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IB Biology Review

Chapters 1, 2, 4, 10
by

Sohyun Kim

on 18 April 2011

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Transcript of IB Biology Review

IB HL BIOLOGY Statistical Analysis Error Bars
used to show either range of data or standard deviation
can be displayed for the values of more than one variable


Mean
sum of all values divided by number of values
average

Standard Deviation
shows spread of data around the mean
measures how widely spread the values in a set of data are
close to mean = small SD; far from mean = large SD; all equal = SD = 0
Variance is the square root of the standard deviation


Regression and Correlation
testing relationship between samples of variables
one variable is dependent on another ---> linear regression technique for line of best fit

Correlation Coefficient
-1 < x < 1
indicates how well experimental data fit the line of best fit
positive correlation: value of X increases = value of Y increases
negative correlation: value of X increases = value of Y decrease
if x = 0, there is no relationship between variables Cells Cell Theory all living organisms are composed of cells
cells are the smallest unit of life
cells only come from pre-existing cells Functions of Life:
metabolism [includes respiration and excretion]
response [to stimuli a.k.a. sensitivity]
growth [in cell size and number]
reproduction [sexual/asexual]
homeostasis [maintaining relatively stable conditions inside the body]
nutrition [source of food] Magnification
magnified size = real size x magnification
magnification = [magnified size (ruler)] ÷ [real size (scale bar)]
real size = [magnifized size (ruler)] ÷ [magnification] Surface Area to Volume Ratio
size of cell is limited by need to exchange with environment
too large = inefficient diffusion; too small = incapable of necessary exchange
rate of heat/waste production and resource consumption :: directly proportial to volume
uptake of resource & removal of heat/waste goes via cell membrane
rate of uptake/removal is proportional to surface area
volume increases more rapidly than surface area

How to Increase Surface Area?
protruding extensions
flattening the cell Emergent Properties
the whole > sum of parts
examples of emergence: termite hill, human brain

multicellular organisms show EP
organism achieves more than individual cells
cells interact and perform tasks that could not be achieved alone individual neurons are not capable of thought
communication and cooperation between neurons make it possible for the brain to think Euchromatin
represents genes used [to transcribe]
Heterochromatin
tends to contain inactive genes Differentiation Stem Cells
unspecialised cells
differentiate into specialized cells when given a certain chemical signal
e.g. embryo, umbilical cord

Different from 'normal' cells in two ways:
undifferentiated: they have not yet specialized into a certain type of cell all (or most) of their genes can still be expressed
self-sustaining: can divide and replicate for long periods of time Cell Therapy
therapeutic use of stem cells
transplanted cells need to become part of the body
need to continue to function well as part of the body

bone marrow transplant for leukemia
graft new skin for burns
grow new corneas for failing eyesight Prokaryotic Cells Cell Wall
made of protein-sugars
gives shape
protects bacterium from external damage
prevents bursting (in a hypotonic medium) Plasma Membrane
controls which materials enter and leave the cell
via active or passive transport
selectively permeable Cytoplasm
watery fluid
contains enzymes that control metabolic reactions
contains the organelles Pili
thin protein tubes
found outside plasma membrane

Two types:
attachment pili (fimbriae)
conjuction pili (sex pili) many attachment pili
sticky section allows prokaryote to stick to surfaces only a few conjuction pili
longer than fimbriae
play a role in bacterial conjugation
build a bridge between two bacterial cells
allows plasmid to be transferred between them Flagella
long thread-like structures
made of protein
attached to cell surface
allow bacterium to move in fluid environment Nucleoid Region
contains the DNA which holds genetic material
controls all processes in the cell Binary Fission
process that divides prokaryotic cells

DNA replication
separation of two circular strands of DNA to either side of the cell
cytokinesis (cell divides into two)
each new cell receives half of the cytoplasm
subsequent growth will restore each cell to full size Eukaryotic Cells Ribosomes
made of two subunits (protein and RNA)
makes proteins used in cell
site of protein synthesis Rough Endoplasmic Reticulum
RER is membrane with ribosomes attached
makes proteins exported via exocytosis (to be used outside cell)
site of protein synthesis Lysosome
contains hydrolytic enzymes
break down substances in cell
fuses and digests old cell organelles
material taken in via endocytosis (intracellular digestion)
can burst and cause autolysis (cell death) Nucleus
largest cell organelle
contains DNA
controls activity of cell by transcribing certain genes Mitochondrion
link reaction and Krebs cycle take place in matrix
electron transport chain is found on cristae of inner membrane
involved in release of energy from organic molecules Golgi Apparatus
stack of flattened, membrane-bound sacs
forms an extensive network
intracellular transport, processing and packaging of proteins Extracellular Components
associated with both plant and animal cells Cellulose
carbohydrate
cell wall is used for carbohydrate storage Cartilage
contains a lot of extracellular matrix (ECM)
ECM of cartilage = gel with certain glycoproteins
associate with water and collagen
responsible for firmness and resilience of cartilage Membranes
fluid mosaic model Two Kinds of Membrane Proteins:

Integral Proteins
found between phospholipid molecules of the membrane
interact with cytoplasm on one side
interact with external molecules
interact with hydrophilic section of the membrane in between

Peripheral Proteins
mostly found outside phospholipid bilayer in cytoplasm
interact with phosphate heads
may not be permanently associated with membrane Summary:
main component of membranes is a phospholipid bilayer
contain integral and peripheral proteins
some proteins are glycoproteins (with carbohydrate attached)
membranes contain cholesterol Functions of Membrane Proteins:

Hormone Binding Sites
hormones transported by blood will only act on cells w/protein receptor on membrane
Immobilised Enzymes
a.k.a membrane bound enzymes
enzymes arranged into systems for easier sequence of reactions to occur
e.g. electron transport chain
Cell Adhesion
integral proteins can stick out
bind to specific protein molecules in adjacent cells
bind to an extracellular matrix
Cell to Cell Communication
via direct contact between membrane proteins of adjacent cells OR
via signals (hormones/neurotransmitters)
Channels for Passive Transport
small proteins
outside is hydrophobic; inside is hydrophilic
allows polar molecules to enter cell
Pumps for Active Transport
Sodium-Potassium pump in nerve cells
use ATP to transport Na+ ions back outside axon & K+ ions back in Diffusion
movement of gas/liquid particles
high concentration ---> low concentration
Osmosis
passive movement
diffusion of water molecules
across a partially permeable embrane
low solute concentration ---> high solute concentration Simple Diffusion
passive transport
possible for small non-polar molecules Facilitated Diffusion
help polar molecules (ions) to cross barrier

Channel proteins
create hydrophilic pore in membrane
Transport proteins
help move substances into cell
binding site for (e.g. glucose) to attach to
change in structure of protein
carries into membrane and releases
returns back to original shape Role of Protein Pumps and ATP
active transport requires energy
moving particles against concentration gradient

Transport Proteins
a.k.a. carrier proteins/membrane pumps

Sodium-potassium pump
protein in plasma membrane
move sodium out and potassium in despite gradient
functioning of nerve cells Transport of Vesicles Between RER, GA, and PM

RER produces proteins inteded for export
Golgi Apparatus prepare substances for exocytosis

nucleus contains chromosomes
contain genes coding for proteins
mRNA made via transcription
move from nucleus to cytoplasm
RER contains ribosomes make proteins via translation
protein goes into lumen of RER
surrounded by membrane then moved to Golgi apparatus
processed into secretory vesicles
leaves cell surface membrane via exocytosis Diffusion Facilitated Diffusion Osmosis Active Transport Endocytosis ATP Required Concentration Gradient no no no yes yes down down down against is possible against is possible Exocytosis
materials removed from cell
requires ATP energy

Endocytosis
process where cell takes up substance by surrounding it with membrane
requires ATP energy
cells need this process to absorb highly polar or large substances
e.g. white blood cells

Two Types:
Pinocytosis (fluid)
Phagocytosis (solid) Cell Division Stage G1
period of cell growth
increase number of cell organelles

Stage S
synthesis of DNA (replication

Stage G2
preparation for mitosis
number of mitochondria and chloroplasts increase

Mitosis
process of nuclear division

Cytokinesis
occurs after mitosis (not included)
actual physical division of cell Stages G1, S, and G2 are called INTERPHASE
very active period NOT resting
biochemical reactions, DNA transcription and translation, and DNA replication occur Mitosis
increase number of cells without changing genetic material
daughter cells chromosomes, genes, alleles = parent cell

4 Phases:
prophase
metaphase
anaphase
telophase a)The cell membrane is intact during this the interphase. The chromosomes cannot be seen during G1,S and G2.

b) G1,Within the nucleus, genes on the chromosome are being expressed to carry out normal cell function (interphase). Remember you cannot see chromosomes at this stage. The diagram has a 'see's through' the nuclear membrane so you can see inside. In reality it would look just like cell a).

c) S-phase in which DNA replication occurs and the chromosomes are copied. The copies called sister chromatids are held together by a protein to form the centromere. It is still not possible to see this happen with an intact cell.

d) Early Prophase in which the sister chromatids have condensed by super coiling. Note the formation of the spindle microtubules and their attachment to centrioles. The nuclear membrane will now break down to reveal sister chromatids. The internal arrangements of chromosomes can now be seen with a light microscope.

e) Metaphase the chromosomes arranged on the equator of the cell each attached to a spindle microtubule at the centromere

f) Anaphase: The spindle microtubules contract and pull apart the sister chromatids one to each pole of the cell. The centromere splits allowing the sister chromatids to be separate.

g) Telophase: at each pole there are separate groups of the replicated chromosomes the spindles is degenerating

h) Cytokinesis: the cell membrane begins to separate, dividing the cell into two new cells. The nuclear membrane is reforming around each cell.

i) Two daughter cells are formed. They are genetically identical to each other and in effect the basis of a clone. (see 2.5.6)

Notice that cell a) begins with one chromosome and that by step h) there are two cells each with a copy of that chromosome.

As suggested by cell theory, all cells have come from other cells Result of Mitosis:
during S phase each chromosome replicates
copies are called sister chromatids
separated during anaphase and moved to each pole
referred to as chromosomes
result is two nuclei, identical to each other and to original nucleus The following processes require mitosis:
growth of tissue
production of muscles
skin regeneration (covering wound)
embryonic development
asexual reproduction
Tumours:

tumour repressor genes produce proteins which inhibit cell division
proto-oncogenes are genese that produce proteins which stimulate growth and cell division
mutations in either gene will result in a tumour (within organ or tissue)
series of genetic changes in a cell is needed before a tumour is formed

some tumours are harmless or benign (e.g. warts)
others are malignant and spread to other tissues/parts of the body (cancer)

Causes:
certain radiation and chemicals are known to be carcinogenic
viruses insert genetic material into host
electromagnetic radiation
ultraviolet light == skin cancer? car·cin·o·gen·ic:
Having the potential to cause cancer Cancer Treatment

Surgical Removal
Radiation Therapy
use strong ionizing/nuclear radiation beam
directed to precise point
'burn' all cells in the area
Chemotherapy
uses chemicals
destroy all rapidly dividing cells
side effects: hair loss, thin gut lining, low sperm count Genetics Meiosis Interphase
cell growth
DNA replication

Prophase 1
chromosomes condense
spindle formation
synapsis (homologous chromosomes pair up = bivalent)
crossing over occurs on points called chiasmata

Metaphase 1
bivalents move to equator

Anaphase 1
homologous pairs split up
one chromosome of each pair goes to each pole

Telophase 1
chromosomes arrive at poles
spindle disappears Prophase 2
new spindles form

Metaphase 2
chromosomes move to equator

Anaphase 2
chromosomes separate
chromatids move to opposite poles

Telophase 2
chromosomes arrive at poles
spindle disappears
nuclear membrane and nucleolus are visible
chromosomes ---> chromatin

Cytokinesis Net Result:

four haploid cells
gametes (sperm/egg)

enables chromosome number of a sexually reproducing species to be kept constant Formation of Chiasmata
combinations of genes within chromosome is possible via crossing over
two chromatids overlap
segments break at chiasmata
reattach to other chromatid

points where two non-sister chromatids overlap form cross-shaped structure = chiasma Mendel's Law of Independent Assortment
second law
'any one pair of characteristics may combine with either one of another pair'
two characteristics must be on different chromosomes Relationship between Mendel and Meiosis
law applies to traits carried on diff. chromosomes
any combination is possible in metaphase 1

crossing 2 plants
heterozygous for both traits (genes)
all combinations will be seen in offspring Pea Plants
Gene: shape of pea
Alleles: wrinkled, round

Gene: color of pea
Alleles: yellow, green Possibilities
Green-round
Green-wrinkled
Yellow-round
Yellow-wrinkled genes for shape and color are inherited independently
there are, however, exceptions to Mendel's 2nd Law Dihybrid Crosses
and
Gene Linkage Dihybrid Cross

Phenotype:
Yellow-Round

Genotype
YYRR

Gametes
YR
Autosomes:
all chromosomes that are not SC
22 pairs

Sex Chromosomes:
2 chromosomes that determine the gender of the individual
XX = Female; XY = Male Linkage Group
group of genes whose loci are on the same chromosome

Mendel's Law of Assortment does not apply to linked genes
genes on same chromosome = inherited together
UNLESS the chiasma is between the two links during cross over

closer loci = fewer recombinants lo·cus
loci, plural

A particular position, point, or place
The position of a gene or mutation on a chromosome Cross between Two Linked Genes

A B
=====
a b

Recombinants in Linked Genes
combinations of genes the parents did not possess Polygenic Inheritance concerns the inheritance of a characteristic that is controlled by more than one gene

Conditions:
human skin color (continuous variation)
shape of the comb in chickens (discontinuous variation)
milk yield in cows (affected by environmental factors)
obesity
cancer
autism
diabetes = 'multifactorial' inheritance described by Mendel Genes for Obesity
leptin = protein hormone
regulates appetite and metabolism
Ob(Lep) located on chromosome 7 for humans

Human Skin Colour
involves at least 3 independent genes
six alleles in total Chapter One Chapter Two Chapter Ten 2.1 2.2 2.3 2.4 2.5 10.1 10.2 10.3 Genetics Chromosomes, Genes,
Alleles, and Mutations Chapter Four 4.1 Prokaryotic chromosomes
circular
small loops = plasmids
found in nucleoid area
contain DNA no protein
Eukaryotic chromosomes
linear
found in nucleus
more than one chromosome
contain DNA and proteins Definitions:

Gene
heritable factor
controls a specific characteristic
on loucs of chromosome

Allele
one specific form of a gene
differ by a few bases

Genome
total genetic material

Gene Pool
total of genes carried by individual members of a population

Gene Mutation
permanent change in sequence of base pairs in DNA

Sickle Cell Anemia
change of only one base leads to a protein with one amino acid changed
GAG (glutamic acid) ---> GTG (valine)
sickle-cell shape blocks capillaries and is inefficient at transporting oxygen

Hemoglobin
4 polypeptide chains
2 alpha and 2 beta chains

Normal: HbA
Sickle Cell: HbS HbAHbS is a carrier of sickle-cell, but there is increased immunity to malaria Meiosis 4.2 BIOLOGY BIOLOGY BIOLOGY BIOLOGY a.k.a. reduction division
daughter cells have only half the # of chromosomes as parent

Purpose:
produce (haploid) gametes
half of (diploid) somatic cells (body cells)
male + female gamete = fertilization = zygote

Chromosomes:
number of chromosomes in haploid = n

Human Somatic Cell: 2n = 46
Gamete of a Camel: n = 35
Apple Somatic Cell: 2n = 34 Homologous Chromosomes
two chromosomes (one from each parent) that look the same
pair and split up during meiosis
same size
same banding pattern in a karyotype
same genes, but may not be same alleles

Example:
Gene = Eye color
Allele = Blue, brown, green, etc Meiosis 1
Meiosis 2

Prophase
Metaphase
Anaphase
Telophase Non-Disjunction
pairing up in Prophase 1 = synapsis
pair = tetrad/bivalent
separation in Anaphase 1 = disjunction
failure to do so = aneuploidy = +/- one chromosome
total non-disjunction = polyploidy = one complete extra set of chromosomes Down Syndrome
chromosome 21
extra copy Karyotyping
process of finding the chromosomal characteristics of a cell
stained to show banding
arrange in pairs (identical sister chromatids) Applications in Pre-natal Testing:

Chorionic Villus Sampling
11-12 weeks
sample of chorionic villi
cells from zygote
Amniocentesis
16th week
sample of amniotic fluid
contains fetal cells Theoretical Genetics 4.3 Definitions:

Genotype
alleles of an organism

Phenotype
all characteristics

Dominant Allele
same effect on phenotype whether it is in a homozygous or heterozygous state

Recessive Allele
only has an effect on phenotype in the homozygous state

Codominant Alleles
pair of alleles that both affect phenotype in heterozygous state

Locus
particular position on homologous chromosomes of a gene

Homozygous
having two identical alleles of a gene

Heterozygous
having two different alleles of a gene

Carrier
has both a dominant and recessive allele

Test Cross
testing a suspected heterozygote with a known homozygous recessive Punnett Square Multiple Alleles
blood type

4 phenotypes: A, B, AB, O
3 alleles: IA, IB, i

CoDominance
IA and IB are codominant
both will affect the phenotype Sex Chromosomes
46 chromosomes in somatic cells
X chromosome > Y size

X-Linked
some genes are only on X-chromosome
females can be hetero (carrier) or homozygous
color blindness
haemophilia

Y-Linked
hairy ears Sex Linkage
occurs when genes are carried on the sex chromosomes
most often on X-chromosome
color blindness and hemophilia Mendel's First Law

Law of Segregation
Parental factors (genes) are in pairs and split so that one factor is present in each gamete Mendel's Second Law

Principle of Independent Assortment
Any of one pair of characteristics may combine with either one of another pair (dihybrid inheritance) Chapter 1: Statistical Analysis
Chapter 2: Cells
Chapter 4: Genetics
Chapter 10: Genetics
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