Biochem Exam 1

covalent bonds

• strong sharing of electrons

• hold atoms together so molecules are formed

noncovalent bonds

weaker bond; do not share electrons

macromolecules

have a sense or directionary

biomolecules

3 dimensional architecture, weak forces

macromolecule examples

proteins, lipids, nucleic acids, polysacharides

monomer examples

amino acids, nucleotides, fatty acids, monosacharides

linkage examples

peptide(amide), glycoside, phosophpodiester, ester

____ forces influence structure and behavior; create interactions that are constantly forming and breaking, restrict organisms to a narrow range of environmental conditions

weak

examples of weak forces

vander Waals interactions, hydrogen bonds, ionic interactions, hydrophobic interactions

prokaryotic cells

single membrane, no nucleus(has a nucleoid) or organelles

eukaryotic cells

much larger, nucleus + many organelles

high BP, heat of vaporization, surface tension, polar

unique properties of water

hydrophilic

water loving, polar/charged, ions, alcohols, proteins, nucleic acids

hydrophobic

water fearing, no polar, oils & cholesterol

amphipathic

both hydrophobic and hydrophilic, polar and non polar ends, fatty acids and detergents

dipeptide

2 residues

each amino acid unit is called a

residue

tripeptide

3 residues

12-20 residues

oligopeptide

many residues

polypeptide

monomeric

only 1 polypeptide chain

multimeric

more than 1 polypeptide chain

homomultimer

one kind of chain

heteromultimer

two or more different chains

isolated system

exchange neither matter or energy with their surroundings

closed system

may exchange energy ; not matter

open system

may exchange matter and/or energy

enthalpy

heat content of a system

heat absorbed in a constant pressure process

endothermic

when heat is absorbed by a system

exothermic

when a system loses heat to the surroundings

entropy

a measure disorder of randomness/disorder in a system

an organized or ordered state is:

low etnropy

a disordered state is:

a high entropy state

1st law of thermodynamics

the total energy of the universe must be constant

• cannot be created or destroyed

2nd law of thermodynamics

the entropy of an isolated system will tend to increase maximum volume

entropy is unchanged by ____ processes

reversible

entropy increases for _____ processes

irreversible

• all naturally occurring processes proceed toward _____, that is, to a state of minimum potential energy

• forward and reverse reactions occur at the same rate

• No net change in reactant or product concentrations

• ΔG = 0

equilibrium

homeostasis

• organisms maintain homeostasis by keeping the concentrations of most metabolites at steady state

• in a steady state, the rate of synthesis of a metabolite equals the rate of breakdown of this metabolite

Reduced coenzymes

NADH and FADH

nucleotide functions

energy for metabolism, enzyme cofactors, signal transduction

nucleic acid functions

storage, processing and transmission of genetic info, protein synthesis

nucleotide components

nitrogenous base, pentose, phosphate

nucleoside components

nitrogenous base, pentose, no phsphate

nitrogenous bases are

planar

nitrogenous bases absorb uv light around

250-270nm

pyrimidines

cytosine, thymine, uracil

purines

adenine and guanine

Nutrigenetics

 embodies the science of intensifying and characterizing gene variants associated differential responses to nutrients and relating this variation to disease status 

• focuses on differences at SNP (single-nucleotide polymorphism) level

Nutrigenonics

studies of constituents of the diet interact with genes and their products and how

• focuses on the effects of nutrients on the genome, protons, and metabolism

↑ Reactants

→ shift toward products

↑ Products

• → shift toward reactants

↑ Temperature

• → favors endothermic reaction

↓ Temperature

• → favors exothermic reaction

↑ Pressure (gases)

• → shift toward fewer gas molecules

↓ Pressure (gases)

• → shift toward more gas molecules

Negative ΔG

 exergonic

Positive ΔG

endergonic

Endergonic reaction

• Requires energy; nonspontaneous

Exergonic reaction

Releases energy; spontaneous

Negative ΔH (energy released)

• favors spontaneity

Positive ΔS (increased disorder)

 favors spontaneity

ΔG

 change in free energy

ΔH

 change in enthalpy (energy in bonds)

ΔS

change in entropy (disorder)

Free Energy (G)

second law in open systems, energy available to do work at constant temperature and pressure

• G=0 is equilibrium/ G>0 is non-spontaneous or endergonic/ G<0 is spontaneous or exogonic

Phospholipids

• polar head + nonpolar fatty acid tails

Fatty acids

charged carboxyl group + hydrocarbon chain

Detergents & bile salts

•  help mix fats with water

Nucleus

Stores DNA; controls gene expression; nucleolus makes ribosomes

Mitochondria

Produces ATP; cellular respiration; regulates apoptosis

Rough ER

Synthesizes proteins for secretion and membranes

Smooth ER

Lipid synthesis; detoxification; calcium storage

Golgi Apparatus

Modifies, sorts, and packages proteins and lipids

Ribosomes

Protein synthesis (free → cytosolic proteins; bound → secreted/membrane proteins)

Lysosomes

Intracellular digestion; breakdown of macromolecules and old organelles

Peroxisomes

Fatty acid oxidation; detoxifies hydrogen peroxide

Cytoskeleton

Cell shape, movement, and intracellular transport

Plasma Membrane

Selective barrier; regulates transport and cell signaling

Chloroplasts (plants)

Photosynthesis

Vacuole

Storage; maintains turgor pressure in plant cells

Cell Wall

Structural support and protection

Centrosome/Centrioles

Microtubule organization; spindle formation during cell division

System

portion of the universe w/which we are concerned 

SNP

 occurs within a gene, having more than one allele 

• may lead to variations in amino acid sequence 

• not just genes

Genome Wide Association Study (GWAS)

working towards detection, treatment, and prevention to find SNP associated with a trait or disease 

Genotyping

• Laboratory method to identify specific genetic variants

• Tells which alleles an individual has

• Does not analyze traits or inheritance

Linkage Analysis

• Family-based method

• Tracks inheritance patterns of traits

• Identifies genes near each other on chromosomes

• Focuses on co-inheritance, not population association

omics

 large-scale study of an entire set of biological molecules in a system

Genomics

•  entire genome (DNA)

Transcriptomics

• all RNA transcripts

Proteomics

• all proteins

Metabolomics:

• all metabolites

Epigenomics

• gene-regulating chemical modifications

Lipidomics

• all lipids

Microbiomics

• microbial communities

Single gene disorder

PKU and lactose intolerance 

Complex disorder

nutritional modifies the expression of genes and metabolism of nutrients varies by genotype 

Thrifty gene hypothesis

obesity used to be beneficial for energy storage, might explain the increase in obesity