribose is pentose sugar (OH on 2)
5. Nitrogenous bases: A C G U

RNA
1. more versatile
2. single stranded form
3. transfers the genetic information for decoding
4. DEOXYribose is pentose sugar (H on 2)
5. Nitrogenous bases: A C G T

Name the properties of water

Cohesive, Adhesive, Thermal, Solvent

Why is water solvent?

Due to polarity, water molecules can separate other polar molecules easily

Why does water have the property of cohesion?

It is due to hydrogen bonds forming between water molecules as a result of polarity (i.e. weak forces of attraction of oxygen and hydrogen atoms)

Why does water have the property of adhesion?

It is due to dipolarity, molecules adhere to polar to hydrophillic surfaces (i.e. atoms in xylem)

What are the thermal properties of water?

High specific heat capacity

High latent heat of vaporization

Why does water have these thermal properties?

Due to STRONG hydrogen bonds, water has high melting and boiling point

What are the benefits of water having a high specific heat capacity?

It remains a constant temperature, fluctuating very little from the mean. This means, that it makes a good habitat for organisms that reside within the sea, ocean or rivers

What are the benefits of water having a high latent heat of vaporization?

It makes a good coolant, as vaporization allows heat to be taken away from body in sweat

What is an example of cohesion benefiting an organism?

Pulling forces can allow water to be transported to areas of a tree above the ground, through the xylem

What is an example of adhesion benefiting an organism?

Adhesive force between water and cellulose wall allows water to be transported from xylem to cell to keep cell wall moist and primed for gas exchange (also applicable to alveoli)

What is an example of the solvent properties of water benefiting an organism?

It allows for blood withing animals to act as a medium of transportation.

Which substances are carried by their blood, and how?

NaCl, ionic compound so dissolves easily into plasma as ions Na and Cl

Glucose and amino acids are polar so water molecules can easily break weak intramolecular molecular forces them to be dissolved in the plasma

Oxygen is non-polar, so must be combined with hemoglobin in erythrocytes to be transported

Metabolism

web of all enzyme-catalysed reactions in a cell or organism

Where does metabolism occur?

Cytoplasm, mitochondria, choloplasts

Anabolism

synthesis of polymers from monomers

Catabolism

breaking down of polymers to form monomers

Hydrolysis reaction

E.g. two amino acids form a dipeptide, linked by a peptide bond and one molecule of water

Condensation reaction

E.g. The peptide bond breaks in a dipeptide and an OH and H atoms saturate bonds forming two amino acids

Polypeptide

amino acid

Polysaccharide

monosaccharide (carbohydrate)

lipids

monoglycerides and fatty acids

nucleic acid

nucleotides

Urea

nitrogenous waste produced by break down of polypeptides

What is significant about urea?

It was synthesized in a laboratory falsifying the theory of Vitalism, instead suggesting organic molecules did not have a 'vital force' and instead are not fundamentally different to inorganic molecules

How do the cohesive properties of water explain its surface tension?

The hydrogen bonding between water molecules allows the liquid to resist low levels of external force (surface tension)

The high surface tension of water makes it sufficiently dense for certain smaller organisms to move along its surface

How do the adhesive properties of water explain capillary action?

Attraction to charged or polar surfaces (e.g. glass) allows water to flow in opposition of gravitational forces (capillary action)

This capillary action is necessary to allow water to be transported up plant stems via a transpiration stream

Organic compound

a compound that contains carbon and is found in living things

Why is carbon the basis for organic life?

it can form four covalent bonds allowing a diversity of stable compounds to exist

What are the main classes of carbon compounds?

Carbohydrates, lipids, nucleic acids, proteins

What is a carbohydrate composed of?

C,H and O atoms in a common ratio - (CH2O)n

What is a lipid?

Non-polar, hydrophobic molecule comes in variety of forms - simple, complex or derived

What is the function of carbohydrates?

a source of energy (and as a short-term energy storage option) and also as

a recognition molecule (glycoproteins) and as

a structural component (part of DNA / RNA)

What is the function of lipids?

component of cell membrane (phospholipid, cholestrol)

long term energy store (fats, oils)

signalling molecule

What is a nucleic acid?

DNA and RNA

What is the function of nucleic acids?

To form genetic material, DNA - master code for protein assembly, RNA - manufactures protein

Proteins are composed of which atoms?

C, H, O, N

What is the role of proteins?

Major regulatory molecules involved in catalysis (enzymes)

structural molecules

role in cellular signalling

Describe the structure of an amino acid

Amine: NH2

Carboxyl: COOH

Variable R group

Hydrogen atom: H

Describe the structure of a nucleotide

Phosphate group: 3(O)-P=O

Pentose sugar

Nitrogenous base

How are glycerol and fatty acids joined to make triglycerides?

ester linkages

How are monosaccharides joined to form polysaccharides?

glycosidic linkages

How are amino acids joined to form polypeptide chains?

peptide bonds

How are nucleotides joined to form polynucleotide chains?

phosphodiester bonds

What are the polymers of glucose?

glycogen, cellulose and starch

Name two reasons for metabolism

They provide a source of energy for cellular processes (growth, reproduction, etc.)

They enable the synthesis and assimilation of new materials for use within the cell

Name three examples of monosaccharides

glucose, galactose, fructose

Name three examples of disaccharides

lactose, maltose and sucrose

Name three examples of polysaccharides

cellulose, glycogen and starch

What is the function of monosaccharides?

immediate energy source

What is the function of disaccharides?

transport

What is the function of polysaccharides?

long-term energy store, cell structure or cell recognition

What is the structure of cellulose?

linear molecule composed of β-glucose subunits (bound in a 1-4 arrangement)

What is the function of cellulose?

structural polysaccharide found in cell wall of plants, cannot easily be digested by most animals due to lacking specific enzyme

What is the structure of starch?

energy storage composed of α-glucose subunits (bound in a 1-4 arrangement) exists in one of two forms - amylose or amylopectin

Distinguish between amylose and amylopectin in terms of structure and function.

Amylose - linear (helical) molecule: harder to digest and less soluble but takes up less space (preferred storage form in plants)

Amylopectin - branched (contains additional 1-6 linkages)

What is the structure of glycogen?

energy store composed of α-glucose subunits linked together by both 1-4 linkages and 1-6 linkages (branching)

It is similar to amylopectin, but more highly branched (every 20 compared to 10)

Fatty acids that possess no double bonds are...

saturated

Fatty acids with double bonds are...

unsaturated

Structure of unsaturated fatty acids

Bent (double bond)

Structure of saturated fatty acids

Linear

Types of fatty acid

saturated, monounsaturated (one double bond), polyunsaturated (several double bonds)

Distinguish between cis and trans unsaturated isomers

Cis: The hydrogen atoms attached to the carbon double bond are on the same side

Trans: The hydrogen atoms attached to the carbon double bond are on different sides

Which isomer of unsaturated fatty acid is not naturally occurring?

Trans, produced by industrial process of hydrogenation to maintain linear structure and thus remains solid at room temperature

How do plants and animals differ in the store of tryglyceride?

Plants: oils (liquid), animals: fats (solid)

Describe the formation of a tryglyceride

One glycerol and three fatty acids.

The hydroxyl groups of glycerol combine with the carboxyl groups of the fatty acids to form an ester linkage

+ three molecules of water

Which fats raise blood cholesterol by increasing LDL levels?

Saturated fats and trans

Which fats lower blood cholesterol by increasing HDL levels?

cis

How are fat and cholesterol transported?

Insoluble, so combine with proteins to form lipoproteins to be carried in blood

What is the function of LDL?

to carry cholesterol from liver to other areas of the body

What is the function of HDL?

to scavenge excess cholesterol and return it to the liver to be disposed of

What are the health risks of high blood cholesterol?

Hardening and narrowing of arteries, LDL deposits form, development of plaques which restrict blood flow. If blocked then CHD will result including heart attacks and strokes

What is the evidence that diets rich in trans and saturated fats increases risk of CHD and that diets rich is cis fats decrease risk of CHD?

Epidemiological studies comparing different population groups

Intervention studies that monitor cohorts following dietary modifications

Experimental designs utilising animal models or data based on autopsies

Evidence and counter evidence for link between fat and CHD.

A positive correlation has been found between the intake of saturated fats and the incidence of CHD in human populations

COUNTER: Certain populations do not fit this trend (e.g. the Maasai tribe in Africa have a fat-rich diet but very low rates of CHD)

4. Intervention studies have shown that lowering dietary intakes of saturated fats reduces factors associated with the development of CHD (e.g. blood cholesterol levels, blood pressure, etc.)

COUNTER: Validity of intervention studies is dependent on size and composition of cohort, as well as the duration of the study

3. In patients who died from CHD, fatty deposits in diseased arteries were found to contain high concentrations of trans fats

COUNTER: Genetic factors may play a role (e.g. blood cholesterol levels only show a weak association to dietary levels)

Proportion of saturated and trans fats in Western diets has decreased over the last 50 years, but incidence of CHD has risen, why might this be?

Counter: Increased carbohydrate intake may cause detrimental health effects associated with CHD (e.g. diabetes, obesity)

Counter: Incidence of CHD dependent on a myriad of factors besides dietary intake (e.g. exercise, access to health care, etc.)

Compare lipids and carbohydrates

S torage (lipids are more suitable for long-term energy storage)
O smolality (lipids have less of an effect on the osmotic pressure of a cell)
D igestion (carbohydrates are easier to digest and utilise)
A TP Yield (lipids store more energy per gram)
S olubility (carbohydrates are easier to transport in the bloodstream)

Formula to calculate BMI

body mass index = mass (kg)/height squared (m)

How many different amino acids are there? Where are they synthesised?

20 different amino acids in polypeptides synthesised on ribosomes

Fold and function of protein differs as a result of what?

Variable side chain and its chemical properties (non-polar, charged etc)

What type of bond is a peptide bond?

covalent (joins amino acids to form polypeptides)

Primary structure of amino acids is...

the order of the amino acid sequence, this determines the way the chain will fold

Two possible secondary structures for amino acids

Alpha helices, when the amino acid sequence folds into a coil/spiral arrangement

Beta-pleated sheets, when the amino acid sequence adopts a directionally-oriented staggered strand conformation

How is the secondary structure of an amino acid determined?

Hydrogen bonds forming between non-adjacent amine and carboxyl groups

Where no secondary structure exists, the polypeptide chain will form...

a random coil

What is the tertiary structure of the protein?

the overall three-dimensional configuration of the protein

How is the tertiary structure of the protein determined?

interactions between the variable side chains (i.e hydrogen bonds, disulphide bridges, ionic interactions, polar associations, etc)

What is the quaternary structure of a protein?

fourth level of structural organisation found in proteins that consist of more than one polypeptide chain linked together or if they include inorganic prosthetic groups in their structure

A proteins have a quaternary structure true or false?

false, many proteins consist of a single polypeptide chain

Give an example of a protein with a quaternary structure

haemoglobin, it is composed of:
1. four polypeptide chains (two alpha chains and two beta chains)
2. iron-containing haeme groups (prosthetic groups responsible for binding oxygen)

Denaturation

a structural change in a protein that results in the loss (usually permanent) of its biological properties

What conditions are likely to cause denaturation?

temperature and pH

What happens if denaturation occurs?

Because the way a protein folds determines its function, any change or abrogation of the tertiary structure will alter its activity

Why is temperature a cause of denaturation?

1. high levels of thermal energy may disrupt hydrogen atoms that hold protein together
2. as hydrogen bond break, protein unfolds and loses intended function
3. proteins usually denature outside of optimum (body temperature)

Why is pH a cause of denaturation?

1. amino acids are neutral molecules possessing both negatively (COO-) and positively (NH3+) charged regions

2. Change in pH alters charge of protein which alters solubility and shape

3. Optimum pH dependent on environment (e.g. stomach proteins require an acidic environment to operate, whereas blood proteins function best at a neutral pH)

Gene

a sequence of DNA which encodes a polypeptide sequence

Transcription

making an mRNA transcript based on a DNA template (occurs within the nucleus)

Translation

using the instructions of the mRNA transcript to link amino acids together (occurs at the ribosome)

Exceptions to the rule that one gene will code for one polypeptide

Genes may be alternatively spliced to generate multiple polypeptide variants

Genes encoding tRNA sequences are transcribed but never translated

Genes may be mutated (their base sequence is changed) and consequently produce an alternative polypeptide sequence

Proteome

the totality of proteins expressed within a cell, tissue or organism at a certain time

Why is the proteome unique for any given individual?

because protein expression patterns are determined by an individual's genes