Chapter 1 - Biochemistry Flashcards
Properties of Water
- Cohesion
- Adhesion
- Specific Heat Capacity
- Specific Heat of Vaporization
- Density
- Strong Polarity (Aq)
- Disassociation of Ions
Cohesion
- The attractive force between like molecules (water molecules are attracted to other molecules)
- This causes water to have a high surface tension
Adhesion
The attraction between two different substances (water and another molecule)
Specific Heat Capacity
- Water has a high specific heat capacity because the hydrogen bonds between the molecules cause water to absorb large amounts of thermal energy as temperature increases or lose large amounts of thermal energy as temperature decreases
- This allows organisms to maintain a constant body temperature
Specific Heat of Vaporization
- Water has a high specific heat of vaporization because the hydrogen bonds absorb large amounts of thermal energy and become vapour
- This has an evaporation and cooling effect on organisms
Density
- Solid water is less dense than liquid water
- As the water reaches 0 degrees Celsius the hydrogen bonds between the molecules push the molecules further apart, thus reducing the density of solid water
- This is why ice floats on water
Strong Polarity
- Water molecules are strongly polar
- Other polar molecules can dissolve in water (they can break the cohesive forces)
- We call these polar molecules that can dissolve hydrophilic molecules
- Those that cant dissolve in water are referred to as hydrophobic molecules
-Small hydrophobic substances are somewhat soluble in water
Disassociation of Ions
- Water is easily able to disassociate into ions
- This process is known as autoionization
- When the concentration of H3O+ in a solution is greater than in the reverse scenario, it has the property of a base
- It is important for living things to maintain the proper pH of their surroundings
Acids
- Conduct electricity
- Increase hydronium ion concentration when dissolved in water
Ionization and pH
- Water has a neutral pH of 7
- Living organisms have some control over the internal pH of their bodies using buffers
- A buffer is a chemical that compensates for pH changes in a solution accepting or donating H+ ions
- eg. One buffer used to help maintain blood in pH humans is carbonic acid (H2CO3)
Carbohydrates
Classified into three main groups: Monosaccharides, Disaccharides, Polysaccharides
Monosaccharides
- Single sugar unit
- Building block for more complex carbs
- Have 3-6 carbons in the molecule
- Overall chemical formula: (CH2O)n
- Occur in a linear form, but when in water (cells) form a ring
- Highly dissolvable making them very sweet
- Three main types are
- Glucose
- Fructose
- Galactose
- All three monosaccharides are isomers of each other
Disaccharides
- Disaccharides consist of two monosaccharides that are joined together by a dehydration synthesis reaction
- A bond called a glycosidic linkage forms between the two monosaccharide units
- Still very soluble in water and sweet, although less so than monosaccharides
- Three main disaccharides:
- Maltose (formed from a glucose + glucose)
- Sucrose ( formed from a glucose + fructose)
- Lactose (formed from a glucose + galactose)
Maltose
- Glucose + glucose (both alpha)
- Found in ‘malt’ which occurs when grains such as barley are soaked
- Alpha 1-4 glycosidic linkage
Sucrose
- Gluctose + fructose
- Found abundantly (produced naturally in plants)
- Alpha 1-5 glycosidic linkage
Lactose
- Glucose + galactose
- Found in milk and dairy products
- Beta 1-4 glycosidic linkage
Polysaccharides
- A polysaccharide is a chain of monosaccharides with many subunits joined by glycosidic linkages
- They are very large molecules (polymers)
- The most common are:
- Starch
- Glycogen
- Cellulose
- Chitin
- Are linear but can be highly branched
- Are polar and hydrophilic. - However, because they are so large, they attract water but cannot dissolve in it
Starch
- Made by plants
- Includes the polysaccharides amylose and amylopectin
- Made up of only alpha-glucose
- Amylose is linear…made up of only 1-4 glycosidic linkages
- Amylopectin is branched…has 1-4 glycosidic linkages but some 1-6 links as well
Glycogen
- ‘Animal’ starch (how animals, fungi, bacteria ‘store’ sugar)
- Made up of glucose with 1-4 and 1-6 glycosidic linkages
Cellulose
- The main component of plant cell walls
- Made up of beta-glucose from beta 1-4 glycosidic linkages
- The most abundant organic molecule on Earth
- The enzyme cellulase is needed to digest it (our digestive system does not contain or produce cellulase)
- Also known as ‘fiber’
Chitin
- Chitin is a polymer of N-acetylglucosamine (a derivative of glucose)
- Found in the cell walls of fungi and the exoskeletons of arthropods
What are Lipids?
- A general term for a variety of non-polar biological molecules
- They are mostly composed of H, C and some O
- They do not dissolve in water
- Function include
- Energy storage
- Hormones
- Component of cell membranes
Fatty Acids - Lipids
- The structural backbone of most Lipids is derived from fatty acids
- They consist of a single Hydrocarbon chain with a carboxyl functional group (COOH) at one end
Saturated - Lipids
- If the Hydrocarbon chain has only single bonds between the carbons, then that chan is said to be saturated with the maximum number of hydrogens
- Fats with fatty acid chains that are saturate
- Solid at room Temperature
- Often originate from animal products
- eg. Butter, coconut milk
Unsaturated - Lipids
- If the Hydrocarbon chain only has one or more double bonds between the carbons, then the chain is unsaturated
- Fats with one or more fatty acid chains that are unsaturated
- Liquid at room temperature
- Often originate from plants
- eg. oils (olive, safflower, etc)
Fats - Lipids
A lipid that is made from two types of molecules: fatty acid and a glycerol molecule. In a triglyceride (most common fat) three fatty acid chains are joined to a single lgycerol molecule
Phospholipid
- A phospholipid is a lipid that consists of two fatty acids and a phosphate group bound to glycerol
- Main component of cell membranes
- The top of the molecule is polar
- The bottom is non-polar
- Phospholipids will arrange themselves in a bilayer or micelle in an Aq solution
Steroids - Lipids
They are the most abunant type of steroid and have a single OH group on the end
Cholesterol - Steroid
- Important part of anial cell membranes (for stabilization)
- Plants have similar sterol (phytosterol)
- Cholesterol converts into Vitamin D
- Too muchcholesterol and saturated fats in the bloodstream has been linked to the development of atherosclerosis
- LDL/HDL
Waxes
- Large liid molecules made of long fatty acid chains linked to alcohols or carbon rings
- Hydrophobic
- Non-polar
- Solids over a range of temperatures
- Eg. cutin is a wax produced by plants for waterproofing
Proteins
- All proteins are polymers that are composed of amino acid monomers
- Proteins fold into three-dimensional structures that specify their function
- Proteins carry out vital structural and functional roles in living things
- All amino acids share the same basic chemical structure - What differs in each is the R group
- In solution, the amino group bonds to an H+ while the carboxyl group releases an H+
Essential Amino Acids
Histidine
Isoleucine
Leucine
Lysine
Methionine
Phenylalanine
Threonine
Tryptophan
Valine
Protein Structure
- Peptide bonds link amino acids together
- A chain of amino acids is referred to as a peptide
- A peptide with more than
- 50 amino acids is a polypeptide
- A protein includes one or more polypeptides that are folded into three-dimensional shapes
- The shape of a protein determines its function
Four Levels of Protein Structure
- Primary
- Secondary
- Tertiary
- Quaternary
Tertiary Structure Stability
- H-bonding
- Ionic bonds
- Van der Waals
- Disulfide bridges
- Proline kinks
What are Enzymes?
They are biological catalysts (usually proteins) that speed up chemical reactions
Substrate
A substance or surface which an organisms grows and lives on and uses as food
Active Site
A pocket or groove in an enzyme
How do Enzymes and Substances Interact?
Induced fit hypothesis
Induced Fit Model
Describes how an enzyme changes shape to better accommodate a substrate
Induced Fit Hypothesis
The enzyme binds to one or more substrates forming an enzyme-substrate complex. The enzymes remain unchanged after the reaction and can bind to other substrates.
Cofactors
A non-protein group that binds precisely to an enzyme eg. Fe, Cu, Zn
Coenzymes
Cofactors that are organic (non-metals) are called coenzymes. They are usually derived from water-soluble vitamins eg. NAD+
Conditions that Affect Enzyme Activity
- Enzyme substrate concentration
- Temperature
- pH
- Control mechanisms (adjust reaction rates)
- Enzyme inhibitors
Competitive Inhibition
A situation in which a competitor substance binds to a normal substrate binding site to block enzyme activity
Non-competitive Inhibition
A situation in which molecules bind to an enzyme at a site that is not the active site, thus blocking enzyme activity
Allosteric Control of Enzyme Activity
- Some molecules behave like non competitive reversible inhibitors
- These molecules bind to an enzyme on a site that is not the active site, called the allosteric site
- This causes a change in the shape of the enzyme, thus affecting the active site
- This regulation of one site on an enzyme by binding to another site on a enzyme is called allosteric regulation
- Allosteric control can be activating or inhibiting. (The allosteric activator can either increase the affinity of the enzyme for the substrate or lower the affinity.)
Feedback Inhibition
- Often, allosteric inhibitors are the very product of the biochemical pathway that it regulates. If the product starts to accumulate, then it will act as an inhibitor to stop or slow down the enzymatic reaction that produces it
- This regulation of a pathway by one of the products of the pathway is called feedback inhibition
