Week 1: Introduction and Protein Structures (Lectures 1-3)

Function of pili

Short hair-like structures that stick to surfaces and other bacteria

Name two unicellular prokaryotes

-Archaea and bacteria

Name a unicellular eukaryote

protists

what can unicellular or multicellular?

fungi

Name two multicellular eukaryotes

plantae and animalia

What's the cell envelope in bacteria and its function?

Cell envelope are all the layers surrounding the cytoplasm

It includes:

1. Cytoplasmic (inner) membrane

2. Peptidoglycan layer

3. Outer membrane (only in Gram‑negative bacteria)

Function: protect the cell, maintain its shape, and regulate interactions with the environment.

What's the function of the nuclear envelope in animal cells?

segregates chromatin (DNA + proteins) from the cytoplasm

double‑membrane barrier that surrounds the nucleus, and its core job is to protect the DNA and control what enters and leaves the nucleus.

What's the function of the nucleolus in animal/plant cells?

site of rRNA synthesis and ribosomal subunits. Subunits leave the nucleus to become full ribosomes in the cytoplasm.

In animal/plant cells, where does protein synthesis occur? Where does lipid synthesis and drug metabolism occur?

-Rough ER

-Smooth ER

What's the role of the Golgi complex in animal/plant cells?

process, package, and target proteins to other organelles or for export

In animal cells, what's the role of transport vesicles?

-shuttles lipids and proteins between the ER's, Golgi, and plasma membrane

In animal cells, what's the function of lysosomes?

-Degrades waste

In animal cells, what's the function of peroxisomes?

oxidizes fatty acids

In plant cells, what is the function of stratch granules?

-temporarily store carbohydrate products of photosynthesis

In plant cells, what are the function of chloroplasts and thylakoids?

-Convert light energy into chemical energy (glucose)

-Carry out the light‑dependent reactions of photosynthesis; produces ATP

How do you calculate the formal charge of an atom?

Formal charge = (Valence electrons) - (Non-bonding electrons) - (1/2 Bonding electrons).

Ex: H2O (6-4-1/2(4) = 0

6 valence e-, 4 non-bonded e-, 4 bonded e-

What's a hydride atom?

hydrogen atom with 2e- (H-)

What do you call a hydrogen atom with no electrons?

A proton (H+)

Define a chiral center

Carbon atom bonded to four different groups.

Define enantiomers

stereoisomers that are mirror images of each other

same formula + same connectivity + different 3D orientation

Define diastereomers

stereoisomers that are not mirror images of each other

Usually differ at one or more (but not all) chiral centers

Define polar covalent bond

a covalent bond between atoms in which the electrons are shared unequally; creates partial negative and partial positive charges due to difference in electronegativity

Define nonpolar covalent bond

a bond in which electrons are shared equally; electronegativity between the atoms is identical or similar

Name the 4 non-covalent interactions

1) Hydrophobic effect

2) ionic interactions (electrostatic)

3) van der waals interactions

4) dipole interactions

Define ionic interactions

interaction between oppositely charged ion (+, -)

-opposite charges attract and like charges repel

Define dipole interactions

intermolecular forces resulting from the attraction of oppositely charged regions of polar molecules; one molecule is partially negative and one is partially positive; think attraction between two water molecules

Define: Van der Waals Interactions

weak, temporary attractions between molecules caused by fluctuations in electron distribution.

arise because electrons are constantly moving. In nonpolar molecules, electrons may momentarily cluster on one side, creating a temporary dipole. This temporary dipole can induce a dipole in a neighboring molecule, leading to a brief attraction.

Define the hydrophobic effect

the tendency of nonpolar molecules to cluster together in water because doing so increases the entropy of the surrounding water

Does the hydrophobic effect favor high or low entropy?

High entropy is favored because water prefers to remain disordered and free, not organized

In the hydrophobic effect what occurs when there is low entropy?

water molecules are forced into organized, structured arrangements, which is unfavorable

In the hydrophobic effect, what occurs when hydrophobic molecules are scattered individually?

water must build many ordered cages and entropy drops a lot

In the hydrophobic effect, what occurs when hydrophobic molecules cluster?

-they reduce the amount of their surface area exposed to water.

-water only needs to organize around one larger surface --> many cages collapse --> water becomes more disordered again --> entropy rises (favorable)

Name 3 buffer system within the living body

-phosphate;

-histidine

-bicarbonate

which buffer system is important in intracellular fluid and kidneys?

phosphate

which buffer system is important in blood plasma?

bicarbonate

which buffer system is efficient in neutral pH?

Histidine

Define primary structures

-linear sequence of amino acids in a polypeptide chain and are held together by peptide bonds

-written from N-terminus to C-terminus

define secondary structures and what holds them together

-the folding of primary structures into alpha helixes or beta pleated sheets/strands; occurs only with backbone atoms (not side chains)

-held together by hydrogen bonds

define tertiary structures

the overall 3D shape of a single polypeptide formed by interactions between side chains

helices + sheets + loops all packed into one functional shape.

Define quaternary structure

the shape resulting from the association of two or more polypeptide subunits; assembles into a functional protein complex

What roles do proteins have in the biological function?

-catalysis; dna polymerase

-transport; hemoglobin

-structure; keratin, collagen

-motion; mysosin/actin

Why do amino acids absorb light at 270-280?

due to their conjugated double bonds

Which amino acid form disulfide bonds?

Cysteine

Define: Post translational modification

changes made to polypeptides following translation

What does it mean when a molecule is deprotonated?

It loses a proton by removing H+, making the molecule more negative

What does it mean when a molecule is protonated?

A molecule gaines a proton (H+), making the molecule more positive

Does a molecule tend to be protonated at a low or high pH?

At low pH, molecules are more likely to be protonated because the solution has a high concentration of protons (H⁺)

Does a molecule tend to be deprotonated at a high or low pH?

molecules tend to be deprotonated at high pH because high pH means a low concentration of hydrogen ions (H⁺), which favors the removal of protons from acids.

What functions do peptides have?

-Hormones (insulin, oxytocin)

-Neuropeptides

-antibiotics

-protection (toxins)

In proteins, what's a cofactor?

-anything that is not an amino acid but is required for a protein's activity

-can be organic (coenzyme/prosthetic group) or inorganic molecule (metal ions)

In proteins, what is a coenzyme and which bond holds the protein and coenzyme together?

-an organic molecule that an enzyme needs in order to carry out its chemical reaction

-coenzymes come and go because they are held through non-covalent interactions

In proteins, what's a prosthetic group?

-non-protein molecule that is tightly or permanently attached to a protein and is essential for that protein's function

-covalently attached

-heme found in hemoglobin

The following modification are considered to be what?

-phosphorylation

-methylation

-acetylation

Post-translational modifications of proteins

When a protein goes through phosphorylation, what occured?

-A phosphoryl group was added along with 2 negative charges

What are phi and psi angles?

-Phi (φ) and psi (ψ) angles are the two backbone rotation angles that determine how a protein chain folds in 3D.

-They are the only flexible rotations in the peptide backbone because the peptide bond itself is rigid.

Where are phi (φ) angles located?

angle around the alpha-carbon—amide nitrogen bond

Where are psi (ψ) angles located?

angle around the alpha-carbon—carbonyl carbon bond

the following characteristics describes what?

-spring shape

-compact

-right-handed

-3.6 amino acids per turn

-backbone held by hydrogen bonds

-side chains point out

alpha helix

Which two amino groups tend to be helix breakers?

Proline and Glycine

In parallel beta sheets, in which direction are the H-bonded strands placed in?

in the same direction

In antiparallel beta sheets, in which direction are the H-bonded strands placed in?

in the opposite direction

Are parallel or anti-parallel beta sheets stronger?

Antiparallel β‑sheets are stronger and more stable than parallel β‑sheets. Since the H-bonded strands run in opposite directions, it allows the hydrogen bonds to form in nearly a straight line, which is the most stable orientation for H-bonds.

-straight=strong

-bent = weak

What are motifs?

-a repeated 3D pattern of secondary structural elements that recurs in many proteins and often supports a specific structural or functional role.

-aka supersecondary structure

What are fibrous proteins?

-strong/insoluble/inflexible material e.g. collagen and keratin

-made from a single secondary structure

What are globular proteins?

-proteins that are water soluble

What makes globular proteins water soluble?

the polypeptide chains are folded such that hydrophobic groups are on the inside, while the hydrophilic groups are on the outside

What allows a globular protein to be lipid-soluble?

-polypeptide chains have hydrophobic amino acids on the surface and hydrophilic residues on the inside; allows globular proteins to enter membranes

How can proteins be denatured?

-heat/cold

-pH extremes

-organic solvents

-chaotropic agents

What are chaotropic agents?

A chaotropic agent is a molecule in water solution that can disrupt the hydrogen bonding network between water molecules. This has an effect on the stability of the native state of other molecules in the solution, mainly macromolecules (proteins, nucleic acids) by weakening the hydrophobic effect

Name 2 chaotropic agents

Urea; disrupts h-bonding and hydrophobic interactions

Guanidinium hydrochloride; unfolds proteins

Describe the ribonuclease refolding experiment

-Chris Anfinsen denatured RNase A using urea to disrupt noncovalent interactions and beta-mercatoethanol to break its 4 disulfide bonds

-RNase A became a random coil with no enzymatic activity

-Anfisen removed urea via dialysis and allowed the protein to exist again in the environmnt

-after the protein reached its correct formation, the disulfide bonds reformed

-demonstrated that the information needed for folding is intrinsic to the protein's primary sequence

What role do chaperone proteins have?

-specialized proteins that help other proteins fold correctly, refold after stress, and avoid clumps of unfolded or misfolded proteins

-prevent misfolding

What role do chaperonin proteins have?

-enclose the misfolded protein inside a chamber (large, barrel-shaped) and uses ATP to reshape the protein. protein is release after a timed folding cycle