IB Bio HL Complete Review

Cell Theory

1. Cells are the basic unit of life

2. All cells originate from pre-existing cells

7 Functions of Life

1. Nutrition - taking in food/nutrients

2. Metabolism - processing the nutrients

3. Excretion - get rid of waste

4. Response to stimuli - reacts to signals from environmental change

5. Homeostasis - maintaining a stable internal environment

6. Growth - increase in size and number

7. Reproduction - pass on genes, sexually or asexually

Cell needs a high surface area to volume ratio because…

Must be able to transport things - food, waste, oxygen - quickly and efficiently through the surface to replenish essential nutrients before the cell dies.

Typical Cell Size

10-100 micrometers

Magnification formula

Magnification = observed size / actual size

Two types of microscopes + differences

1. Light - black and white, preserves the specimen (does not kill)

2. Electron - higher resolution image, must kill specimen

Cell differentiation

The process by which some genes are switched on or off (in other words, some expressed, some not), creating cells with specified functions

Stem cells

Undifferentiated cells that can divide and differentiate into any cell and thus acquire any functions

Prokaryotes vs Eukaryotes

Proks: unicellular, simple structure, smaller

Euks: multicellular or unicellular, bigger, complex organelle based function

Prokaryote structures + functions

• cell wall - protection and pressure maintenance

• cell membrane - transport of materials

• cytoplasm - contains enzymes, food, medium for rxns

• 70S ribosomes - protein synthesis

• nucleoid - naked DNA

• plasmid - extra genetic material

• pili - communication, DNA exchange, attachment

• flagella - movement

Eukaryotic cells structures and functions

• 80S ribosome - protein synthesis

• Rough ER - protein modifications

• Golgi apparatus - protein packaging

• Mitochondrion - site of cell respiration (double membrane)

• Nucleus - contains genetic material

• Lysosome - degradation enzyme storage

• Centrioles - chromosome separation during mitosis (animal cells only)

• Vacuole - food and water storage, separates from rest of cell

• Cell Wall - maintenance of cell pressure (plant cells only)

• Chloroplast - site of photosynthesis (plant cells only)

• Cell membrane - encloses, protects cell

Phospholipids

Glycerol head - hydrophilic, polar

Hydrocarbon tail - hydrophobic, non-polar

Integral protein

Spans lipid bilayer, helps with diffusion of large and/or non-polar molecules across membrane

Peripheral protein

attached to inner or outer side of membrane

active transport

movement of molecules up the concentration gradient (from area of lower to area of higher concentration) with the use of ATP

Passive transport

movement of molecules down the concentration gradient (higher to lower concentration)

Simple diffusion

passive transport of molecules through a membrane without the need of protein channels (common example: oxygen)

facilitated diffusion

passive transport of molecules facilitated by channel or carrier proteins

osmosis

diffusion of water across a membrane from an area of lower solute concentration to an area of higher solute concentration

Exocytosis

transport of molecules out of the cell by vesicles which fuse with the plasma membrane and expel the contents

Endocytosis

infolding of a molecule/cell into the cell to form a phospholipid vesicle containing molecule

Osmolarity (hypo- and hyper-tonic)

Osmolarity: measure of a solute concentration in a given system

Hypotonic: low solute concentration - system loses water

Hypertonic: high solute concentration - system gains water

Endosymbiotic theory

Complex eukaryotic cells have evolved from prokaryotic cells through a symbiotic process

Mitochondria and Chloroplasts as evidence for endosymbiotic theory

• double membrane - engulfed

• own 70S ribosomes

• make own proteins

• about the size of a prokaryotic cell

• replication

Phases of mitosis

1. Prophase (prepare): supercoiling of chromosomes w/ help of histone proteins, nuclear membrane disappears, MTOC’s (microtubule organising centres) move to poles and create spindle apparatus (centrioles in animal cells)

2. Metaphase (middle): chromosomes moved by spindle apparatus to line up on metaphase plate, each chromatid attached to a fibre

3. Anaphase (away): sister chromatids split and move to poles, now called daughter chromosomes

4. Telophase (two): chromosomes uncoil, spindle apparatus disappears, two cells form

   • cytokinesis - not part of mitosis - formation of cleavage furrow and splitting of cytoplasm to form 2 daughter cells

Cell Cycle

G₁ - the phase which cells spend the majority of their lifespan: growth and performance of daily functions

S - the phase that occurs once the cell has decided to undergo mitosis: period of DNA synthesis (replication)

G₂ - the phase where cell does last preparations for mitosis: cell duplicates organelles, prepares enzymes and proteins needed for mitosis

mitotic index

number of cells undergoing mitosis / total number of cells

How many covalent bonds can Carbon form?

4 - allows for the formation of a wide variety of stable and complex compounds

Components of an amino acid structure

Amine group, R-group, carboxyl group

Metabolism

Web of all enzyme-catalysed rxns in a system. Metabolic pathways can consist of chains or cycles, and can be anabolic or catabolic

Anabolism

Synthesis of complex molecules from simpler ones (e.g. formation of macromolecules from monomers by condensation rxns). Associated with condensation rxns - removal of a water molecule each time a monomer is added to a polymer chain or other monomer.

Catabolism

Breakdown of complex molecules into simpler ones (e.g. hydrolysis of macromolecules into monomers). Associated with hydrolysis rxns.

Polar molecule

a molecule that has an uneven distribution of charges across the molecule (e.g. more negative at one end and more positive at the other)

• water is polar

Non-polar molecule

a molecule that has an even distribution of charges across the molecule, so no positive or negative poles are formed

Thermal properties of water

• high specific heat: large amounts of energy required to raise water’s temp.

  • Takes lots of energy to break H bonds

• High latent heat of vaporisation: H bonds between water molecules make it hard for single molecules to escape as vapour

  • energy necessary to break bonds high compared to other liquids

• High latent heat of fusion: water at 0ºC must lose a lot of energy before forming ice crystals

  • water expands as it freezes, so ice floats on water

Cohesive properties of water

• water molecules can stick to each other through the formation of H bonds between H of one and O of another water molecule

  • can explain the formation of water droplets, why some organisms can ‘walk on water’, etc.

Adhesive properties of water

Water can adhere to charged surfaces through the formation of H bonds due to its polarity

Solvent properties of water

Water is an excellent solvent for polar molecules that attract the charged poles of water molecules

• water forms bonds around other polar compounds, separating them

• compounds and molecules that dissolve in water are hydrophilic

Hydrophilic

all molecules that can readily dissolve in water and can freely associate with it by forming intramolecular bonds (e.g. polar molecules and ionic compounds)

• e.g. Glucose

Hydrophobic

all molecules that cannot associate with water molecules or easily dissolve in it (e.g. large and non-polar molecules)

• e.g. cholesterol and fats

Carbohydrates

organic molecules composed of hydrogen, oxygen, and carbon atoms. Monosaccharides are the monomers of carbs, and are building blocks to more complex carbs

Monomer, dimer, polymer

Monomer: the building block or basic unit of a class of compounds that can be polymerised to make larger compounds

Dimer: a compound made from the bonding of 2 monomers

Polymer: two or more repeated monomers from a class of compounds bound together, forming a more complex molecule

monomer, dimer, polymer —> carbohydrate terms

monomer = monosaccharide

dimer = disaccharide

polymer = polysaccharide

Examples of monosaccharides

Glucose, Fructose, Galactose

Examples of disaccharides + composition

maltose (glu + glu), sucrose (glu + fru), lactose (glu + gal)

Examples of polysaccharides

cellulose, glycogen, starch (all polymers of glu)

Important functions of lipids

• long term energy storage

• heat insulation

• buoyancy

• shock absorption

Saturated fatty acids

all carbon atoms in fatty acid chain connected by single covalent bonds, so number of hydrogen atoms connected to each carbon cannot be increased (e.g. butter)

Trans unsaturated fats

hydrogen atoms are bonded to carbon on the opposite sides of the double bond (e.g. margarine)

cis unsaturated fats

hydrogen atoms are bonded to carbon on the same side of the double bond (e.g. olive oil)

Are lipids or carbs more easily digested?

Carbs - good for energy storage that needs to be rapidly released

Do lipids or carbs store more energy per gram?

lipids - good for long term energy storage

monomers of proteins

amino acids

how many different amino acids are there?

20

essential vs non-essential amino acids

Essential - cannot be produced (in sufficient quantity) by the human body, so must be obtained through diet

non-essential - are made by the body in sufficient quantity

for humans: 9 essential, 11 non-essential

4 levels of protein structure

Primary: amino acid sequence

Secondary: formation of alpha helices and beta pleated sheets, stabilised by formation of hydrogen bonds

Tertiary: formation of 3D structure of polypeptide due to interactions between R groups of amino acids

Quaternary: multiple polypeptide chains combined to form a single protein

Functions of proteins

structural - e.g. collagen, which strengthens bone, tendon, and skin

transport - e.g. hemoglobin, which binds oxygen in the lungs and transports to other tissues

movement - e.g. actin, which is involved in muscle contraction

defence - e.g. immunoglobulins, which act as antibodies

proteome

entire set of proteins expressed by a genome, cell, tissue, or organism at a given time (each individual has unique proteome, like fingerprints)

substrates and enzymes must ——————— with one another to react

collide

• more collisions = faster rxn

lock and key model

substrate and enzyme have shapes that make them fit perfectly with each other, enzyme catalyses specific rxn

induced fit model

as substrate and enzyme approach each other, their interactions make them shift physically so that they fit perfectly together

Effect of temperature on enzyme activity

as temperature increases enzyme activity also increases, until it reaches a point that is too hot, where the enzymes will start to denature and enzyme activity will rapidly decrease and then stop

Effect of pH on enzyme activity

Enzymes have an optimal pH, above or below which activity is decreased and/or the enzyme is denatured

Effect of substrate concentration on enzyme activity

as substrate concentration increases, more collisions between enzymes and substrate will occur, meaning more successful collisions will occur, increasing enzyme activity

Nucleotide structure

phosphate group, pentose sugar (either ribose or deoxyribose), nitrogenous base

Bases of RNA and pairs

Purines: Adenine (A), Guanine (G)

Pyrimidines: Cytosine (C), Uracil (U)

Pairs: A-U, G-C

DNA bases and pairs

Purines: Adenine (A), Guanine (G)

Pyrimidines: Cytosine (C), Thymine (T)

Pairs: A-T (2 H bonds), G-C (3 H bonds)

DNA replication

1. Helicase unwinds double helix and breaks hydrogen bonds to separate strands

   • 2 parent strands are templates

2. Single-Strand binding proteins bind to the outside of the strands, preventing the double helix from reforming

3. DNA primase puts a short RNA primer on each template strand

4. DNA polymerase III adds nucleotides to complementary bases on each strand

   • leading strand: starts at 3’ end of parent strand, synthesises continuously

   • lagging strand: DNA primase places RNA primers along the strand, as DNA can only synthesise in the 5’ to 3’ direction, and DNA polymerase III goes and fills them in, forming Okazaki fragments

5. DNA polymerase I goes along the lagging strand replacing RNA primers with DNA nucleotides

6. DNA ligase then goes in and fills the gaps in the fragments of the lagging strand

7. Result is 2 identical daughter DNA strands

Transcription

RNA polymerase makes a new strand of RNA from DNA in the 5’ to 3’ direction

1. Initiation: RNA polymerase binds to location on DNA called promoter near the start of the gene

2. Elongation: RNA polymerase moves along separating DNA into single strands and pairing RNA nucleotides with complementary bases

   • RNA polymerase forms covalent bonds between RNA nucleotides

   • RNA separates from DNA and double helix reforms

3. Termination: transcription stops at end of gene (terminator sequence) and RNA transcript is released. RNA polymerase detaches

• Template strand = anti-sense strand because it is complementary, other strand is sense strand bc identical (except for T instead of U)

• RNA processing occurs before DNA exits nucleus

  • 5’ end gets a ‘cap’ (special G nucleotide)

  • 3’ end gets a poly-A tail

  • both used to help RNA exit nucleus, serve as protection, and help attachment to ribosome

• RNA splicing

  • introns cut out before exiting nucleus

  • exons spliced together

  • shortens RNA, now called mRNA

Translation

RNA-directed synthesis of a polypeptide

• Initiation: activating enzyme attaches to methionine to initiator tRNA

  • Initiator tRNA binds to small subunit of ribosome, producing ternary complex

  • Ternary complex binds to 5’ end of mRNA and slides along, scanning for AUG

  • Small subunit stops and links anticodon to AUG codon w/ hydrogen bonds

  • Large subunit binds to small w/ initiator at P site, completing translation initiation complex

• Elongation: tRNA w/ anticodon complimentary to next codon on RNA binds to a site

  • peptide bond formed between amino acids on A and P sites

  • ribosome translocates tRNA in A site to P site, and tRNA in P site to E site for release

  • process repeats

• Termination: Elongations continues until stop signal on mRNA is reached

  • connection to tRNA at P-site is broken off

  • everything detaches - the tRNAs, the large and small ribosomal subunits, etc

  • protein will get modified

Glycolysis

occurs in cytoplasm, glucose in, 2 pyruvates out, 2 net ATP produced, 2 reduced NAD

• phosphorylation - glucose phosphorylated by 2 ATP molecules to form a hexose bisphosphate (6C sugar)

• lysis - 6C sugar split into 2 triose phosphates (3C sugars)

• oxidation - H atoms removed from each 3C sugar via oxidation to reduce NAD, producing 2 red. NAD molecules

• ATP formation - 4 molecules of ATP generated during glycolysis, pyruvate formed

Link Reaction

occurs in mitochondria, 2 pyruvate in, 2 acetyl CoA out, 2CO₂ out, 2 reduced NAD produced

• pyruvate transported to mito matrix by carrier proteins on mito membrane

• pyruvate loses a C molecule, forming CO₂

• 2C compound forms acetyl group when it loses H via oxidation (reduces NAD)

• acetyl compound transferred to CoA to form acetyl CoA

Krebs Cycle

occurs in matrix of mito, 2 acetyl CoA in, 4 CO₂ out, 2 ATP, 6 reduced NAD, 2 reduced FAD

• oxaloacetate accepts acetyl group from acetyl CoA to make citrate

• citrate loses 2 C molecules through decarboxylation

• 3 NAD and 1 FAD reduced = 3 red. NAD, 1 red. FAD

• ADP —> ATP (1)

• oxaloacetate regenerated

• products go to oxidative phosphorylation

oxidative phosphorylation

occurs in inner membrane of mito, 10 red. NAD and 2 red. FAD in, 24-28 more ATP + water produced

• Reduced NAD and FAD delivers electrons to the ETC, changing it back to NAD and FAD

  • H moves up to form proton gradient in the intermembrane space

• electrons are passed between carriers as they move down the ETC, which consists of transmembrane protein complexes

• as electrons move down the chain, they lose energy, which is used by the chain to pump protons up to form the proton gradient

• buildup of protons in intermembrane space causes protons to diffuse back down to an area of lower concentration

  • does this by going through ATP synthase, rotating it

• ATP synthase generates additional 25-28 ATP molecules

• Oxygen is the last electron carrier and combines with free protons in matrix to form water

best light for photosynthesis

red and blue - chlorophyll reflects

absorbs green

limiting factors of photosynthesis

• light intensity - main factor at night, limits production of reduced NADP and ATP, shuts down calvin cycle during reduction phase

• CO₂ concentration - often limiting factor, shuts down carbon fixation step of calvin cycle

• temperature - at low temps, enzymes are slow causing red. NADP to accumulate, stopping reduction step. At high temps, rubisco denatures

Calvin cycle

occurs in stroma of chloroplasts

• start with RuBP - 5C

• carbon fixation - CO₂ added and then split into 2 glycerate-3-phosphates

• reduction phase - 2 ATP and 2 reduced NADP used to make 2 triose phosphates

  • 1/6 of triose phosphate goes to make glucose, starch, etc (only ½ of a sugar molecule, so calvin cycle x2 to produce a single glucose monomer)

• regeneration - other 5/6 regenerates RuBP (requires ATP)

• enzyme called rubisco catalyses rxn between RuBP and CO₂

Light dependent rxns

occur in thylakoid membrane and thylakoid space, red NADP and ATP reduced

• absorption of light by PSII and PSI generates excited electrons

• photolysis of water generates electrons for use

• excited electrons are carried by plastoquinone to the cytochrome complex from PSII, where they enter the ETC and lose energy, helping pump protons into the thylakoid space

• Plastocyanin moves electrons to PSI, where light excites them again

• excited electrons are moved by ferrodoxin into NADP reductase to form reduced NADP

• reduced NADP and ATP (products of light dependent rxns) go to calvin cycle

gene

a DNA sequence that defines a certain heritable characteristic

• one DNA molecule contains many genes, but not all are expressed

chromosome

a DNA molecule that carries genes

how many chromosomes do humans have

46, meaning 23 pairs of chromosomes

allele

a variation of a certain gene, differing from the other allele of the same gene by a few bases. different alleles code for different variations of the trait coded for by that gene

• result of mutations in the gene sequence

homozygous

if an organism has 2 of the same alleles, it is homozygous for the trait

heterozygous

if an organism has 2 different alleles, it is heterozygous for the trait

alleles can be _______ or __________

dominant, recessive - dominant alleles always expressed if present, recessive only expressed if homozygous

traits of sickle cell anemia

• moon-shaped red blood cells with lower oxygen carrying capacity compared to normal

• malaria less likely to infect sickle cells

genome

entire genetic information of an organism - includes genes, introns, exons

human genome project

project aiming to sequence the entire human genome

• humans share most of their genetic sequence, with the exception of short nucleotide polymorphisms (SNPs)

Does the size of the genome/number of genes relate to the complexity of an organism?

No

Karyogram

an image of all the chromosomes of an organism’s cell, shown in decreasing size of homologous pairs

• can help determine sex and possible chromosomal irregularities

  • e.g. trisomy 21, also known as down syndrome, is an extra copy of a chromosome in the 21st pair

karyotype

the characteristic pattern of chromosomes of an organism, referring to their size, shape, and banding pattern

meiosis

a type of cell division in which one cell with a diploid nucleus divides into 4 genetically distinct cells with haploid nuclei. Process by which gametes are made

diploid cells

have two variations of each chromosome (one maternal and one paternally derived)

haploid cells

have one variation of each chromosome (either a maternal or paternally derived one)

aim of meiosis

to create cells with half the number of chromosomes so that during fertilisation, each parent can contribute their own set of genes to the offspring and thereby conserve the number of chromosomes of a species and promote variation

Meiosis I

• homologous chromosomes separated, end up w 2 haploid cells with duplicated chromosomes

• DNA duplicates before prophase I

• prophase I - crossing over between nonsister chromatids, DNA supercoils and chromosomes shorten, nuclear envelope breaks down, centrioles move to poles

• metaphase I - homologous chromosomes pair up on metaphase plate, spindle fibre attaches to one chromosome from each homologous pair

• anaphase I - homologs separate, start to move towards opposite poles, cell starts to elongate

• telophase I - chromosomes assemble in 2 poles, some species form new nuclear envelopes and chromosomes decondense, but not in others, cleavage furrow/vesicles and cytokinesis

meiosis II

• sister chromatids separate, resulting in 4 haploid cells

• prophase II - chromosomes supercoil and become shorter, centrioles move to poles of the cell, nuclear envelopes break down

• metaphase II - chromosomes line up at metaphase plate, one next to each other, spindle fibres attach to centromeres of chromosomes

• anaphase II - spindle fibres pull sister chromatids apart (one chromatid of each chromosome travels to opposite pole), each pole of the cell will receive one DNA copy of each chromosome

• telophase II - nuclear envelopes form and cell divides into two cells

crossing over

process through which the nonsister chromatids within a homologous pair exchange genetic material during prophase I

• through crossing over, gametes end up with chromosomes with new gene combinations that were not present before - contributes to genetic variation

genotype

combination of alleles of one or more genes

phenotype

the physical trait that is expressed by a certain genotype, observable characteristics