Untitled Quiz

Biochemistry Study Notes

• Biochemistry aims to explain biological form and function in chemical/molecular terms.
• Living organisms share remarkable similarity in their chemical makeup, distinct from non-living matter.
• Fewer than 30 naturally occurring chemical elements are essential to organisms.
• Hydrogen, Oxygen, Nitrogen, and Carbon make up 99% of living matter.
• The lightest elements form the strongest bonds.
• Trace elements are important for enzymes and other specific functions of proteins. Hemoglobin, for instance, needs iron to transport oxygen.
• Red- structural components of cells, required to eat grams/day.
• Yellow - trace elements required for specific pathways, requires only a few mg/day
• Biomolecules are compounds of Carbon with a variety of functional groups.
• Versatility of carbon bonding is a major factor in selecting carbon compounds for molecular machinery during evolution.
• No other element can form molecules of such widely different sizes, shapes, and compositions.
• Free rotation differs for C-C single and double bonds. Single bonds allow for free rotation unless large or charged groups are attached, while double bonds do not.
• Common functional groups are important for macromolecules: Methyl, Ethyl, Phenyl, Amino (protonated), Carbonyl (aldehyde), Carbonyl (ketone), Carboxylate (carboxyl), Hydroxyl (alcohol), Sulfhydryl, Disulfide, Phosphoryl.
• Many biomolecules are polyfunctional, meaning they contain multiple functional groups.
• The chemical "personality" of a molecule is determined by the chemistry of its functional groups and their orientation in 3D space.
• Most macromolecules are polymers with molecular weights above ~5,000 Da.
• Macromolecules are assembled from relatively simple monomers.
• Examples of macromolecules include proteins, nucleic acids, and polysaccharides.
• Lipids are important but technically not macromolecules (not polymers).
• Proteins and nucleic acids are informational macromolecules. The monomers are amino acids, monosaccharides, lipid monomers, and nucleotides respectively, while the polymers are proteins, polysaccharides, lipids, and DNA/RNA respectively.
• In informational macromolecules, the order of monomers affects the function. The sequence of different amino acids in a protein, for example, determines its 3D structure and function.

Water Study Notes

• Water is the medium for life, typically comprising 70-90% of organisms.
• Biochemical reactions mostly occur in the aqueous environment of the cytoplasm.
• Water is a critical determinant of the structure and function of proteins, nucleic acids, and membranes.
• Water has relatively higher melting and boiling points compared to other common solvents.
• Water's properties like this are due to hydrogen bonding between adjacent water molecules.
• Attractions between adjacent water molecules lead to high internal cohesion.
• At room temperature (RT), thermal energy is similar to the energy required to break hydrogen bonds. Therefore, hydrogen bonds form and break rapidly in water.
• Hydrogen bonds are longer and weaker than covalent bonds
• Water molecules are dipolar, with partial positive charges around their hydrogen atoms.
• These partial charges lead to electrostatic attraction between water molecules.
• The oxygen nucleus attracts electrons more strongly than hydrogen. Oxygen is more electronegative.
• Shared electrons are on average more near the oxygen atoms, resulting in two dipoles.
• Each hydrogen atom has a partial positive, and the oxygen a partial negative charge. This leads to the electrostatic attraction between the hydrogen of one water molecule and the oxygen of another.
• The result is that many water molecules can interact simultaneously through hydrogen bonding—like a 'network'.
• The number of other water molecules a single water can form H bonds with is four in ice or 3.4 on average in water.
• Water's regular crystal lattice structure in ice is why ice is less dense than liquid water and why ice floats on water.
• In liquid water, H-bonds are constantly forming and breaking.
• H- bonds are important in orienting interacting molecules in 3D space (orientation).
• There are two types of bonds in water: Covalent and hydrogen.

Weak Interactions Study Notes

• Weak interactions are attractive or repulsive forces between molecules and non-bonded atoms.
• These forces can be, for example, electrostatic interactions, hydrogen bonding, van der Waal's interactions or hydrophobic interactions.
• Covalent bonds represent a stronger force of attraction compared with the weak interactions.
• Covalent bonds are crucial to biological processes. If covalent bonds had to be broken every time biological processes occurred, it would be an energetically costly process.
• Hydrogen bonding interactions are responsible for the properties of water.
• Electrostatic interactions are crucial in determining the structure and function of proteins.
• Hydrophobic interactions are caused by the interaction of hydrophobic molecules in water.
• Van der Waal's forces are very weak attractions.
• These weak interactions result from temporary fluctuations in electron distribution around atoms and molecules.
• When these temporary dipoles approach, they influence each other giving rise to a very weak attractive forces between them.
• The strength of Van Der Waals is much less than H-bonding, but they add up when there is a large number of molecules.
• These interactions are essential to the structure and function of proteins, DNA, and other biological molecules.
• These interactions can be crucial to keeping molecules in particular 3D arrangements

Macromolecules Study Notes

• Macromolecules are polymers assembled from relatively simple monomers. These have molecular weights above ~5,000 Da.
• Proteins, nucleic acids and polysaccharides are examples of macromolecules.

Thermodynamics Study Notes

• The chemical composition of living organisms changes with environmental changes (e.g., temperature).

• However, changes in the population of the molecules within organisms are minimal.

• Living things are constantly making new molecules. The rates of synthesis and breakdown are often equivalent.

• Small and large molecules are constantly being synthesized and broken down in chemical reactions, leading to a constant flux of mass and energy within living systems.

• A chemical reaction is defined as either exergonic or endergonic depending on whether or not free energy is released.

• In a closed system, chemical reactions will proceed spontaneously until equilibrium is achieved.

• Equilibrium means that the rate of product formation equals the rate of conversion to starting reactants. No net change in the concentrations of components.

• In an open system (e.g., living cells), chemical reactions can proceed spontaneously until equilibrium is reached.

• The entropy of the universe is continually increasing. The more disordered a system is, the higher the entropy.

• A biological process that requires energy is called endergonic, while one that releases energy is called exergonic (both are spontaneous.)

• The criterion for spontaneous reactions is ΔG (negative value).

• The values of ΔG are affected by both heat content (ΔH) and randomness (ΔS).

• When ΔG is negative, the reaction is exergonic; when ΔG is positive it is endergonic.

• Large changes in ΔGº lead to large changes in K'eq since there is a relationship between the two values.

• Standard free energy changes (ΔGº) are standard conditions; 25°C, 1 M, 1 atm of pressure.

• Biochemists use (AG') to reflect the typical conditions found in biological systems.