Topic 2: Molecular Biology

What is metabolism?

The totality of chemical processes that occur within a living organism in order to maintain life; it is the web of all enzyme-catalysed reactions that occur within a particular cell or organism explained in terms of the molecules involved

What are organic compounds?

Molecules that contain carbon and are found in living things, with the exceptions of carbonates and oxides of carbon

Why do carbon atoms form the basis of organic life?

Because of their capacity to form four covalent bonds, allowing for a diversity of stable compounds to exist

What are the four main groups of organic compounds in cells?

Carbohydrates, lipids, proteins, and nucleic acids, with carbs, proteins, and nucleic acids being made up of recurring subunits called monomers

What are the monomers and polymers for carbohydrates?

Monomer: Monosaccharides

Polymer: Polysaccharides

What are the monomers and polymers for proteins?

Monomer: Amino acids

Polymer: Polypeptides

What are the monomers and polymers for nucleic acids?

Monomer: Nucleotides

Polymer: DNA/RNA

How are lipids composed?

Not of monomers, but instead smaller non-repeating subunits, such as triglycerides containing one glycerol and three fatty acids

What are the two main types of reactions?

Anabolic and catabolic reactions

What is anabolism?

• The synthesis of complex molecules from simpler ones

• Involves condensation reactions (water is produced)

• An example of an anabolic reaction is photosynthesis

What is catabolism?

• The breakdown of complex molecules into simpler ones

• Involves hydrolysis reactions (water is consumed)

• An example of a catabolic reaction is cellular respiration

What is the theory of vitalism?

A doctrine that dictated that organic molecules could only by synthesized by living systems, and that living organisms contained a “vital force” that was required to manufacture organic molecules

How was vitalism falsified?

In 1828, Frederick Woehler artifically synthesized urea by heating the inorganic salt ammonium cyanate

How is water composed?

Water is made up of two hydrogen atoms covalently bonded to an oxygen atom (H₂O), and since oxygen has a higher electronegativity, attracting the shared electrons more strongly, the molecule is polar

What is hydrogen bonding?

An intermolecular force occurring with hydrogen, especially between multiple water molecules

How can water interact with other molecules?

Water can form intermolecular associations with other molecules that share common properties, like polarity

What is cohesion of water?

When water can form hydrogen bonds with other water molecules (like the molecules stick together)

What is adhesion of water?

When water can form polar associations with charged molecules (molecules aren’t sticking together)

What is the result of the cohesive properties of water?

A relatively high surface tension that can resist low level external forces

What is the result of the adhesive properties of water?

A potential capillary action

Why is water called the universal solvent?

Because of its capacity to dissolve a large number of substances (ionic/polar) and its ability to weaken forces and form dispersive hydration shells

What are substances that can dissolve in water called?

Hydrophilic (glucose, amino acids, sodium chloride, oxygen)

What are substance that cannot dissolve in water called?

Hydrophobic (lipids → fats and cholesterol)

Why are the solvent properties of water important?

They make water an important medium for metabolic reactions, as well as a necessary transport medium

What are the thermal properties of water?

Water has the capacity to absorb large amounts of heath energy before undergoing a resultant change in state (only after extensive hydrogen bonding has been broken)

Does water have a high or low specific heat capacity?

High → hydrogen bonds are strong

Why are the thermal properties of water important?

They are what make water a very effective coolant, such as in sweat

What are two other properties of water?

Transparency:

• Light can pass through water

• Important for photosynthesis and vision

Expansion when frozen:

• Water becomes less dense as ice

• Important for life as ice floats, meaning oceans beneath do not automatically freeze

Why are water and methane compared?

They have similar structures, weight, and size

Why are water and methane different?

Water is polar and can form intermolecular hydrogen bonds

What are the differences between methane and water?

Methane:

• CH₄

• Non-polar

• Heat capacity of ~2

• Boiling point of -161

Water:

• H₂O

• Polar

• Heat capacity ~4

• Boiling point 100

What is a monosaccharide?

The monomer of a carbohydrate, with the primary function as being an energy source

What are two example of monosaccharides?

Glucose (both alpha and beta) as well as ribose

How are polysaccharides formed?

Monosaccharides are covalently joined by glycosidic linkages by condensation reactions to form polymers, which are then joined into disaccharides for easy transport or more complex polysaccharides

What can polysaccharides be used for?

• Short term energy storage (glycogen, starch)

• Structural components (cellulose)

• Recognition/receptors (glycoproteins)

How is the carbohydrate formed determined?

By the monosaccharide subunit used and the bonding arrangement between them

What are three types of polysaccharides?

Cellulose, starch, and glycogen

What is cellulose?

• Component of plant cell wall

• Linear molecule made of ß-glucose subunits

• Subunits bound in a 1-4 arrangement

What is starch?

• Energy storage in plants

• Composed of α-glucose subunits and exists in two forms

• Amylose is linear (helical) and bound in 1-4 arrangements

• Amylopectin is branched (bound in 1-4 and 1-6 arrangements)

What is glycogen?

• Energy storage in animals

• Branched molecule composed of α-glucose subunits

• Is like amylopectin but with more frequent 1-6 bonding

How do carbohydrate and lipids differ in energy storage?

SODAS:

Storage - lipids used for long term storage
Osomotic pressure - lipids easier to store
Digestion - carbohydrates easier to ulilise
ATP yield - lipids store more energy per gram
Solubility - lipids insoluble/harder to transport

What can be a downside to carbohydrates and lipids?

While they are important components to a healthy diet, excess intake can impact body mass

How is BMI calculated?

BMI = Mass in kg ÷ (height in m)²

What is the name for the alignment chart used to classify BMI?

A nomogram

Why is BMI sometimes inaccurate?

It was created based upon the average white male, making it not applicable for many females and those of different races. Additionally it does not take into account variables like muscle mass

What are lipids?

A class of non-polar organic molecules, including triglycerides (adipose tissue), phospholipids (bilayer), cholesterol (animal cell membrane), and steroids (hormones)

What are the functions of lipids?

SHIPS:
Storage of energy (triglycerides)
Hormonal roles (steroids)
Insulation (thermal)
Protection of organs
Structural roles (cholesterol)

What are triglycerides?

Lipids used for long-term energy storage that are composed of a glycerol molecules covalently linked to three fatty acid chains through condensation reactions

What are fatty acids?

Long hydrocarbon chains found in certain lipids, mainly in triglycerides and phospholipids

What are the two types of fatty acids?

Saturated and unsaturated fatty acids

What are saturated fatty acids?

Fatty acids that:

• Posses no double bonds in the hydrocarbon chain

• Are generally solid at room temperatures

What are unsaturated fatty acids?

Fatty acids that:

• Posses double bonds (mono = one, poly = many)

• Are generally liquid at room temperature

What are the two isomers of unsaturated fatty acids?

Cis and trans unsaturated fatty acids

What are the differences between cis and trans unsaturated fatty acids?

Cis:

• H atoms on sae side

• Double bonds creates kink in fatty acid chain

• Loosely packed and usually liquid

• Occur commonly in nature

• Generally good for health

Trans:

• H atoms on different sides

• Double bond does not create kink (linear chain)

• Are tightly packed and usually solid

• Occurs in processed food

• Generally bad for health

Why can lipids pose health risks?

Fats and cholesterol cannot dissolve in the blood and so are packaged with proteins (lipoproteins) for transport

What are the two types of lipoproteins and their impact on health?

• Low density lipoproteins (LDLs) → transport cholesterol from the liver to the rest of the body (bad for health)

• High density lipoproteins (HDLs) → scavenge excess cholesterol and return it to the liver for disposal (good)

How can fatty acids influence the levels of lipoproteins?

• Cis fats raise levels of HDL (lower cholesterol)

• Saturated fats raise levels of LDL (raise cholesterol)

• Trans fats raise levels of LDL and lower levels of HDL

Why are high levels of blood cholesterol bad?

They can cause atherosclerosis and lead to health issues like coronary heart disease (CHD)

What are amino acids?

They monomer of a protein, linked together to form polypeptides

How is variation in proteins achieved?

There are 20 different amino acids that can be linked in any sequence to create variation

How are polypeptide chains formed?

By amino acids covalently joining by peptide bonds and condensation reactions

What determines the sequence of amino acids?

Genes

What are the different protein structures?

Primary, secondary, tertiary, and quaternary

What is primary protein structure?

• Order of amino acid sequence

• Formed by covalent peptide bonds

What is secondary protein structure?

• Folding into repeat patterns (α-helix or ß-pleated sheet)

• By hydrogen bonds between amine and carboxyl groups

What is tertiary protein structure?

• Overall three-dimensional arrangement of a polypeptide

• Determined by the interactions between variable side chains

What are the functions of proteins?

SHITS ME

Structure (collagen, spider silk)
Hormonal (insulin, glucagon)
Immunity (immunoglobulins)
Transport (haemoglobin)
Sensation (rhodopsin)

Movement (actin, myosin)
Enzymatic (rubisco, catalase)

What is the proteome?

The totality of all proteins that are expressed within a cell, tissue, or organism at a certain time, which will be unique, since protein expression patterns are influenced by a genome

What is denaturation?

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

What conditions can caused denaturation?

• Temperature (heat can break structural bonds)

• pH (alters protein charge → changes solubility and shape)

What is an enzyme?

An enzyme is a globular protein which speeds up the rate of a chemical reaction by lowering the activation energy required while not being consumed by the reaction

What is a substrate?

The molecule(s) the enzyme react with

What is the active site?

The complementary region on the enzyme’s surface to which a substrate binds

What is the lock and key model?

This illustrates how enzymes and substrates work:

• Enzyme and substrate complement each other precisely in terms of both their shape and chemical properties

• The active site and the substrate will share specificity

What is the induced fit model?

The illustrates how enzymes and substrates work:

• Active site is not a rigid fit fore the substrate and changes its conformation to better accommodate the substrate

• This stresses the substrate bonds and induces catalysis

What factors impact enzyme activity?

Temperature, pH, and substrate concentration

How does temperature impact enzyme activity?

• Increases enzyme activity

• Enzyme peaks at an optimal temperature

• Higher temperature decrease activity

How does pH impact enzyme activity?

• Enzyme activity is highest at an optimal pH range

• Activity decreases outside of this range

How does substrate concentration impact enzyme activity?

• Increases enzyme activity

• At a certain point, activity plateaus

How can the rate of enzyme catalysis be increased?

By increasing the frequency of enzyme-substrate collisions (molecular motion)

How can the rate of enzyme catalysis be decreased?

Denaturation

What enzymes are used in industrial practices?

Immoblised enzymes:

• They are fixed to a static surface to prevent enzyme loss

• This improves separation of a product and purity of yield

How does the production of lactose-free milk involve enzymes?

• Lactase digests lactose into glucose and galactose

• Lactase is fixed to an inert surface like alginate beads

• Milk is passed over this surface to become lactose free

What are the benefits of lactose-free milk?

• Provides a source of dairy for lactose-intolerant people

• Increases sweetness of milk (less need for sweeteners)

• Reduces crystallization and production times for cheese

What is a nucleotide?

• Monomer of nucleic acids

• Consists of pentose sugar, phosphate group, and nitrogenous base

What are the different nitrogenous bases?

Adenine, Thymine, Cytosine, Guanine, and Uracil

What are the two types of nitrogenous bases?

Purines (A, G) and pyrimidines (T, C, U)

What is the difference in nitrogenous bases between RNA and DNA?

RNA will have uracil anywhere DNA has thymine

How are nucleotides linked together?

They are linked in a single strand through condensation reactions between a 5’ phosphate and a 3’ hydroxyl group

What is the result of the arrangement of nucleotides?

A sugar-phosphate backbone covalently linked by phosphodiester bonds

What is the structure of DNA?

Two complementary strands line up in opposite directions, anti-parallel, with the bases facing inwards and connected by hydrogen bonds (A-T, C-G), with the double stranded molecule twisting in order to adopt a more stable energy configuration (double helix)

What is the structure of RNA?

The polynucleotide chain remains single stranded, but may fold upon itself to form double stranded motifs (cloverleaf shape of a tRNA molecule)

What are the differences between DNA and RNA?

DNA:

• Sugar is deoxyribose

• Has thymine

• Is double stranded

RNA:

• Sugar is ribose

• Has uracil

• Is single stranded

Who discovered the structure of DNA?

Watson and Crick (using Franklin’s model that they stole from her desk without asking)

What did Watson and Crick’s model demonstrate?

• A double helix structure composed of antiparallel DNA strands

• Internally facing bases with complementary pairing

What does it mean if DNA replication is semi-conservative?

One strand is from an original template molecule and one strand is newly synthesised, because each base pair will only pair with its complementary partner and thus ensure the sequence is conserved

What does helicase do?

• Unwinds and separates the double stranded DNA

• Breaks the hydrogen bonds between the base pairs

What does DNA polymerase III do?

• Free nucleotides line up opposite complementary partners

• DNA Polymerase III covalently joins the free nucleotides together

What did the Meselson-Stahl experiment support?

The theory that DNA replication occurred via a semi-conservative process

How did the Meselson-Stahl work?

They incorporated radioactive nitrogen isotopes into DNA

• Templates were prepared with the heavier ¹⁵N

• New sequences were replicated with lighter ¹⁴N

The DNA was separated via centrifugation in order to determine its composition of radioisotopes