Chapter 6:Energy,enzymes and metabolism

Reusing Organic
Molecules

Enzymes and Rribozymes

Metabolism

A biological catalyst is an enzyme. RNA molecules with catalytic capabilities are called ribozymes.

Activation energy is reduced by enzymes by Reactants are positioned in close proximity to one another to facilitate bonding and contain straining bands that facilitate the transition stage. The local ecology is evolving. involvement directly through transient bonding

Plateau of saturation where almost all active sites are taken up by substrate

Competitive inhibitor:
The binding of a molecule to the active site prevents the substrate from binding.

Noncompetitive inhibitor:Allosteric site, not active site, is where inhibitor binds. alters the enzyme's structure

Michaelis constant, concentration of substrate at which velocity is half of its maximum value

Proteasome: A big complex that uses protease enzymes to break down proteins
An amino acid's link is broken by proteases. Ubiquitin marks proteins to be broken down and recycled by the proteasome. The cellular process of ubiquitin tagging enables the degradation of misfolded proteins. quickly break down proteins in response to shifting cellular environments

mRNA Degradation:
1-Exonucleases are enzymes that cut nucleotides off at the end.
2-Exosomes: Exonucleases are used by multiprotein complexes

Hydrolases are found in lysosomes, which aid in the breakdown of lipids, proteins, carbohydrates, and nucleic acids. Break down materials that endocytosis takes up.


Autophagy: utilizing an autophagosome to recycle deteriorated organelles

Energy

ATP hydrolysis: Numerous biological functions are powered by the energy released during this process.

The first law of thermodynamics states that although energy cannot be generated or destroyed, it can change into different forms.
The second law of thermodynamics states that a system's entropy increases when energy is transferred from one form to another.

1-Exergonic = spontaneous(negative free energy)releases energy


2-Endergonic = not spontaneous(positive free charge) requires enrgy to complete the reaction

The energy required to produce ATP is derived from chemical processes.exergonic is the bust.

Energy for endergonic cellular functions is obtained by ATP hydrolysis.

Anabolic Pathway: Cellular components synthesized. Endergonic Reaction and Exergonic Reaction Must Be Coupled

Metabolic pathway regulation: Gene regulation
Activate or deactivate genes cellular control hormone-like mechanisms for cell signaling. Biological control Early stages are inhibited by feedback inhibition, a pathway product, to avoid overexposure and excessive buildup.

Catabolic pathway(exergonic) : breakdown cellular components

reactions involving biosynthesis
Make bigger macromolecules or smaller molecules unavailable from diet Utilize intermediary energy sources (ATP or NADH) to power processes

Disintegration of Reactants


1-utilized to recycle construction materials


2-utilized as fuel to power endergonic reactions


There are two methods for producing ATP:

  1. The enzyme responsible for substrate-level phosphorylation moves phosphate straight from one molecule to another.
    1. Osmosis An electrochemical gradient's stored energy is used to convert ADP and Pi into ATP.


Organic compounds oxidize to release electrons, which are then used to produce energy intermediates like NADH.

Feedback inhibition:
When the end product concentration rises, it will bind to enzyme 1 and alter its conformation, preventing the enzyme from converting the original substrate into intermediate 1.

Chapter 3:The Chemical Basis of Life

Proteins

nucleic acids

Carbohydrates: C,H,O

lipids

triglycerides

Tertiary structure: Folding gives protein complex 3D shape
This is the final level of structure for a single polypeptide chain

simple sugars

Responsible for the storage, expression, and transmission of genetic information

complex sugars

Disaccharides: Composed of two monosaccharides , eg: sucrose

Polysaccharides:Many monosaccharides linked together to form long polymers

Monosaccharides: simplest sugars , its structure could be ring or linear , eg: glucose

assimilable, for example starch

non assimilable ,for example chitin

steroids

phospholipids

Formed from glycerol, two fatty acids and a phosphate group.Phospholipids are amphipathic molecules


Formed by bonding glycerol to 3 fatty acids.

saturated:
all carbons linked by single bonds
Tend to be solid at room temperature
ex: animal fats

unsaturated:
contain one or more double bonds
Tend to be liquid at room temperature
ex:vegetables oil

Four interconnected rings of carbon atoms.Usually insoluble in water
ex: Cholesterol

Secondary Structure: Chemical and physical interactions cause protein folding,α helices and β pleated sheets and Random coiled regions”


Quaternary structure: Made up of two or more polypeptides

Primary structure: Amino acid sequence
Encoded directly by genes

Ribonucleic acid (RNA): single strand,URACIL, several forms

Deoxyribonucleic acid (DNA) :2 strand double helix,THYMINE, one form

Chapter 5: Membrane Structure,Synthesis and Transport

synthesis: Cytosol and Endomembrane system

Membrane Structure:Selectively permeable


transport

Chapter 4: General Features of Cells

prokaryotes:Simple cell structure with
No nucleus

cell theory:

protein sorting

eukaryotes:Complex cells,DNA enclosed within membrane-bound nucleus

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1-All living organisms are composed of one or more cells

2-Cells are the smallest units of life

3-new cells exist because of a cell division of a previous cell

Plant cell

Archaea

Bacteria

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Cytoplasm – contained within plasma membrane

Nucleoid region – where DNA is located

Ribosomes – synthesize proteins

Cell wall – provides support and protection

Glycocalyx – traps water, gives protection, help evade immune system

Appendages – pilli (attachment), flagella (movement)

Animal cell

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vacuole: central, contractile and phagocytic

Lysosome

nucleus and indomembrane system

cytosol

cytoskeleton

motor protein: caries cargo, moves and bends filaments

actin filaments

microtubules

intermediate filaments

endoplasmic riticulum: smooth and rough

golgi: stacks and vesicles

nucleus

peroxisome

nuclear envelope

plasma membrane

semiautonomous organelles

mitochondria

chloroplast

Post-translational

Cotranslational

Phospholipid
bilayer

Protein and
carbohydrates

semifluid

1-Essential molecules enter 2-Metabolic intermediates remain 3-Waste product exit

Flip-flop of lipids from
one leaflet to another

requires Flippase

carbohydrates

Glycosylation: Attaching carbohydrates
to protein or lipids

covalently attached carbohydrate to a protein or lipid

proteins

synthesize lipids using fatty acids

transported via vesicles

N linked

O linked

diffuse laterally

found in smooth ER

in rough ER

transferred via vesicles

active:requires energy

passive:No energy is required

primary:Uses pump

secondary:Uses different
gradient

Passive
diffusion

Facilitated
diffusion:transports large molecules

types of transporters

symporter

Antiporter

Uniporter

extra information

channels

open passageway, direct diffusion ex:ex: Aquaporin

osmosis

tonicity

cell gradient

movement of water when solute cannot move,

hypotonic

isotonic

hypertonic

cytosis active transport

endocytosis

exocytosis

materials are sent out via vesicles

receptor mediated endocytosis, pinocytosis, and phagocytosis

used for large molecules

chapter8 :Photosynthesis

extra information

light reactions:uses energy ,produces ATP, NADPH and O2

Dark Reactions

chloroplast:1-carries out photosynthesis 2-has pigments that enable maximum absorbance of light 3-contained by mesophylls

parts

stroma

intermembrane space

grana

inner and outer membrane envelopes

cyclic

non cyclic

requires PS 1 ,produces ATP

reaction centre P700

releases H+ into the lumen driving ATP synthesis

requires both PS 1 and 2 ,begins at PS 2

starts by breakdown of H2O ,reaction centres P680 and P700

produces both ATP and NADPH in equal amounts

C3:all reactions held in mesophyll chloroplast

CAM

C4:

MESOPHYL:4 carbon compund is transferred that releases
CO2 minimizing photorespiration

sheath: CO2 is used to make 4 carbon oxaloacetic acid

phases

uses less energy in cooler enironments

photorespiration

first CO2 receiver is phosphoenol pyruvic acid

conserves water in dry warm climates

CO2 is broken down during day for c3 cycle

CO2 and oxaloacetate are converted to malate

opens stomata at night ,closes stomata during day to conserve water

more likely in hot and dry environments , usage of O2 and liberating of CO2 when rubisco acts as
oxygenase

second: reduction and CO2 production

third: regenration of RuBP

first: carbon fixation

enhancement effect

trophic levels

ATP synthesis in chloroplasts

H+ gradient

achieved by photophosphorylation ATP synthesis in chloroplasts and driven by the flow of H+ from lumen to the stroma

P680 activates PS 2

P700 activates PS 1

heterotroph: depends on others for energy

autotroph:produces make its food using available energy

photoautotroph:carries out photosynthesis

enhanced by ETC pumping H+ into the lumen , enhanced by H2O oxidation

photosynthesis facts

anabolic and endergonic

enhanced by less light intensity, more temperature and more
water vapor

not spontaneous