Exam 2!! Biol 1306, Cheek, IN PROGRESS

Steps of Secretory pathway of proteins

1. synthesis and entry into rough ER -polypeptide synthesized

2. transport vescile transport into golgi’s cis face

3. processing in the golgi

4. secretory vescile leaves trans face of golgi

5. secretory vescicle fuses with plasma membrane , releasing protein outside cell and adding vesicle membrane to plasma membrane

cisternae

individual membrane-bound compartments that make up golgi apparatus

How are proteins directed to the ER? (generic signal hypothesis)

1. free ribosome has ER signal sequence

2. translation of protein is paused

3. ribosome goes to rough ER and docks onto it

4. Translation resumes, so protein grows into ER lumen

5. newly made protein in ER

primary protein structure (define and held by what?)

• unique AA sequqnce

• held by peptide bonds

• ex: sickle cell disease

secondary protein structure

• a helices (coils), b pleated sheets

• held together by H bonds between fucntional groups in the peptide backbone

• very stable structures!

tertiary protein structure

• 3d shape of a polypeptide!

• help together by R-group interactions

  • H bonds

  • hydrophobic interactions

  • Disulfide bonds

  • Ionic bonds

• Creates very specific shapes that a protein needs (ex: a protein’s active site!)

• NP R groups =causes R groups to be in interior = away from water

  • P R groups= causes R groups to be in exterior= facing water

Quaternary Structure

• many polypeptide units combines

• multiple chains

primary hemoglobin structure

• AA sequence

  • changing one AA = Sickle cell anemia

secondary hemoglobin structure

• 2 helices + 2 sheets

tertiary hemoglobin structure

• 3d shape

• made mostly of coiled a-helices.

quaternary hemoglobin structure

• 4 subunits (helices+sheets) into 1 unit

Denaturation

• destroys tertiary structure

  • destroys active site

  • loss of fxn

Purines?

• PURe As Gold

• Adenine, Guanine

• 2 Rings (2 ring wedding band)

Pyrimidines

• CUT Pie

• Cytosine, Uracil, Thymine

• 1 ring (pyramid=one)

how is a phosphodiester bond formed?

formed by condensation of 3’ OH on sugar + 5’ phosphate of next nucleotide!!

Where is the phosphate in the nucleotide?

5’ Sugar

Where is the base in the nucleotide?

on 1’ Carbon

What’s the identifying detail of a ribose sugar?

OH on the 2’ Carabon

What’s the identifying detail of a deoxyribose sugar?

Only H on the 2’ Carbon

primary DNA structure

sequence of nucleotides connected by phosphodiester bonds

secondary hemoglobin structure

Antiparralel double helix held by H bonds

Difference between secondary structure between protein vs DNA

• Protein secondary structure uses backbone H bonds

• DNA uses base H bonds

tertiary DNA structure

Compact 3d shapes

Amount of bonds between both pairs of nucleotide pairs?

• A=T : Double H bonds

  • C㆔G : Triple bonds

primary RNA structure

• sequence of nucleotides continaing Ribose & Uracil instead of Thymine

  • ⭐Ribose has a 2’ OH , makes RNA less stable than DNA, enables catalysis

secondary RNA structure

• single strand folds on itself using H bonds b/t complimentary bases on the same strand, forms stem & loop (hairpin) structures

tertiary RNA structure

secondary structures fold into complex 3d shapes (ex: pseudoknots)

Why does DNA store information well but cannot catalyze?

• High stability: Regular geometry, hidden bases, strong bonds make DNA ideal for long term storage

• No catalytic activity: Lacks exposed functional groups and diverse 3d shapes required fpr active sites. RNA/Proteins do catalysis instead.

Why can RNA catalyze?

• Shape diversity: single strand allows more shapes, creating active site pockets for substrates

• Chemical reactivity: —OH group acts as reactive functional group

  • Ribozymes: Catalytic RNA mlcls

Why RNA World Hypothesis ?

Because RNA can store information + caralyze reactions, RNA likely existed before DNA

DNA

• uniform shape

• ✅ storage

• ❌ Catalysis

RNA

• sequence directly determines secondary and tertiary shapes

• Diverse functions

• ✅ Catalysis

Prokaryote characteristics

• no membrane bound nucleus

• plasmids

• ribosomes

• chromosomes

  • cell wall- resists osmotic pressure

    • bacteria: made of peptidoglycan

    • archaens: cell walls LACK peptidoglycan

eukaryote characteristics

• Nucleus—store DNA, site of transcription (DNA→RNA), nuceolus inside builds ribosome components

• Ribosomes- Assembles RNA+ Protein that builds protein

  • (free protein= cytosol/nucleus protein)

  • (ER bound= membrane=exported proteins)

Rough ER

studded w/ ribosomes, folds + processes protein in it’s lumen

single membrane

Smooth ER

synthesizes lipids (phospholipids, steroids), detoxifies chemicals, stores Ca2+

Golgi apparatus

stacked slattened sacs (cisternae) with polarity.

Cis Face recieves cargo from ER; Trans face ships processed cargo out

Lysosomes

• In animals

• Digestion +recycling center

• ~40 acid hydrolases, proton pump keeps lumen acidic (ph=5)

Mitochondria

• ATP production site

• Contains inner+ outer membranes, folded cristae, and a central matrix.

• Has it’s own circular DNA + Ribosomes

Chloroplasts

• Plants/Algae

• photosynthesis site.

• Contains stacked grana (thykaloid discs) in fluid.

• Stroma. Has it’s own DNA + Ribosomes

Endomembrane System

ER →Golgi → Lysosome/vescicles/Plasma membrane (last bit works as one unit)

Exocytosis → Secreted Protein Path

ribosome on rough ER→ ER Lumen → transport vescicle → golgi cis face → cisternae → golgi trans face→vescicle → plasma membrane

Rough ER fx

Protein Synthesis + Processive

Key features: Ribosomes attached: has receptors that allow entry of selected proteins

Smooth ER fx

Lipid Synthesis + Processing

Key features: Has enzymes for making phospholipids

Golgi Apparatus fx

Protein, lipid, and carbohydrate processing

Key features: Stack of flattenede cisternae, has receptors for rough ER products.

Lysosomes fx

Digestion + Recycling

Key features: Contains hydrolases (breaks down macromlcls) + protein pump ON lysosomal membrane. Keeps inside acidic.

Cytoskeleton Fx

1. Structural Support

2. Movement of materials

3. Movement of whole cell in some species

Components of cytoskeleton

1. Microfilaments

2. intermediate filaments

3. microtubules

Microfilaments Fx

• Resists Tension (pull)

• Cell crawling + contraction

• cytokinesis in animal cells

• move organelles+cytoplasm

intermediate filaments fx

• Resists tension (pull)

• anchor nucleus +some organelles

microtubules fx

• Resists compression (push)

• move cells via flagella or cilia

• move chromosomes in cell division

• tracks for vescicle transport

Where does protein synthesis start?

cytoplasm.

glycosidic linkage

covalent bond between 2 monosaccharides

polysaccharide

3 or more monosaccharides, covalently bonded

• ex: starch- polymer of glucose; made by plants

• ex: glycogen- polysaccharide of glucose; made in animal cells

Fx of carbs

• monosaccharides

  • fuel for cellular respiration

• polysachharides (starch/glycogen)=fuel storage + structural support

  • ex: cellulose= plant cell walls

  • ex: chitin= in arthropod exoskeletons

Fx of fats

• metabolic fuel

  • glycerol + fatty acids can be used in cell. resp. as reactants.

  • glycerol and FAs can be seperated for different reactions

• stored fuel

  • triglycerides, not reactants in cell. resp.

OIL RIG

Oxidation is Loss of electrons

Reduction is Gain of electrons

Catabolism

breaking dowm mlcls + releasing energy

NAD+

Nicotinamide Adenine Dinucleotide

• building block= Niacin (Vit. B3)

  • NAD+ = oxidized state

    • can accept electrons as H- / Has already donated electrons

  • NADH = reduced state

    • NADH is carrying electrons or has already accepted electrons

FAD

Flavin Adenine Dinucleotide

• building block =riboflavin (Vit B2)

  • FAD= oxidized state

    • can accept electrons as 2H- ; or already has donated electrons

  • FADH2

    • carrying electrons ; or has already accepted electrons

Fermentation

Occurs if O2 is absent

Occurs in Cytoplasm

If pyruvate accepts electrons from NADH and is converted to lactate → NADH oxidized to NAD+ → NAD+ now available to accept electrons from reactions of glycolysis

Pyruvate Oxidation

In presence of O2

Location of CAC in eukaryotes

Mitochondrial Matrix

Location of CAC in prokaryotes

Cytosol

What is in mitochondria?

• it’s own ribosomes

• it’s own chromosomes

Where does CAC/TCA cycle occur?

mitochrondrial matrix

Where are electron transport complexes located?

Inner membrane of mitochondria

Where does oxidative phoshporylation occur in mitochrondria?

Inner membrane (where the electron transport chain and ATP synthase perform oxidative phosphorylation to make ATP).

Location of pyruvate oxidation

Mitochondrial matrix (after pyruvate is transported across the inner mitochondrial membrane from the cytosol).

double check

reacctions of pyruvate oxidation

‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ NAD+ Coenzyme A

‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ↓ ↓

pyruvate —↓—--↓———→ Acetyl CoA

‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎ ‎CO2 NADH

Acetyl CoA

not done

participates in CAC reactions!

Reactions of CAC

Reactions release electrons

Inputs of CAC reactions

• 1 Acetyl CoA

• 3 NAD+

• ADP/GDP

• 1 FAD

Outputs of CAC reactions

• 2 CO2

• 3 NADH

• 1ATP/GTP

• 1 FADH2

NADH + FADH = electron carriers

Which products of the CAC reactions are electron carriers?

NADH and FADH2

Source of substrates of CAC

glucose yields pyruvate

fatty acids yield Acetyl CoA

AAs yield pyruvate + other intermediates in CAC

Location of electron transport in eukaryotes

inner mitochondrial membrane

dots= ETC

Where is ETC in prokaryotes?

ETC in prokaryotes: ETC proteins embedded in infoldings of plasma membrane

Where is ETC in eukaryotes?

ETC in eukaryotes: NADH + FADH2 in mitochondrial matrix, Donates electrons to the ETC proteins in inner mitochondrial membrane

Where are ETC complexes and what do they do?

• protein complexes in inner mitochondrial membrane that accept and donate electrons in a sequence

  • Many of these proteins contain Iron (Fe)

• sequence ends with O2 accepting electrons to become H2O

Where does H+ gradient come from in electron transport?

energy from ETC pumps H+ from matrix → intermembrane space

glucose in linear form

glucose recognizable by?

• 3 or more C atoms

• —OH (hydroxyl)

• —C=O (carbonyl)

glucose in ring structure

also glucose in ring structure

how are glycosidic linkages made?

through dehydration synthesis. H and OH from two different monosaccharides are removed to produce H2O and fuse to make a disaccharide

Reactants of Glycolysis

• glyceraldehyde-3-phosphate (also an intermediate)

• glucose

products of glycolysis

• 2 pyruvates

• 1 ATP

• NADH

inputs of pyruvate oxidation

• 2 pyruvates

• NAD+

• Coenzyme A

Outputs of pyruvate oxidation

• 2 Acetyl CoA

• 2 CO2

• 2 NADH

because of 2 pyruvates!

Chemiosmosis

Diffusion of H+ through ATP synthase in inner mitochondrial membrane

Proton Motive Force

• Kinetic energy created by H+ gradient across the inner membrane

• H+ moves a rotor protein that is part of ATP synthase

1 ATP forms for every

4 H+that flow through

1000s ATP synthase mlcls per

1 mitochondrion

how many mitochondria per liver of muscle cell

1000s of mitochondria

how much atp / sec/ muscle cell?

10 × 10⁶ ATP/sec/muscle cell

Partial Presure of gases

pressure exerted by a particular gas in a mix of gasses

1 ATM=

760mmHg

Respiratory Medium= Air

• 21% O2

• Low density

• Low viscosity

• easy to move ocer a surface and through vessels

• dehydrates organism

Respiratory Medium= Water

• 4-8 mL of O2 per L /0.4-0.8% O2 per L of H2O

• O2 solubility decreased by increased temp. and increased salt concentration

• Dense

• Viscous

• more work to move over surface