chemical bonds, cell structure and functions

membranes are found around the cell and each organelle

The cell boundary

seperates cellular materials from external environment

regulates which materials can enter and exit the cell

maintains homeostasis in cell

Semipermeable membranes

membranes that allow certain materials to pass through based on certain properties

size, hydrophobicity, charge

The fluid mosaic model

the membrane is made up of many smaller parts and the structure moves likes a fluid

Phospholipids and proteins

make up most of the membrane

cholesterol helps with flexibility and carbohydrate chains help communicate with other cells

phospholipid: 2 fatty acid tails and a phosphate head

phospholipid bilayer forms because the inside and outside of the cell are mostly water

semipermeable because it only allows certain molecules to cross

Hydrophilic, polar, large and charged molecules must use a transport Protein to enter/exit the cell.

The proteins are specific; glucose can only pass through a glucose transport protein.

transport proteins

There are two types of Transport Proteins: Protein Channels: a special entryway for large, polar, hydrophilic and charged ions to diffuse through the cell membraneThis is called Facilitated Diffusion.

chemical evolution hypothesis

three domains of life

bacteria

c

no nucleus

DNA in nucleoid

no membrane bound organelles

membranes

plasma membrane

consists of phospholipid bilayer that is semipermeable

hydrophobic fatty acid tail (away from water) and a hydrophilic head (faces water)

amphipathic

cholesterol

hydrophilic becuase of phophate group

regulate cell's tarffic

membrane fluidity

temp affects the fluidity

above temp lipid is in liquid crystalline phase and is fluid

below temp lipid is in gel phase and is rigid

Each phospholipid has a specific temp

membrane proteins

functions

transport

passive transoport

diffusion of a substance across a membrane with no energy investment

example includes osmosis

water balance of cells

tonicity

ability of a surrounding solution to cause a cell to gain or lose water

isotonic

solute concentration is the same as inside the cell; no net water movement across the plasma membrane

hypertonic

solute concentration is greater than that inside the cell; cell loses water

hypotonic

solute concentration is less than that inside the cell; cell gains water

facilitated diffusion

passive transport aided by proteins

active transport

movement of substances from low to high concentrations

maintains a concentration gradient

uses energy

specific case of active transport is the sodium-potassium pump

enzymatic actvity

signal transduction

cell-cell recognition

intercellular joining

attachment to ECM an cytoskeleton

eukaria

made up of eukaryotes

cells have membrane bound nucleus

most of the DNA is in the nucleus

nucleus is an organelle that is bounded by a double membrane

archaea

branched membrane lipids

extreme halophiles: live in saline environments

extreme thermophiles: very hot environments

methanogens live in swamps and produce methane as a waste product

strict anaerobes

Proteins

protein polymers

bonded through peptide bonds

has directionality (N- terminal & C-terminal ends)

Structure and Organization

Primary: types, quantity, and sequence of amino acids

Secondary: formation of α helices or β pleated sheets

occurs due to the formation of hydrogen bonds

Tertiary: 3D-shape of polypeptide chain

determined by R group interactions

Quartenary: arrangement of multiple polypetide chains to form a protein

monomers: amino acids

Nucleic Acids

bonded through phosphodiester bonds

is formed through dehydration synthesis

also known as condensation reaction

results in the sugar-phopshate backbone

has directionality (5' & 3' ends)

polymers:

RNA

base pairs:

adenine (A)

uracil (U)

cytosine (C)

guanine (G)

sugar molecule: ribose

forms a single-stranded nucleotide chain

DNA

base pairs:

adenine (A)

thymine (T)

cytosine (C)

guanine (G)

sugar molecule: deoxyribose

forms a double helix
with anti-parallel strands

connected by base-pair hydrogen bonding

monomer: nucleotide

nitrogenous bases

pyrimidines

cytosine

thymine

uracil

purines

adenine

guanine

sugar molecule

phosphate group

Carbohydrates

carbon-based molecules hydrated with many hydroxyl groups (-OH)

monomers: monosaccharides

polymers: polysaccharides

bonded through glycosidic linkages

form via a dehydration reaction

types:

simple carbohydrates

most abudant is glucose

C6H12O6

complex carbohydrates

cellulose

composed of beta glucose molecules

cannot be digest by humans because we
lack the necessary enzyme needed to break it down

starch

composed of alpha glucose molecules

can be digest by humans due to the
amylase enzyme

Lipids

fatty acids

saturated

saturated with hydrogen

single bonds

able to pack closely together

higher melting points

solid at room temperatue

unsaturated

not fully saturated with hydrogens

double bonds

causes kinks in the chain

liquid at room temperature

phospholipids

contains a phosphate group

otherwise known as the "head"

hydrophilic

composes all cell membranes

has two fatty acid chains

otherwise known as the "tail"

hydrophobic

triglycerides

a lipid with 3 fatty acid chains

linked to a glycerol molecule

occurs through a dehydration reaction

steroids

made up of 4 fused carbon ring structures

cholesterol

essential for the structure of
animal cell membranes

waxes

functions:

protection

prevention of water loss

fatty acids bound to long chain alcohol molecules

Covalent bonds

strongest bond: sharing of electron pairs

two types:

polar covalent

unevenly matched, but willing to share

example of covalent bond: two hydrogen bonds getting close together, the attraction is balanced in both directions. Hydrogen gas is formed.

nonpolar covalent

evenly matched

Add your text

Ionic bonds

attraction between ions of opposite charges

complete transfer of valence electrons between atoms

metal loses electrons to become a positively charged cation

non metal accepts these electrons to become a negatively charged anion

example of ionic bond: Na and Cl

Ion- dipole

attractive forces between polar molecules and ions

Hydrogen bonds

attractive force between the hydrogen attached to an electronegative atom of one molecule and one from a different molecule

the electronegative atom is usually oxygen, nitrogen, or fluorine.

these have partial negative charges

example of hydrogen bond: a hydrogen atom covalently bonded to an oxygen via a shared pair of electrons

Metallic bonds

type of bonding found in metallic elements

electrostatic force of attraction between positively charged ions and delocalized outer electrons

refers to an interaction between delocalized electrons and the metal nuclei

Example of metallic bonding: if metal cations and electrons are oppositely charged they will be attracted to each other and also other metal cations

Peptide bond

proteins are linear polymers composed of amino acids linked by a peptide bond

chains containing less than 50 amino acids are peptides

chains containing greater than 50 amino acids are called proteins

peptide bonds are formed by the condensation of the carboxyl group of amino acid and the amino group of the second amino acid with the elimination of water

Phosphodiester bond

make up backbone strands of DNA and RNA

this bond is the linkage between the 3" carbon atom of one sugar molecule and the 5" carbon atom of another

these bonds are central to all life on earth

Glycosidic bond

type of covalent bond that joins a sugar molecule to another group which could be another carbohydrate.

covalent

holds together the long chains of macromolecules (DNA, RNA, and Proteins)

ionic

compounds with ionic bonds split into ions in water. Ions conduct electricity. Gives specialized cells excitable properties

hydrogen

makes water molecules stick together. responsible of the properties of water.

cause protein chains to spiral and bend, giving unique shapes

chemical bond is a link between 2 atoms to give a molecule

provides energy necessary to form a chemical

strength of the bond depends on the molecules involved in the process of bond formation

the chemical bond is composed by 2 electrons coming from the outer layer of each different atom to make a pair of electronds

shared electrons=pair of electrons

types of R groups present

polar

nonpolar

acidic

basic

the ability to do work

Kinetic Energy

energy of motion

e.g. muscle contractions

e.g. light energy

Potential Energy

stored energy available to do work

e.g gravitational energy

e.g. chemical energy

it is used, stored, and transformed in living systems

metabolism: the totality of the chemical reactions of an organism's body

a starting molecule is converted into a product through the used of intermediates

catalyzed by specific enzymes suited for the reaction

enzymes help to lower the energy barrier which reactant need to overcome before they can form products

substrate: the small molecule that an enzyme binds to

active site: where on the enzyme the substrate binds to

binding of a susbtrate forms weak bonds, changing the shape of the enzyme

weak bonds include hydrogen bonds and ionic bonds

regulation of enzyme function

inhibition of enzyme activity

competitive inhibition: a competitive inhibitor mimics a substrate, competing for the active site

noncompetitive inhibition: a noncompetitive inhibitor binds to the enzyme away from the active site, changing its shape so that the active site functions much less effectively

feedback inhibition: when the end product of a process stops the process from continuing

allosteric regulation

regulatory molecule binds to a protein
at one site which then affects the protein's function at another site

regulatory molecule

inhibitor: inhibits enzyme activity

activator: stimulates enzyme activity

e.g. cooperativity: when one substrate molecule binds to an active sits allowing all other subunits to go into active form

chemical reactions can be broken down into two pathways

catabolic

breaking down complex molecules into simpler compounds, releasing energy

e.g. cell respiration

exergonic

spontaneous

anabolic

when simpler molecules are converted into complex molecules, consuming energy

e.g. photosynthesis

endergonic

nonspontaneous

it is constantly being changed from one type of energy to another

e.g. photosynthesis: when light energy (kinetic energy)is converted into chemical energy (potential energy) to transform it into glucose

6CO2 +6H2O -> C6H12O6 +6O2

products are provided to the mitochondria

goes through cellular respiration
C6H12O6+6O2 -> 6CO2+6H2O+ATP

aerobic respiration: occurs with oxygen and releases energy slowly

C6H12O6+6O2 -> 6CO2+6H2O+ATP

products (minus ATP!) are used as reactants for photosynthesis

anaerobic respiration: occurs without oxygen and releases energy quickly

alcoholic fermentation: a pyruvate (2) forms acetyl-dehyde which gets reduced with the electrons from NADH forming alcohol

humans can't do this

lactic acid fermentation: pyruvate (2) is directly reduced, grabbing electrons from NADH, forming lactate (2)

humans can do this

broken up into two stages

light reactions

converts light (photons) & H2O into chemical energy (ATP & NADPH) while producing O2 as a byproduct.

chemical energy will be used to power the Calvin Cycle

NADPH: electron donor

ATP: energy currency of the cell

renewable resource regenerated by the addition of a phosphate group to ADP

catabolic reactions in the cell power the phosphorylation of ADP

different ways to synthesize ATP in cells

substrate level phosphorylation: when a phosphorylated substrate and ADP interacts with an enzyme which leads to a formation of a product (substrate) and ATP (when the phosphate group from the substarte is transferred to ATP)

glycolysis

you start with glucose and ATP (2)

occurs in the cytoplasm (outside the mitochondria so it does NOT need oxygen; also known as anaerobic respiration)

energy investment: the first five steps you use ATP

energy payoff phase: the last five steps you make more ATP than you used

net number of molecules:
ATP: 2 (2 used and 4 formed)
NADH: 2
Pyruvate: 2

citric acid cycle

following glycolysis, the two pyruvate formed are oxidized to form acetyl-Coa, our starting molecule.

molecules per acetyl-Coa formed: (there are 2 acetyl-Coa present! so each molecule times two)

ATP: 1
NADH: 3
FADH2:1

Oxidative phosphorylation: electrons from NADH and FADH2 transfer to oxygen, generating ATP; occurs in the mitochondria

electron transport chain (ETC)

NADH brings electrons from glycolysis and citric acid cycle where they move down complexes 1, Q, 2,3, cyctochrome c, 4, and finally oxygen to form water. While this is occuring, there is a release of energy.

the energy produced is used to pump H+ against their concentration gradient (proton gradient) into the intermembrane space

an example of active transport

chemiosomosis

following ETC, so many protons are now being pumped into the intermembrane space, and they now want to go back their concentration gradient into the matrix trhough facilitated diffusion.

facilitated diffusion occurs through the used of the enzyme, ATP synthase. This results in the synthesis of ATP

26-28 ATP

occurs in the thylakoid membrane/space

calvin cycle

uses CO2 & chemical energy to synthesize glucose

broken up into three stages

carbon fixation

catalyzed by enzyme Rubisco

G3P synthesis

gl

RuBP Regeneration

a series of enzymatic reactions driven by ATP

thermodynamics: the study of energy transformations

system: the matter under study

closed system

open system

surroundings: matter in the rest of the universe

first law of thermodynamics: energy can be transferred or transformed but it cannot be created nor destroyed

second law: every energy transfer or transformation increases the entropy of the universe

entropy (S): measure of disorder

Gibbs free energy (G): helps to predict the spontaneity (or lack thereof) of a reaction at constant temperature and pressure

ΔG=ΔH-TΔS

ΔG<0 implies that ΔStotal>0

spontaneous

exergonic

ΔG=0 implies that ΔStotal=0

ΔG>0 implies that ΔStotal<0

nonspontaneous

sending and receives signals

local signaling

paracrine & synaptic

long distance signaling

hormonal signaling

two types of receptors

membrane receptors

G protein linked receptor

steps at reception:

signal molecule binds to GPCR

allows G protein to bind

causes GDP to be replaced with GTP

*G protein switch removes phosphate group from GTP to make GDP

active G protein activates enzyme

Tyrosine Kinase receptor

made of two polypeptides which dimerize when a signal molecule is bound to each polypeptide

each polypeptide takes a phosphate group from ATP and adds it to the other polypeptide

called autophosphorylation

Ion Channel receptor

intracellular receptors

transduction

second messenger

cyclic AMP (cAMP)

formed from ATP using Adenylyl Cyclase

converted to AMP by phosphodiesterase

Phospholipids

glycerol

2 fatty acids

phosphate

basic component

selectively permeable

types of membrane transport

simple passive

facilitated diffusion

active transport

three major steps

opening of the double helix and separation of the strands

priming of template strands

assemply of new DNA segment

monomer

nucleotides

hydrogen bonds connect complementary nucleotides

a double helix formed from two complementary strands of nucleotides held together by hydrogen bonds between G-C and A-T base pairs.

cytosine, guanine, thymine, adenine

DNA strand is used as template strand to create new complementary strand

both prokaryotic & eukaryotic cells have the ability to regulate their gene expression

gene expression: the ability to express a gene to produce products such as proteins and non-coding RNA molecules

can be controlled at any of these 5 stages:

chromatin rearrangements: regulates chromatin conformation & DNA's accessibility for transcription

chromatin: loosely coiled nucleosomes

nucleosomes: DNA wrapped around units of 8 histone proteins (octamer)

histones: proteins that binds the DNA (first level of packaging

H1

it is NOT involed in the octamer (it acts independently)

H2A

H2B

H3

H4

transcriptional control: regulates RNA polymerase binding to a promoter & initiation of transcription

most prokaryotic gene regulation occurs at this stage

transcription intiation in Eukaryotes requires a complex of trancription factors bound to the promoter sequence so then RNA pol II can bind

transcription factors: proteins that bind to specific DNA sequences & regulates transcription initiation

recruited by the TATA box

TATA box sequence of A & T repeats located in the promoter

general: bind to (or near) the promoter

brings about low levels of transcription (background/basal)

recruits RNA polymerase to the promoter region of a gene

specific: bind to distal control elements called enhancers

activators: bring about increased level of transcription

repressors: brings about low levels of transcription

post-transcriptional control: regulates modifications to RNA after transcription

alternative RNA splicing

spliceosome: the RNA protein complex that removes introns from premature RNA

introns: noncoding section of an RNA trancription and interrupts the sequence of genes

results in different protein products form the same mRNA transcript

RNA processing adds 5' Cap & poly-A tail to mRNA for protection from RNA degrading enzymes in the cytoplasm

small noncoding RNA block translation of target mRNA molecules

mRNA is degraded

ribosome is blocked from binding

translational control: regulates initiation and elongation steps of translation

post-translational control: regulates modifications to proteins after translation

can activate/inactivate a protein for degradation by proteases

proteases: enzyme that degrades proteins by breaking polypeptide bonds making single amino acids

differential gene expression: process that allows multi-cellular orgnaism to express genes differently in different cells

all cells of a multi-cellular organism have the same genome, but have different sets of proteins

fundamental to eukaryotes

regulated in 2 ways:

positive regulation

stimulates gene expression by turning "on" the gene; genes are allowed to be expressed

negative regulation

prevents gene expression by turning "off" the gene

prokaryotes need to often change their metabolic pathways due the availability of nutrients, which can be done by regulating expression of certain genes

most common way they regulate genes is through the use of operons

operon: a group of prokaryotic genes of related function which are controlled by a single promoter

promoter: a region of DNA that initates transcripiton of a gene

it is located at the beginning of the gene

operator: regulates transcription of the operon; decides whether the gene should be "off" or "on" through the binding of regulatory proteins

regulatory proteins: binds to the operator and affects RNA polymerase binding to the promoter

activator: promotes RNA polymerase binding
(stimulates transcription)

repressor: blocks RNA polymerase binding
(prevents transcription)

Lac I: active repressor protein that normally represses transcription when bound to lac operator

lac operon: inducible operon with 3 genes encoding enzymes that metabolize lactose for energy; only in the presence of lactose (& absence of glucose) is the lac operon transcribed

Lac Z

Lac Y

Lac A

glucose impact on lac operon:

glucose is the preferred energy source even in the presence of lactose in most prokaryotes

if glucose is available, the lac operon should be turned "off"

glucose levels are linked to cyclic AMP (cAMP)

when glucose is low/absent. cellular levels of cAMP increases

high cellular cAMP levels increases the rate of transcription of the lac operon

membranes and organelles in eukaryotic cells

package, transport, and export the proteins made in cell

protein could either function as membrane protein or be secreted outside of the cell

composed of nuclear envelope, endoplasmic reticulum, Golgi Apparatus, vesicles, lysosomes, and vacuoles.

a theory stating that genetic information only flows one direction^

DNA to RNA to Protein

DNA is transferred to mRNA molecule by a process called transcription

mRNA is bound by ribosomes which read mRNA to produce chain of amino acids

RNA directly to protein