UNIT 1: BIOCHEMISTRY

Why is water cohesive/adhesive

Water’s hydrogen bonds cause a high level of polarity (and strong attractive partial charges) which allows for bonding with other water molecules and other polar molecules.

Why does water have a high specific heat capacity.

Water’s strong hydrogen bonding and as you must break those bonds to heat it up, a lot of energy must be used

Why is water the perfect solvent

Water is highly soluble because polar molecules can easily ionize with the positive and negative ions of other molecules

Why is ice less dense than water

Ice is less dense than water because when water freezes, the molecules slow down and their tetrahedral position becomes fixed, leaving empty space within the barriers of the molecules and decreasing its densit

Why is carbon so fundamental

1. Can make 4 bonds

2. Large and stable molecules can be formed

3. Formed stable bonds at moderate energy levels that won’t be broken spontaneously

4. Relatively small amount of energy is needed to break and reform bonds

Hydroxyl

Carboxyl

Carbonyl

Amino

Sulfhydryl

Phosphate

Properties of hydroxyl

• Polar covalent

• Soluble in water

Properties of carboxyl

• Weakly ionic

• Acidic

• Soluble

Properties of carbonyl

• Weakly polar

• Soluble in water

Properties of aminos

• Ionic

• Basic

• Soluble

Properties of sulfhydryls

• Non-polar

• Insoluble in water

Properties of phosphates

• Ionic

• acidic

• soluble in water

single unit of molecule

monomer

repeated string of monomers (100s-1000s)

polymers

oligomers

short polymers (≈3-20)

how do you build polymers

condensation or dehydration synthesis

• removing water from two monomers

• each monomer joins at hydroxyl

• h from one monomer attaches to oh from second creating water and a greater string of monomers

how do you break up polymers

hydrolysis

• adding water to split polymers

• h goes to one string of monomers and oh goes to other string

what basic biomolecule does not have true monomers

lipids

What is the typical molar ratio of a carbohydrate

CH₂O or 1:2:1

What are the elements of carbohydrates

Carbon, hydrogen, and oxygen

What are some structures/functions of carbohydrates

• Suitable for energy storage

• Play a structural role in the cell wall of plants

What is the monomer of a carbohydrate

monosaccharides

What are some key features of monosaccharides

• Small

• Polar (water soluble)

• Rich in chemical energy

• Form ring structures in solution

What differentiates α-glucose and β-glucose

α-glucose

• hydroxyl group points down

• used for energy

β-glucose

• hydroxyl group points up

• used for structure

What are the benefits of disaccharides

• Twice as much energy per molecule of monosaccharide

• Less osmosis which disrupts cell processes

What are the common disaccharides

• Maltose

• Lactose

• Sucrose

What are the common monosaccharides

• Glucose

• Galactose

• Frutose

What are the characteristics of polysaccharides

• Good for long-term energy storage

• Insoluble due to shape

What are the α-glucose polysaccharides

• Amylose

• Amylopectin

• Glycogen

What are the β-glucose polysaccharides

• Cellulose

• Chitlin

What are the characteristics of amylose

• Helix shape

• Made by plants for energy

• Starch

What are the characteristics of amylopectin

• Helix shape (w additional branches from 1,6 glycosidic bond)

• Made by plants for energy

• Even more starch than amylose

What are the characteristics of glycogen

• Helix shape with many branches

• Animal starch stored in liver and skeleton

• Breaks down faster as it has increased surface area

What are the characteristics of cellulose

• Strong and rigid

• In the cell walls of animals/plants

What are the characteristics of chitin

• Heightened strength due to additional amino groups

• In exoskeletons of insects/bugs

• Extra H bonds

What are the characteristics of lipids

• CHO

• less oxygen and more CH than carbs

• 2x as much usable energy as carbs (reserve of stored energy)

• non polar (insoluble in water)

What are the functions of lipids

• Waterproof (hydrophobic because of non-polarity)

• Protect vital organs

• Insulation (strong insulators against heat and electricity)

• Long-term energy storage (2x as much usable energy as carbs)

What are the types of lipids and how do you distinguish them

• Triglycerides

  • Glycerol condensed with 3 fatty acids

• Phospholipids

  • Two fatty acids attached to a phosphate group and a polar head

• Wax

  • Ester with long chain alcohol bonded to fatty acid (H’s are removed in the bond)

• Steroids

  • 3 hexagons and 1 pentagon

What is a membrane?

• A barrier that separates aqueous cell contents from the environment

• Made up of phospholipids

What are the types of membrane transport

• Passive (including facilitated)

• Active

How does regular passive transport work?

Regular:

• When molecules are small and non-polar enough they diffuse naturally (eg. O₂ and CO₂)

How does active transport work.

• Active transport goes against the concentration gradient and uses ATP to change protein shape

What is a hypotonic solution?

• A solution with a low amount of solute relative to the other side of the membrane and a positive net movement of water

What is an isotonic solution

• A solution with an equal amount of solute as the other side of the membrane and no net movement of water

What is a hypertonic solution

• A solution with a high concentration of solute relative to the other side of the membrane and therefore a negative net movement of water

How does osmosis work

Water molecules go from a dilute solution with a low concentration of solute to a concentrated solution with a high concentration of solute, leading to a positive net movement of water

What is bulk transport

Taking many things and moving them across the membrane (the membrane uses ATP to change shape to facilitate this)

What is endocystosis and three main types

Bulk transport into the cell

• Phagocytosis - cell eating (plasma membrane absorbs cells)

• Pinocytosis - cell drinking (plasma membrane absorbs extracellular fluid)

• Receptor-mediated endocytosis - specific eating (plasma membrane absorbs specific particles)

What is exocytosis

Bulk transport out of the cell

How does facilitated passive transport work

Facilitated:

• Go through proteins

• Channel protein is opening for molecules to go through

• Carrier proteins change shape for molecules

What is a protein

• Polymer of amino acids with complex 3-dimensional folding

What is the monomer of a protein

Amino acid

What are the key defining features of amino acids

• An amino

• Carboxyl

• R group

How does polymerization of amino acids work

• 2 amino acids link by the oh of the carboxyl on one and the H of the amino on the other to form a a peptide bond.

What is the difference between a polypeptide and a protein

• Any protein is a polypeptide but polypeptides are only called proteins if they have a specific function

What is the primary polypeptide structure

• A sequence/chain of amino acids

What is the secondary polypeptide structure

• When hydrogen bonds in the peptide chain interact causing folding in a repeated pattern

What is the tertiary polypeptide structure

• When interactions between remote R groups based on charges, attraction to water, size and shape

• This is when they are called proteins (typically in a globular form)

What types of interactions cause tertiary folding

• Hydrophobic exclusion

• Hydrogen bond

• Disulfide bridge

• Ionic bond

• van der Waals interaction

What is hydrophobic exclusion

• When non-polar hydrophobic R groups cluster together in the inside of the protein leaving hydrophilic amino acids to bond with water on the outside)

How does hydrogen bonding affect protein shape

• Some polar R groups can undergo hydrogen bonding, bending their respective polypeptide chains

What is a disulfide bridge

• Covalent links between the sulfur-having side chains of the R group cysteine (strongest of all the bonds that contribute to tertiary structures)

How do ionic bonds affect protein shape

• R groups with different charges can undergo ionic bonding, bending their respective polypeptide chains

What is a van der Waals interaction

• When two molecules come very close to each other inducing electrical charges

What is a quartenary polypeptide structure

• When multiple amino chains (typically secondary) attach

What kind of things can change the shape of a protein

• Any change in environment (eg. temperature or pH)

What is an enzyme and how does it work

• A protein that acts as a catalyst for a chemical reaction

• Each protein has an ‘active site‘ that is shaped for a substrate and therefore binds to it

• After they bind, the enzyme typically bends the substrate contorting the bonds and making them weaker/easier to break

What is the typical naming structure of an enzyme

(thing it breaks up/builds up)-ase

What are the key features that must be in the naming of a protein

• Polarity (non-polar or polar)

• Charge (negative or positive charge)

What are cofactors/coenzymes

• Things that bind to the active site to create a better fit and facilitate the building up or breaking down of molecules

• cofactors are typically metal ions while coenzymes are organic molecules

What is induced fit

• When an enzyme slightly changes shape to better bind to substrates

What structure can form enzymes

• At least tertiary structure is needed

What are the types of enzymes and what do they do

• Hydrolase: catalyzes hydrolysis

• Lyase: cleaves covalent bonds (without hydrolysis)

• Ligase: combines 2 molecules

• Transferase: transfers functional groups between molecules

• Isomerase: catalyzes spatial rearrangement of substrate

• Oxidoreductase: transfers electrons between molecules

What are the 6 components of membranes and what do they do?

Phospholipids

• Provides permeability barrier and matrix for protein

Transmembrane proteins

• Active and passive transport and transmission of information into cell

Interior proteins:

• Determines the shape of cells and act as anchor sites for proteins

Glycoproteins:

• Self recognition (your cells are your cells)

Glycolipids:

• Tissue recognition

Cholesterol:

• Membrane fluidity

What is the difference between diffusion and osmosis

• Osmosis is the movement of water through the membrane

• Diffusion is the movement of a solute in solution through the membrane

Which molecules can typically undergo diffusion?

• oxygen

• carbon dioxide