Cell Structure and Function Test 1

First Cell Discovery

Robert Hooke discovered the first cell using a compound microscope (1655). It was a dead cork cell.

First living cell discovery

Anton van Leework discovered the first living single celled organism in the late 1600s using an improved compound microscope

3 Tenets of the cell theory (1800s)

1. All living organisms are made up of one or more cells

2. the cell is the basic unit of structure for all organisms

3. all cells arise from preexisting cells

Cytological Biology

Uses microscopy to study the structure of a cell

Kinds of microscopy

electron microscopy is significantly more detailed than light microscopy (higher resolution)

Biochemical Biology

identifies molecules and their structure and function

Louis Pasteur + The Buchners

Found that yeast could ferment sugar into alcohol. The Buchners found yeast extract can do the same. These observations led to the discovery that enzymes are biological catalysts,

subcellular fractionation

uses a centrifuge to separate/isolate different structures and macromolecules

ultracentrifugation

can isolate small to large macromolecular assemblies

chromatography

separates single proteins and molecules from a solution based on size, charge and or chemical affinity

electrophoresis

uses electrical field to move proteins, DNA or RNA through a medium based on size/charge

mass spectrometry

used to determine the size and composition of individual proteins 

x-ray crystallography

used to determine the 3-D structure of individual molecules and complexes 

Genetic Biology

Studies the inheritance of characteristics from generation to generations. Genes were discovered in the 19th century

Central Dogma of Molecular Biology

DNA replication —> DNA —> transcription —> RNA —> transcription —> protein

Watson and Crick

proposed the double helix model in 1953, in the late 1960s advancements were made which led to the central dogma

Recombinant DNA technology, DNA sequencing

uses restriction enzymes to cut DNA at specific places, allowing scientists to create DNA with DNA from different sources

Bond Strength

triple > double > single

Chemical bonds

• Ionic bonding (gains or loses e-) - strongest bond 

• Covalent – shares orbital electrons, strong 

• Di-sulfide bonding – type of covalent bond, strong 

• Hydrogen bonding – milder 

• Van derWaalsforces – weak interactions 

• Hydrophobic interactions – interactions for fear of water 

Steps for macromolecular synthesis

• 1 – monomers with available H and OH groups are activated by coupling them into a carrier molecule (monomer activation) 

• 2 – the two activated molecules are condensed and one of the carrier molecules gets released (monomer condensation) 

• 3 – the next activated monomer is added to another one (polymerization) 

(molecule of water is remove to form a bond)

macromolecular synthesis concepts

condensation only occurs with activated monomers. The process of adding a new monomer to a polymer requires energy (ATP). The two ends are chemically different.

Monomers of proteins

proteins are made up of amino acids

Amino acids

there are over 20 different kinds, each one contains a central carbon, a carboxyl group and an amino group, each has a unique R group

Nonpolar R groups

contain mainly hydrogen and carbon atoms, lack any charge (hydrophobic)

polar uncharged R groups

contain polar covalent bonds (hydrophillic)

polar charged R groups

include acidic and basic amino acids (hydrophillic)

polypeptide

polymer of amino acids. In a growing polypeptide, a new bond is formed between the carboxyl group (C) of the last amino acid and the amino group (n) of the new amino acid. polypeptides have directionallity

Primary structure

amino acid sequence made up of covalent peptide bonds, order is genetically determined (mRNA)

secondary structure

sequences fold into an alpha helix or beta sheet or a random coil. Hydrogen bonds form between NH and CO groups of peptide bonds in the backbone. Beta sheet has maximum hydrogen bonding.

tertiary structure

three-dimensional folding of a single polypeptide chain - disulfide bonds, hydrogen bonds, ionic bonds, van der Waals interactions and hydrophobic interactions

quaternary Structure

- association of multiple polypeptides to form a multimeric protein. same bonds as tertiary structure

How do enzymes work

they bind to substrates at their activation site, forming an enzyme substrate complex

oxidoreductases (enzyme class)

oxidation-reduction reactions

transferases (enzymes)

Transfer of functional groups from one molecule to another

hydrolases (enzyme)

hydrolytic cleavage of one molecule into two molecules

lyases (enzyme)

removal of a group from or addition of a group to a molecule

isomerases

movement of a functional group within a molecule

ligases

joining of two molecules to form a single molecule

ribozymes

special RNA molecules that catalyze chemical reactions (most enzymes are proteins)

Temperature dependence (enzymes)

At lower temps, molecules have less energy which leads to fewer interactions between the active site and substrate. There is an optimal temp for each enzyme where it works the best. When an enzyme goes above the optimal temperature, the structure begins to break down and denature, changing the shape of the active site.  

pH (enzymes)

Each enzyme has an optimal pH where it functions most efficiently. PH changes affect the ionization of amino acids and alter the proteins shape and the charge of the active site. Extreme pH changes can lead to denaturation as well. 

Active site formation

The active site is where the substrate bonds. If an enzyme denatures, the substrate will no longer be able to bind effectively to the active site 

induced fit model

when the substrate bonds, the active site has a slight shape change to create a tighter, more precise fit 

competitive inhibition

the inhibitor and substrate both bind to the active site of the enzyme, which esubstrate binding and inhibits the enzymes activity (dependent on substrate concentration) 

noncompetitive inhibition

the inhibitor and substrate bind to different sites on the enzyme. The inhibitor distorts the enzyme preventing the substrate from binding (independent of substrate concentration) 

reversible inhibitors

Reversible inhibitors bind to enzymes non-covalently and can dissociate from the enzyme (dependent on concentration)

irreversible inhibitors

bind to the enzyme covalently and lead to a permanent loss of catalytic activity  

allosteric site

This is when a regulatory molecule binds to an enzyme at a site separate from the active site (allosteric site) and causes a structural change 

feedback inhibition

This is a type of allosteric regulation where the product of a metabolic pathway binds to the enzyme that starts the pathway. This helps cells conserve energy and maintain metabolic homeostasis. 

nucleic acid monomers

nucleotides make up nucleic acid (DNA and RNA)

DNA vs RNA

DNA uses thymine (T) to bind to A, RNA has uracil (U) which binds to A

3’,5’ phosphodiester bond. 

A phosphate group linked to two adjacent nucleotides via two phosphodiester bonds.  

Nucleic acid directionality

• The polynucleotide formed hy this process has a 5’phosphate group at one end and a 3’ hydroxyl group at the other 

• These sequences are conventionally written in the 5’ to 3’ direction 

polar nucleic acid part

sugar-phosphate backbone which makes the outer helical part of DNA

nonpolar part of nucleic acid

nitrogenous bases (adenine, guanine, cytosine, thymine) are nonpolar and found in the interior of the double helix

purines

adenine, guanine

pyrimidines

thymine, cytosine and uracil

pairs

A-T, A-U, G-C

aplh glucose

repeated unit that makes up glycogen and starch, forms helicies

b-glucose

unit that makes up cellulose, forms strands

glycosidic bond

covalent linkage between two monosaccharides

fatty-acid

long unbranched, amphipathic hydrocarbon chain with a carboxyl group. makes up lipids (triacylglycerols, phospholipids, glycolipids)

saturated fatty acid

hydrocarbon chain with a single bond. This makes them solid at room temp

unsaturated fatty acid

one or more double bond which causes a kink, prevents dense packing

triacylglycerols

function as long term storage, mostly stored as fat

phospholipids

main component of a cell membrane, forms the phospholipid bilayer