Lecture 6 + 7

Primordial soup

Fundamental Ingredients: Water, heat, organic molecules, time

>200 million years of stuff sloshing around before first cell

Organic Molecules

make up 98% the dry weight of cells

Macronutrients

carbon based life forms

C is the most abundant element along with H, O, N, S, P

Micronutrients

in lower amounts: Na, K, Cl, Mg, Fe, Ca, etc

Carbin is an important building block

Stable bonds between carbons and stable bonds to many other atoms

Shape of organic molecules

3-D shape

Diverse functional groups

give organic molecules their distinct chemical properties

polarity of organic molecules

determines whether they are hydrophilic or hydrophobic

Hydrophobic

decrease solubility

• regions with many C-C and C-H bonds dont form H-bonds with water

Hydrophilic

they increase solubility

• most bonds involving non-C atoms can participated in H-Bonds

Four fundamental classes of macromolecules

carbohydrates

lipids

proteins

nucleic acids

what is often polymers?

bonds between carbon atoms form the backbone of some large biomolecules

carbohydrates

mostly C, H, O most or all carbon atoms are bound to oxygen (Typically: C2H2nOn)

N,P,S can also occur in functional groups

Large number of O and OH groups make sugars highly polar and soluble

Monosaccharide

a single sugar

can interconvert between linear and ring structures

isomers

same atoms in a different arrangement. The ring form is more stable and more commons

Ribose

component of RNA

core metabolic pathways

structured to utilize glucose as input

Grouping of monosaccharides

multiple monosaccharides can form disaccharides and polysaccharides through glycosidic bonds

Dehydration synthesis reaction

Two OH groups react, and one H2O molecule is lost

What are both formed from glucose?

Maltose and lactose but with different linkage

polysaccharides

longer carbohydrate polymers

can be linear, branched, or crosslinked

What is the most abundant biomolecule on earth

carbohydrates mainly due to cellulose

Lipids are composed of primarily?

C and H

possesses long hydrocarbon chains

Lipids are hydrophobic

avoid water and tend to cluster together

lipid single bond

saturated

lipid double bonds

unsaturated

lipid head group

polar

fatty acid head group

simple carboxylic acid headgroup and single hydrocarbon chain

Triacylglycerides

have a core glycerol molecule attached to three fatty acid chains

lipids are

important energy storage molecules

phospholipids

-are important components of biological membranes

-amphipathic

amphipathic

both polar and hydrophobic groups

this allows lipids to self-assemble into the lipid bilayer

phospholipid structure

A core glycerol is attached to two fatty acid chains, and to a modified phosphate group.

When bacteria is cultured?

fatty acids are extracted and analyzed in a gas chromatograph. Different fatty acids give distinct peaks in the resulting data which allows this to serve as a fingerprint for specific bacterial species

proteins

polymers of amino acids

amino acids contain

amine group

carboxylic acid group

central carbon with a side chain

(20 standard)

amino acids structure wise

has a different side chain with different chemical properties

How are amino acids linked?

linked by peptide bonds between amine and carboxylic acid groups

polypeptide

polymer of amino acids

backbone is flexible

primary structure

amino acid structure

polypeptides folding

unique 3d structure. The structure gives protein its structural and chemical properties.

Folding drive

to bury hydrophobic side chains from bulk water

what stabilizes the 3D protein structure?

electrostatic interactions between charged side chains, hydrophobic interactions, hydrogen bonds, covalent disulfide bonds between cysteine side chains

protein secondary structure

local folding of the backbone, stabilized by hydrogen bonds among backbone atoms

protein tertiary structure

three dimensional structure of a single polypeptide chain

proteins quaternary structure

interactions between multiple folded protein chains

-oligomeric state is often linked to function

proteins can be chemically modified

this influences function ((phosphorylation, glycosylation, etc)

protein function

determined by structure and primary sequence

Changes to the primary sequence can disrupt folding or function

nucleic acid

nitrogenous base, phosphate (negatively charged), deoxyribose

nucleotides are linked by

phosphodiester bonds between 3’ carbon and 5’ carbon

how do bases interact in nucleic acids

hydrogen bonding patterns forming base pairs

adenine: thymine

guanine: cytosine

this allows strands to hybridize, they run antiparallel directions

Metabolism

encompasses all the chemical reactions inside a cell

exergonic (energy)

reactions are spontaneous and release energy

endergonic (energy)

reactions consume energy

catabolism (biological molecules)

reactions that break down complex molecules into smaller components, releasing energy

anabolism (biological molecules)

reactions that build complex molecules from simple components, req energy input

autotrophs

convert inorganic CO2 into organic carbon molecules

heterotrophs

use existing organic molecules as nutrients (originally created by autotrophs)

phototrophs

energy captured by light

chemotrophs

energy from breaking chemical bonds

organotrophs (chemical)

use organic compounds

lithotrophs (chemical)

use inorganic sources

chemoautotrophs

chemical reactions provide energy, and inorganic carbon serves as the carbon source

chemoheterotrophs (most organism/bacteria)

break down organic molecules for energy and as a carbon source

photoautotrophs

energy from light, and uses CO2 as a carbon source (cyanobacteria)

photoheterotroph

get energy from light, but cannot use CO2 as a carbon source. They must consume organic compounds (purple nonsulfur bacteria)

energy is stored

in high energy electrons

redox reactions

transfer electrons allow the cell to harness this energy

redox: oxidation reactions

remove electrons from donor molecules, leaving them oxidized

redox: reduction reactions

adds electrons to acceptor molecules, leaving them reduced

When cells break chemical bonds in organic molecules

they capture energy either by extracting a high energy electron or storing energy in the bonds of ATP

Electron carriers

bind high energy electrons and shuttle them around the cell

NAD+/NADH

nicotinamide adenine dinucleotide

NADP+/NADPH

nicotine adenine dinucleotide phosphate

FAD/FADH2

flavin adenine dinucleotide

NADH reduced form

carries a high energy electron

NAD+

can capture an electron from reduced substrates, NAD+ reducing to NADH and oxidizing the substrate

Other ways cells store energy

within high energy bonds of phosphorylated compounds especially ATP

ATP

most common currency of cellular energy

Hydrolysis

of the phosphate bond yields free energy that can be harnessed for chemical reactions or mechanical work

cleavage of phosphate from ATP

highly exergonic, it releases lots of energy. This can be couples to endergonic reactions to drive them forward.

activation energy

all reactions have, energy that must be invested for them to move

Enzymes

catalyze chemical reactions by lowering th activation energy, helping the reaction move forward faster

Enzymes are reusable

not consumed in the process

Enzyme 3D fold

required for its catalytic activity

catalytic site

enzymes typically have this site that matches the shape of the substrate molecule

Enzymatic reactions

Enzymes are often dynamic.

• The enzyme may change shape upon binding of substrate(s) – the induced fit hypothesis.

• After the reaction happens, this helps kick out products to reset the enzyme.

Enzymes required specific local environmental conditions

pH, substrate concentration, temperature

Extreme temperatures or unfavorable conditions on enzymes

may cause enzymes to denature (unfold) and lose activity

Enzymes may need

cofactors or coenzymes to function

holozyme

enzyme + cofactor/coenzyme

apoenzyme

enzyme without cofactor/coenzyme

Enzymes activity is often heavily regulated by

by the cell – one mechanism is through inhibition.

Competitive inhibition

occurs when an inhibitor directly competes with substrate for binding to the active site

Sulfa drugs

an example of competitive inhibition. They look like a natural substrate and compete for binding to the enzyme. Sulfa drugs block synthesis of folate, an essential cofactor

noncompetitive inhibition

occurs when an inhibitor binds somewhere other than the active site.

allosteric regulation

Noncompetitive inhibitor binding typically changes the shape of the enzyme to prevent activity.

molecules that act allosterically

can change the shape of an enzyme to activate it

biochemical pathways

Metabolic reactions organized into multistep

metabolites

Product of one reaction is substrate for next