EXAM 1 CONTENT

dehydration synthesis

when monomers combine to form polymers and release water as a byproduct

• monomer → polymer

hydrolysis

when polymers (w/ water) break down into monomers

• polymer → monomer

What is denaturation, and what causes it?

Changes to the protein’s shape, leading to a loss of function caused by:

• Exposure to chemicals

• Changes in temp & pH

amino acid (draw it too)

monomers that comprise proteins

• amino group (NH₂)

• carboxyl group (COOH)

• H atom

• R group / side chain (determines nature of amino acid; whether its acidic)

primary structure

sequence of amino acids; held by peptide bonds

secondary structure

how amino acids fold (alpha helix or beta pleated sheet); held by backbone H-bonds

tertiary structure

3D shape of a polypeptide; held by ionic bonds, H-bonds, hydrophobic effect, & van der waals

quaternary structure

3D of MULTIPLE polypeptides; held by ionic bonds, H-bonds, hydrophobic effect, van der waals, & disulfide bonds

α-carbon

central carbon of amino acid

What are the different terminals of a polypeptide?

• amino group end → (amino) N terminal

• carboxyl ground end → (carboxyl) C terminal

heroin vs. fentanyl

• heroin: semi-synthetic

• fentanyl: synthetic & more deadly due to how it changes the shape of the receptor

opioid receptors

receptors on the surface of nerve cells that heroin, fentanyl, & narcan bind to

antagonist

can block agonists from binding to receptors & binds to the receptors w/o changing shape

agonist

activates a cell receptor to produce a response

How does narcan save lives?

it doesn’t change the shape of the receptor AND blocks heroin & fentanyl from binding

Water is special because it has…

• resistance to rapid temperature change

• ability to extract & dissolve many molecules

• ability to exclude other molecules

• cohesiveness that allows pushing & pulling it in columns

all bc of molecular stickiness (has + & - partial charge)

What is crucial to H bonds and why?

angle & distance bc “wiggling” (caused by thermal motion) makes them loose

monomer of proteins

amino acids

amino acid polymer

peptide

what drives a protein’s shape?

the order and composition of the side chains

hydrophilic

on the OUTSIDE of protein so it can interact w/ water

• ionic, polar = hydrophilic (charged side chains can form ionic bonds)

hydrophobic

on the INSIDE of protein to avoid water interactions

Two general rules of proteins

1. hydrophobic amino acids will avoid water interactions

2. the number of H bonds in proteins in maximized

Cystic Fibrosis

caused by missing CFTR protein; most common variant when 1 amino acid is missing, causing it to fold incorrectly; CFTR is located in ER

• incorrect folding = peptide never leaves ER = degraded by quality control enzymes

phospholipids

• amphiphillic

  • polar head (hydrophilic)

  • nonpolar tails (hydrophobic)

saturated fatty acids

• hydrocarbons saturated w/ H

• solid @ room temp (ex. butter)

unsaturated fatty acids

• hydrocarbons not saturated w/ H

• liquid @ room temp (ex. oil)

@ warm temps, sterols (ex. cholesterol) keep the membrane from…

getting too fluid

@ cold temps, sterols (ex. cholesterol) keep the membrane from…

getting too rigid

FRAP

cell absorbs fluorescent molecules → high intensity laser concentrated on one part of cell (photobleaching) → decreases fluorescence → fluorescent molecules diffuse back

• used to study rate of diffusion

• proves bilayer is fluid & can move laterally

↑ double bonds in the membrane =

↑ fluidity (bc the kinked effect creates more space)

↑ tail length of phospholipids in membrane =

↓ fluidity (bc more hydrophobic effect so they hold together more)

↑ temp of membrane =

↑ fluidity (bc ↓ van der waals & space)

lipid rafts

membrane microdomains enriched in cholesterol, sphingolipids, & glycosphingolipids

• more ordered than the surroundings = more rigid & less fluid

• diffuses slower in FRAP

transmembrane proteins

span the bilayer & conduct transport

Transport is affected by:

property of the molecule

• small, nonpolar → moves across easily

• small, uncharged polar → moves across a lil harder but still easy

• large, uncharged polar → much harder but possible

• Ions → not possible w/o help

concentration gradient

high → low

hypotonic

more solute INSIDE; water rushes in (swells up)

isotonic

solute even on both sides

hypertonic

more solute OUTSIDE; water rushes out (shrivels)

passive transport

moves across concentration gradient

• simple - no channel needed

• facilitated - channel needed

active transport

helps move AGAINST concentration gradient (requires energy); maintains imbalance of ion concentrations across the membranes (acts as a biological battery)

aquaporin

channels that allow water to diffuse freely (still passive, just facilitated)

kinase

enzymes that do phosphorylation

phosphorylation

addition of phosphate group (PO₄)

proton pumps

uses energy from ATP hydrolysis to move protons against gradient

Na⁺/K⁺ ATPase

• moves Na⁺ and K⁺ AGAINST their concentration gradients

• uses ATP to fuel this process

• -ase: enzyme that breaks something down

shape driven by cycle of phosphorylation

endomembrane system

collection of interconnected, membrane-bound organelles in eukaryotic cells

nuclear envelope

• connected to ER

• separates the nucleus from the cytoplasm

nuclear pores

channel for RNA & proteins to travel from nucleus → cytocol & vice versa

lamina

provides structural support to the nuclear envelope & provides a place for chromatin to attach during interphase of cell division

Rough ER functions

• covered in ribosomes

• extra cytoplasmic protein synthesis (proteins located in endomembrane or secreted from the cell)

• protein modifications

• membrane assembly

Smooth ER functions

• no ribosomes

• synthesizes lipids (steroid)

• metabolizes carbs (gylcogen metabolism)

• stores calcium

• detoxifies poison & drugs

Golgi body (appartus) function

receiving, shipping, & modification center

lysosome function

• can digest food (phagocytosis)

• break down damaged organelles (autophagy)

• uses enzymes & acidic pH

vesicles

vessels for transporting, storing, & recycling materials in eukaryotic cells; NOT unidirectional

secretory pathway

secreting or releasing things out of the cell

1. ER synthesizes lipids & proteins

2. Transport vesicle moves it to cis golgi body

3. Golgi modifies, stores, & secretes cargo

4. Transport vesicles move it to trans golgi bosy → early/late endosomes & sends some out

retrival pathway

brings something into the cell; opposite of secretory

1. Bring something to golgi to figure out what it does

2. Send back to ER

Endocytic

when things come in the cell and get digested immediately

endosome

special early vesicles that form when you bring something into the cell & will fuse w/ another vesicle to turn into a lysosome

constitutive secretion

constant, unregulated release of the same molecule

regulated secretion

receives a signal to make a molecule (ex. hormones & neurotransmitters)

pancreas secretes…

insulin

insulin “cycle”

insulin released to insulin receptors → tells GLUT4 (carrier protein) to allow glucose in the cell

what happens in type 1 diabetes?

don’t make insulin so glucose levels can’t be naturally regulated

stomach cells secrete…

ghrelin (hunger hormone)

topologically equivalent

organelles that share the same internal environment, allowing molecules to move between them w/o crossing a membrane

ex. ER, golgi, lysosomes, & endosomes

COP l

protein coat that directs vesicles from golgi → ER (retrograde); recycling

COP ll

protein coat that directs vesicles from ER → golgi (anterograde); new proteins & lipids

endocytosis & the different types

process of bringing something into the cell

• phagocytosis: cell eating (solids)

• pinocytosis: cell drinking (fluids)

• receptor-mediated endocytosis: bind proteins in membrane to tell it to take it in the molecule

receptor-mediated endocytosis examples

• Covid binds to ACE2

• transport of cholesterol into cells using LDL receptors (ApoB binds to LDL receptors → cholesterol taken in)

uniport

moves a single molecule down the concentration gradient (facilitated)

symport

two different substances move in the same direction at the same time; one molecule moves down its gradient, which provides the energy to pull the other molecule against its gradient (ex. Na⁺/glucose symporter)

antiport

two different substances move in opposite directions; the movement of one ion down its gradient powers the transport of the other substance

Which transport/diffusion for each one?

1. Requires a transmembrane protein

2. Involves ATP hydrolysis

3. Moves molecules from lower to higher concentration

4. Applies mainly to small, nonpolar molecules

5. Transports ions across the membrane

6. Applies to water molecules

7. Transport can go in either direction across the membrane, depending on concentration gradient

8. Applies to ion channels

1. Requires a transmembrane protein : F, A

2. Involves ATP hydrolysis: A

3. Moves molecules from lower to higher concentration: A

4. Applies mainly to small, nonpolar molecules: S

5. Transports ions across the membrane: F, A

6. Applies to water molecules: S, F

7. Transport can go in either direction across the membrane, depending on concentration gradient: S, F

8. Applies to ion channels: F

familial hypercholesterolemia (FH)

no uptake of LDL which leaves excess LDL in the bloodstream

normal cells vs FH cells (cell culture)

• normal: most LDL surface bound @ first → decreases as more becomes internalized & degraded

• FH: more LCL stays surface-bound → less gets internalized & degraded

  • LDL receptors are likely mutated

carrier protein vs channel protein

• carrier proteins can be passive or active while channel proteins are ONLY passive

• carrier proteins undergo conformational (shape) change

  • carrier protein example: GLUT1 & Na/K pump

  • channel protein example: aquaporins

Voltage-Gated Channels

Open and close in response to changes in the electric voltage

• Transports ions like Na⁺, Cl^-

Ligand-Gated Channels

Open when a specific chemical molecule (the ligand), such as a neurotransmitter, binds to the receptor protein

Mechanically-Gated Channel

Open or close in response to physical stress, stretching, or mechanical pressure on the cell membrane