BCH Week 1 - Lec 1 - Biomolecules

what are the two main types of bonding patterns

covalent bonds and non-covalent bonds

covalent bonds

• atoms share electrons in covalent bonding

• biomolecules are held together through these bonds

non-covalent bonds

• bonds not involving electron sharing

  • i.e. hydrogen bonds (Van der Waals), ionic bonds, hydrophobic interactions

polarity of covalent bonds - what determines this

• covalent bonds can be polar or non-polar

  • polar - unequal e- sharing which creates ± dipoles

  • non-polar - equal e- sharing

• if the difference in electronegativity between the atoms is >0.5, the atom with the higher EN attracts more e-s

what are ionic bonds (aka electrostatic interactions)?

• attractions between oppositely charged molecules

  • i.e. Na+ and Cl-

what are hydrogen bonds?

• dipole-dipole interactions between a partially positive hydrogen atom (covalently bonded to electronegative N, O, or F) and another electronegative atom with a lone pair

what are hydrophobic interactions?

• the exclusion of non-polar (like oil) substances from water (which is polar)

• non-polar molecules will aggregate together

what is the cell membrane like?

• the phospholipid bilayer makes up cell membranes

• membranes have a hydrophobic interior due to the hydrophobic tails

• extracellular and intracellular surfaces of the bilayer are hydrophilic

can hydrophilic, hydrophobic, and charged molecules pass through the bilayer structure easily?

no, therefore, cells need transporters to support the movement of molecules that struggle to pass through the lipid bilayer

what are functional groups?

functional groups are formed by atoms found in organic molecules, they have predictable non-covalent bonding patterns based on their polarities

what group is this?

hydroxyl group

what group is this?

sulfhydryl group

what group is this?

carbonyl group

• ketone on top (COR)

• aldehyde on bottom (COH)

what group is this?

carboxyl group

what group is this?

ester group

what group is this?

phosphoryl group

what group is this?

amino group

what group is this?

amido group aka amide

what group is this?

methyl group

what group is this?

thioester group

what functional groups can participate in H bonding

• hydroxyl

• carboxyl (uncharged)

• amino (uncharged)

• amido (uncharged)

what functional groups participate in ionic bonds?

• carboxyl (RCO²-)

• phosphoryl (–PO4²-)

• amino (RNH³+)

what functional groups participate in hydrophobic interactions?

• methyl

Why do you think the addition or removal of a phosphoryl group can completely change the function of the molecule?

The addition or removal of a phosphoryl group dramatically changes a molecule’s charge and conformation due to the highly EN O atoms, altering its interactions and switching enzyme activity on or off.

why does the cleavage of phosphate from ATP release energy?

ATP hydrolysis releases energy because the products are more stable than ATP due to reduced electrostatic repulsion, increased resonance stabilization, and improved hydration.

what are monosaccharides, what atoms do they contain?

• monosaccharides are the monomers of carbohydrates

• they contain carbon atoms and water (H2O)

carbohydrate composition and general naming

• carbs have a minimum of 3 Cs and each has a hydroxy group except one, which is either an aldehyde or a ketone

• general naming of carbs is based on the number of Cs and whether it is an aldehyde or ketone

are monosaccharides linear or cyclic?

they can exist as linear that can be converted to cyclic

• this is because linear carbs react in solution as certain C positions (i.e. aldehydes at C5) to form a ring structure

  • aldohexose → glucose

  • ketohexose → fructose

what type of carbs make up dietary carbs? what foods contain these carbs?

• dietary carbs are polymers of hexose monosaccharides

• specifically, glucose, fructose, galactose

  • Starches & grains → glucose

  • Fruits & sweeteners → fructose

  • Dairy → galactose

how do monosaccharides bond to one another?

• via glycosidic bonds to form disaccharides and polysaccharides

• very strong binding

  • glucose + glucose = maltose

fatty acid key functions in the body

• fatty acids are a main lipid category

  • they provide fuel for cells, have structural functions (phospholipids), are used in recognition (glycolipids), etc.

dietary sources of lipids

nuts, cheese, oil, fast food, etc.

how do you differentiate between saturated and unsaturated fatty acids?

• saturated - the hydrocarbon chains in saturated fatty acids are linked by single bonds, giving them a higher melting point because they can pack better together

• unsaturated - cis double bonds in the hydrocarbon chain create a kink in the molecule, making the section very hydrophobic, and the double bonds decrease the melting point of the fatty acids

what type of functional groups do fatty acids have at the end?

carboxyl

what do fatty acids link themselves to and how? what is the attachment pattern usually like?

fatty acids attach to a glycerol backbone via ester linkages (very strong)

• they create mono, di, or tri-glycerides - this is how we store fatty acids in our body

• the first fatty acid attached is usually saturated, second is usually unsaturated, and third can be either or

• fatty acids are stored in adipocytes and when oxidized, release a considerable amount of ATP

what are amino acids and what are some functions?

• amino acids are the building blocks of proteins in the body

• some functions

  • enzymes - each have their respective locations, descriptive names

  • transporters - deliver materials across PM of cells

    • i.e. albumin - found in plasma binds to fatty acids and delivers to cells to use as a fuel source

    • lipoproteins - transport lipid material (LDL, HDL, VODL)

  • many other functions in cells and body

what are some dietary sources of protein?

• nuts

• lentils

• beans

• cheese

• tofu

• meat

general structure of amino acids

• a central carbon that holds: an amino group + R group + carboxyl group

• the R group varies based on the specific amino acid

what amino acids are polar? and what non-covalent bonds do neutral polar amino acid R groups participate in?

serine, threonine, tyrosine (np ring but OH group likes water), asparagine, glutamine, cysteine

they participate in hydrogen bonds

what amino acids are non-polar? and what non-covalent bonds do neutral non-polar amino acids participate in?

they participate in hydrophobic interactions

which amino acids are negatively charged? what are their characteristics and what type of bonding do they take part in?

• at a pH of 7, the acidic R groups of these amino acids are negatively charged

• and they take part in ionic bonds (aka salt bridges)

which amino acids are positively charged? what are their characteristics and what type of bonding do they take part in?

• at a pH of 7, the basic R groups will be positively charged

• they take part in ionic bonding (aka salt bridges)

what amino acids should we know for quiz 1 and test 1?

• Cysteine

• Glutamate

• Aspartate

• Asparagine

• Glutamine

• Proline

• Methionine

• Serine

• Valine

• Tryptophan

• Glycine

• Histidine

what bonds do amino acids form with one another?

• peptide bonds to be incorporated into proteins - very strong

  • H bonding between the negatively charged O on the carboxyl group of one amino acid and the H from the positively charged amino group on the other amino acid

• the R groups of amino acids determine the overall shape of each protein

general nucleotide structure

• nitrogenous base

• 5-C sugar (ribose in RNA, deoxyribose in DNA where one OH is not present)

• phosphate group

what are the two nitrogenous base types?

purines - double ring structure

• include adenine and guanine

pyrimidines - single ring structure

• thymine, uracil, cytosine

what are some examples of nucleotides in the body?

• nucleic acid - DNA/RNA

• various coenzymes - NAD+, NADP+

• energy molecules - ATP, GTP

what bonding helps to synthesize nucleic acids from nucleotides?

• phosphodiester bonds