ib biology topic 2

what are Light Dependent Reactions ?

Light energy is converted into chemical energy • Light is absorbed by chlorophyll to produce ATP • The photolysis of water forms oxygen and hydrogen

what are Light Independent Reactions ?

Carbon compounds are made from the chemical energy • ATP and hydrogen are fixed with carbon dioxide • This results in the formation of organic molecules

Pigments can be separated by what and how?

chromatography

\- Pigments are dissolved in fluid • The fluid is passed through a static material • Pigments are separated according to size A retardation factor

Rf =

distance of pigment ÷ distance of solvent

what is a limmiting factor?

When a process depends on more than one condition, the rate will be limited by the factor nearest its minimum value

Limiting factors in photosynthesis include what?

Temperature (influences photosynthetic enzymes) • Light intensity (required for chlorophyll photoactivation) • Carbon dioxide concentrations (CO2 is a core substrate)

what is an action spectrum?

indicates the overall rate of photosynthetic activity at each wavelength of light

what is the genetic code?

the set of rules by which information encoded in mRNA sequences is converted into a polypeptide sequence

what are codons?

Triplets of bases which correspond to a particular amino acid

A coding sequence always begins with what?

with a start codon (AUG)

what is traslation?

Translation is the process of polypeptide synthesis by the ribosome

process of translation ?

Messenger RNA (mRNA) is transported to the ribosome - A ribosome reads an mRNA sequence in base triplets called codons - Each codon codes for a specific amino acid (as per the genetic code) - Amino acids are transported to ribosomes by transfer RNA (tRNA) - Each tRNA aligns opposite a codon via a complementary anticodon - The ribosome moves along the mRNA sequence (5’ → 3’) and joins amino acids together with peptide bonds (condensation reaction) - The synthesis of a polypeptide is initiated at a start codon (AUG) and is completed when the ribosome reaches a STOP codon

what is A gene ?

is a sequence of DNA which encodes a polypeptide sequence • One gene = one polypeptide (proteins may have multiple polypeptides)

what are the exceptions to One gene = one polypeptide rule?

Genes may be alternatively spliced (one gene = many polypeptides) -Genes encoding tRNA or rRNA are transcribed but not translated -Genes may be mutated to alter the original polypeptide product

what is metabolisum?

Metabolism describes the totality of chemical processes that occur within a living organism in order to maintain life

It is the web of all enzyme–catalysed reactions that occur within a particular cell or organism

what are organic compounds?

Organic compounds are molecules that contain carbon and are found in living things

\-Exceptions include carbonates and oxides of carbon

Carbon atoms form the basis of organic life due to what?

their capacity to form four covalent bonds - This allows a diversity of stable compounds to exist

what are the four main groups of organic compounds in cells?

Carbohydrates, lipids, proteins and nucleic acids

carbohydrate polymer and monomer?

MONOMER: Monosaccharide - POLYMER : Polysaccharide

protein polymer and monomer?

MONOMER: Amino acid - POLYMER : Polypeptide

nucleic acid polymer and monomer?

MONOMER: Nucleotide - POLYMER : DNA / RNA

Lipids are not composed of repeating monomers, but may contain smaller subunits (e.g?

Triglyceride- subunit= Glycerol + Fatty Acid (×3)

what is Anabolism reaction?

The synthesis of complex molecules from simpler ones

\-Involves condensation reactions (water is produced)

\-An example of an anabolic reaction is photosynthesis

what is Catabolisum reaction?

The breakdown of complex molecules into simpler ones

\-Involves hydrolysis reactions (water is consumed)

\- An example of a catabolic reaction is cellular respiration

what is the Theory of Vitalism ?

Vitalism was a doctrine that dictated that organic molecules could only be synthesized by living systems

\- Living organisms were thought to possess a “vital force” that was required to manufacture organic molecules

what was the Falsification of Vitalism?

In 1828, Frederick Woehler disproved the theory of vitalism by artificially synthesizing an organic molecule

\-He heated an inorganic salt (ammonium cyanate) under laboratory conditions to produce urea (organic)

what is waters structure?

Water is made up of two hydrogen atoms covalently bonded to an oxygen atom (molecular formula: H2O)

Oxygen has a higher electronegativity that attracts what?

the shared electrons more strongly, resulting in polarity

The dipolarity of the water molecule enables what?

water to form polar associations with other charged molecules (polar or ionic)

Water molecules can also form hydrogen bonds with other water molecules (between an δ+ hydrogen and an δ– oxygen)

what are cohesive properties of water?

Water can form intermolecular associations with other molecules that share common properties (e.g. polarity)

\-Water can form hydrogen bonds with other water molecules (cohesion: like molecules stick together)

\-Water can form polar associations with charged molecules (adhesion: unlike molecules stick together)

The cohesive properties of water results in what?

a relatively high surface tension (can resist low level external forces)

The adhesive properties of water result in what?

it allows for potential capillary action (e.g. transpiration stream in plants)

Water is commonly referred to as the universal solvent due to what?

its capacity to dissolve a large number of substances (ionic / polar)

\- Large quantities of water molecules can sufficiently weaken forces (e.g. ionic bonds) and form dispersive hydration shells

Substances that can dissolve in water are called what ? examples?

hydrophilic and Includes glucose, amino acids, sodium chloride, oxygen (low)

Substances that cant dissolve in water are called what ? examples?

hydrophobic and Includes lipids (fats and cholesterol)

what are water’s thermal properties?

Water has high specific heat capacity, heat of vaporization, and heat of fusion. These properties help regulate temperature in living organisms and weather patterns on Earth.

why is it important for Water to be transparent?

as it allows light to pass through it

\-Important for photosynthesis and also for vision

Water expands when ….? and why is this important?

frozen, becoming less dense

\-important for life on Earth as it means ice floats and the oceans underneath don’t automatically freeze

what is a monosaccharide?

The monomer of a carbohydrate

\-Monosaccharides primarily function as an energy source and Examples of monosaccharides include glucose and ribose

Monosaccharides are covalently joined by glycosidic linkages to form what?

polymers (requires condensation reactions)

Polysaccharides may be used for what cell functions?

Short term energy storage (e.g. glycogen, starch)

Structural components (e.g. cellulose)

Recognition / receptors (e.g. glycoproteins)

Types of Polysaccharides ?

Cellulose - Amylose - Glycogen - Amylopectin

what is cellulose?

component of plant cell walls

Linear molecule made of β-glucose subunits • Subunits bound in a 1-4 arrangement

what is starch?

energy storage in plants

Composed of α-glucose subunits and exists in two forms • Amylose is linear (helical) and bound in 1-4 arrangements • Amylopectin is branched (bound in 1-4 and 1-6 arrangements)

what is glycogen?

(energy storage in animals)

• Branched molecule composed of α-glucose subunits

• Is like amylopectin but with more frequent 1-6 bonding

how do Carbohydrates and lipids differ as energy storage molecules?

\-Storage (lipids used for long term storage)

\-Osmotic pressure (lipids easier to store)

\-Digestion (carbohydrates easier to utilise)

\-ATP yield (lipids store more energy per gram)

\-Solubility (lipids insoluble / harder to transport)

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SODAS

BMI =

Mass in kg ÷ (Height in m)2

what are lipids ? and examples?

Lipids are a class of non-polar organic molecules

Include triglyceride (adipose tissue), phospholipid (bilayer), cholesterol (animal cell membrane), steroids (hormones)

Lipids may serve a variety of cellular functions, including:

\-Storage of energy (triglycerides)

\-Hormonal roles (steroids)

\-Insulation (thermal)

\-Protection of organs

\-Structural roles (cholesterol)

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SHIPS

what are Triglycerides?

lipids used for long-term energy storage -

They are composed of a glycerol molecule covalently linked to three fatty acid chains (via condensation reactions)

what are fatty acids ?

long hydrocarbon chains found in certain lipids - Principally found in triglycerides and phospholipids

what are saturated fatty acids ?

Possess no double bonds in the hydrocarbon chain

\-Are generally solid at room temperatures (e.g. animal fat)

what are unsaturated fatty acids ?

Possess double bonds (mono = one ; poly = many)

\-Are generally liquid at room temperature (e.g. plant oils)

Unsaturated fatty acids occur in what two distinct configurations?

Cis Isomer - Trans Isomer

Cis fatty acids?

H atoms on the same side - Double bond creates kink in fatty acid chain - Are loosely packed and usually liquid - Occur commonly in nature - Generally good for health

trans fatty acids?

H atoms on different sides - Double bond does not create kink (linear chain) - Are tightly packed and usually solid - Occurs in processed food - Generally bad for health

Low density lipoproteins (LDLs) ?

transport cholesterol from the liver to the rest of the body (bad for health)

High density lipoproteins (HDLs) ?

scavenge excess cholesterol and return it to the liver for disposal (good)

how do Fatty acids influence the levels of lipoproteins?

Cis fats raise levels of HDL (⇩ blood cholesterol)

Saturated fats raise levels of LDL (⇧ blood cholesterol)

Trans fats raise levels of LDL and lower levels of HDL

High levels of blood cholesterol can cause what?

atherosclerosis and lead to health issues like coronary heart disease (CHD)

what is an amino acid?

The monomer of a protein and Amino acids are linked together to form polypeptides

how many amino acids are there?

There are 20 different amino acids that form polypeptides • These can be linked in any sequence to create variation

Amino acids are covalently joined by peptide bonds to form what?

polypeptide chains (requires condensation reactions)

where dose The sequence of amino acids is encoded by genes and the assembly of a polypeptide occour

in the ribosome

what is the Primary Structure of a protein?

1º structure = sequence and number of amino acids

2º structure = folding into α-helix or β-pleated sheet

3º structure = three-dimensional shape of a polypeptide

4º structure = presence of multiple polypeptide chains

some functions of Proteins ?

\-Structure (collagen, spider silk)

\-Hormonal (insulin, glucagon)

\-Immunity (immunoglobulins)

\-Transport (haemoglobin)

\-Sensation (rhodopsin)

\-Movement (actin, myosin)

\-Enzymatic (Rubisco, catalase)

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SHIT ME

what is a proteome ?

The totality of all proteins that are expressed within a cell, tissue or organism at a certain time

\-The proteome of any given individual will be unique as protein expression patterns are influenced by a genome

what is denaturation?

Denaturation is a structural change in a protein that results in the loss (usually permanent) of its biological properties

Denaturation can be caused by what certain conditions?

Temperature (heat may break structural bonds)

\- pH (alters protein charge ➡ changes solubility & shape)

what is an enzyme?

a globular protein which speeds up the rate of a chemical equation by lowering the activation energy (i.e. it is a biological catalyst)

\-Enzymes are not consumed by the reactions and can be re-used

what is the substrate and the active site?

The molecule(s) the enzyme reacts with is called the substrate, which binds to a complementary region on the enzyme’s surface (active site)

what is the Lock and Key Model?

Enzyme and substrate complement each other precisely in terms of both their shape and chemical properties

\-The active site and the substrate will share specificity

what is the Induced Fit Model?

Active site is not a rigid fit for the substrate and changes its conformation to better accommodate the substrate

\-This stresses the substrate bonds and induces catalysis

how dose Temperature effect enzyme activity?

Increases enzyme activity (more kinetic energy = more collisions)

\-Enzyme activity peaks at an optimal temperature

\-Higher temperatures decrease activity (causes denaturation)

how dose PH effect enzyme activity?

• Enzyme activity is highest at an optimal pH range

\-Activity decreases outside of this range (due to denaturation)

how dose Substrate Concentration effect enzyme activity?

Increases enzyme activity (more particles = more collisions)

\- At a certain point, activity plateaus (saturation of active sites)

how can The rate of enzyme catalysis be increased?

d by increasing the frequency of enzyme-substrate collisions (molecular motion)

\-The rate of enzyme catalysis is decreased by denaturation

why are Immobilised enzymes often used in industrial practices?

They are fixed to a static surface to prevent enzyme loss

\-This improves separation of product and purity of yield

what is One application for immobilised enzymes?

the production of lactose-free milk and associated dairy products

how is lactose-free milk produced?

Lactase (enzyme) digests lactose into glucose / galactose

\-Lactase is fixed to an inert surface (e.g. alginate beads)

\-Milk is passed over this surface to become lactose free

benefits to lactose free milk?

Provides a source of dairy for lactose-intolerant people

Increases sweetness of milk (less need for sweeteners)

Reduces crystallization and production times for cheese

what is a nucleotide ?

The monomer of a nucleic acid

Each nucleotide consists of what three basic components?

• A pentose sugar • A phosphate group • A nitrogenous base

Each nucleotide possesses one of five different nitrogenous bases wich ones?

Adenine, Guanine, Cytosine, Thymine or Uracil

\-Bases may either be purines (A, G) or pyrimidines (C, T, U) • T is present in DNA, whereas U is present in RNA

Nucleotides are linked together into a single strand via what?

condensation reactions - (between a 5’-phosphate and a 3’-hydroxyl group of adjacent nucleotides)

a polynucleotide arrangement results in what?

he formation of a sugar-phosphate backbone that is covalently linked together by phosphodiester bonds

what is DNA structure?

Two complementary strands line up in opposite directions (anti-parallel) with the bases facing inwards and connected by hydrogen bonds (G ≡ C and A = T)

\-The double stranded molecule then twists in order to adopt a more stable energy configuration – a double helix

what is RNA structure?

The polynucleotide chain remains single stranded, but may fold upon itself to form double stranded motifs (e.g. the cloverleaf shape of a tRNA molecule)

The structure of DNA was elucidated by who? and when?

Watson and Crick in 1953

what dose semi-conservative replication mean?

DNA replication is semi-conservative – one strand is from an original template molecule and one strand is newly synthesised

\-This occurs because each base will only pair with its complementary partner and thus ensure the sequence is conserved

what dose Helicase: do?

Unwinds and separates the double stranded DNA

\-Breaks the hydrogen bonds between the base pairs

what dose DNA Polymerase III do?

Free nucleotides line up opposite complementary partners

\- DNA Pol III covalently joins the free nucleotides together

what was the The Meselson-Stahl experiment?

experiment that supported the theory that DNA replication occurred via a semi-conservative process

what occurred in the Meselson-Stahl experiment?

They incorporated radioactive nitrogen isotopes into DNA

\- Templates were prepared with heavier 15N

\- New sequences were replicated with lighter 14N

\-The DNA was then separated via centrifugation in order to determine its composition of radioisotopes

\- 1st division: DNA had 15N and 14N (i.e. mixed)

\- 2nd division: DNA is mixed or has 14N only

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\-The results were consistent with a semi-conservative model

what is The polymerase chain reaction (PCR)?

an artificial method of DNA replication that is used to rapidly copy sequences

PCR occurs in a thermal cycler over what three repeating steps?

Denaturation: DNA heated in order to separate strands

\-Annealing: Primers attach to ends of a target sequence

\-Elongation: A heat-tolerant polymerase copies strands

what is Transcription?

the synthesis of an RNA sequence from a DNA template • This process occurs within the nucleus of a cell