Biology

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Unit 1: Biochemistry

A Rにより

Psychological Perspectives on the Problem of Losing Weight

Michael Brittにより

Kingdom Protista

RR - 12PC 658658 Lincoln Alexander SSにより

BADMINTON

Amir Aiman Bin Ismailにより

Fermentation

Fermentation is an anaerobic process in which energy can be released from glucose even though oxygen is not available.

When oxygen is lacking glucose is still metabolized to pyruvic acid via glycolysis. The pyruvic acid is converted first to acetaldehyde and then to ethyl alcohol. The net gain of ATP to the yeast cell is two molecules—the two molecules of ATP normally produced in glycolysis.

Metabolism

All of the chemical reactions that take place inside of a cell are collectively called the cell’s metabolism.

Building Up Glucose: Photosynthesis

Sugars like glucose are made by plants in a process called photosynthesis. In photosynthesis, plants use the energy of sunlight to convert carbon dioxide gas into sugar molecules.

Breaking Down Glucose: Cellular Respiration

Breaking down glucose releases energy, which is captured by the cell in the form of adenosine triphosphate, or ATP. ATP is a small molecule that gives cells a convenient way to briefly store energy.

To catalyze a reaction, an enzyme will grab on (bind) to one or more reactant molecules. These molecules are the enzyme's substrates.

ΔG=ΔH−TΔS

Types of Receptors

Tyrosine Kinase Receptor

These receptors have a catalytic activity that is activated by binding of the ligand. Binding of an often dimeric ligand induces dimerization of the receptors that leads to cross phosphorylation of the cytosolic domains and phosphorylation of other proteins.

G-Protein Coupled Receptors

The conformational change in the receptor upon ligand binding activates a G protein, which in turns activates an effector protein that generates a second messenger.

Enzymes

Enzymes perform the critical task of lowering a reaction's activation energy—that is, the amount of energy that must be put in for the reaction to begin. Enzymes work by binding to reactant molecules and holding them in such a way that the chemical bond-breaking and bond-forming processes take place more readily.

Enzymes lower the energy of the transition state, an unstable state that products must pass through in order to become reactants.

A substance that speeds up a chemical reaction—without being a reactant—is called a catalyst. The catalysts for biochemical reactions that happen in living organisms are called enzymes. Enzymes are usually proteins, though some ribonucleic acid (RNA) molecules act as enzymes too.

Facilitated Diffusion

Movement of specific molecules across cell membranes through protein channels

DNA Replication

The RNA primers are removed and replaced by DNA through the activity of DNA polymerase 1, the other polymerase involved in replication. The nicks that remain after the primers are replaced get sealed by the enzyme DNA ligase.

Topoisomerase also plays an important maintenance role during DNA replication, This enzyme prevents the DNA double helix ahead of the replication fork from getting too tightly wound as the DNA is opened up. It acts by making temporary nicks in the helix to release the tension, then sealing the nicks to aviod permanent damage.

Lagging strand: runs 5' to 3' away from the fork. This strand is made in fragments because, as the fork moves forward, the DNA polymerase must come off and reattach on the newly exposed DNA. The small fragments are called Okazaki fragments.

Leading strand: Runs 5' to 3' towards the replication fork. This strand is made continuousaly.

Specialized proteins recognize the origin, bind to this site, and open up the DNA. As the DNA opens, two Y-shaped structures called replication forks are formed, together making up what's called a replication bubble. The replication forks will move in oppositie directrions as replication proceeds.

Proteins called single-strand binding proteins coat the separated strands of DNA near the replication fork, keeping them from coming back together into a double helix.

DNA polymerases starts at a specific locations on the DNA, called origins of replication and are recognized by their sequence.

DNA polymerases are responsible for synthesizing DNA: they add nucleotides one by one to the growing DNA chain, incorporating only those that are complementary to the template.

They always need a template, can only add nucleotides to the 3' end of a DNA strand. Can't start making a DNA chain from scratch, but require a preexisting chain or short stretch of nucleotides called a primer.

DNA replication is semiconservative, meaning that each strand in the DNA double helix acts as a template for the synthesis of a new, complementary strand.

Membranes

In order to survive, the cell needs to maintain it's own internal chemistry
 and protect it from the outside 
environment. To do this, 
cells surround themselves 
with a structure called 
the plasma membrane.

Cell membranes need to be semi-permeable. Only certain kinds of chemical compounds can pass through the membrane and sometimes only in one direction. Very few molecules that are soluble in water can dissolve in these oily lipids or pass through to the other side.

Diffusion: Occurs because molecules constantly move and collide with each other

Gene Expression

Nucleus separates transcription and translation

Translation

happens in cytoplasm

mRNA is decoded to build a protein that contains a specific series of amino acid.

In a mRNA, the instructions for building a polypeptide are RNA nucleotides (As, Us, Cs, and Gs) read in groups of three. These groups are called codons.

Amino acid chains gets longer. mRNA is read one codon at a time and the amino acid matching each codon is added to a growing protein chain.

The stage is when the finished polypeptide chain is released. It begins when a stop codon enters the ribosome, triggering a series of events that separate the chain from its tRNA and allow it to drift out of the ribosome.

mRNA is being read and tRNA carries the first amino acid methionine (the start codon)

Transcription

1st step in gene expression.Pre-mRNA must be modified by RNA poly. II to RNA processing. Mature mRNA leaves by pore.

Initiation

RNA polymerase binds to a sequence of DNA Called the promoter, found near the beginning of gene. Each gene has its own promotor.

Elongation

One strand of DNA, the template strand, acts as a template for RNA polymerase. The polymerase builds an RNA molecule out of complementary nucleotides, making a chain that grows from 5' to 3'. RNA transcript carries the same info as the non-template (coding) strand of DNA, but it contains the base uracil instead of thymine.

Termination

Seeuences called terminator signal that the RNA transcript is complete. Once they are transcribed, they cause the transcript to be released from ther RNA polymerase.

Makes mRNA

Transcription and Translation are couple, happens at the same time in the cytosol.

Forms RNA: mRNA, tRNA, rRNA

Double membrane

Centrioles Centrosomes small vacuoles cilia/flagella-re long, hair-like structures that extend from the cell surface and are used to move an entire cell lysosome: sack of enzymes, acid hydrolases, hydrolysis, high proton concentration, breaks down covalent bonds peroxisomes

Endoplasmic reticulum:modification of proteins and the synthesis of lipids. Golgi apparatus: package, one membrane Nucleus

Chloroplast

Mitochondria

Active Transport

An energy-requiring process that moves material across a cell membrane against a concentration gradient

Passive Transport

The movement of substances across a cell membrane without the use of energy by the cell.

Osmosis

Diffusion of molecules through a semipermeable membrane from a place of higher concentration to a place of lower concentration until the concentration on both sides is equal.

Hypertonic Solution

A solution in which the concentration of solutes is greater than that of the cell that resides in the solution which causes a cell to shrink.

Isotonic Solution

A solution with the same concentration of water and solutes as inside a cell, resulting in the cell retaining its normal shape because there is no net movement of water.

Hypotonic Solution

A solution in which the concentration of the solute is less than that inside of the cell which causes a cell to lyse.

Floating topic

THE CYCLE OF LIFE

Recombinant DNA and Cloning

Involves creating an animal that is genetically identical to a donor animal through somatic cell nuclear transfer.

In reproductive cloning, the newly created embryo is placed back into the uterine environment where it can implant and develop. Dolly the sheep is perhaps the most well known example.

Restriction endonuclease refers to a group of endonucleases which cleaves the DNA at specific points known as recognition sequences or sites.

Reverse Transcriptase: Its functions include synthesis of cDNA using RNA template and this property of reverse transcriptase is used to create cDNA libraries.

Cloning Vector Uses

1.modify DNA sequences with a unique segment DNA 2. make multiple copies or RNA copies of specific DNA sequence 3. store DNA in stable construct

Steps:

Cut open the plasmid and "paste" in the gene. This process relies on restriction enzymes (which cut DNA) and DNA ligase (which joins DNA)

Transform the plasmid into bacteria. Use antibiotic selection to identify the bacteria that took up the plasmid.

Grow up lots of plasmid-carrying bacteria and use them as "factories" to make the protein. Harvest the protein from the bacteria and purify it.

Potential problems:

If a Eukaryotic gene is expressed in bacteria is might not be a functional gene due to the fact that the gene wouldn’t be modified by the Golgi and ER because a prokaryotic cell (bacteria) does not contain these organelles.

Unit 2

Endosymbiotic Theory

The Cell

Extracellular Matrix

Regulating cell differentiation

4 things in all cells: ribosomes: make protein, made of protein and RNA cytoplasm DNA plasma membrane

Two main types

Eukaryotes

Membrane junctions

Plasmodesmata

places where a hole is punched in the cell wall to allow direct cytoplasmic exchange between two cells.

gap junction

transmembrane proteins form pores that allow small molecules to pass from cell to cell

desmosome

anchoring junctions bind adjacent cells and help form an internal tension-reduction network of fibers

tight junction

prevents fluid and most molecules from moving between cells

Cytoskeletal elements

Actin Filaments Intermediate Filaments Microtubules

Microtubules: cylinders made of tubular that function in motility (flagella and cilia), support of cell shape, or transport of chromosomes and vesicles. Microfilaments: 2 actin polymers that function in cell shape, muscle action w/ myosin, cytoplasmic streaming, cell division and motility, and anchoring proteins in the plasma membrane.

Multi- cellular

Plant cell

Cell wall vacuoles

Animal cell

Prokaryotes

Unicellular cellular

Organelles

Capsule: pilus: cell wall nucleoid (DNA) flagellum

Unit 4

Energy Flow in an Ecosystem

an ecosystem consists of all the organisms living in a community

Energy coupling using ATP hydrolysis

Exergonic reaction: Delta G is negative, reaction is spontaneous

Endergonic reaction: Delta G is positive, reaction is not spontaneous

Gibbs Free Energy:

Delta G < 0 A reaction/process can occur spontaneously Delta G = 0 A system is at equilibrium: no net change occurs Delta G > 0 A reaction/process cannot occur spontaneously. An input of free energy is required to drive the reaction.

Photosynthesis

Photosynthesis and cellular respiration both involve a series of redox reactions (reactions involving electron transfers). In cellular respiration, electrons flow from glucose to oxygen, forming water and releasing energy. In photosynthesis, they go in the opposite direction, starting in water and winding up in glucose—an energy-requiring process powered by light. Like cellular respiration, photosynthesis also uses an electron transport chain to make a H+ concentration gradient, which drives ATP synthesis by chemiosmosis.

. The glucose molecules serve as fuel for cells: their chemical energy can be harvested through processes like cellular respiration and fermentation, which generate adenosine triphosphate

The cells in a middle layer of leaf tissue called the mesophyll are the primary site of photosynthesis.

Small pores called stomata are found on the surface of leaves in most plants, and they let carbon dioxide diffuse into the mesophyll layer and oxygen diffuse out.

The glucose molecules provide organisms with two crucial resources: energy and fixed—organic—carbon.

Is the process in which light energy is converted to chemical energy in the form of sugars. In a process driven by light energy, glucose molecules (or other sugars) are constructed from water and carbon dioxide, and oxygen is released as a byproduct.

Thermodynamics

System-matter within defined region of space

Closed System: Open System. Surrounding: matter in the rest of the universe

The second law of thermodynamics

overall entropy of the universe always increases. Entropy: the degree of randomness or disorder in a system

First Law of Thermodynamics

total energy of a system and its surroundings is constant

Respiration

Oxidative phosphorylation

Kreb cycle (citric acid cycle)

Location: matrix mitochondria Input: 2 Acetyl coA, 2 Oxaloacetate, Output: 6 NADH, 2 FADH2, 2 ATP, Process to produce ATP: substrate level phosphorylation and oxidative phosphorylation

Location: inner membrane of mitochondria Input: 10 NADH, 2 FADH2 Output: H2O Process of produce ATP: ATP synthase (26-28 ATP)

Pyruvate oxidation

Location: start in cytosol then moves into the matrix, Input 2 pyruvate, 2 coA, 2 Acetyl coA, 2 NADH, (per glucose), Process to produce ATP; NO ATP made

Glycolysis

Location: outside the mitochondria in the cytosol. Input is 2 ATP, 1 Glucose Output 2 pyruvate, 4 ATP, 2 NADH. Net is 2 ATP, 2 Pyruvate, Process to produce ATP is substrate level phosphorylation and oxidative phosphorylation

Unit 1

3 Domains of Life

Eukarya

Nuclear envelope: present Membrane enclosed organelles: present Peptidoglycan in cell walls: absent Membrane lipids: unbranched hydrocarbon

Nuclear envelope: absent Membrane enclosed organelles: absent Peptidoglycan in cell walls: absent Membrane lipids: some branched CH

Bacteria

Nuclear envelope: absent Membrane enclosed organelles: absent Peptidoglycan in cell walls: present Membrane lipids: unbranched hydrocarbon

Chemical Evolution Hypothesis:

process where simple molecules containing C,H,O,N underfoot complex chemical reactions to form organic compounds w/ C-C bonds

Archaea

methanogens

produce methane gas as a process of making energy, release methane as a way to obtain energy

helophites

love salty conditions

thermophites

love hot conditions

Experiments:

Miller and Urey's Experiment:

condenser

electrodes (electricity)

chamber (atmosphere)

heated water (ocean)

Acid and Base

Buffers:

protects the PH; a buffer is a salt and WA or WB

PH Scale:

Basic

8-14

Neutral

7

Acidic

1-6

Base

a substance that reduces the hydrogen ion concentration of a solution (some reduce H+ conc. by accepting H+ ions).

Acid

a substance that increases the hydrogen ion conc. of solution

Biological Molecules

Nucleic Acid

2 types:

RNA

used to form proteins

DNA

info in DNA is transmitted to RNA

carries our genetic material

Made up of 4 types of nucleotides:

Nucleoside=5 carbon sugar + nitrogenous base

Nucleotides= 5 carbon sugar + nitrogenous base + phosphate group

Purines

Pyrimidines

Cytosine, Thymine, Uracil (in RNA)

Cytosine

Guanine

Thymine

Adenine

Proteins

Denaturation:

disrupts secondary and tertiary and quandary.

it involves the breaking of all bonds expect peptide bonds

unfold, lose their functionality

Subtopic

Quaternary

proteins consisting of more than one polypeptide chain

Ex.) hemoglobin

Tertiary Structure:

side chain interactions of the amino acids (ex: hydrophobic interaction)

Secondary Structure:

the 3-D shape of proteins in contributed to by the child and folds of the polypeptide backbone.

Primary Structure:

defined by the specific sequence of amino acids found in the polypeptide

made up of amino acids; 20 different types

exist as long chains called polymers

polymers are made up by smaller components called monomers

Carbohydrates

Cellulose

plants use glucose chains in their cell walls (but w/ different forms of glucose); Beta 1-4 Glycosidic linkage

Starch

Humans can digest starch (alpha linkage) but not cellulose (beta linkage)

Amylopectin

Glycogen has the same bond types as amylopectin but its more branches thus faster to digest

alpha 1-6 glycosidic linkage

Amylose

slowest to digest

made of glucose rings attached in a line (alpha 1-4 glycosidic linkage)

Polysaccharide

Glycogen and starch are storage polysaccharide

many monosaccharides linked together

Glucose

can be broken down to make fuel

Monossacharides

2 monosaccharides make 1 dissacharide

Ex: Glucose or Fructose

Sucrose=Glucose+Fructose

Lactose=Glucose+Galactose

starch, glucose, lactose, etc

energy generation; sugar

Lipids

Phospholipids

head is polar; tail in non polar

major component of cell membranes; glycerol backbone w/ 2 fatty acid tails and one charged phosphorus head.

Unsaturated

kinks in the fatty acid tails preventing solidification

liquid at room temp. Ex: olive oil

Saturated

solid at room temp. Ex: Butter

Two classes:

2nd Class

Sterols

fused carbon rings; Ex: cholesterol and hormones

Cholesterol; will interact w/ phospholipids in cell membrane; mainly hydrophobic.

Cholesterol: crucial in animals. Common component of animal cell membranes. Help synthesize other steroids like sex hormones.

Steroids: lipids characterized by a carbon skeleton of 4 fused rings; cholesterol

1st Class

Based on Glycerol

larger than simple sugars and amino acids

they're made in our cells; fats and cholesterol

they synthesize hormones, and generate energy

presented in our cells (plasma membrane)

Functional Groups

Methyl; CH3

Phosphate; PO4

Sulfhydryl; SH

Amino; NH2

Carboxyl; COOH

Carbonyl; CO

Aldehyde; carbonyl group is at the end of a carbon skeleton

Ketone; carbonyl group is within a carbon skeleton

Hydroxyl; OH

Atom

Isomers

compounds w/ the same # of atoms of the same elements but different structures

Enantiomers

isomers that are mirror images of each other and that differ in shape due to the presence of an asymmetric carbon (one that is attached to 4 different atoms or groups of atoms)

Cis-trans Isomer (geometric isomers)

Trans isomer; 2 atoms on opposite sides

Cis isomer; 2 atoms on the same side

carbons have covalent bonds to the same atoms, but these atoms differ in their spatial arrangements due to inflexibility of double bonds

Structural Isomer

differ in covalent arrangements of their atoms

temperature is a measure of energy

Kinetic Energy

anything that moves, energy of motion

highest energy level is the shell farthest away from the nucleus

lowest energy level is the shell closest to the nucleus

capacity to do work

Smallest unit of matter that still retains properties of an element

Neutron

Isotopes

elements have the same # of protons but different number of neutrons. Ex: C-12 or C-13

Neutral charged particle in nucleus

Electron

Electronegativity

the attraction of electrons to an atom. A high electronegativity means that the atom is very attracted to the electron.

Electron shells

electrons can move shells by absorbing or losing energy (energy absorbed = moves to a higher shell level #) (energy released = moves to a lower shell level #)

each shells has a specific distance and energy level

Anion

an ion w/ more electrons (-)

Cation

an ion w/ fewer electrons (+)

Negatively charged particle in cloud around nucleus

Proton

Positively charged particle in nucleus

Bonds

Double

two pairs of shared electron

Single

a pair of shared electron

Van der Waal interaction

Ex: allows geckos to walk up a wall

everything has these; interaction of electrons of non polar substances

Individually = weak - Together = strong

Hydrogen

weak attraction

sharing H with N, O, or F

Water

Floating of ice on liquid water

Evaporative cooling

molecules that move fast will evaporate. Those that are fast at low temps may eventually evaporate too.

Adhesion

the clinging of one substance to another

Cohesion

theres a strong attraction between within molecules (why water forms droplets)

Hydrolysis reactions

water molecule added to break bonds

Condensation reactions (dehydration synthesis)

water molecule removed to bring bonds together

High specific heat; water can absorb a lot of heat before changing temperature.

High surface tension; force that causes molecules on surface to be pushed together.

Hydrophilic

polar

atoms are pulling unevenly; H2O

loves water, can form H-bonds w/ water; example glucose

Hydrophobic

non polar

Hydrocarbons

organic molecules that have only Carbon and Hydrogen; non polar beings

atoms are pulling evenly; O2

scared of water, molecules cluster together in avoidance of water; example is oil

Covalent

Polar covalent

atoms don't have the same electronegativity so one atom is pulling more than the other; Ex: OH

Nonpolar covalent

atoms w/ the same electronegativity, so the electrons are shared equally; Ex: H2

sharing electrons

Ionic

complete transfer of electrons

Unit 3

Cell Cycle

The cell cycle involves many repetitions of cellular growth and reproduction.

Meiosis

Meiosis II

Prophase II: Prophase II is similar to the prophase of mitosis. The chromatin material condenses, and each chromosome contains two chromatids attached by the centromere. The 23 chromatid pairs, a total of 46 chromatids, then move to the equatorial plate.

Metaphase II: In metaphase II of meiosis, the 23 chromatid pairs gather at the center of the cell prior to separation. This process is identical to metaphase in mitosis, except that this is occurring in a haploid versus a diploid cell.

Anaphase II: During anaphase II of meiosis, the centromeres divide and sister chromatids separate, at which time they are referred to as non-replicated chromosomes. Spindle fibers move chromosomes to each pole. In all, 23 chromosomes move to each pole. The forces and attachments that operate in mitosis also operate in anaphase II.

Telophase II: During telophase II, the chromosomes gather at the poles of the cells and become indistinct. Again, they form a mass of chromatin. The nuclear envelope develops, the nucleoli reappear, and the cells undergo cytokinesis.

Meiosis I

Prophase I: Prophase I is similar in some ways to prophase in mitosis. The chromatids shorten and thicken and become visible under a microscope. An important difference, however, is that a process called synapsis occurs. Synapsis is when the homologous chromosomes migrate toward one another and join to form a tetrad (the combination of four chromatids, two from each homologous chromosome). A second process called crossing over also takes place during prophase I. In this process, segments of DNA from one chromatid in the tetrad pass to another chromatid in the tetrad. These exchanges of chromosomal segments occur in a complex and poorly understood manner. They result in a genetically new chromatid. Crossing over is an important driving force of evolution. After crossing over has taken place, the homologous pair of chromosomes is genetically different.

Metaphase I: In metaphase I of meiosis, the tetrads align on the equatorial plate (as in mitosis). The centromeres attach to spindle fibers, which extend from the poles of the cell. One centromere attaches per spindle fiber.

Anaphase I: In anaphase I, the homologous chromosomes or tetrads separate. One homologous chromosome (consisting of two chromatids) moves to one side of the cell, while the other homologous chromosome (consisting of two chromatids) moves to the other side of the cell. The result is that 23 chromosomes (each consisting of two chromatids) move to one pole, and 23 chromosomes (each consisting of two chromatids) move to the other pole. Essentially, the chromosome number of the cell is halved once meiosis I is completed. For this reason the process is a reduction-division.

Telophase I: In telophase I of meiosis, the nucleus reorganizes, the chromosomes become chromatin, and the cell membrane begins to pinch inward. Cytokinesis occurs immediately following telophase I. This process occurs differently in plant and animal cells, just as in mitosis.

Mitosis

Prophase: Mitosis begins with the condensing of the chromatin to form chromosomes in the phase called prophase. Two copies of each chromosome exist; each one is a chromatid. Two chromatids are joined to one another at a region called the centromere. As prophase unfolds, the chromatids become visible in pairs (called sister chromatids), the spindle fibers form, the nucleoli disappear, and the nuclear envelope dissolves.

Metaphase: Metaphase is the stage of mitosis in which the pairs of chromatids line up on the equatorial plate. This region is also called the metaphase plate. In a human cell, 92 chromosomes in 46 pairs align at the equatorial plate. Each pair is connected at the centromere, where the spindle fiber is attached (more specifically at the kinetochore).

Anaphase: At the beginning of anaphase, the sister chromatids move apart from one another. The chromatids are called chromosomes after the separation. Each chromosome is attached to a spindle fiber, and the members of each chromosome pair are drawn to opposite poles of the cell by the spindle fibers. During anaphase, the chromosomes can be seen moving. They take on a rough V shape because of their midregion attachment to the spindle fibers. The movement toward the poles is accomplished by several mechanisms, such as an elongation of the spindle fibers, which results in pushing the poles apart. The result of anaphase is an equal separation and distribution of the chromosomes. In human cells, a total of 46 chromosomes move to each pole as the process of mitosis continues.

Telophase: In telophase, the chromosomes finally arrive at the opposite poles of the cell. The distinct chromosomes begin to fade from sight as masses of chromatin are formed again. The events of telophase are essentially the reverse of those in prophase. The spindle is dismantled and its amino acids are recycled, the nucleoli reappear, and the nuclear envelope is reformed.

Cytokinesis: Cytokinesis is the process in which the cytoplasm divides and two separate cells form. Note that cytokinesis is separate from the four stages of mitosis. In animal cells, cytokinesis begins with the formation of a cleavage furrow in the center of the cell. With the formation of the furrow, the cell membrane begins to pinch into the cytoplasm, and the formation of two cells begins. This process is often referred to as cell cleavage. Microfilaments contract during cleavage and assist the division of the cell into two daughter cells.

Interphase

G2 Phase

In the G2 phase, the cell prepares for mitosis. Proteins organize themselves to form a series of fibers called the spindle, which is involved in chromosome movement during mitosis. The spindle is constructed from amino acids for each mitosis, and then taken apart at the conclusion of the process. Spindle fibers are composed of microtubules.

S Phase

During the S phase of the cell cycle, the DNA within the nucleus replicates. During this process, each chromosome is faithfully copied, so by the end of the S phase, two DNA molecules exist for each one formerly present in the G1 phase. Human cells contain 92 chromosomes per cell in the S phase.

G1 Phase

During the G1 phase, each chromosome consists of a single molecule of DNA and its associated histone protein. In normal human cells, there are 46 chromosomes per cell (except in sex cells with 23 chromosomes and red blood cells with no nucleus and, hence, no chromosomes).

Gene regulation

activators - binds DNA to stimulate transcription initiation -catabolite activator protein (CAP) - activator protein stimulating transcription for operons coding for sugar catabolism -binding controlled by cAMP (inversely related to glucose level) -little glucose >> lots of cAMP >> CAP able to bind to DNA >> stops catabolic operons

repressors - proteins that bind to regulatory sites on DNA >> prevent start of transcription -trp operon - repressed in presence of -tryptophan, induced in absence of tryptophan -tryptophan repressor can’t bind to DNA unless it binds to 2 tryptophan molecules first

operons - multiple genes part of a single gene expression unit -All part of same mRNA >> controlled by same promoter -Genes for same biochemical pathway organized this way

lac operon - makes enzymes when lactose available -lack of lactose >> lack of allolactose (metabolite of lactose) >> repressor allowed to bind to DNA >> stops production of enzymes for lactose

Signal Transduction

1. Synthesis of signaling molecule by signaling cell (e.g. hormones by pituitary gland) 2. Release of signaling molecule (e.g. into blood or extracellular matrix) 3. Transport to receiving cell (e.g. in blood) 4. Binding to receptor 5. Initiation of intracellular signal transduction 6. Resultant changes to cellular functions functions (e.g. activating enzymes would be a fast response, changing gene expression would be a slower response) 7. Feedback regulation: removal of signaling molecule or disabling of receptor (e.g. via endocytosis)

Energy

Energy has been expressed in terms of reliable observations known as the laws of thermodynamics.

The Second Law of Thermodynamics

The second law of thermodynamics states that the amount of available energy in a closed system is decreasing constantly. Energy becomes unavailable for use by living things because of entropy, which is the degree of disorder or randomness of a system. The entropy of any closed system is constantly increasing. In essence, any closed system tends toward disorganization.

Endergonic: Energy is absorbed from the surroundings. The bonds being formed are weaker than the bonds being broken.

Exergonic: Energy is released to the surroundings. The bonds being formed are stronger than the bonds being broken.

The First Law of Thermodynamics

The first law of thermodynamics states that energy can neither be created nor destroyed. This law implies that the total amount of energy in a closed system (for example, the universe) remains constant.

Cell signaling