BI220 Week 2 Lecture 5 (Living Chemistry: from atoms to cells)

macromolecule

lg organic molecule containing thosuands of carbon-carbon bonds

essential for life because they perform critical functions in biological systems in humans and microbes

make up the structure of both human and microbial cells and have specific roles in cell function

4 types of macromolecules

lipids, carbohudrates, nucleic acids, proteins

water

not macromolecule not biomolecule, but necessary for maintaining life in cells due to its role in faciliting chemical reactions and transport in cells

hydrophobic vs hydrophilic

lipids

are organic molecules that serve as stuctural components of membranes and other parts of cells

fatty acids, triglycerides, phophsolipids

make up cell membranes

hydrophobic lipids

region of fatty acids are “water fearing” because they are uncharged

hydrophilic lipids

regions of fatty acids are “water loving” because they are polar covalent around the O-H bond at the top of the molecule

fatty acids

are a component of phospholipids, which are an important structural component of microbial cell membranes

carbohydrates

sugars, monosacchardies (simple sugars), disacchardies, polysaccharides

function of carbohydrates

energy source in cells (nutrient source for some microbes, imporant for microbial growth)

found on cell surfaces (mimic the sugars found on human cells to help avoid immune cell detecting by mimicking human cell structure)

can also b structural parts of cell walls of microbes (lipopolysaccharides, glycoproteins)

sugars can take on mirror forms where only one enzyme can utlize that sugar for catalyzing reactions (D-form or L-Form humans= L bacteria=both)

nucleic acids

help store, transmit, express genetic instructures that allow microbes to function as living cells (growth, reproduction, energy generation, function)

nucelic acids are

long chains composed of nucleotides

three compements of nucleotides

five-carbon sugar

phosphate group

nucelobase

nucelic acid (DNA) deoxyribonelenic acid

encodes genetic info in genes

all living cells have dna based genomes

nucleic acid (RNA) ribonuclic acid

transfer of info from gene to protein

some viruses store their gentic info w RNA based genomes

nucleobase

adenine, guanine, cytosine, thymine, uracil

one change of nuclease within a gene can cause a mutation, can b fatal for organism

The DNA double helix

chromosomes of all cells consist of dna that is double stranded or duplex

sugar in dna is

deoxyribose

dna is a living cells

hereditary material

forms the chrosomes and contains the entire genone of a cell

genome

complete set of genetic instructions contained within a organism

bacterial genomic dna helps

determine which antibiotixs will b able to b used against the organism and how it will survive under specific cond.

e.g bacteria w the gene for the enzyme beta-galactsosidase can make that enzynme when lactose is present, which helps break down the surgar for energy

nucleobase pairings in DNA

A (adenine) T (thymine) a-t bonds

G (guanine) and © cytosine G-C bonds

why is dna imporant for microbes

stores genetic info

bacterial genomic dna helps determine which antibiotics will b able to b used against the organism

the accessible portions of DNA are accessible by

regulatory proteins

dna can b changed or repaird through these regions aswell

mutations in dna can help,hurt, or cause no chnage to a microbe depending on teh mutation itself

vibrio cholera

thes eorganims have proteins that detect enviormental temp and PH

helps organism determine that it has entered a host and needs to to then start its disease process

rna is important for creating

proteins via translation

ribonucleic acid (RNA) surgar in this is

ribose

RNA can make base pairs like DNA bur

uses uracil rather than thymine

A-U bonding

G-C bonding

can sometimes form double helix like DNA (common in rna only viruses)

usually single stranded in cells

rna carries genetic info translated by

ribesomes to fomr various proteins necessary for cellular processes via translation

mRNA (messenger RNA)

is transcribes from a gene

encodes the info from a gene to specify a protein

base pairings between RNA and DNA is used to make mRNA from a DNA template

rRNA (ribosomal RNA)

is pt, of a ribosome

direct the catalyic steps of protein synthesis

stitch together amino acids to make a protein molecule

tRNA (transfer RNA)

carries amino acids to mRNA

transfers the appropiate amino acid to the ribosome during protein synthesis

some viruses such as influenza and HIV have genomes made of RNA only (Highly susceptible to mutations)

protein function

catalyzing biochemical reactions to serving as receptors adn transporters to providing structure and aiding movement

cells can make thousands of

diff. proteins and could contain upwards of 2 mill. proyein molecules at any time

potein structure

chains of diff. amino acids that fold together inro a specidic shape to b functional

20 amino acids w diff R groups can make up a proteins

protein structure: protein fold into

three dimensional structures that may fit together in a complex

e.g chloerla toxin is composed of two types of protein chains that form a complex to b functional

amino acids

building blocks of proteins

20 diff amino acids used to build proteins

what determins how proteins get synthesiszed

teh sequence of amino acids in peptide chain

arrangement of amino acids around chial carbon matters

isomers

mirror images of one another

L amino acids

are used by ribosomes to make proteins in cells

bacteria uses what amino acid

 D-amino acids to build their cell walls

D-amino acids are found in antibiotics to try to halt cell wall synthesis in bacteria

Mutations to DNA or RNA can lead to

misfolded/non-functional proteins!

proteins must b what to b functional

folded correctly

levels of protein folding

primary, seocundary, tertiary, quantanary

primary structure portein folding

refers to the linear sequence of amino acids. 

amino acids are held together by

peptide bond

amino acid chains get numbered from the

amino terminus to the carboxyl terminus

proteins can contain

hundred of amino acid residues in one chain

seocundary structure protein folding

the regular pattern of amino acid residues that form over short regions of the polypeptide chain.

• Two main secondary structures 

  • Alpha helix

  • Beta sheet

seocunday structure of protein is very imporant

Very important for how antibodies recognize antigens and how pathogens cause disease

Very beginning of protein folding from the primary structure

tertiarty structure protein

is its uniquw three dimensional shape

Regions distant in the primary structure may be brought closer together during this level of protein organization

tetritary structrue protein folding imporant because

• determining how a protein folds into its final structure. 

• Folding influenced by hydrogen bonding between different amino acids within the protein chain

• 
  

• Folding leads to protein functionality at this stage!

  • Function of proteins is determined by the unique shape of the protein after folding

proteins produced in the ribosomes are bound to chaperone…

proteins that then get folded into their functional shape

native conformation

Functional shape of proteins called

folding of proteins occur because of

• ionic bonds and hydrogen bonds forming between side chains of amino acids

incorrectly folded proteins are

not functional because they can’t tightly bind to their target molecules!

quaternary structure

proteins form stable, functional complexes with other proteins, forming

antibodies are

• common types of protein complexes that are made up of light and heavy chains of amino acids

Toxins often are found in protein complexes

• Example: Cholera Toxin

function of proteins for microbes

• Help microbes sense their environment and make changes based on the environmental stimuli

• Microbes can secrete proteins that affect surrounding microbes and cells

• Important for nutrient uptake and catabolism

• Allow for the attachment to other proteins or cells

• Allow for biofilm formation 

• Speed up chemical reactions (enzymes)

catabolism

 is when complex molecules are broken down into simpler ones, releasing energy in the process

prions

are misfolded protein that induces misfolding in normal variants of the same protein, leading to cellular death

Prion diseases are transmissible and often neurodegenerative

• Often fatal 

normal prions

•  consists of mainly alpha helices

  • Under conditions where they are causing disease they transition to the abnormal conformation consisting of beta sheets, which then causes other proteins to also misfold

• Example: Mad Cow Disease

Where do living cells get the fuel to drive their reactions?

Synthesis of molecules requires energy

energy

ability to do work

It is important for energy to be conserved by organisms and only used when necessary

first always of thermodynamics

 states that matter and energy are neither created nor destroyed.

secound law of thermodynamics

states that, in all energy transformations, some energy becomes unavailable to do work and is lost as entropy, or disorder.

Free energy change (ΔG)

of a reaction depends on the intrinsic energy and entropy changes of the molecules as well as the concentrations of reactants and products. 

free energy change (concentration)

 is presented in terms of molarity.

• There also needs to be a change in free energy for a reaction to go forward

Activation energy (E_a)

is the energy needed to reach this transition state.

A spontaneous reaction will be slow if it must pass through a high-energy transition state on the way to forming products.

entropy

This energy that is now unavailable to do work is called

Entropy can be reduced by adding more energy to the reaction

Reactions that increase entropy…

may go forward

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