Bio Sata Exam 3

Define metabolism, anabolism and catabolism and give examples for each.

Metabolism- sum of all chemical reactions within a cell, including ones that use energy and ones that release energy

Anabolism- building, simple → complex molecules, respiration

Catabolism- degradation, complex → simple molecules, photosynthesis

Describe how the two laws of thermodynamics apply to biological systems with examples.

Energy can be transferred, but neither created nor destroyed

Plants convert sunlight energy into chemical energy within organic molecules

Energy transfer leads to increased randomness of the universe

Energy is lost as heat during cellular metabolic reactions

Define entropy, enthalpy and free energy and give examples. Understand how they are related to each other in the free energy equation.

ΔG = ΔH - TxΔS

Entropy- disorder, randomness, unusable energy, ΔS

Enthalpy- heat energy, ΔH

Free energy- combining enthalpy and entropy, energy available to perform work, ΔG

Know examples of exergonic, endergonic, exothermic and endothermic reactions and combinations of the same. No need to memorize the bond energies.

Exergonic- -ΔG, release of energy, spontaneous

Endergonic- +ΔG, absorption of energy, non-spontaneous

Exothermic- heat is released, -ΔH

Endothermic- heat is absorbed, +ΔH

Examples

Breaking sugar down into simple molecules is exergonic

Melting ice cubes is endothermic

Respiration is exergonic and exothermic

Photosynthesis is endergonic and endothermic

Understand and practice how Keq is calculated with given concentrations of reactants and products.

(C x D) / (A x B)

What is ATP and how it is used to drive endergonic processes through energy coupling?

Organic compound that provides energy to cells

ATP hydrolysis is exergonic and favorable, so it can be coupled with endergonic, unfavorable reactions

It drives reactions forward when they are not spontaneous (ex. Glucose + fructose → sucrose)

Describe enzymes and how they help in a biochemical reaction.

Biological catalysts that lower activation energy

They have a specificity for a specific substrate and fits into it via induced fit

Know the relationship between the enzyme active site, free energy and activation energy changes.

Active site- site of an interaction between enzyme and its substrate

Free energy- energy available to do work

Ea is what changes

Enzymes do not change ΔG, they just lower ΔG of activation

Be able to identify Vmax and Km in a given graph or Table.

Vmax- highest velocity of enzyme, highest the line goes

Km- the X axis where ½ Vmax is

Know the 5 different factors affecting enzyme activity and examples.

TPSSC

Temperature- each enzyme has optimal temp (37 degrees C in humans)

pH- optimal pH (ex. 2 for pepsin in stomach)

Salt- require presence of certain ions or salts (ex. DNA polymerase requires Mg2+)

Substrate- needs the right kind of substrate. Vmax is achieved when all active sites are saturated

Cofactors- accept or donate electrons to help enzymes work

How does substrate concentration, competitive inhibitors, non-competitive inhibitors affect enzyme activity? How do these inhibitors affect the Vmax and Km?

Competitive inhibitors- compete with substrate for the same active site, keep enzyme from working, higher concentration of substrate needed, Vmax is not altered but Km increases

Noncompetitive- bind to different spot, change shape to make enzyme less active or inactive, Vmax decreases and Km stays the same

Briefly describe allosteric, feedback and chemical modification and how they regulate enzyme activity with examples.

Allosteric- active and inactive forms, activator or inhibitor changes to respective form, cooperativity among bonding with activator (ex. PFK)

Feedback- end product of one biological pathway inhibits an earlier enzyme and stops pathway (ex. Valine inhibits acetolactate synthase in amino acid pathway)

Chemical modification- modified to make active or inactive (ex. Phosphorylation of amino acids)

Explain how the energy stored in different types of food molecules is released in a series of redox processes to produce ATP by substrate-level phosphorylation and oxidative phosphorylation.

Food (glucose) becomes ATP

Substrate level: transferring phosphate from high energy molecule to ADP

Oxidative: Proton motive force. NADH and FADH2 transfer electrons from food molecules thru the electron transport train and they are accepted by O2. During the process, protons are pumped into the intermembrane space, creating a proton gradient. ATP-synthase then combines ADP with a Pi. When protons go back out into the matrix, they release the ATP.

Remember where the different processes of cellular respiration occur in prokaryotic and eukaryotic cells, and explain the role of mitochondrial structure in such processes.

Production of ATP via chemiosmosis is called oxidative phosphorylation

Chemiosmosis takes place in the mitochondria in a eukaryotic cell, and in cell membrane in a prokaryotic cell

Describe how cellular respiration is regulated in cells. Be able to predict responses to changing conditions such as lack of oxygen, lack of carbohydrate fuels, relative abundance of ATP/ADP, or the presence of specific toxins.

Multiple controls are needed to use/make ATP when appropriate

If no oxygen, then anaerobic fermentation

GLUT proteins transport glucose into cells, so facilitate glycolysis

High levels of ATP inhibit PFK, which does step 3 of glycolysis, so step 3 occurs slower. Citrate also does this.

High levels of ADP induce PFK, so step 3 occurs faster (more ATP needed)

Connect how the outputs of one process become inputs of another process of aerobic respiration (glycolysis, acetyl CoA formation, Krebs cycle and oxidative phosphorylation).

Pyruvate from glycolysis goes into acetyl CoA formation

Acetyl CoA goes into the Krebs cycle

CoA from the Krebs cycle goes back into acetyl CoA formation

NADH and FADH2 from the Krebs cycle go into oxidative phosphorylation

There is no need to memorize all steps of Glycolysis, Krebs cycle or oxidative phosphorylation. Remember only the first committed step 1 and the rate-limiting step 3 in both processes.

First committed step (1)

Glycolysis- performed by hexokinase, forms glucose-6 phosphate

Krebs- performed by citrate synthase, induced by AMP and inhibited by ATP

Rate limiting step (3)

Glycolysis- performed by PFK (also need Mg2+), which can make it go faster or slower, induced by ADP and AMP, inhibited by high levels of ATP and citrate

Krebs- performed by isocitrate dehydrogenase, stimulated by ADP and inhibited by high levels of ATP and NADH

Know why fermentation occurs in the absence of O2, which organisms can perform this, and how it helps make ATP.

Because no molecule can accept the electrons from the transport chain

Animals and bacteria

NAD+ needs to be regenerated to keep it moving. 2 pyruvates from glycolysis and NADH make lactic acid and NAD+

Know how various molecules such as carbohydrates, proteins and lipids will enter the various stages of cellular respiration.

Glycolysis → acetyl CoA → Krebs: the molecules enter at different stages

Carbs- enter the process at glycolysis

Fats- enter the process at acetyl CoA production

Proteins- enter at Krebs cycle after the amino acids have been deaminated

what is my favorite color

green

Summarize why photosynthesis is important to life on earth and remember the summary equation for photosynthesis, identifying the inputs and outputs.

Only biological process that can utilize sources like light, plants depend on it and animals depend on plants

Equation: CO2 + 2H2O (light)→ CH2O + O2 + H2O

Identify parts of the leaf and chloroplast where light reactions and Calvin cycle takes place

Light reactions take place in thylakoid membranes, and protons are pumped there from stroma

The Calvin Cycle occurs in the stroma

Describe how light energy is harvested and how its absorption is related to wavelength.

Photosystems I and II, 700 nm and 680 nm wavelength respectively, do ATP synthesis

PS I

NAD+ → NADH

Cyclic and non-cyclic reactions

Primitive

PS 2

Water split to 2 H+, 2 e-, ½ O2

Only in non-cyclic

More recent

Trace the path of an excited electron from its absorption of solar energy to the production of ATP and NADPH.

Received by photosystem II (electrons lost after receiving photons, but replaced by splitting of water, O2 is also released here) → primary electron acceptor → electron transport chain → photosystem I → primary electron acceptor → NADPH (used to reduce NAD+)

The whole transfer process provides energy for ATP by the electrons losing energy

Discuss cyclic vs noncyclic electron flow, and the net inputs and outputs of each.

Cyclic

No water split

No NADPH made

Electrons start at PS I and end back at PS I

Creates proton gradient that drives ATP synthesis

Noncyclic

Water and NADPH made

Electrons start at PS II and end up making NADPH

Generates ATP by transfer from PS II to PS I

Compare and contrast chemiosmosis and ATP production in mitochondria and chloroplasts.

Chemiosmosis- movement of electrons from high to low concentration to generate membrane potential, proton motive force

Oxidative phosphorylation- ATP synthase makes 30-32 ATP (in humans)

Both M and C make ATP, have ETC, and have ATP synthase

Mitochondria

All plants and animals

ETC along inner mitochondrial membrane

High proton concentration in intermembrane space

Chloroplasts-

Plants and cyanobacteria only

ETC along thylakoid membrane

High proton concentration within thylakoids

Describe the Calvin cycle, including the role of ATP and NADH, net inputs and the ultimate product(s) of the reaction.

Occurs in stroma

Needs 6 turns to make 1 C6H12O6

Steps

RuBisCo is the main enzyme and does carbon fixation

Reduction

Regeneration of RuBP

They use ATP and NADH previously produced in cyclic or noncyclic electron flow

Inputs: CO2, ATP, NADPH

Outputs: CH2O, ADP, Pi, NADP+

Know the rate limiting step 1 and enzyme, RuBisCO of Calvin cycle and how it is regulated.

Carbon fixation done by RuBisCO

3CO2 → 3-phosphoglycerate

Regulation of RuBisCO

Concentration of O2 and CO2 in the cell- functions most when CO2 goes down

Mg 2+ concentration- needed

pH- optimal is 8, achieved when light reactions happen

NADPH levels- greater levels stimulate

How does photorespiration affect photosynthesis in C3 plants and how it can be minimized with PEP carboxylase in C4 and CAM plants?

On hot, dry, sunny days

CO2 is low, O2 is high, rubisco turns O2 into RuBP and releases CO2

C3 plants like rice and wheat only have C3 pathway, photosynthesis inhibited

C4 plants like corn and sugarcane have additional C4 pathway, PEP carboxylase is used to turn CO2 into 4-C sugars, PEP has no affinity for O2

CAM plants are similar to C4, but they do not have separate cells for C4 and C3 pathways, C3 is performed during day and C4 during night

Compare and contrast C3, C4 and CAM plants in terms of their structure and how they minimize photorespiration.

C3- rice, wheat, only C3 plants, not as successful as minimizing photorespiration

C4- corn, sugarcane, have C3 and C4 pathway, use PEP carboxylase to minimize photorespiration, C3 pathway is limited to bundle sheath cells and C4 pathway is mesophyll cells close to surface

CAM- pineapple, cacti, night/day reactions

take a deep breath

done

Know the three different types of lipids and their functions.

Carotenoids- photosynthesis and antioxidants

Phospholipids- make up cell membrane

Sterols- precursors for steroid hormones like estrogen

Connect the various processes such as photosynthesis, respiration and lipid synthesis

Photosynthesis is the primary source for all organic molecules

The glucose made in photosynthesis goes through glycolysis, and the 2 3-C molecules become glycerol. This, combined with fatty acids, make fats.

Acetyl CoA, produced by respiration, is an central precursor for lipid synthesis

Understand how the intermediates and end products in respiration are used to make fats and phospholipids.

Acetyl CoA, produced by respiration, is an central precursor for lipid synthesis

Acetyl CoA is used to make Malonyl CoA, which is the first committed step of fatty acid synthesis

The phosphates produced during the respiration process combine are used to make phospholipids

Remember the precursor and key enzyme in steroid biosynthesis

HMG-CoA is the precursor, regulated by HMG-CoA reductase

Know the precursor of carotenoid biosynthesis.

Isoprenoids

Understand how fats and steroids are broken down by the cells.

Lipase

Fatty acids are broken down in the mitochondrial matrix by beta-oxidation

Fatty acyl-CoA hydrogenase needed

Beta oxidation and CoA → acetyl CoA and NADH

The Acetyl CoA then goes into the Krebs cycle and becomes CO2

Recognize and remember the cell structures involved in lipid metabolism.

Takes place in cytoplasm

Enzymes and stuff used

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