blg307 mol bio

the 4 major macromolecules

nucleic acids (DNA/RNA), proteins, carbohydrates, lipids

what are macromolecules built from?

from small organic molecules; cells are carbon-based

covalent bonds

STRONG electron sharing between atoms

noncovalent bonds

weak interactions that attract molecules without electron sharing; hydrogen bonds, ionic interactions, van der Waals forces

water as a solvent

drives hydrophilic vs hydrophobic interactions

hydrophilic molecules

interacts with water, often polar/charged

hydrophobic molecules

avoids water, nonpolar, cluster together in aqueous environments

phosphate groups

central to energy transfer and regulation

position of phosphate matters in SOME reactions

ATP ⇄ ADP cycle

main energy currency in phosphate groups

ATP hydrolysis

provides energy for synthesis of macromolecules and cellular work

pyrophosphate formation

one of the important energy release mechanisms

glycolysis

central ATP producing pathway

fermentation

ATP production without oxygen

citric acid cycle

generates NADH by oxidizing acetyl-CoA to CO₂

energy storage

sugars & fats stored; between meals, fatty acids supply energy

isomeric sugars

molecules with same formula but different structures

derivatives

-OH groups replaced with other functional groups

glycosidic linkages

α vs β positions → very different properties

amino acids

20 of them, polar, nonpolar, acidic or basic

polar amino acids

SOME have nonpolar characteristics, ex; Tyr, Thr

disulfide bonds

covalent bond between 2 cysteine side chains

protein folding

guided by α helices & β sheets (weak noncovalent bonds)

central dogma

DNA → RNA → Protein (flows in ONE direction)

second law of thermodynamics

heat flows spontaneously from hotter to colder objects, NEVER in reverse

total disorder of closed system always increases over time

phosphorylation

addition of a phosphate group to a molecule (regulatory or energetic role)

entropy

measure of disorder, increases spontaneously unless energy is added

what drives the folding of proteins in aqueous environments?

hydrophobic interactions and noncovalent bonds

what bond forms between two cysteine side chains?

disulfide bond

what’s the difference between α and β glycosidic bonds?

differ in orientation of the -OH group, leads to different structural/functional properties

central dogma

DNA → RNA → protein

4 major families of small organic molecules

sugars, fatty acids, amino acids, nucleotides

structural feature makes sugar hydrophillic

presence of multiple -OH groups

what defines alpha vs beta sugars?

orientation of -OH groups on anomeric carbon, determines properties of polysaccharide

part of fatty acid is hydrophobic?

long hydrocarbon chain

part of fatty acid is hydrophillic?

carboxylic acid head group

4 components bonded to central alpha carbon in amino acids?

amino group (-NH₂), carboxyl group (-COOH), hydrogen (-H), variable side chain (R group)

which amino acid can form covalent disulfide bonds?

cysteine, bond forms between sulfur atoms in their side chains

3 components of a nucleotide?

nitrogenous base, pentose sugar, 1 or more phosphate group

primary role of ATP in cell?

universal energy currency, hydrolysis to ADP releases energy to drive endergonic reactions

phosphorylation

addition of phosphate group, key for regulating protein activity and transferring energy

3 types noncovalent bonds

ionic, hydrogen, van der waals

how do noncovalent bonds stabilize large protein?

weak bonds acting together create strong force to stabilize proteins 3D structure

2nd law thermodynamics

towards disorder (increased entropy) creating order requires input of energy

biochem vs genetics

chemistry and function of molecules (vitro) vs genes and heredity in living systems (vivo)

founder effect

genetic drift = new population is founded by small number of individuals, loss of genetic variation, higher frequencies of rare alleles from original population

founder effect by natural selection?

no, by chance sampling during formation of new isolated population

humans (homo sapiens)

in Africa 200-300k yrs ago

migration out of Africa

approx 10k individuals migrated out 60-80k yrs ago (founders effect)

what supports “out of Africa”?

fossil evidence, anthropological studies, genome sequencing, shows non African populations carry traces of Neanderthal & Denisovan

interphase

cell growth, gene expression, DNA replication (S phase)

sister chromatids

2 identical copies of duplicated chromosomes

centromere

region where sister chromatids are joined

which phase of cell cycle is most variable in length?

G1 phase

Griffiths experiment with S & R bacteria

a transforming principle from dead S bacteria can change traits of live R bacteria

how did the Avery-MacLeod-McCarty experiment identify DNA as the genetic material?

destroying DNA in S strain extract removed its ability to transform R bacteria

crossing over (recombination)

exchange of DNA between homologous chromosomes during meiosis, creates new combination of alleles

mitosis

produces 2 genetically identical diploid cells for growth

meiosis

produces 4 genetically unique haploid cells for reproduction

chromosome theory

segregation & independent assortment of chromosomes during meiosis mirrors those of Mendel’s genes

what bond links nucleotides together in DNA strand

phosphodiester bond (between 5’ phosphate of one and 3’ OH of next)

antiparallel DNA strands

two strands run in opposite directions; 5'→3' and 3'→5'

Chargaff’s rules

DNA: %A=%T and %G=%C

why does a G-C base pair have a higher melting temperature than an A-T base pair?

G-C pairs are held together by 3 hydrogen bonds (STRONGER AND MORE STABLE) vs A-T pair with 2 hydrogen bonds

2 chemical features that stabilize DNA double helix

hydrogen bonding between base pairs and hydrophobic base stacking in interior

Rosalind Franklin

provided critical evidence for helical structure, diameter and spacing of bases

watson & crick model

suggested mechanism for how DNA could be replicated because each strand could serve as template for new complementary strand

purine found in DNA

double ring nitrogenous base, Adenine and Guanine

pyrimidine

single ring nitrogenous base, cytosine and thymine

melting temperature of DNA

temperature at which half DNA double helices separate into single strands

melting (tm) of DNA

temp at which 50% of DNA double helices are denatured into single strands and 50% is double stranded

GC content affect tm of DNA

higher gc → higher tm, G-C base pairs are more stable than A-T pairs

tm calculation

(A+T) x 2 + (G+C) x 4