Biochemistry Chapter 1-3

Smallest organisms

single cell, microscope

Larger multicellular organism

many cell, vary in shape size function

Plasma membrane

lipid +protein semipermeable membrane

Transport proteins

let specific things in/out

Receptor Proteins

signal transmission

Membrane enzymes

Reaction pathways

cytoplasm

everything inside the membrane

Cytosol

fluid part of membrane, contains small organic molecules (central metabolites)

Nucleoid

Bacteria/Archaea: no membrane around it

Nucleus

Eukaryotes, encolsed in double membrane

Lower size limit

minimum number is biomolecules needed to function

Upper size limit

diffusion, nutrients in, waste out

Three Domains of Life

Bacteria: single celled, no nuclear membrane, common environments

Archaea: single celled, no nuclear membrane, extreme environments

Eukarya: membrane bound organelles

Aerobic Habitat

plenty of oxygen, derive energy from transfer of electrons from fuel molecules to oxygen within cell

Anaerobic Habitat

devoid oxygen, microorganisms obtain energy by transferring electrons to N2, H2S, CO2

Photoautotroph

CO2 + light: dandilion

Photoheterotroph

organic compound + light: Heliobacteria

Chemoautotroph

CO2 + inorganic compound: hydrogen bacteria

Chemoheterotrophs

organic compounds + organic compounds: Humans

Cell envelope

plasma membrane + outer layers

Endoplasmic Reticulum/Golgi Complex

lipid/protein synthesis and processing

Peroxisomes

fatty acid oxidation

Lysosomes

digest cellular debris

Vacuoles

storage of organic acids

Actin filaments

thinnest, movement

Microtubules

help organism move/chromosomes

Intermediate filaments

structural support

Endomembrane system

segregates specific metabolic processes and provides surfaces for enzyme catalyzed reactions

Structural Hierarchy (small—> large)

Monomers, Macromolecules, Supermolecular Complexes, Organelles

Monomers

Nucleotides, amino acids, sugars

Macromolecules

Nucleic Acids, Proteins, Lipids, Carbs

Polymers with MW above 5,000

Supermolecular Complexes

Chromatin, Plasma membrane, cell wall

In vitro

studies cleaner can miss real cellular context

In vivo

crowded, other molecules interfere/interact

Goal of biochemistry

To understand the chemical basis of life by studying the structures, properties, and functions of biological molecules and the reactions they undergo.

Study of biochemistry

The study of the chemical substances and processes that occur in living organisms

Most abundant elements

C,N,O,H

Can form 1-4 bonds

Lighter elements, stronger bonds

Trace elements

Fe, Cu, Zn often needed for specific enzyme/proteins to function

Biomolecules

hydrocarbons + function groups swapped in for H

Methyl

CH3

Ethyl

C2H5

Phenyl

cyclohexene

Carbonyl (aldehyde)

COH

Carbonyl (ketone)

CO

Carboxyl

COO-

Hydroxyl

OH

Enol

Ether

Ester

Acetyl

Anhydride

Amino

NH3+

Amido

Imine

Guanidinium

Imidazole

Sulfhydryl

Disulfide

Thioester

Phosphoryl

Cyano

Phosphoanhydride

Proteins

Monomer: amino acid

Function: enzymes, structure, transport, signaling

Nucleic Acids

Monomer: nucleotides

Function: store, transmit genetic info

Metabolome

full set of small molecules in a cell under given conditions

Polysaccharides

Monomer: Sugars

Function: energy storage, structure, cell regulation

Proteome

Sum of all proteins functioning in given cell

Genome

sequence of cells DNA

Informational Macromolecules

Proteins and Nucleic Acids

Configuration

Breaking covalent bonds, Fixed, Cis/Trans, chiral centers

Conformation

Free rotation around single bonds, freely, rotational states

Sterioisomers

molecules with same chemical bonds and formula but different configuration

Stereospecific

requiring specific configurations in interacting molecules

Geometric (cis/trans) isomers

form non rotating double bonds

Chiral centers

carbon bonded to 4 diff groups

enantiomers vs diasteromers

mirror image vs not mirrored

Stereospecificity

All amino acids (-Glycine) L, Glucose/Sugars D

Dynamic Steady State

concentrations stay constant, molecules constantly being replaced

Open system

exchanges energy and matter

Closed system

exchanges energy not matter

Isolated system

exchanges neither

Organisms obtain energy in 2 ways

oxidizing chemical fuels, absorb sunlight

Entropy

randomness/disorder of a system

Entropy Glucose Oxidation

Aerobic organisms extract energy from glucose from their surroundings and oxidize it

Entropy Information

Living organisms highly ordered, information rich and entropy poor

Gibbs Free Energy

Delta G = Delta H-TDeltaS

Entropy Teakettle

heat spontaneously spreads out and randomizes

Delta G Negative

Exergonic, release energy, spontaneous (ATP→ADP)

Delta G Positive

Endergonic, gain energy, non spontaneous (ADP→ATP)

Bioenergentics

study of energy transformation in living systems

Keq

How far reaction proceeds before stopping

Enzymes

Mostly proteins, determine how matter and energy are channeled into cellular activities

Metabolism

catabolism + anabolism

Catabolism

break down molecules, release energy, ATP NAD(P)H

Anabolism

Builds up molecules, requires energy, proteins, nucleic acids

Genetic continuity

living things reproduce with near perfect fidelity across billions of years

DNA replication

strands separate, act as template, build new complementary strand produce 2 identical double helicases,

DNA Repair

Damaged strand uses other template to repair nucleotides

DNA → Protein

DNA transcribed to RNA, RNA translated into amino acid chain