B1: Form and Function Molecules

Learning outcomes:

• descibe nature of covalent bond and that a carbon atoms can form up to four single bonds and other bonds with other atoms

• expain macro molecules, such as polysacharides are formed by condensation reaction that link monomers to form a polymer

• explain that wa wa molecules are split to provide the -H and -OH groups incorpotated to produce monomers in a hydrolysis reaction

Carbon and the covalent bond

• found in cabrs, lipids, proteins and nucleic acids

• C forms covalent bonds

  • enables variety of stable compounds to exist. covalent bond = stable

• longer chain of C-C bonds the more stable

  • distinct feature of a fatty acid

Carbon rings

• carbon can also form rings

• example of this is glucose

• many carbon rings can also join together to form branched structures such as glycogen, which is a polymer of many glucose molecules joined together

Macromolecules

= large molecules made up of smaller building blocks called monomers

• individual sub units that can be linked together to form longer chains called polymers

Four main classes of macromolecules:

• Carbs

• lipids

• proteins

• nucleic acids

Formation of condensation reactions

• macromolecules formed = monomers must join together by a type of chemical reaction called condensation reaction

• condensation reaction = polymersation reaction in which 2 molecules join, one molecule loses a hydroxyl group (-OH) and the other loses a hydrogen atom (-H), forming a water molecule and resulting in the formation of a new covalent bond

• condesnation reactions = formation of macromolecules

• -Oh group on carbon 1 of glucose molecule attacthed to the -OH group on a carbon 4 of the other glucose molecules, results in a covalent bond between two molecules, and relase of a molcule of water.

• glycosidic bond = O atom shared between two glucose molecules that are joined together, when two glucose molecules join together they are called a diashacaride

• more then two join together = polysacharide

• celluose is an example of polysacharide

Breakdown of hydrolosis reactions

• our bodys break down large polymers into constituient monomers to use them for energy or to build new macromolecules ur body needs

• process of breaking down macromolecules into monomers = hydrolosis

• reverse reaction for the condensation polymerisation reaction

• water molecules break the covalent bonds between monomers that make up a polymer making them available for biological processes

Carbohydrates:

• recognise monosacharides (pentose and hexoses) and know the properties of glucose (glucose in soluble, stable and can be oxidised).

• outline the role of polysacharides as energy storage compounds and as structural components

• explain the role of glycoprtiens in cell - cell recognition

Introduction to monosaccharides

• monosacharides are dundemental

• source of energy for cells

• simplest form of a carb, consisting of a single sugar unit that cannot be broken down into smaller molecules by hydrolysis.

Types of monosaccharides

• calsified by number of carbon atoms they have

• pentoses have 5 carbon atoms, such as ribose, whereas hexose has six, like glucose, galctose and fructose.

  Fructose:

  • sugar naturally found in fruits whereas galactose is a type of sugar that is found in dairy products glucose = most common monosacharide found in nature and is an important source of energy for many organisms.

Properties of glucose

Glucose has two isomers

• most common monosaccharide found in nature & properties are esential to its roles

• glucose = two isomers = alpha glucose (a-glucose) and beta-glucose (B-glucose)

• in the alpha glucose the -OH group is oriented downwards, wheras in beta it is oriented upards

• diff structures are a result of diff combinations of the different isomers

Glucose is a soluble molecule

• glucose is polar becasue it contains several -OH group

• oxygen atom present in the glucose ring has a partial negative charge the carbon - hydrogen (C-H) groups linked to it have a partial positive charge.

• in water solution, glucose is in equilibrium with open-chain form, where C1 atom is able to rotate

Glucose is a stable molecule

• sturcutal role of the polysaccharide cellulose in plants

Glucose can be oxidised

Oxidation is a chemical reaction that involves the loss of electrons from an atom or molecule

Metabolism

all of the enzye reactions that take place inside a living organism

Anabalism

Def: the sythesis of complex macromolecules from monomers

Energy use: requires input of energy

Type of reactions: condensation reactions

Examples: amino acids from protiens, glucose forms startch

Catabolism

Def: the breakdown of macromolecules into monomers

Energu use: energy is realised in the process

Type of reaction: hydrolysis

Ex: the breakdown of sugars (including glycolysis) or fats to release energy

Hydrolosis

the breaking od chemical bonds by the addition of water molecules

Condensation reaction

reactio in which two smaller organic molecules combine to form a larger molecule with the accomponies formation of water or some other simple molecule

Monosachardies

• single sugar monomers used to build larger comples carbs; polar and water soluble

• 

Disaccharides

two sugar monomers joined by a glycosidic bond thru condesation reaction; polar and water soluble

Example: glucose + fructose = sucrose

or glucose + glucose = maltose

Polysaccharides

Macromolecules made of many sugar monomers joined thry condensation reactions; not soluble in water

• use glucoe as monomer

• very abundant on earth

• plants store startch in roots and cells

• carbs also make up chitin exosckleleton of isects and crustaceans

Cellulose

• beta glucose monomers flip 180 degerss every other glucose to form straight un-branched chain

• H bonds between chains provide stability

• plants use celluclose as a strucural component, can be used as biofuel

Glycogen

• animals use glycogen to store energy

• very similar in structure to amylopectin (branched chain of alpha glucose monoers)

Glycoportiens

Def: protiens with one or more carbs attatched to them

Roles include

• cell-cell recognition

• receptors

• ligands

• structural support

  

Properties of lipids

Lipids: class of hydrophobic, non-polar molecules

• insoluble in water, will dissolve in other non-polar solvents

Includes triglcerides, wax, steroids & cholesterol

• triglycerides: synthesized by liver, found in foods (buuter, lard, olive oil)

• wax: high melting point, often solid at room temp; found on surface of leaves to reduce transpiration

Formation of phospholpids

• similar to triglycerides except with 2 fatty acid tails and a phosphate group joined to glycerol

Fatty acid structure

Saturated: all single bonds, each C fully saturated with H (4 bonds) —> straight chains that pack together easily —> solid at room temp

Unsaturated: one or more C-C double bonds —> results in kinks or bends in the chain —> harder to pack together —> liquid at room temp

Lipids for energy storage

• lipids vs carbs: lipids have higher energy content per gram and are thermal insulators

• carbs: 17kL/g vs Fats: 37 kJ/g —> twice the energy per gram

• Eg: fat isulated wwhales during winter

Lipids as long term storage:

glycogen (carbs energy stores in animals_ associated with 2g water per gram glycogen

• lipids stored w/no addtional water —> smaller contribution to body mass —> lighter overall body mass possible, enhances mobility while retaintaing a lot of energy

• can form waterpoof layer in plants and animals

• plants store fats (often unsaurated) in seeds as energy for germinating seedling

Phospholipids

• negativley charged hydrophilic phospahte head + non-polar long fatty acid tails

• hydrophilic + hydrophobic = amphipathic

• in water, hydrophobic tails will orite themselves towards other tails (away from water molecules) —> spontanous fomation of bilayers

  

Membranes as a barrier

• core of phospholipid bilayer made of fatty acid tails —> hydrophobic

• low permeability to hydrophilic molecules (ions and large polar molecules) because of interactions w/ hydrophobic core

• low permeability to large molecules due to size

• result: membranes can prevent many kinds of particles from diffusing across without the help of membrane protiens

Steroids

• category of hormones which regulate a wide range of functions in the body

• share similar carbo 4-ring structure with diff function groups

• cholesterol is the base for steriod hormones

• hydrophobic —> able to pass thry phospholipid membrane easily —> steroid hormones can deliver their message more efficiently

Proteins: Essential structures for life

• huge range of functions:

  • enzymes

  • hormones

  • pumps

  • receptors

  • immune protiens (antibodies)

  • structural protiens

  • keratin —> hair, nails, claws

Gene

Section of DNA that codes for the amino acid sequence of one polypepetide/protien.

Genes and Protiens

• DNA is transcribed as mRNA

• mRNA is read (translated) by ribosomes, which build the amino acid chain based on the mRNA instruction

• resulting amino acid chain is a polypeptide which will fold innto its final protien configuration

Amino Acids: The building blocks

• all protiens are made of chains of amino acids

• amino acid structure: central carbo with amino group NH₂ carboxyl group (COOH), and R group (20 kinds)

20 Diff Kinds of Amino Acids

Some are essential —> cannot be sythensized in the human body, so must come from outside sources:

• Histidine

• Isoleucine

• Leucine

• Lysine

• Methionine

• Phenylalanine

• Threonine

• Tryptophan

• Valine

Dipeptide

two amino aicds joined by a peptide bond (formed via condensation reaction)

Polypeptide

Def: Many amino acids joined by a peptide bonds

Protiens can be a single polypeptide chain, or several chains combined, like hemoglobin

Peptide bonds

Bonds that join amino acids together

Polypepetide

• chain of many amino acids, used interchangeably with protien, usually longer chains folded into secondary structures

Peptide

• smaller chains of amino acids, between 2-50

Dipeptide

• two amino acids joined by a bond

Polymer

Polymer: general term for a large molecule made of monomers

Examples of polypeptides

Lysozyme: enzyme made of 129 amino acids; found in tears and salvia; disrupts bacteria cell walls

Alpha-neurtoxins: polypeptides in snake venom which target and disrupt nervous system by inhibiting receptors; 60 - 75 amino acids

Glucagon: made of 29 amino acids; secreted by pancreas; increases blood sugar levels by breaking down glycogen stores

Myoglobin: oxygen-binding protien found in muscle tissues; made of 153 amino acids

Optimum temp and pH

• devations from optimum temp and pH reduce function and cause denaturation of protiens

• Temp: high temps cause denatureation resulting in changed interaction between amun acud R-groups, sometimes irreversible

Optimum pH

• very alkaline or acidic solution can break bonds within quaternary, tertiary and secondary structure

Membrane structure

• membranes are fluid, flexable and dynamic

• maintains internal enviorment of the cell, allows for exchange with outer enviorment

• key player in homeostasis

Fluid mosaic model

• membranes composed of phospholipid bilayer w/embended protiens and chlesterold

Phospholipid biylaer

• two layers of phospholipids( tails on inside, heads on outside)

  • polar phosphate head —> hydrophilic

  • two (non-polar) fatty acid tails —> hydrophobic

  • hydrophilic + hydrophobic = ampipathic

• hydrophobic tails “hide” from water between the hydrophilic phosphate heads, which are attratced to water

• low permability to hydrophilic molecules because of interactions w/hydrophobic core

• low permability to large molecules

• membranes can prevent many kinds of particles from diffusing across

Diffusion O₂ and CO₂

• small non-polarticles like O₂ and CO₂ can diffuse easily across phospholipid bilayer

• passive transport

• moves down conc gradient from higher to low

Membrane protiens

Intergral: embeded in membrane; amphipathic

Peripheral: attatched to outside of membrane hydrophilic

Chanels: passive transport

Carriers: substrate binds to one side, protien changes shape to carry thru

Recognition: helps cell differentiate between self and non-self

Receptors: relay info from inside or outside cell

Enzymes: increase rate of reactions

Other parts of cell membrane

• glycolipids = branching carb attatched to the head of phospholipid

  • maintain structure, help cells identify “self”

• glycoprotien = branching carb attatched to a protien

  • enormos range of functions

Drawing fluid mosaic model

Represent phospholipids as circle w/ two parallel lines

Represent cholesterol as a short chain of hexagons amongst hydrocarbon tails

Include range of integral and peripheral proteins

Include and label the following structures:

Phospholipid bilayer

Phospholipid molecule

Glycoprotein

Glycolipid

Integral and peripheral proteins

Cholesterol

Import and export thru membrane

import materials for metabolism

• glucose

• hormones

• ions

Export toxic wates and useful products made by the cell

• other functions: cell defence and homeostasis

Passive transport

Simple diffusion: particles pass directley thru membrane

• faciliated diffusion: particles move thry a chanel/carrier protien

  • larger particles, ions (repelled by hydrophobic tails)

  • channels and carriers spesific to certain sizes and shapes of molecules

Facilated diffusion of K+ ions

• during action potential, K+ floods into axon

• axon needs to repolarize by moving K+ out of axon

• specialized K+ channels move K+ down its conc gradient

• K+ channels are voltage gated

Organelles

structures in a cell that preform spesific functions (like organs in your body).

Membrane bound organelles

• many organlles are memrane bound (surrounded by plasma membrane)

• only eukaryotic cells have membrane bound organelles

Compartmentalisation

Def: organising certain functions or processes inside structures bound by plasma membranes

• allows for developemnt of specialized cell structures

• allows for diff interal conditions

Lysosomes

• found in eukaryotic cells: enzyme-filled compartments that break down wastes in cell

Pagocytic vacules

Found in macrophages; use enzymes to break down pathogens into parts (part of immune response)

What isn’t an organelle

• organelles need to have specialised function/role: usually related to metabolism

• cytoskeleton, cell wall, and cytoplasm are not organelles

Ribosomes

are organelles

• they make protiens

• not membrane bound

Role of nucleus

• DNA is housed in nucleus

• DNA —> mRNA —> protien

• segments of DNA (genes) are transcribed into mRNA

• mRNA leaves nucleus to be translated into protien by the ribosomes in cytoplasm

Role of nucleus in gene expression

• before mRNA leaves nucleus, post transcriptional modification

• allows modification to be made before ribsomes can access mRNA transcript

• prokaryotes are unable to do this

• compartmentalisation of nucleus from cytoplasm allows cytoplasm to send signals to nucleus

• extrcellular signals like hormones, recieved by cytoplasm

  • passed to nucleus to alter rate of transcription

Stem Cells

• every organism starts as a single, upecialized cell (zygote)

• first cells need to be able to differentiate to make specialized tissues of a complate organism

• these fist cells are called stem cells

• diff kinds based on where they come from and limits of their differentiation

General charactaeristics of stem cells

All stem cells are unspecialises

• devide indefitinley to keep making more of that kidn of stem cells

• differentiate into difff kinds of cells when given the right stimulus

Differentiation

Def: unspecialised cells developing into cells with a distrinct structure and cell function

• certain sections of the genome are turned on for spesific “instructions” for diff kinds of cells

Embryonic development

• sperm + egg = zygote

• morula: solid ball of cells after first few divisions (16-32)

• blastocyst: hollow ball of cells consisting of trophoblast and iner cell mass ICM

• trophoblast will become placenta, ICM will become embyro

• Other cells “read: their distance away from source in conc grandent thry receptors on surface and devlop accordingly 

  • Result: early embryonic cell differentiations 

From Unicellular to multiceullular organisms 

• Since organisms has multiple cells, those cells could specialise thru differientiation 

Stem cell niche: 

Def: the micromoment within the organism with adult stem cells live and recieve instructions

• Includes cell-to-cell interactions between cell na d extracellular fluid 

• Signaling molecules can activate, or prevent genes from transcribing → leads to activation of supression of cells. 

Bone marrow/blood cell niche 

• Bone barrow niche consits of cells that make bloof cells and supportive cells

Hair follicles: 

• Have cycles of degeneration growth and rest so that your body is alwaus covered with mature hair shaft

  • These are stem cells responsible for the proliferation of hair found in the “buldge”

Surface to colume ratio: cells 

• Will eventually be to much volume to be supported by not enough surface area 

• Wont be enough membrane space allow enough nutrients in watses out to maintian full volume of the cell