BIO150 Final

Protein

Monomer:

Covalent Bonds:

Non-Covalent Bonds:

Key Roles:

Amino Acids

Peptide Bonds

H-Bonds, ionic, hydrophobic, Van Der Waals, disulfide interactions

Enzymes, large structures, signaling, connecting cells

DNA/RNA

Monomer:

Covalent Bonds:

Non-Covalent Bonds:

Key Roles:

Nucleotides

Phosphodiester Bonds

H bonds (b/w bases) & Van Der Waals (Base Stacking)

Info storage, gene control, protien production

Carbohydrates

Monomer:

Covalent Bonds:

Non-Covalent Bonds:

Key Roles:

Monosaccarhides

Glycosidic Bonds with a/B linkages

H-bonds, Van der Waals

short-term energy (glycogen & starch), structural support (cellulose & chitin), cell recognition

Lipids

Monomer:

Covalent Bonds:

Non-Covalent Bonds:

Key Roles:

Glycerol and Fatty Acids

Ester Bonds w/ triglycerides & phospholipids

Hydrophobic interactions & Van der Waals

Energy Storage, Membranes, & Signaling

Condensation Reaction

Forming Macromolecules with water as a byproduct

Hydrolysis

Breaking down macromolecules by adding water

Central Dogma

DNA -(transcription)→ RNA -(translation)→ Protiens

Prokaryotic protein production

Speed is the priority; transcription and translation happen in the cytoplasm; transcribed genes are translated immediately

Eukaryotic protein production

Fine control is the priority; transcription in the nucleus; translation in the cytoplasm; transcription and translation are independently regulated

Transcription

How RNA is made; DNA copied into RNA by complementary base pairing; forms raw RNA, which must be edited; many RNAs are never translated into proteins but proteins are the final working molecule

Complementary Pairing

Complementary bases prefer to H-bond with each other; A-T (U in RNA) has 2 H-bonds and G-C has 3 H-bonds

Primary Structure

Amino acid sequence, covalent bonds between peptide sequence

Secondary Structure

Alpha helix and beta pleated sheets. A-helices have right-handed (most common), coiled-coil, amphipathic, Beta sheets have parallel, antiparallel (most stable), mixed. Different amino acids prefer to bond with different structures. They bond by forming H-bonds between the backbone atoms

Tertiary Structure

R group interactions, non-covalent interactions with some covalent bonds, are affected by environmental conditions (pH, ions, temperature, chemical modifications)

Quaternary Structure

Multiple Subunits; folding driven by non-covalent interactions between tertiary subunits

Translation

Proteins fold as they are translated. Evolution favors fast folding; the final shape is thermodynamically favored but not guaranteed. Chaperones assist folding by preventing aggregation, providing a safe environment, and using ATP-driven cycles to give proteins multiple chances to reach their proper structure. The N-C-C backbone of a misfolded protein attracts chaperones

Directionality of protiens

-N-C-C- Chain in center, polarity, gives directionality to entire macromolecule

Disulfide Bonds in proteins

between cysteines, connect two different parts of a chain

Van der waals in proteins

complementary shapes bind together

H-bonds in proteins

between side chain and backbone or between side chain and another side chain

Hydrophobic interactions in proteins

R groups avoid water and aggregate

Carbohydrate structure: monomers

monomers: carbon backbones with multiple OH groups and one double-bonded O group. Can spontaneously form a ring (-O-)

Carbohydrate Structure: Polymers

disaccharides and polysaccharides; glycosidic bonds link because of condensation reaction, they form between 2 -OH groups

Small sugars are used for:

Bulk Transport because they are a source for rapid release energy (ex: glucose)

Polysaccharides

They form long fibers (ropes), strands have covalent and non-covalent interactions, used for storage and structural support (ex: cellulose)

Charged polysaccharides

attract water, form a cheap space filling mass (ex: pectin in plant cell wall, mesoglea in jellyfish)

Fatty Acids

Carboxyl head group (-COOH) → Charged; nonpolar (C:H) tails that differ in length and number of double bonds (saturation)

Triglycerides

Also called triglycerols (TAGs), 3 fatty acids linked to glycerol via ester linkage, hydrophobic

Functions: energy storage, physical padding, insulation

Phospholipids

2 fatty acid chains linked to glycerol, phosphate linked to 1 of 4 possible head groups, they are amphipathic

Steroids

3 6-Carbon rings and 1 5-Carbon ring, side chains, and Carbon Carbon double bonds that modify function.

Function: membrane fluidity (cholesterol) and signaling molecules (testosterone, estrogen)

Phospholipid Bilayer: Fluid Mosaic Model

The lipid bilayer is the main barrier; integral proteins, outside surface has glycoproteins attached

Phospholipid bilayer structure

Hydrophilic heads on the outside (attract solutes and interact with H2O); Hydrophobic tails are on the inside (Hydrophobic effect causes them to cluster together so fewer of them are exposed to water; water pushes them together), they form a semi-permeable membrane

Fluidity Depends On:

Proportion, Saturation, Cholesterol/Steriods

Proportion of head groups and tails on packing

Bigger heads = less packing

shorter tails = less packing ( decrease in hydrophobic interactions)

Saturation of C C double bonds on packing

more C C double bonds = less packing

more C C double bonds = melt at a lower temperature

Cholesterol/Steroids on packing

High Temp: Reduce fluidity = reduces movement

Low Temp: Increase fluidity = prevents tight packing

Steroids act as a buffer, stabilizing membrane fluidity

How do bacteria maintain fluidity?

change length and saturation

How do eukaryotes maintain fluidity?

modify melting properties with steriods

Channels/Pores

fast, let the solute diffuse down the gradient

can be open continuously but most are gated

filter by size/charge → lets selected ions and small molecules move in

uses simple diffusion

less specefic

Transporters

Carriers and Pumps

bind, transport specific solutes

Carriers

Type of transporter

Use passive, facilitated diffusion

move solutes through membranes by making conformational changes

Bind and transport to specific solutes

Rate plateaus (like enzymes)

Ex: GLUT1

Pumps

Active transport, Endergonic (movement against the gradient) coupled with exergonic reaction (ATP → ADP)

Primary Active Transport

exergonic process is ATP breakdown; creates own gradient

Secondary Active Transport

Indirectly, energy is from a concentration gradient; it uses the existing gradient created by primary transport, used by prokaryotes and eukaryotes

Ex: SGLT, glucose is transported used Na+ gradient

More efficient because if glucose pimp was used, you would need 1 ATP for each glucose. This amplifies the energy and is easier to control/regulate

Types of Membrane Protiens

Integral and Peripheral

Integral proteins

Single or Multi-pass

always a-helices, have side groups that bind to lipid tails, can form pores and channels when paired

Peripheral

On either side of the membrane, anchored by a covalent bond to lipid/protein or by a non-covalent interaction

Endocrine

Long distance

Paracrine

Short Distance

Gases and Non-polar molecules as a stimulus

diffuse through the bilayer to a macromolecule ( ex: enzyme) that causes a response or an intracellular receptor in the cytoplasm, signal is not amplified, slower response

Small polar molecule as a stimulus

Can’t diffuse through bilayers, uses surface receptors, signal is amplified so faster response

Surface Receptor Types

Ion channels, G Protein, and Kinase

G-Protein coupled receptors (GCPRs) Steps

1) ligand changes the receptor’s shape

2) The new shape attracts the G-protein, which turns on the alpha subunit by GTP exchange

3) a- subunit leaves and turns on the enzyme generating secondary messengers

4) Secondary messengers activate protein kinase A

5) Protein kinase a activates new enzymes to control downstream events and/or a change in transcription factors that control DNA

G-Protein coupled receptors (GCPRs) Deactivation

1) release/destroy ligand

2) turn off the receptor

3) switch G protein off (GTP→GDP); done by G-protein coupled receptor kinases

4) destroy secondary messengers

5) turn off kinases, turn on phosphatases

What molecules are GCPRs used for

small soluble molecules

Kinase Receptors

1) ligand (small proteins) binds to receptors

2) receptors dimerize, trans-phosphorylate (they phosphorylate each other)

3) Adaptor proteins bind, and Ras (G-Protein) is activated

4) Ras activates phosphorylation cascade of MAP kinases

5) final kinase turns on transcription factors and/or increases expression of cell growth genes

Deactivating Kinase Receptors

Takes longer than GCPRs

Phosphatases remove phosphates from kinases and transcription factors; gene products must be degraded

ECM

A network of proteins that surrounds the cell

Made of:

• Water

• Jelly-like ground substance

• fibers

• secreted ions/molecules

• adhesion molecules

Plant ECM

Cell Wall

Made of:

• Pectin polysaccharides (space filling/jelly/adhesive)

• Cellulose/ hemi-cellulose (strength)

• Lignin (harden walls), silica

Stable, Stiff, not flexible

Fungal ECM

Cell Wall

Made of:

• Glucans (space filling polysaccharide)

• Chitin (Strength)

• Glycoproteins (Cell-Cell Adhesion)

Septal pores: let adjacent cell membranes communicate

Properties of Animal ECM

Mechanical strength, protection, organization, specialization

Ground Substances

GAGS (glycosaminoglycans): chains of disaccharides, they attract Water and Na+ ions

Proteoglycans (GAGs + Protein anchor): The size of proteins and the number of GAGs control how much water it binds to (stiffness), resists compression forces, and is a cheap, adjustable filler

Fibers

Collagen, Elastin, and Fibrillin

Collagen

Many Types:

• Fiber/Cable like → Type 1 (Cable), Type 3 (Fibers)

• Net/Mesh like → Type 3 and 4

Fibers built from fibrils

• Fibrils are 3 protein triple helix

High Tensile Strength: Resist stretch and length pulling

How collagen is produced

1) mRNAs translated into the ER Lumen

2) Golgi modifies some proteins to hydroxyproline, adds O-linked sugar

3) assemble procollagen triple helix

4) secreted with loose ends via vesicles

5) ends are trimmed

6) self-assemble into fibrils, then fibers

• Stabilized by H-Bonds and cross-links

• can bend but will not stretch in length

Elastin and Filbrillin

Elastin → Stretch

Fibrillin → limit

Found in all tissues that stretch, produced and secreted like collagen but elastin coils/links randomly; elastin will stretch until break without fibrillin

Adhesion Molecules

Fibronectin and Laminin

secreted out of the cell into the ECM, connect other parts of ECM to each other, help attach and create anchor points for cell

Fibronectin

Large protein in the ECM, V-shaped dimer, 2 covalently bonded chains, containing binding sites for integrins, collagen, and other ECM components

Laminin

T-shaped trimer, arms join to form flat sheet in the ground substance of the basal lamina → creates a selective barrier with epithelial tissue, separates cells from connective tissue; Tails form a triple helix which binds to cells

Secreted Materials

Minerals: stiffness and strength

• Ca2+ and PO43-

Signal Factors

• Tell cell what type of ECM

• History

Growth Factors

• Released for repair

• Inactive when healthy

Metabolism

chemical reactions that sustain life

catabolism

breaking down molecules, releases energy

anabolism

building up molecules, uses energy

Endergonic Reaction

absorbs energy, Delta G is less than 0

Exergonic Reaction

Releases energy, Delta G is greater than 0

Endergonic Reactions are driven by:

coupling an unfavorable (endergonic) reaction with a favorable (exergonic) one

Steady State

Cells maintain a steady state, not equilibrium because they need ATP levels to be x10 higher than ADP

Enzymes

Catalyze Reactions:

lower activation energy, alters the rate of spontaneous reactions (causes spontaneous reactions to not be spontaneous anymore). Does not change delta G or make an endergonic reaction exergonic

How do enzymes catalyze reactions?

1) align substrates so productive collisions are more likely

2) rearrange electrons so the substrate will spend more time in the transition state

3) distort bonds/shape of substrate so the binding site puts stress under bound substrate

How are enzymes regulated?

Chemical Modification: kinases and phosphatases

Activators: Small ions/molecules that can be required partners

Inhibitors:

• Bind reversibly/irreversibly by a covalent bond

• competitive

• non-competitive inhibition

Allosteric Regulation

Competitive Inhibiton

inhibitor molecule binds to the active site, competing w/ substrate

Noncompetitive Inhibition

inhibitor molecule binds outside the active site and changes the enzyme shape so the substrate cannot bind to the active site

Allosteric Regulation

a downstream product directly inhibits an enzyme near the start of a series, this links products to production levels

Endomembrane system

ER → Golgi → vesicles

Rough ER

protein synthesis and initial processing

• begins glycosylation (folding and modification)

• proteins made to be secreted are made by the ribosomes attached to the rough ER

Smooth ER

Lipid synthesis, detoxification, and Ca²⁺ storage

• makes phospholipids and steroids

• detoxifies drugs (liver cells)

• Stores Ca²⁺ for muscle contraction

Golgi

Modifies, sorts, and ships proteins

• receives proteins and lipids from the ER

• modifies (glycosylation)

• sorts based on signals

Lysosomes

Breakdown and digestion

• contains digestive enzymes

• breaks down macromolecules, old organelles, and pathogens

Nuclear Membrane

A double-membraned structure that separates DNA from the cytoplasm

• the outer membrane is continuous with the RER

Nuclear Pores

large protein complexes that control what enters/leaves

• highly regulated transport

• regulate: transcription factors, other proteins get in to control DNA expression, and ribosomes get out

Endosymbiosis

theory of how plastids (mitochondria and chloroplasts) were created. Cyanobacteria → chloroplasts and purple aerobic bacteria → mitochondria

Glycolysis

Glucose → 2 ATP + 2 NADH

• Preparatory phase: consumption of 2 ATP

  • Glucose-6-phosphate is formed and trapped in cell because it is negatively charged

  • Fructose 6-phosphate is the irreversible step, dedicated to energy extraction after this step

• Cleavage and rearrangement: 6C → 2 3C

• Payoff

  • Reaction Releases energy and stores it in ATP via substrate phosphorylation

Takes place in the cytoplasm

Pyruvate Oxidation

3C pyruvate → 2C Acetyl +CO₂

Acetyl + Coenzyme A → Acetyl CoA

• Acetyl CoA is locked into the mitochondria

Citric Acid Cycle

Energy from oxidation reactions is captured and used elsewhere

Products: 10 NADH, 2 FADH₂, 4 ATP, 2 CO₂

Oxidative Phosphorylation

Regenerate FADH and NAD+

ATP Synthase

Uses H+ gradient to generate ATP

F₁ (ATP Synthase)

uses rotational energy to catalyze ATP synthesis

F₀

forms a channel that rotates as protons pass through

Degrading Fats

Beta oxidation

Degrading Amino Acids

Remove N-Group and rearrange backbone to be a more burnable molecule