Polymers (Lecture 2)

What is the central dogma of biology?

DNA → RNA → Protein

The process of DNA using DNA to make more DNA

Replication

The process of turning DNA into RNA

Transcription

The process of turning RNA into protein

Translation

DNA is made of…

two paired polymers made of nucleotides

The shape of DNA in a solution of water…

does not depend on its sequence

A strand of DNA is grown from the….

3 prime end during replication

How do molecules “see” each other?

Molecules can sense only the pattern of positive, negative, and neutral charges across a surface

Water has a molecular dipole with…

A partial negative on oxygen and a partial positive on hydrogen

mRNA

used to carry information in the cell

When does mRNA in a eukaryotic cell begin translation?

When it reaches the cytoplasm

Process of cutting out introns from mRNA happens in…

the nucleus

tRNA (translational RNA)

brings amino acids to ribosomes during translation; its shape matter when finding correct amino acid to bring to ribosome, but once amino acid is attached all tRNA can fit into the ribosome

rRNA (ribosomal RNA)

forms the core part of the ribosome; the shape of rRNA is VERY important, because this is how the enzyme will build proteins

Primary structure of proteins

a long chain of amino acids

Tertiary structure of proteins

Proteins fold into shapes that allow them to function (caused by interactions between R groups and polypeptide backbone)

Lock-and-key concept of proteins

-Proteins have an active site that is a particular shape, and only substrates with the correct shape can bind to that active site

-Protein active sites also have a particular charge (negative or positive) and the substrate must have and OPPOSITE CHARGE to bind (with neutral regions in the same places)

Strawberry DNA experiment

-get the DNA out of a strawberry (very slimy and gloopy in large quantities)

-in small quantities it is fairly stable when wet or dry

What happens to RNA to protect our body from viruses

Our body produces enzymes that destroy rapidly RNA to protect us from viruses (don’t want harmful RNA making proteins that could hurt you)

Isolated proteins

powdery substance

The purifying for specific types of molecules

-allows us to learn how specific molecules like proteins, nucleic acids, etc. function

-allows us to see how we can use them in medicine

What are all purification methods based on?

Physical properties that allow us to separate different molecules from one another

(“How dense is it?”, “How big is it?”, “Is it positively or negatively charged?”, “Does it dissolve well/poorly in different solvents, or very salty solutions?”)

Charge of all nucleic acids (DNA and RNA)

Negative; they have no hydrophobic (non-polar) regions, and have a negative charge on every nucleotide (the oxygen bound to the phosphate)

Double-stranded RNA is more _______ than DNA

negative

Electrical charge of proteins

neutral (although some proteins have charged R groups)

Do proteins dissolve in water?

Proteins dissolve in water ONLY WHEN FOLDED CORRECTLY; if they are not folded correctly, they will not dissolve in water

What is the difference in properties that will help us separate nucleic acids (DNA and RNA) from proteins?

Nucleic acids are negatively charged (polar) and will dissolve in water, while proteins and neutral (non-polar) and will not dissolve in water

Sonication

smashing bacteria cells with very high frequency sound waves, which makes them vibrate to death

Lysis buffers

Can be used with soap to rupture bacteria cells (a methods of smashing cells to study them)

How are mammalian cells smashed for studying?

Specific organs can be collected and thrown in a blender; this can be done because animal cells have no cell wall, and are larger than bacterial cells

Protease inhibitors

Special buffers for animal cells that destroy the proteins of animal cells that would destroy the released material of the cells (aka kill the cell by eating up released material)

Centrifugation

a laboratory technique that uses rapid spinning and centrifugal force to separate different components of a cell based on their size, shape, and density

you add your smashed cells into the centrifuge, and depending on how fast you spin, that effects what parts of the cells will sink or float

In a centrifuge larger, denser materials sink _______

faster

Why do centrifuges spin?

The spinning dramatically increases the forces applied, reducing the time needed for big dense things to sink

Why would a denser liquid (like a sugar solution) be used in a centrifuge instead of water?

Some proteins that would sink in water (more dense that water), would float in a denser solution (less dense than the solution)

What happens to PROTEINS when you increase the ammonium sulfate salt concentration in the buffer of your centrifuge?

The proteins clump together (precipitate) and sink to the bottom

What happens to nucleic acids when you increase the ethanol concentration in the buffer of your centrifuge?

The nucleic acids will clump together (precipitate) and sink to the bottom

Chromatography

A laboratory technique used to separate the individual components of a mixture

The two main components of all types of chromatography

Stationary phase and mobile phase

Stationary phase

A fixed solid or liquid material that stays in one place; something for your sample to interact with

You can change the stationary phase to purify a sample by….

radius - size exclusion chromatography

charge - ion exchange chromatography

specific binding interactions - affinity chromatography

Banting and Best

Scientists that purified insulin from cow pancreas using differential solubility, filtration, etc. and were able to cure diabetes patients; Proved why purification is important (won noble prize)

Brinkley

Scientist that injected unpurified material from goat testicles directly into patients, causing them to die; proved the danger of not purifying samples (sued for malpractice, wrongful death)