Molecular Biology

Define metabolism

The collection of enzyme catalyzed chemical reactions that occur in a living thing and require a solvent

Define cohesion

hydrogen bonds between polar water molecules cause them to cohere to each other

Explain cohesion in plants

• Allows for transpiration in plants moving water against gravity from the roots up the xylem to the leaves

• If a molecule evaporates at the leaf another is pulled up

Define adhesion

water molecules form hydrogen bonds with other polar molecules

Explain adhesion in plants

• Water adheres to cellulose in plants which prevents the water column from breaking and assists in transpiration

• This is an example of capillary action

Define capillary action

The adhesion of water to the walls of a narrow tube, drawing the water upwards

State the solvent properties of water

• Water dissolves polar molecules

• This is necessary for metabolism

• Enzymes catalyze reactions in aqueous solutions

• Non polar substances are hydrophobic

Explain an example of a non-polar substance

Steroid hormones can diffuse through membranes because they are hydrophobic and not repelled by fatty acid tails of membranes

• membrane proteins have hydrophobic regions allowing them to contact the hydrophobic hydrocarbon tails

Explain adaptations for the thermal properties of water

• water has a high thermal conductivity so warm blooded animals that live in water need a layer of fat to prevent heat loss

• high specific heat capacity

• high viscosity selects for animals with streamlined bodies

• high buoyancy allows air breathing animals to remain near surface

State the chemical properties of carbon

• Forms four covalent bonds leading to a diversity of possible stable compounds

• Can form single or double bonds allowing for long chains or rings

Monomer

The individual units of a polymer

Polymer

A long chain of monomer units covalently bonded

Explain anabolic reactions

• Turn monomers into polymers by linking them together through condensation synthesis

• Require energy in the form of ATP

• Produce water as a byproduct

What is the polymer for a monosaccharide + example

• polysaccharide

• Glucose links together to form glycogen

Outline catabolic reactions

• digest polymers by turning them into monomers

• Requires water

• Requires energy

Describe glucose

• Hexose monosaccharide

• Alpha glucose has a hydrogen at the top of carbon 1

• Beta glucose has the hydroxyl at the top of carbon 1

Outline the form and function of glucose as an example of a monosaccharide

• glucose is polar covalent

• Polar = soluble in water and easy to transport

• Covalent bonds = stable but a lot of energy released when bonds are broken in cell respiration

What is an example of a pentose monosaccharide

DNA/ RNA

Describe the structure of starch

• alpha glucose linked at carbons one and four

• All glucoses oriented the same way

• Curved chain

• Amylose: unbranched helix

• Amylopectin: branched globular shape due to additional links at carbons 1 and 6

• Short term energy storage in plants

Describe the structure and function of glycogen

• similar to amylopectin with more branching

• Short term energy storage in animals

• Stored in the liver

How are polysaccharides suited to storage

• insoluble due to size

• Linked with a bond called a glycosidic bond

• They can be broken down into monosaccharides through hydrolysis

Describe the structure and function of cellulose

• provides rigidity and strength in plant cell walls

• B glucose linked at 1 and 4

• Glucoses alternate

• Unbranched chain

• Chains can be grouped in bundles and linked with hydrogen bonds for more strength

Describe the hydrophobic properties of lipids

• lipids include long carbon chains

• Steroids found in animals are cholesterol based but they are still lipids

• They are not very soluble

Outline the formation of triglycerides

• three separate condensation reactions linked three fatty acid monomers to a glycerol

• This forms one triglyceride and three waters

• Stored as fate in adipose tissue used for long term energy storage and insulation

What is the structure of a phospholipid

The same as a triglyceride but with one phosphate group instead of a fatty acid group

What is the function of unsaturated fatty acids in membranes

In phospholipids: preventing phospholipids from packing as tightly allowing for membrane fluidity

Draw an amino acid

Explain the formation of an amino acid Chain (polypeptide)

• two amino acids are linked by condensation synthesis producing a protein

Outline the different amino acids

• there are 20 amino acids

• Humans require all 20

• About half of the amino acids are essential meaning they must be ingested and we cannot produce them

Explain the variety of proteins possible

• every protein has a different sequence of amino acids

• Because proteins can be any length there is an infinite variety of possible polypeptide chains

Outline the denaturation of proteins

• changes in the 3d structure of a protein due to changes in the bonds holding its shape

• Structure dictates function so changes in the structure alter or halt the function

• High temps and extreme ph can cause denaturation

How do enzymes affect metabolic reactions

• catalyse them

• Unique enzymes exist for thousands of unique metabolic reactions

• Reactions can be controlled by activating or deactivating enzymes

Contrast the activation energy of metabolic reactions

• catabolic: exergonic release energy

• Anabolic: endergonic require energy

• The transition state of an enzyme catalyzed reaction has a lower energy than non enzyme catalyzed, lowering activation energy

• Net energy absorbed or released is not changed

Define enzyme

A globular protein functioning as a biological catalyst speeding up metabolic exactions by lowering the activation energy

Explain active sites

• the site on the surface of an enzyme to which a substrate binds and catalyses a chemical reaction

• When a enzyme binds to substrate it is referred to as an enzyme-substrate complex

• Diff enzyme for almost every substrate

• Specificity of the enzyme is determined by the shape and chemical composition of the active site

• Determined by the amino acids making up the enzyme

• As the substrate approaches the active site the shape of the active site changes slightly to fit the shape of the substrate

• Bonds of the substrate weaken and it changes shape too

• This is the induced fit model explaining broad specificity

How does kinetic molecular theory relate to enzymes

• molecular motion increases with increasing temperature

• In order for an enzyme to catalyse it must collide with reactant molecules

• Increased frequency of catalyst and reactant molecules leaves to an increase in enzyme activity up to the optimal temp where it is denatured

• The catalyst may be immobilized in a membrane

What is an optimal pH

The pH at which the active site best fits the substrate (not denatured)

Explain the relationship between substrate concentration and activity

• more substrate = more collisions = more product formed

• Until the saturation point at which all of the active sites are occupied

State two ways to measure the rate of enzyme catalysed reactions

• production of product per unit time

• Reduction of reactant per unit time

What is the relationship between photosynthesis and cell respiration

• complementary processes

• The products of photosynthesis are used for cellular respiration and vice versa

• Photosynthesis is performed in choroplasts

• Cellular respiration is performed in the mitochondria of eukaryotic cells

What is atp

• cells require energy in the form of atp

• A nucleotide that can diffuse to any part of the cell and release energy

• Every cell produces its own atp

State three functions atp is used for

1. Anabolic reactions like synthesizing polymers

2. Active transport using membrane pumps

3. Movement within a cell or as the entire cell

Relationship between adp and atp

• energy from cell respiration attaches an inorganic phosphate to adp making atp

• The high energy bond of atp is hydrolyzed then adp and phosphate are reformed and energy is released

What compounds can be used for cellular respiration

• glucose/fatty acids or other organic compounds

Aerobic versus anaerobic respiration

• aerobic: uses oxygen and make a lot of atp slowly

• Anaerobic: does not involve oxygen and makes a little atp quickly

Outline anaerobic respiration

• Glucose is converted to pyruvate in the cytoplasm producing a small amount of atp

• If no oxygen is available the pyruvate remains in the cytoplasm and is converted into a waste product (lactate in humans)

Outline aerobic respiration

• Glucose is converted to pyruvate in the cytoplasm producing a small amount of atp

• if oxygen is available the pyruvate is absorbed into a mitochondrion and broken down into co2 and water producing a large amount of ATP

• Higher yield of ATP per gram of glucose

Define photosynthesis

The process by which algae and some bacteria produce organic carbon compounds

Photosynthesis converts light energy into chemical energy

What is photolysis

• light energy is used to split water into oxygen gas and hydrogen used for carbon fixation

• Photosynthetic pigments absorb light energy and convert it into atp

• Energy from atp is used to fix carbon dioxide (turn it into organic molecules) by combining it with the hydrogen

What happens to the oxygen produced by photolysis

• waste product

• Diffuses out of the plant

• All atmospheric oxygen is a result

Describe photosynthetic pigments

• absorb light and convert it into chemical energy

• Chlorophyll is green and the most common

• Other pigments are called accessory pigments

Describe the visible light spectrum

• em radiation of wavelength 400 to 700 nm

• 400 - 525 violet - blue

• 525 - 625 green - yellow

• 625 - 700 orange - red

Outline chlorophyll’s absorption

Greatest absorption of violet - blue

High absorption of red

Green to yellow not absorbed and reflected

Explain photoactivation

• absorbed light energy excites electrons

• Jump to higher energy level

• This is photoactivation

• Diff pigments are activated by diff wavelengths

What is an absorption spectrum

• wavelengths or frequency of light absorbed by each pigment

What is an action spectrum

• the rate of photosynthesis for each wavelength or frequency measured in o2 produced or co2 consumed

• Strong correlation to pigment absorption peaks

Explain the relationship between co2 concentration and photosynthesis rate

• Low levels = less carbon for fixation

• Increase = increase in rate up to max

• At the max another factor is usually limiting

• Co2 is usually liming factor at atmospheric levels

Why is there a maximum in the relationship between light and rate of photosynthesis

• chlorophyll cannot absorb any more light

• Usually not a limiting factor

Why are co2 rich lab experiments not accurate for photosynthesis

• higher co2 concentration is shown to lead to more photosynthesis in the lab

• Not accurate in the field because high co2 = high temp which decreases rate of photosynthetic activity (denaturation)

Rf formula

distance moved by pigment/distance moved by solvent