Ls3 - Lecture 2

Front 1

Proteins

Back 1

Proteins are polymers made from a unique arrangement of 20 common amino acids

Front 2

What are amino acids made up of?

Back 2

Carbon, Hydrogen, Oxygen & Nitrogen

Front 3

What determines the 3D shape & function of a protein?

Back 3

The sequence of amino acids

Front 4

Polypetides

Back 4

A polypeptide is a linear polymer of amino acids. Peptides usually contain less than 20-30 aa.

Proteins usually contain 100 or more aa.

Front 5

Describe the structure of amino acids

Back 5

Amino acids are composed of a central, alpha carbon. Attached to the carbon are a Hydrogen, a Carboxyl group, an Amino group and a R variable.

Front 6

The backbone of a polypeptide contains?

Back 6

Carbon & Nitrogen. They contain C & N because polypeptides are made of amino acids. An amino acid contains C & N.

Front 7

Describe the properties of amino acids.

Back 7

The properties of the aa side chain determine the properties of the final protein. AA facing the interior of the cell membrane are non-polar, hydrophobic. AA facing the exterior of the cell membrane are polar, hydrophilic. Non-covalent bonds (Ionic + -, Hydrogen bonds, Waals interactions & Hydrophobic interactions) are critical for interactions between macromolecules.

Front 8

What kind of bonds are critical for interactions between these macromolecules?

Back 8

Non-covalent bonds are important.

Front 9

What is a peptide bond?

How are peptide bonds formed?

Back 9

The covalent link between two adjacent amino acids is called a peptide bond. The carboxyl group from one monomer reacts with the amino group from another monomer. This releases H2O. A covalent bond is now formed. This covalent bond is also a peptide bond. This is a condensation reaction because water is released.

Front 10

How can you determine which is the peptide bond?

Back 10

1 amino acid = N, C, C, O. The peptide bond is where one amino acid meets another. Where the N meets the C.

Front 11

Are peptide bonds planar?

Back 11

Yes, they are planar. They have resonance and this makes them planar and can only rotate around the alpha carbons.

Front 12

What allows proteins to form 3D structures & perform different activities?

Back 12

The R groups (side chains) attached. The overall charge is given by the side chain.

Front 13

How are amino acid side chains classified?

Back 13

They are classified based on their propensity to be in contact with polar solvents.

Front 14

Hydrophobic Side Chains & location

Back 14

Have low tendency to be in contact with water. These include nonpolar, aromatic R groups & nonpolar, allphatic R groups. They are located towards the interior of the proteins.

Front 15

Polar/Charged Side Chains

Back 15

Are energetically favorable to be in contact with water. They face the aqueous environment of the protein. Hydrophilic aa dissolve easily in H2O. Acidic aa readily donate a proton. Basic aa take up a proton. They are often found in the active site of a protein. The charged side chains of hydrophilic aa can form H-bonds or ionic bonds with aa of opposite charge.

Front 16

How come some polar aa that are uncharged in physiological conditions but can form H bonds?

Back 16

The side chains tend to have a partial + - charge. This allows them to form H-bonds with other aa and associate with water.

Front 17

Non-polar Amino Acids

Back 17

These side chains often point to the inside of the protein where they form hydrophobic associations with each other.

Front 18

What are some notable amino acids?

Back 18

Cysteine, Glycine & Proline.

Front 19

Cysteine

Back 19

Forms covalent disulfide bonds primarily in secreted proteins. You rarely see disulfide bridges in the cell because cytosol is a reducing environment. A disulfide bond greatly increases the stability of a folded protein because of the strength of covalent bonds & crosslinks between different segments/regions/proteins.

Front 20

Do disulfide bonds form in oxidizing or reducing environments?

Back 20

They only form in oxidizing environments. In reducing environments, disulfide bonds are unstable so they wont form.

Front 21

Glycine

Back 21

It's the smallest R-Group. See it often in stems and loops of proteins

Front 22

Proline

Back 22

Forms bends/kinks & disrupts protein structure

Front 23

What are the 3 key experiments that led to the discover of DNA vs Protein in Genetic Info?

Back 23

Griffith Experiment (1920s)

Avery, MacCleod, McCarty Experiment (1940s)

Hershey Chase Experiment (1950s)

Front 24

Griffith Experiment

Back 24

Studies S. Pneumonia bacteria. It existed in two types; Non-Virulent (rough) & Virulent (smooth). When the smooth was injected into a mouse, it died. When the rough was injected in the mouse, it lived. When the heat-killed smooth was injected in the mouse, it lived. When heat-killed and rough were injected in the mouse, it died.

Front 25

Avery Experiment

Back 25

Took vile of heat killed strain (smooth) * combined it with enzymes to break down RNA, DNA, Lipids & Carbohydrates. He then added them to the vile of live R strain to see what resulted. DNAse would have destroyed the ability for the R strain to become virulent from the S strain, so in the solution with DNase, only the R strain showed up because the DNase destroyed the S strain DNA.

The DNase-treated extract lost the capacity to transform nonvirulent rough-colony cells into a virulent smooth-colony strain. The researchers then extracted DNA from virulent bacteria, purified it of contaminating proteins and RNA, and showed that this pure DNA was still capable of transforming nonvirulent bacteria into the virulent strain

Front 26

What was concluded from the Avery Experiment?

Back 26

DNase destroys the ability of heated extract to transform the R strain into lethal, smooth (S) strain. DNA must contain the transforming agent. DNA must contain the genetic info.

Front 27

Hershey-Chase Experiment

Back 27

Used phages with radioactive DNA & Protein. The phages will inject their genes into the bacteria & leave ghost phages (their bodies). The ghost phages are then removed with centrifugation. The radioactive DNA would go to the bottom and the radioactive Protein would go to the top because the phages had a protein coat (was part of the body) and not injected in the bacteria. Protein was labeled with S35. DNA was labeled with P32.

Front 28

Non-Polar Aliphatic R Groups

Back 28

Aliphatic side chains are those composed only of hydrocarbon chains (–CH2–), which are nonpolar and quite hydrophobic. These residues tend to cluster inside proteins and stabilize the structure through hydrophobic effects.

Front 29

Polar, Uncharged R Groups

Back 29

Polar, uncharged R groups can interact extensively with water, or with atoms in other side chains, through hydrogen bonds. Hydrogen bonds are interactions between a donor hydrogen atom that is covalently bonded to an electronegative atom and an acceptor atom that usually has a lone pair of electrons.

Front 30

Polar Charged R Groups

Back 30

Charged side chains can form hydrogen bonds and can form ionic interactions with amino acids of opposite charge.

Front 31

Nonpolar Aromatic R Groups

Back 31

Phenylalanine, tyrosine, and tryptophan contain aromatic side chains and therefore are hydrophobic.

Front 32

In peptide bonds, is cis or trans favored?

Back 32

Trans. This is because the peptide bond has a partial pi bond which restricts movement. Movement is also restricted due to the proximity of adjacent side chains.