Cell Biology Exam 2

Bioenergetics

The study of the various types of energy transformations that occur in living organisms

Energy

capacity to do work, or the capacity to change or move something

Thermodynamics

the study of the changes in energy that accompany events in the universe

First Law of Thermodynamics

The law of conservation of energy states that energy can neither be created nor destroyed. Cells are capable of energy transduction. The universe can be divided into systems and surroundings.

Second Law of Thermodynamics

events in the universe tend to proceed from a state of higher energy to a state of lower energy (spontaneous events). Every event is accompanied by an increase in the entropy of the universe

Transduction

conversion of energy from one form to another

Examples of energy transduction

electric energy can be transduced to mechanical energy when we plug a clock in. Chemical energy is converted to mechanical energy when heat is released during muscle contraction. Animals, such as fireflies and luminous fish, are able to convert chemical energy back to light

Where is chemical energy stored?

In certain biological molecules like ATP

photosynthesis

conversion of sunlight into chemical energy

What is a system?

a subset of the universe under study

What are the surroundings in a system?

everything that is not a part of a systemthat interacts with the system.

internal energy

energy of the system. change in Eis related to heat and work.

Exothermic reactions

reactions that lose heat

Endothermic

reactions that gain heat

First law of thermodynamics equation

change in E = Q - W, where E is internal energy, Q is heat energy, and W is the work energy

Spontaneous events

events that occur without the input of external energy (second law of thermodynamics)

Entropy

measure of randomness or disorder. associated with random movements of particles or matter

First and Second Law combined equation

change in H = change in G + T change in S, where free energy is change in G, enthlapy is change in H, change in s is change in entropy. change in g is spontaneity of the reaction. <0 reaction is exergonic, >0 it is endergonic

Enzymes

catalysts that speed up chemical reactions. almost always proteins. Can be conjugated with non-protein components

Cofactors

inorganic enzyme conjugates

Coenzymes

organic enzyme conjugates

Properties of enzymes

Present in small amounts, not permanently altered during course of reaction, can’t affect thermodynamics of reactions (only rates), highly specific for their particular reactants called substrates, produce only appropriate metabolic products, and can be regulated to meet needs of cell

Activation Energy

small energy input that is required for any chemical transformation. It slows the progress of thermodynamically unstable reactants

transition state

reactant molecules that reach the peak of the EA barrier

What happens without an enzyme?

only a few substrate molecules reach transition state

What happens when there is a catalyst?

a large proportion of substrate molecules can reach the transition state

Enzyme-substrate complex

when an enzyme interacts with its substrate if forms this (active sites)

active sites

substrate that binds to a portion of the enzyme. have complementary shapes with substrates that allow substrate specificity

What is the formation of an enzyme-substrate complex?

pyruvate kinase, PEP, and ATP

induced fit

shifts in the conformation after binding.

How have researchers determined the three dimension structure of an enzyme at successive stages during a reaction?

By using time-resolved crystallography

3 ways enzymes accelerate reactions

substrate orientation, changing substrate reactivity, and inducing strain in the substrate

How can Enzymes accelerate reactions through substrate orientation?

multiple substrates brought together in correct orientation to catalyze reactions. Changes in atomic and electronic structure occur in both enzyme and substrate during reaction.

How can enzymes accelerate reactions through changing substrate reactivity?

Substrate influenced by amino acid side chains at active site that alter chemical properties (e.g. charge) of substrate. This temporarily stabilizes the transition site.

How do enzymes accelerate reactions by inducing strain in the substrate?

enzyme changes conformation of substrate to being closer to conformation of transition state. Shifts in the conformation after binding cause an induced fit between enzyme and substrate. Covalent bonds are strained

Examples of ways enzymes accelerate reactions through changing substrate reactivity

Acidic or basic R groups on the enzyme may change the charge of substrate. Charged R groups may attract substrate. Cofactors of enzyme increase the reactivity of substrate by removing or donating electrons

Kinetics

Study of rates of enzymatic reactions under various experimental conditions. These rates can increase with increasing substrate concentrations until the enzyme is saturated

What happens when an enzyme is saturated?

Every enzyme is working at maximum capacity

Maximal velocity or Vmax

velocity at saturation

turnover number

number of substrate molecules converted to product per minute per enzyme molecule at Vmax

Michaelis Constant (KM)

substrate concentration at one-half of Vmax. Units of KM are concentration units. The KM may reflect the affinity of the enzyme for the substrate.

What do Lineweaver-Burk plots show?

plots of the inverses of velocity versus substrate concentrations. facilitate estimating Vmax and KM

Enzyme inhibitors

slow the rates for enzymatic reactions

irreversible enzyme inhibitors

bind tightly to the enzyme

Reversible enzyme inhibitors

bind loosely to the enzyme

Competitive enzyme inhibitors

compete with the substrate for active sites. usually resemble the substrate in structure and can be overcome with high substrate/inhibitor ratios

What do non-competitive inhibitors do?

bind to sites other than active sites and inactivate the enzyme. The maximum velocity of enzyme molecules cant be reached nor overcome with high substrate/inhibitor ratios

How do antibiotics help humans?

it targets human metabolism without harming the human host

How have antibiotics been misused and what consequences do they have?

Susceptible cells are destroyed, leaving rare and resistant cells to survive and replicate. Bacteria become resistant to antibiotics by acquiring genes from other bacteria by various mechanisms

Metabolism

collection of bio-chemical reactions that occur within a cell

metabolic pathways

sequences of chemical reactions. each reaction in the sequence is catalyzed by a specific enzyme. Pathways are usually confined to specific locations. Pathways convert substrates into end products via a series of metabolic intermediates

Catabolic pathways

break down complex substrates into simple end products. provide raw materials and chemical energy for cell

anabolic pathways

synthesize complex end products from simple substrates. requires energy and use ATP and NADPH from catabolic pathways

Three stages of metabolism

Stage 1: macromolecules are hydrolyzed into their building blocks. Stage 2: building blocks are further degraded into a few common metabolites. Stage 3: small molecular weight metabolites (like acetyl-CoA) are degraded yielding ATP

Oxidation-Reduction (redox) reactions

involve a change in the electronic state of reactants. When substrate gains electrons it is reduced. When substrate loses electrons it is oxidized. When one substrate gains or loses electrons, another substance must donate or accept those electrons

Reducing agent

substrate that donates electrons

oxidizing agent

substrate that gains electrons

Reduced atoms

can be oxidized, releasing energy to do work. The more a substance is reduced, the more energy that can be released

glycosis

first stage in the catabolism of glucose, and occurs in the soluble portion of cytoplasm

Tricarboxylic (TCA) cycle

second stage in catabolism of glucose and it occurs in the mitochondria of eukaryotic cells

Steps of glycolysis

1. glucose is phosphorylated to glucose 6-phosphate by using ATP

2. Glucose 6-phosphate is isomerized to fructose 6-phosphate

3. Fructose 6-phosphate is phosphorylated to fructose 1, 6-biophosphate using another ATP

4. Fructose 1, 6-biphosphate is split into two three-carbon phosphorylated compounds by the enzyme aldolase. These are DHAP and GAP

5. DHAP is rapidly converted into GAP by triose-phosphate isomerase

6. NAD + is reduced to NADH when glyceraldehyde 3-phosphate is converted to 1, 3-bisphosphoglycerate (BPG)

7. The two BPG molecules donate a phosphate group to an ADP molecule, forming 2 molecules of ATP and 2 molecules of 3 phosphoglycerate (PGA)

8. Phosphoglyceromutase converts the two 3 PGA molecules into 2 PGA

9. enolase removes a water molecule from each of the 2 PGA molecules. This creates 2 molecules of phosphoenolpyruvate (PEP)

10. phosphate group is transferred from PEP to ADP. creates two molecules of ATP and two molecules of pyruvate

dehydrogenase enzymes

oxidize and reduce cofactors

kinase enzymes

transfer phosphate groups

substrate-level phosphorylation

occurs when ATP is formed by a kinase enzyme

transfer potential

shown when molecules higher on the scale have less affinity for the group being transferred than are the ones lower on the scale. Lower affinity = better the donor

anaerobic pathway

occurs in absence of oxygen

fermentation

restores NAD+ from NADH. NADH is oxidized to NAD+ by reducing pyruvate. inefficient with only about 8% of the energy of glucose captured as ATP

What do anabolic pathways require to form larger molecules?

a source of electrons like NADPH

Transhydrogenase Enzyme

catalyzes the transfer of hydrogen atoms from one cofactor to another

Metabolic regulation

may involve controlling key enzymes of metabolic pathways. Enzymes are controlled by alteration in active sites

protein kinases

covalent modification of enzymes regulated by phosphorylation

allosteric modulation

mechanism in which the activity of an enzyme is either inhibited or stimulated by a compound that binds to a site that is spatially distinct from the enzyme’s active site

Feedback inhibition

the product of the pathway allosterically inhibits one of the first enzymes of the pathway

What are the catabolic and anabolic pathways of glucose metabolism?

Glycolysis and gluconeogenesis

Plasma Membrane

outer boundary of the cell. Has trilaminar appearance in electron micrographs. “Moat around the castle” has a general barrier yet have bridges that promote the movement of select elements into and out of the enclosed living space

Membrane compartmentalization

allows specialized activities to proceed without external interference and enables cellular activities to be regulated independently of one another

Membrane’s transport machinery

allows a cell to accumulate substances, such as sugars and amino acids, that are necessary to fuel its metabolism and build its macromolecules. Proteins that move things across membrane

How does the membrane respond to external signals?

they have receptors located on surface of the cell

intercellular interaction

interactions between cells

What are membranes made of and why?

Found to be mostly composed of lipids because their dissolving power matched that of oil

lipid bilayer

the plasma membrane contains a biomolecular layer of lipids. The polar groups are directed outward toward the aqueous environment.

What do protein-lined pores account for?

movement of polar solutes and ions across membranes

integral membrane proteins

proteins imbedded in membrane

Membrane composition

lipid and protein components bound together by non-covalent bonds, membranes also contain carbohydrates. protein/lipid rations vary among membrane types

Amphipathic

have both polar and nonpolar parts. membrane lipids

Three types of membrane lipids

1. phosphoglycerides

2. sphingolipids

3. cholesterol

phosphoglycerides

diacylglycerides with small functional head groups linked to the glycerol backbone by phosphate ester bone

sphingolipids

ceramides formed by the attachment of sphingosine to fatty acids

cholesterol

smaller and less amphipathic lipid that is only found in animals

What do lipids do?

give membranes the ability to fuse, form networks, and separate charge. Lipid bilayers assemble spontaneously in aqueous solutions as in liposomes

Asymmetry of membrane lipids

inner/outer membrane leaflets have different lipid composition. This provides different physicochemical properties appropriate for different interactions

Blood Type O

Universal Donor

Blood Type A

Can give blood to type A and AB

Blood type B

can give blood to blood types B and AB

antigen

something thats immugenic. causes immune response

Three classes of membrane proteins

1. integral membrane (bound)

2. Peripheral membrane (affiliated not bound)

3. GPI anchored

Freeze-fracture technique

divides the phospholipid leaflets of the membrane (freeze and smash). Use when proteins are hard to get out of membrane

How can orientation of integral proteins be determined?

using nonpenetrating agents that label proteins. Can also solubilize protein out of membrane detergence

site-directed mutagenesis

replacing specific amino acids with others. This identifies some spatial relationships

Electron spin resonance

identifies some conformational changes that occur when integral proteins function