IB BIOLOGY, Unit 2 - Molecular Biology

what do 'cis' fatty acids have to cause its properties

"cis" fatty acids have a kink at the double bonds, causing the fatty acids to pack more loosely, lowering the melting point and making them liquid at room temperature

what do 'trans' fatty acids have to cause its properties

"trans" fatty acids do not have the kink at the double bond, can pack more tightly, have a higher melting point and are solid at room temperature.

state the properties of carbon

1. Carbon atoms form covalent bonds with other atoms. These bonds are very strong between atoms so stable molecules can be produced. 2. each carbon atom can form up to 4 covalent bonds so these molecules can have complex structures. 3. Its ability to form long chains of carbon. No other element can bond like carbon does. The reason carbon can do this is that carbon-carbon bonds are extremely strong. This allows carbon to make up many of the basic building blocks of life

state the functions of proteins

1. catalysis 2. muscle contractions 3. cytoskeletons 4. tensile strengthening 5. blood clotting 6. transport of nutrients and gases 7. cell adhesion 8. membrane transport 9. hormones 10. receptors 11. packing of DNA during mitosis 12. Immunity

Why are lipids more useful than carbohydrates for long-term energy storage?

1. the amount of energy released in cell respiration per gram of lipids is double the amount released from a gram of carbohydrates. fats form pure droplets of cells with no water associated, whereas each gram of glycogen is associated with about 2 grams of water. So lipids are actually 6 times more effective in the amount of energy that can be stored per gram of body mass. This is important because we have to carry our energy stores around with us all the time. 2. Because lipids are poor conductors of heat, they can be used as heat insulators. This is why our fat is deposited just under the skin. 3. Fat is liquid at body temperatures, it can also act as a shock absorber. This is why we have fat around our organs.

how much of genes store the amino acids sequence?

3 bases of a gene is needed to code for each amino acid.

explain its thermal property of a high boiling point

A lot of heat is required to evaporate water as hydrogen bonds have to be broken. therefore the boiling point of high.

what is a proteome?

A proteome is all of the different kinds of proteins produced by a genome, cell, tissue or organism at a certain time. Each individual has a unique proteome as they change not only in their cell activity but also in their variations in the amino acid sequences.

what's the type of bonds formed between each fatty acid and and the glycerol?

An ester bond. This is formed when when an acid reacts with OH group in an alcohol.

use of water as a cooling process by sweat

As humans sweat, the water droplets absorb heat from the blood flowing under our skin causing the water to evaporate and our blood to cool down. This will in turn cool our whole body down. This cooling is controlled by negative feedback through receptors in the hypothalamus If the body is overheated, receptors in the hypothalamus sense this and stimulate the sweat glands to secrete sweat Some reptiles such as crocodiles cool by opening their mouths (gaping). Dogs also pant which causes water to evaporate from their upper respiratory tract.

what and where is the carboxyl group?

At one end of the fatty acid chain is the acidic carboxyl group. it's represented as COOH.

state the 4 carbon compounds

Carbohydrates Lipids Proteins Nucleic acid

what is rubisco

Catalyzes reactions that fixes CO2 from the atmosphere into organic carbon to be used by living organisms to produce the carbon compounds need for life. It is one of the most abundant and important enzyme in the world

what is cellulose made up of? and by which bonds the molecules are held together with?

Cellulose are unbranched straight chains of β (beta) glucose molecules, held together with glycosidic bonds

provide examples of protein structures that have more than 1 polypeptide

Collagen consists of 3 long polypeptides wound together to form a rope-like molecule. It has a greater tensile strength than the three polypeptides would if they were alone. This bonding allows a small amount of stretching, reducing the chance of the molecule breaking. Haemoglobin has 4 polypeptide with associated non-polypeptide structures. The four parts of haemoglobin interact to transport oxygen more effectively to tissues that need it than of they were separate.

what is the main concern of fats for human health?

Coronary disease where the coronary arteries are blocked with fat deposits leading to clots and heart attacks. It is not only caused by saturated fats but can be caused by other factors such as low intake of dietary fibre.

how specific are enzymes? and why?

Each enzyme catalyzes a specific reaction for a specific substrate. Enzymes are very specific, because both the enzyme and the substrate possess specific complementary shapes that fit into one another.

describe the general conformation of proteins

Fibrous proteins like collagen are elongated. But many proteins are globular.

explain its thermal property of a high specific heat capacity

Hydrogen bonds restricted the motion of water molecules and high temperatures are required to break the bonds. Therefore, the energy needed to raise the temperature of water is relatively large.

describe the position of hydrophobic and hydrophilic R groups in a protein when it is soluble in water?

Hydrophilic R groups are usually outside the molecule and hydrophobic R groups are on the inside.

what does it mean when the isomer have 'cis' in the name

If the hydrogen atoms are on the same side of the double bond then the isomer is "cis"

state the difference between them

In alpha glucose the OH points downwards and in beta glucose it points upwards.

provide an example of a condensation reaction that is used in life processes

In plants, many glucose molecules combine through condensation reactions to form the polysaccharide starch.

what is glycogen? and how are the molecules linked?

Is a multi-branched energy storage polysaccharide for animals. Glycogen consists of many α (alpha) glucose molecules linked by glycosidic bonds.

Why does heat cause denaturing?

It causes vibrations within the molecule that can break the intermolecular bonds or interactions.

How is glycogen a good molecular structure for energy storage?

It is highly branched, making the molecule more compact and a perfect molecule for energy storage

are enzymes used up in chemical reactions?

No

what is an enzyme?

Proteins that catalyze chemical reactions (increase the rate by lowering the activation energy)

Saturated fatty acids are saturated with hydrogen. Why so?

Saturated FA's are all single bonds and are therefore saturated with the most hydrogen they could have.

How is cellulose a good molecular structure for providing strength for cell walls in plant cells?

Since the -OH groups point out in opposite directions and every other β glucose is flipped 180 degrees, cellulose forms a nice straight chain These straight chains also allow cellulose to form bundles linked by H-bonds. This is essential for cellulose's function, which is to provide strength for cell walls in plant cells

How is starch a good molecular structure for storing glucose in plants?

Since the bonds in starch are α-glucose, the -OH groups from the glucose molecules are always pointed down, causing starch to have a curved appearance. This makes starch a good molecule for storing glucose in plants

How can the number of amino acids be estimated in a polypeptide?

Since there are 20 amino acids, an enormous variety of polypeptides can be produced Basically the number of different polypeptides that can be produced is 20^n, where 20 represents the number of amino acids that can be used and n represents the number of AA's in a particular polypeptide.

provide an example of a hydrolysis reaction that is useful in life processes

Starch and glycogen are broken down by the addition of water into glucose molecules which is to be used in aerobic respiration.

when are successful reactions occurred?

Successful reactions only occur if the substrate and the active site of the enzyme are correctly aligned and the collide with sufficient KE

what is the active site?

The area or the pocket on the enzyme where the substrate binds.

how is the product substrate made?

The binding of the substrate to the enzyme causes the chemical bonds of the substrate to weaken. This eventually causes the reactions that take place that form the products. After the products are released, the enzyme can bind to another substrate, because enzymes are not used up in these chemical reactions.

what is meant by condensation reactions?

The building of large macromolecules (polymers) by the removal of water molecules (OH from one and H from the other) when monomers combine. Each time two monomers combine, one water is removed.

explain its thermal property of a high latent heat of vaporisation

The heat needed to evaporate a molecules from other one is referred to this. Evaporisation has a cooling effect. A lot of heat is required to evaporate water as hydrogen bonds have to be broken. This makes it a good vaporisation coolant.

what is water's solvent properties

The polar water molecules mean that they form shells around charged and polar molecules preventing them from clumping together and keeping them in solution. water forms hydrogen bonds with polar molecules. Its partially negative oxygen pole is attracted to positively charged ions and its partially positive hydrogen pole is attracted to negatively charged ions, so both dissolve.

Why is the bonding of a water molecules a polar covalent bond?

This is so because the nucleus of the oxygen atom is more attractive to electrons than the nucleus of the hydrogen atoms.

Why do unsaturated fatty acids do not have the most Hydrogens they could have?

Unsaturated FA's contain a double bond or double bonds.

provide an example of a compound that is produced by living organisms but which can also be artificially synthesised

Urea is a nitrogen containing compound. It's produced when there's an excess of amino acids in the body. The making of urine takes place in the liver. Urea produced artificially is identically the same but doesn't require the conditions in which is made in the body. It's used as a nitrogen fertiliser on crops.

When two monomers combine together they form.....

a dimer / disaccharide eg. maltose

what is starch made up of? and what's its function?

a long chain of α (alpha) glucose molecules used as a glucose storage by plants

what is a dipeptide?

a molecule consisting of 2 amino acids linked by a peptide bond.

what is a polypeptide?

a molecule consisting of many amino acids linked by peptide bonds.

When many monomers combine together they form......

a polymer

what are proteins composed of?

amino acids and they are composed of carbon, hydrogen, oxygen and nitrogen (mostly)

why does pH cause denaturing?

because charged on R groups are changed, breaking the ionic bonds within the protein or causing new ones to form. The 3D shape is altered and many soluble proteins become insoluble.

how, why and what are the charges of the particles in the water molecule?

because of the unequal sharing of electrons in water molecules, the hydrogen atoms have a partial positive charge and oxygen has a partial negative charge. This attraction is small as they are not full ions but they still have significant effects.

how are amino acids diverse?

because they have different R groups

hydrolysis

break down of larger polysaccharides into smaller monosaccharides through the addition of water

how are triglycerides formed? and provide an example

by condensation reactions from 3 fatty acids and 1 glycerol the oil in sunflower seeds

how can one explain the diversity of compound structures?

by explaining their properties

what are carbohydrates composed of and state its functions

carbon, hydrogen and oxygen Many carbohydrates are used for energy or structural purposes

what are hormones

chemical messengers that help coordinate certain regulatory activities

what are the properties of water?

cohesion adhesion high specific heat capacity high latent heat of vaporisation high boiling point

list some of the processes which are catabolistic

digestion of food cell respiration in which glucose is oxidised to CO2 and H2O

give 3 examples of monosaccharides

glucose fructose ribose

what carbohydrate is used for energy storage? and why?

glycogen this is because glycogen can be easily and quickly broken down into glucose and then transported by the bloodstream wherever it is needed. Fats can not be immobilised as quickly. Glucose is useful for both aerobic and anaerobic respiration but fats are only useful for aerobic.

explain its adhesive properties

hydrogen bonds can form between water and other polar molecules, causing water to stick to them. This is useful in leaves where water adheres to cellulose molecules in cell walls.

what does it mean when the isomer has 'trans' in the name

if the hydrogens are on opposite side of the double bond then the isomer is "trans"

what are the hydrophobic molecules? and why are they called that?

if they don't have a charge and are non-polar. it means they are insoluble

catabolism

is the breakdown of complex molecules into simpler molecules including the hydrolysis of macromolecules onto monomers released energy

Anabolism

is the synthesis of complex molecules from simper molecules including the formation of macromolecules from monomers by condensation reactions. Usually requiring energy in the form of ATP

describe the condensation reaction of polypeptides?

it involves the amino group (NH2) of one amino acid and the carboxyl group (COOH) of another. Water is eliminated and a peptide bond is formed.

what is the conformation and how is it determined?

it's the 3D structure of a protein and is determined by the amino acid sequence of a protein and its constituent polypeptides.

What is vitalism?

it's the theory that the origin and phenomena of life is due to a vital principle (which is different from pure chemical and physical forces). eg. psyche - soul

what is insulin? and what's its function?

its a hormone produced by the beta cells of the pancreas that reduces the blood glucose levels by promoting the absorption of glucose from the blood to the skeletal muscles and tissue Insulin binds reversibly to receptors in the cell membrane to promote uptake

what is collagen? where is it found?

its a main structure molecule in various connective tissues such as skin, blood vessels and ligaments They are fibrous rope-like proteins made from 3 polypeptides. Most abundant protein in the body.

what is more suitable as long-term storage: carbohydrates or lipids?

lipids

what are polysaccharides? and what are they held by?

long chains of monosaccharides held together with glycosidic linkages made by condensation reactions

how are polypeptides made?

made by linking amino acids together by condensation reactions on ribosomes

how is BMI calculated? units?

mass in kg / (height in metres)^2 Units: kgm^-2

Enzyme catalysis involves.....

molecular motion and the collision of substrates with the active site.

When a fatty acid has one double bond what is it referred to?

monounsaturated

draw the structures of ribose, glucose, a fatty acid and an amino acid

p.65 in the text book

When a fatty acid has more than one double bond what is it referred to?

polyunsaturated

compare thermal properties of methane and water

pp. 71

be able to find BMI using a nomogram

pp. 81

list some of the processes which are anabolistic

protein synthesis using ribosomes Photosynthesis

what is Rhodopsin?

rhodopsin is a biological pigment in the photoreceptor cells of the retina It consists of a light sensitive retinal molecule surrounded by an opsin polypeptide When the retinal absorbs light through the eye, it changes it's shape and the shape of the opsin. This sends a nerve impulse through the optic nerve to the brain

what are monosaccharides

single sugar units

state the properties (abilities) of spider silk for human use

spider silk consists of many different types with different functions dragline silk is stronger than steel and tougher than Kevlar used in bulletproof vests used in the spokes of a web and when a spider suspends itself very extensible and resistant to breaking relative to its size

give examples of lipids are fatty acids polar?

steroids waxes fatty acids triglycerides Fatty acids are non-polar and therefore hydrophobic Chains consist of covalently bonded carbon with hydrogen

What helps falsify vitalism?

the artificial synthesis of urea in 1830 using silver isocyanate and ammonium chloride. It was important because no vital step was needed. This reaction reveals that if urea can be artificially made then other organic compounds can be made without a vital principle too.

what's a hydrogen bond?

the attraction between water molecules. It's an intermolecular force rather than a bond. It forms when a hydrogen atom in one polar molecule is attracted to a slightly negative atom of another polar covalent molecule. These bonds are weak but collectively they give water its unique properties.

What is denaturing

the change in conformation of the protein by the breaking or disruption of bonds between R groups of amino acids within the protein.

what is catalysis

the enzymes catalyze biochemical reactions by lowering the activation energy needed for the reaction to take place

How do globular proteins develop their final conformation?

the polypeptide gradually fold up as they are made. This is stabilised by bonds between the R groups of the amino acids that have been Brough together by folding. This does not happen in fibrous proteins.

why are the substrates and the enzymes are in continuous motion?

the substrate is dissolved in water around the enzyme

What is metabolism?

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

what are immunoglobulins? and what is their role?

these are also known as "antibodies" They are Y shaped proteins produced by cells to identify and neutralize foreign pathogens like bacteria and viruses they act as markers to identify these pathogens for destruction by large white blood cells called Phagocytes each antibody is specific for a specific pathogen

why are methane and water physical properties very different?

they are both small molecules and have atoms linked by single covalent bonds. but water molecule are polar and can form hydrogen bonds, whereas methane molecules are non-polar and do not form hydrogen bonds.

what are nucleic acids? and what do they contain?

they are chains of subunits called nucleotides and they contain carbon, hydrogen, oxygen, nitrogen and phosphorus.

Why soluble proteins often become insoluble and form percipitates?

this is due to the hydrophobic R group in the centre of the molecule becoming exposed to the water around by the change in the conformation.

explain its cohesive properties

this means they stick to each other due to their hydrogen bonds. This is useful for water transport in plants.

what is cytoskeletons?

tubules is the subunit of microtubules that give animals cells their shape and pull on chromosomes during mitosis.