404 Exam 1 with amino acids

Glycine

neutral, but hydrophobic at times; uncharged

Alanine

hydrophobic; uncharged; nonpolar

Valine

hydrophobic; non polar

Leucine

hydrophobic; nonpolar

Isoleucine

hydrophobic; nonpolar

Proline

hydrophobic; nonpolar

Methionine

hydrophobic; uncharged

Phenylalanine

hydrophobic; uncharged

Tyrosine

hydrophilic; polar

Tryptophan

hydrophobic; nonpolar

Serine

hydrophilic; polar

Threonine

hydrophilic; polar

Cysteine

hydrophilic; polar

Asparagine

hydrophilic; polar

Glutamine

hydrophilic; polar

Lysine

hydrophilic; charged

Arginine

hydrophilic; charged

Histidine

hydrophilic; charged

Aspartate

hydrophilic; charged

Glutamate

hydrophilic; charged

a-Ketoglutarate amino acid derivatives

Glutamate, glutamine, proline, arginine

Oxalocacetate amino acid derivatives

Aspartate, Asparagine, Threonine, Isoleucine, Methionine, Lysine

3-Phospho-glycerate amino acid derivatives

Serine, Glycine, Cysteine

phosphoenol-pyruvate amino acid derivatives

Tryptophan, Tyrosine, Phenylalanine

pyruvate amino acid derivatives

Alanine, Leucine, Valine

the # of amino acids for building protein

20

What are the amino acids that create the start codon

AUG

What are the amino acids to create stop codons

UGA, UAA, UAG

(U Get A, U Are Awesome, U Are Great)

What does nonessential vs essential amino acids mean

nonessential: can synthesize ourselves; make it on our own

essential: cannot synthesize our selves efficiently; get from food bc its less of an investment and energy to make it ourselves

**does not apply to plants bc they create #essential

In humans, what is the most costly amino acid

Arginine

• NH2- and NH and NH2 in top group => urea cycle

3 rules of amino acid synthesis

1. different metabolic substrates

2. incorporate N2 into NH4 (amino groups)

3. feedback and control mechanisms to balance the levels of all 20 amino acids

What is the main nitrogen fixation cycle for amino acid biosynthesis

Nitrification of Nitrite (NO2-) → Nitrate (NO3-) → Denitrification to N2 → nitrogen fixation → Ammonia (NH4+)

How to attach nitrogen/ammonia to molecule to make amino acids?

Glutamine & free ammonium

What is the importance and difference between GS1 and GS2

compartmentation of isoenzymes of glutamine synthetase (GS)

GS1 only functions in cytosol

GS2 only functions in plastid

In plastids, which amino acids are derived from aspartate

Threonine

Methionine

Isoleucine

Lysine

Where are most biosynthesis of amino acids found in plant cell

Chloroplasts or plastids

What is the main mode of action of the Methionine-SAM cycle

transfer of methyl groups from methionine-SAM to charge and move methyl

What is unique about methionine

first amino acid in the start codon

Where in the pathway do substrates target when overproduced

the earliest enzyme → nip production in the bud without wasting any byproduct by going up the pathway

What is the key enzyme for branched chain amino acid synthesis

Acetohydroxy acid synthase (AHAS)

What is the function/mode of action of herbicides

inhibit certain pathways for plants biosyntheses

for AHAS enzymes, herbicides mimic the structure of Hydroxyethyl-TPP to glue the enzyme shut and inhibit function = kill plant

Why is ESPS synthase important

creates precursor chorismate for aromatic amino acids (rings)

the synthase can be targeted by RoundUp (Glyphosate) = no aromatic amino acids

What amino acid is biosynthesized through the shikimate pathway

Chorismate

What does allosteric regulation of chorismate mutase (CM) mean?

depends on context and where the substrate will bind to the enzyme => can either be promoter or inhibitor

What are the 5 enzymes of tryptophan biosynthesis

1. AnS (first step & feedback regulation)

2. PAT

3. PAI

4. IGPS

5. Tryptophan synthase (TS)

what is genetic redundancy

Multiple genes that have similar functions or code for the same products

some may be “dormant” when the DNA is methylated (regulated to demethylate when product is low in cell)

What do southern, western, and northern blot dectect?

Southern: DNA

Western: proteins

Northern: mRNA

4 parts of plant cell

• cell wall

• plasma membrane

• cytoplasm & organelles

• air space

what are membrane lipids built from

bilayer of amphipathic bipolar lipids (hydrophilic and hydrophobic tails — hydrophilic being on the outside and hydrophobic inside

What makes up the fluid mosaic membrane model

fluid membrane with:

• integral membrane proteins

• peripheral membrane proteins

• GPI/lipid anchored proteins

• oligosaccharide side chains

What is the plasmodesmata

channels through cell wall to connect neighboring cytoplasm

What is the function of the endoplasmic reticulum

the highway system to connect nucleus to rest of cell and cell to cell interactions

sorts proteins

movement of organelle

difference between the rough and smooth ER

Rough:

• ribosomes

• makes membrane protein (protein body ER)

Smooth:

• no ribosomes

• makes lipids (oil bodies)

Function of the golgi apparatus

work with the ER for retrograde transport (ER → golgi → ER)

rides along actin filaments with motors

what are the 3 mechanisms of membrane trafficking and recycling

1. cell expansion (use up membrane)

2. formation of clathrin-coated vesicles (CCV) (endocytosis)

3. direct lipid transfer from PM to ER

Function of vacuoles

build large cells for cheap (turgot pressure)

storage, digestion, pH homeostatis, defense

What organelles contain their own DNA

nucelus, mitochondria, plastids

(all double membraned)

how and why to remove cell wall

pectinase and cellulase

deliver reagents easier without the barrier of wall

what makes fungal cell wall diff than plant cell wall

fungal walls are made of chitin

long chain polymer of derivative of glucose (N-acetylglucosamine)

what is the function of plastids

handle the manufacture and storage of essential food and chemical compounds

what is the function of mitochondria

ATP synthase, electron transport chain complexes, porin channels with its own DNA in the mitochondria

What are peroxisomes

single membrane organelles for photorespiration, ROS control, and make long fatty acid chains

what is the function of the nucleus

store genetic material and safeguard/regulate molecules with the nuclear pore complex and cytosol

which organelles are important for the cell membrane system

plastma membrane, ER, golgi

What are the 5 amino acid derivatives

1. α-ketoglutarate

2. Oxlacacetate

3. 3-phospho-glycerate

4. Phosphonoenol-pyruvate

5. Pyruvate

What is a lipid

• organic compounds that are fatty acids or derivatives

• insoluble in water

• soluble in organic solvent

What are the 3 general classes of lipids

• phospholipids

• triglycerides (triacylglycerol)

• steriods

Function of lipid molecules in plants

• membrane structure

• storage

• protein modification

• signaling

• defense

• cold weather protection

How many fatty acid tails do phosphatidylcholine have

2

How many fatty acid tails do tricylglycerol have

3

What is the structural and shorthand abbreviation difference between saturated and unsaturated fatty acids?

Saturated Fatty Acids:

(total # carbons: 0)

• Only single carbon-carbon bonds (C-C); fully packed with hydrogen atoms. Straight chains that stack tightly (solid at room temperature)

Unsaturated Fatty Acids:

[Total Carbons]:[Number of double bonds] Δ^[positions of double bonds]

• Contains one or more carbon-carbon double bonds (C=C), causing a "kink" or bend. Prevents tight stacking (liquid at room temperature).

Simple definition of the sanger sequencing process

(the chain-termination method) determines the exact nucleotide order of a DNA strand using regular building blocks and fluorescent stop signals

Steps of sanger sequencing

• Denature: Heat the DNA to separate it into single strands.

• Anneal: Cool the mixture = the primer to the target DNA.

• Extend: The polymerase adds normal dNTPs to grow the new DNA strand.

• Terminate: A colored ddNTP is randomly added instead of a normal base. It stops the chain because it lacks a required 3'-OH group.

• Repeat: The reaction creates many fragments of different lengths, all ending in a colored stop base.

• Separate and Read: Capillary electrophoresis sorts the fragments by size, and a laser reads the fluorescent colors in order from shortest to longest to reveal the DNA sequence.

What is one basic mechanism for plants to recognize fungal pathogens and how can one engineer disease resistance to fungus?

Pathogen-Associated Molecular Pattern pathway with PRR where cell-surface receptors detect chitin found in fungal cell walls

overexpress chitin receptors or plant chitinases to boost detection

What does amphipathic for mem. lipid mean

It has a hydrophilic (polar) head group AND hydrophobic tail(s) (fatty acids). In water the tails hide from water and the heads face it

How do sterols control membrane fluidity?

They wedge between phospholipid tails.

high temperature: restrain movement

low temperature: prevent tight packing (keep it from solidifying).

Net effect: a fluidity buffer.

State the fluid-mosaic model.

membrane is a fluid phospholipid bilayer in which proteins float like a 'mosaic'

Lipids and many proteins can diffuse laterally.

Components: lipid bilayer, integral proteins, peripheral proteins, lipid-anchored proteins, and oligosaccharide (carbohydrate) chains on the outer face.

List the 5 types of phospholipid movement

1. Lateral diffusion (neighbor swap on same side)

2. Rotation (spinning about the long axis)

3. Flexion (bend tail)

4. Bobbing

5. Flip-flop (transverse movement to the other side, need phospholipid translocators)

Structure of the nuclear pore complex (NPC).

Embedded where the inner and outer nuclear membranes fuse.

Parts: cytoplasmic filaments, cytoplasmic ring, luminal ring, scaffold, nuclear ring, central channel (transporter), and nuclear basket. Built from ~30 nucleoporin proteins.

How do proteins get through nuclear pores?

Small molecules (< ~40 kDa) diffuse freely.

Larger proteins need a nuclear localization signal (NLS) that binds importin = pulled through the central channel by binding FG-nucleoporins.

How does the Ran gradient make nuclear transport directional?

nucleus Ran-GTP causes cargo release. Export uses a nuclear export signal (NES) + exportin + Ran-GTP. Ran-GTP/GDP gradient gives direction and requires energy (GTP

List the all membrane systems/organelles

Plasma membrane, ER, Golgi, vacuoles, plastids (chloroplast, amyloplast; absent in fungi), mitochondria, peroxisome, nucleus.

How can you determine the subcellular localization of a protein? (list methods)

(1) Fuse a fluorescent protein (GFP) to your protein; express in protoplasts, image by confocal with organelle marker co-localization.

(2) Immunolocalization with a specific antibody (immunofluorescence)

(3) Subcellular fractionation + Western blot with organelle marker antibodies.

(4) In silico prediction (signal peptides)

When and how is the plant cell wall formed?

During cytokinesis

• Golgi-derived vesicles guided by the phragmoplast (microtubules + actin) fuse at the cell plate = grows outward to fuse with the parent wall

• The cell plate matures into the middle lamella, and each daughter cell then lays down its own primary wall.

List ALL major components of the plant cell wall

Cellulose microfibrils

cross-linking glycans (hemicelluloses) (bind cellulose)

pectins (middle lamella is pectin rich and is like a glue with pore size of wall)

structural proteins (PRP, GRP)

phenolic polymers lignin and suberin (secondary walls/special cells)

water

Cellulose: monomer, bond, and structure

Linear glucan chains of beta-D-glucose joined by beta-1,4-glycosidic linkages

held by hydrogen bonds into crystalline microfibrils

Which sugar nucleotides are the 'active building blocks' of wall polysaccharide synthesis?

UDP-glucose and GDP-glucose

Glycosyltransferases transfer the sugar from the nucleotide sugar to the growing chain, releasing UDP/GDP.

List the 3 families of Structural proteins of the wall

1. Hydroxyproline-rich glycoproteins (HRGPs)

2. Proline-rich proteins (PRPs)

3. Glycine-rich proteins (GRPs)

List Wall-related water transport pathways

Apoplastic: through cell walls and intercellular spaces (fast, but blocked by waterproof lignin/suberin in the Casparian strip).

Symplastic: through the cytoplasm via plasmodesmata.

Transcellular: crossing plasma membranes through aquaporins. Waterproof suberin/lignin forces water into the symplast/transcellular route at the endodermis.

How is an actin filament assembled and disassembled?

Dynamic cycle

adding ATP-bound G-actin monomers to the plus (ATP is hydrolyzed within the filament) end and disassemble by releasing ADP-bound monomers from the minus (pointed) end

Free ADP-actin is recharged to ATP-actin and reused = treadmilling. Capping protein blocks ends;

How are the cytoskeleton and the cell wall coordinated?

Microtubules lie beneath the plasma membrane and guide cellulose synthase complexes

Actin/myosin-driven vesicles deliver matrix polysaccharides and CESA to the wall. Wall status feeds back on the cytoskeleton.

List hydrophobic amino acics

Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Proline, Phenylalanine, Tryptophan

List hydrophilic amino acids

Serine, Threonine, Cysteine, Tyrosine, Asparagine, Glutamine

List charged & acidic amino acids

Aspartate, Glutamate

List charged & basic amino acids

Lysine, Arginine, Histidine

Four major roles of nucleotides

1. Building blocks of nucleic acids

2. energy currency

3. activated intermediates/derivatives in biosynthesis

4. cell signaling

Purines vs pyrimidines

Purines (A, G): two-ring structure (6+5-membered fused).

Pyrimidines (C, T, U): single six-membered ring.

DNA: A, G, C, T.

RNA: A, G, C, U.

What are the two routes of nucleotide synthesis?

• De novo pathway: build the ring from simple precursors (amino acids, CO2, formate/THF, NH3) on activated ribose (PRPP), costly in ATP.

• Salvage pathway: recycle free bases/nucleosides by attaching them to PRPP (cheap, base + PRPP → nucleotide).

De novo pyrimidine synthesis: list enzymes in order (to UMP)

1. (CPS): Gln (NH3) + HCO3- + 2 ATP -> carbamoyl phosphate.

2. (ATCase): + Asp -> carbamoyl aspartate.

3. Dihydroorotase: ring closure -> dihydroorotate

4. Dihydroorotate dehydrogenase (DHODH; uses CoQ or NAD+) -> orotate

5. Orotate phosphoribosyltransferase (+PRPP) -> OMP

6. OMP decarboxylase -> UMP.

Regulation of pyrimidine synthesis

Feedback at the first committed enzyme (CPS): PRPP (and ATP) activate (positive);

end products UDP/UTP (and downstream nucleotides) inhibit (negative).

PRPP availability also acts as feed-forward control.