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BIOL &160, Polymers: Cells make most of their macromolecules by…
BIOL &160
CHAPTER 1:
Biology: Exploring Life
What is life?
Growth and development
Energy processing
Regulation
Evolutionary adaption
Order
Reproduction
Biologists arrange the diversity of life into three domains:
Domain Archaea
Domain Eukarya
Protists
Plantae
Fungi
Animalia
Domain Bacteria
Structural Levels of Hierarchy:
Biosphere
Ecosystem
Community
Population
Organism
Organs and Organ System
Tissue
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The process of Science
Process of Science: Forming and testing hypotheses
Can be tested using observational data
Hypotheses can be tested using controlled experiments
Independent Variable
Dependent Variable
Controlled experiment
Biology, Technology, and Society are connected in important ways
Five Unifying Themes in Biology
Artificial Selection: Selective breeding of plants and animals, humans also acts as agents of evolution.
DNA
A genes information is first transcribed from DNA to an intermediate molecule, RNA
RNA
Protein-manufacturing machinery
Gene Expression
RNA:
A, C, and G
Genes consist of DNA
DNA
: A, T, C, and G
Contains two polynucleotides which form
double helix
Darwin's theory of Evolution
Natural Selection: Organism environment selecting for adaptive traits
Observation #1: Individual Variation
Observation #2: Overproduction of Offspring
Interference #1: Unequal reproductive success
Interference #2: Accumulation of favorable traits over time
CHAPTER 2:
The Chemical Basis of Life
Elements, Atoms, and Compounds
matter: space and mass
Electrons are what can interact with each other
non polar
- electrons are shared equally
Some trace elements are required to prevent diseases
each element has a unique atom
isotope
- happens when you change the number of neutrons
ion
- messing with number of electrons present
Organisms are composed of Elements, Atoms, and usually combined into Compound
Atoms
atom is smallest unit of matter:
Nucleus
protons
atomic number
Neutrons
isotope
radioactive isotope
Nucleus has DNA
DNA & RNA are nucleic acids
Electrons
Chemical Bonds
Hydrogen bond- weak but vital
Oxygen is slightly negative
hydrogen is slightly positive
connect and try to flirt with other hydrogen bonds
Covalent Bonds
A molecule consists of two or more atoms held together by covalent bonds.
Polar
Nonpolar
Water's Life-supporting Properties
Property 1: Cohesion :
Property 2: Moderates temperature changes
Property 3: Ice floats
Property 4: Versatile solvent
Solute is getting dissolved
gas, liquid, or solid
hydrogen bonds make ice less dense than water
kinetic and thermal energy
Evaporative cooling
Adhesion
- sticking to something of a different type
The chemistry of life
Acid
Use pH scale to describe how acidic or basic a solution is
Base
CHAPTER 3:
The Molecules of Cells
Introduction to Organic Compounds
Organic Compounds:
Carbon-based molecules
Isomers:
Compounds with the same formula but different structural arrangements.
Hydrocarbons:
composed of only carbon and hydrogen
Functional groups
Hydroxyl
Carbonyl
Carboxyl
Amino
Phosphate
Methyl
Macromolecules :
Cells make large molecules from a limited set of small molecules
Carbohydrates
Proteins
Lipids
Non-polar bonds and Hydrophobic
No polymers or monomers
Mostly hydro carbon and stores lot of energy
Fats:
large lipid made from two smaller molecules: glycerol and fatty acids
Saturated fatty acid
Unsaturated fatty acid
Transfat
Phospholipids
Steroids
Cholesterol and some hormones
Nucleic acids
Stores information
Genes
Chromosomes
Sugar
: Deoxyribose and Ribose
CHAPTER 4:
A Tour of the Cell
Discovery of Cells
eukaryotes
extracellular matrix
junctions
tight
water tight
anchoring
made of intermediate filaments; really strong connection between cells to prevent other cells from being pulled away
gap
protein tunnel to send rapid messages
animal cells
plant cells
cell wall
plasmodesma
chloroplasts
prokaryotes
flagella
Cytosol
Cytoplasm
Prokaryotes
bacteria
archaea
nuceloid
cilia
Plasma membrane
Plasma membrane in plants is cell membrane
Chromosomes
Genes
DNA
Ribosomes
The Endomembrane System
organelles
smooth ER
rough ER
ribosomes
lysosomes
mitochondria
golgi apparatus
nucleus
nuclear envelope
chromatin
nucleolus
vesicles
The Cytoskeleton and Cell Surfaces
microfilaments
support shape, pseudopodia, muscle cell contraction, cytoplasmic streaming
intermediate filaments
reinforce shape, fix organelle position, permanent framework, nucleus is locked in position
microtubules
hollow, biggest, thickest in diameter
Microscopes
Microscopes reveal the world of the cell
CHAPTER 5:
The Working Cell
Plasma Membrane
Fluid Mosaic Model
Proteins
Proteins perform various functions
Junction protein
Active transport protein
Attachment protein
Receptor protein
Channel transport protein
Aquaporin: The very rapid diffusion of water into and out of such cells is made possible by a protein channel called an aquaporin.
Glycoprotein
Phospholipid
Cholestrol
Enzyme
Molecules
Solute molecules
Signaling molecule
Nonpolar molecules
Oxygen
Carbondioxide
Molecules have a type of energy called Thermal Energy due to their constant motion
One result of that motion is Diffusion
Transport of Large Molecules
Exocytosis:
Cell uses this to export bulky materials such as proteins or polysaccharides.
Endocytosis:
It is a transport process through which a cell takes in large molecules or droplets of fluid.
Phagocytosis or cellular eating
Receptor-mediated endocytosis
Cytoplasm
It has selective permeability
Membranes are fluid mosaics of lipids and proteins with many functions.
Diffusion
Passive Transport :
Diffusion across a membrane with no energy investment
Facilitated Diffusion:
Hydrophilic molecules and ions require the help of specific transport proteins to move across a membrane and that assisted transport is called facilitated diffusion.
Osmosis:
Diffusion of water across a membrane
Lower concentration of solute
Higher concentration of solute
More equal concentrations of solute
Tonicity:
The ability of a surrounding solution to cause a cell to gain or lose water.
Isotonic
Depends on the cell type
Hypotonic
Cells swell
Hypertonic
Cells shrink
Chemical reactions either release or store energy
Energy Coupling
ATP
Energy Molecule
ATP
supplies energy for most active transport
ATP drives cellular work by coupling exergonic and endergonic reactions
Chemical work
Transport work
Mechanical work
Phosphorylation
Exergonic reactions:
Releases energy
Endergonic reactions:
Require energy and yield products rich in potential energy.
Metabolism
Metabolic pathway
Energy and the Cell:
Cells transform energy and matter as they perform work
Forms of Energy
Kinetic energy
Thermal energy
Type of Kinetic energy associated with the random movement of atoms or molecules.
Potential energy
Chemical energy
Cellular respiration:
The chemical energy stored in organic molecules is used to produce ATP
Energy Transformations
Thermodynamics
First law of Thermodynamics:
Law of energy conservation
Energy can change form but cannot be created or destroyed
Second law of Thermodynamics:
Every energy conversion increases the entropy (disorder) of the universe.
Energy transfers or transformations increase disorder with some energy being lost as heat.
Entropy:
Measure of disorder
How Enzymes Function
Protein Catalysts
Enzymes speed up the cell's chemical reactions by lowering energy barriers.
Optimal conditions
Temperature
pH
Cofactors
Coenzymes
Activation Energy
A specific enzyme catalyzes each cellular reaction
Substrate
Active site
Induced fit
Enzyme inhibition can regulate enzyme activity in cell
Noncompetitive inhibitor
Competitive inhibitor
Feedback inhibition
Metabolic pathways are often regulated by feedback inhibition
CHAPTER 6:
How Cells Harvest Chemical Energy
Cellular Respiration: Aerobic Harvesting of Energy
Photosynthesis
The energy of sunlight is used to rearrange the atoms of CO2 and H2O producing organic molecules and releasing Oxygen.
Sugar and Oxygen are produced
Cellular respiration
Oxygen is consumed as organic molecules are broken down to CO2 and H2O and the cell captures the energy released in ATP.
Provides energy for body maintenance and voluntary activities.
Stages of Cellular Respiration
Stage 1: Glycolysis
Stage 2: Pyruvate Oxidation and the citric acid cycle
Stage 3: Oxidative phosphorylation
Chemiosmosis
ATP Synthase
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Electron Transport Chain
Location: Inner Mitochondrial membrane
Location: Mitochondria
ATP is formed
Location: Cytosol
Respiration:
It is referred to as an exchange of gases.
Cells capture energy from electrons 'falling' from organic fuels to oxygen
Redox Reactions
Oxidation
Reduction
Photosynthesis = Redox process
Cellular respiration
NADH
Electron transport chain
Fermentation
enables cells to produce ATP without oxygen
Lactic Acid Fermentation
NAD+ is regenerated as pyruvate is reduced to lactate
Alcohol Fermentation
NAD+ is regenerated as pyruvate is broken down to CO2 and ethanol
Types of Anaerobes
Obligate anaerobes : Require anaerobic conditions and are poisoned by oxygen
Facultative anaerobes: They make ATP either by fermentation of by oxidative phosphorylation
Organic Molecules
Cells use many kinds of organic molecules as fuel for cellular respiration
Carbohydrates
Sugars
Glucose -> G3P -> Pyruvate
ATP
Fats
Glycerol
Fatty Acids
Acetyl CoA
Citric Acid cycle
Proteins
Amino Acids
Cells, Tissues, Organisms
CHAPTER 7:
Photosynthesis: Using Light to Make Food
Photosynthesis fuels the biosphere
Autotrophs
Photoautotrophs: Which use light energy
Heterotrophs
Decomposers
Photosynthesis occurs in Chloroplasts in plant cells
Plant Leaf
Stomata
Chloroplast
Stroma
Thylakoid
Grana
Chlorophyll
Cell membrane
Mesophyll
Photosynthesis
Occurs in two stages
Light Reactions
Thylakoids
Make ATP + NADPH
Converting Solar Energy to Chemical Energy
Visible radiation absorbed by pigments drives the light reactions
The nature of sunlight
Electromagnetic spectrum
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Photosynthetic Pigments
RGB
CMY
Calvin Cycle
Stroma
Carbon Fixation
Formula:
6 CO2 + 6 H2O -------> C6H12O6 + 6O2
Photosystems capture solar energy
Reaction-center complex
Light-harvesting complexes
PH I
Electrons are passed to NAP + reducing it to NADPH
Goes to Calvin Cycle
Step 1: Carbon Fixation
Step 2: Reduction
Step 3: Release of G3P
Step 4: Regeneration of RuBP
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with help of Rubisco Enzyme
Other methods of Carbon fixation in plants
C3 plants
Uses photorespiration instead of calvin cycle
CAM plants
Light reaction
Calvin Cycle
Stomata closes and uses Calvin cycle when there's light
C4 plants
Reducing CO2 to sugar
PH II
Connected by Electron transport chain
Greenhouse effect
CHAPTER 8:
The Cellular Basis of Reproduction and Inheritance
Cell Division and Reproduction
Cell Division
Plays many important roles in the lives of organisms
Asexual Reproduction
Organisms reproduce by dividing in half, and the offspring are genetic replicas
Prokaryotes reproduce by
Binary Fission
As the cell replicates its chromosome
The plasma membrane pinches inward
Copies move apart
More cell wall is made, which eventually divides the parent cell into two daughter cells
Creating of genetically identical offspring by a single parent, without the participation of sperm and egg.
An individual that reproduces asexually gives rise to
Clone
Sexual reproduction
The lone parent and each of its offspring have identical genes.
Requires the fusion of gametes, egg and sperm
Production of gametes involves a particular type of cell division that occurs only in reproductive organs such as testes and ovaries in humans
Has only half as many
Chromosomes
as the parent cell that give rise to it
Contains unique combinations of genes
Enables organisms to develop from a single cell - the fertilized egg, or zygote into an adult organism.
Not identical to their parents or to each other with the exception of identical twins
2 Individuals contributing to form an offspring
The Eukaryotic Cell Cycle and Mitosis
Eukaryotic cells
Eukaryotic cells are more complex and much larger than prokaryotic cells
Have more genes
Genes found in cell Nucleus, grouped into multiple
CHROMOSOMES
Each Chromosome consists of one long
DNA
molecule
Bears hundreds or thousands of genes
equal amounts of DNA and protein
Chromatin
Chromosomes are duplicated before they condense and the cell divides
DNA molecule of each chromosome is replicated and new protein molecules attach as needed to main the chromosome's structure and regulate its genes.
Each chromosome now consists of two copies of
Sister Chromotids
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Reproduction
The Cell cycle includes growth and division phases
Cell Cycle
G1 (First gap)
S (DNA synthesis)
G2 (Second gap)
Mitotic phase
Mitosis
Prophase
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Cytokinesis
Checking
Growing
Spent in interphase
The rate of cell division is affected by environmental factors
Nutrition
Growth factor
PDGF
Signal the cell cycle control system
G1 checkpoint
G2 checkpoint
M checkpoint
G0
Density-dependent
Anchorage-dependent
Growing out of control, cancer cells produce malignant tumors
Tumor cells
Benign tumor
Malignant tumor
Cancer
Metastasis
Chromosomes are matched in homologous pairs
Somatic cells
Homologous chromosomes
Locus
Gametes have a single set of chromosomes
Somatic
Diploid (2n)
Gametes
Haploid (n)
Meiosis reduces the chromosome number from diploid to haploid
PMAT PMAT
Interphase, Meiosis I and Meiosis II
G1 (First gap)
S (DNA synthesis)
G2 (Second gap)
Mitotic phase
Mitosis
Meiosis I
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Cytokinesis
Checking
Growing
Crossing over further increases genetic variability
Chiasma
Alterations of Chromosome number and structure
Nondisjunction
Trisomy 21
Down syndrome
Abnormal numbers of sex chromosomes do not usually affect survival
XXX
XYY
XXY
Karyotype
Deletion
Duplication
Inversion
Translocation
CHAPTER 9:
Patterns of Inheritance
MENDEL'S LAWS
There are alternative versions of genes that account for variations in inherited characters.
Alternative versions of genes are called
alleles
.
Pedigree
Many inherited traits in humans are controlled by a single gene
Recessive Disorders
Dominant Disorders
Disorders can be tested by
Fetal Testing
Newborn Screening
Genetic Testing
Fetal Imaging
For each character, an organism inherits two alleles of a gene, one from each parent.
An organism that has two identical alleles for a gene is called
homozygous
and an organism that has two different alleles for a gene is said to be
heterozygous
.
Locus
If the two alleles of an inherited pair differ, then one determines the organism's appearance and is called the
dominant allele
and the other has no noticeable effect on the organism's appearance and is called the
recessive allele
.
A sperm or egg carries only one allele for each inherited character because allele pairs separate from each other during the production of gametes. This statement is called the
law of segregation
.
Law of independent assortment
Monohybrid cross
Dihybrid cross
Punnet Square & Foil
Phenotypes
Genotypes
Finding unknown genotype by
Testcross
.
Homozygous
Heterozygous
True-breeding
P generation
Hybrids
F1 generation
Genetic Cross
F2 generation
Rules of probability
Rule of multiplication
"AND"
Rule of addition
"OR"
The science of genetics began in an abbey garden
Heredity:
The transmission of traits from one generation to the next
Genetics:
Scientific study of heredity
Character:
Heritable feature that varies among individuals
Trait:
Each variant for a character
Variations on Mendel's Laws
Complete Dominance
Incomplete Dominance
Codominant
ABO Blood group
Blood Type A
Carbohydrate A
Anti-B
Blood Type B
Carbohydrate B
Anti-A
Blood Type AB
Carbohydrate A and Carbohydrate B
No Antibodies present in blood
Blood Type O
No Carbohydrates present on Red Blood Cells
Anti-A and Anti-B
A single gene may affect many phenotypic characters
Pleiotropy
Sickle-cell Disease
A Single character may be influenced by many genes
Polygenic inheritance
The environment affects many characters
Nature vs. Nurture
The Chromosomal Basis of Inheritance
Chromosome theory of inheritance
Genes occupy specific loci (positions) on chromosomes.
Chromosomes undergo segregation and independent assortment during meiosis.
Violations of mendelian genetics
Linked genes
Crossing over produces new combination of alleles
Wild-type
Mutant
Recombination frequency
Geneticists use crossover data to map genes
Genetic map
Linkage map
Sex Chromosomes and Sex-Linked Genes
Autosomes
X-Linked gene
CHAPTER 10:
Molecular Biology of the Gene
The structure of the Genetic Material
Bacteriophages
A phage attaches itself to a bacterial cell
The phage injects its DNA into bacterium
The phage DNA directs the host cell to make more phage DNA and proteins; new phages assemble
The cell lyses and releases the new phages
DNA and RNA are polymers of Nucleotides
polynucleotide
Sugar-phosphate backbone
DNA
A
T
C
G
RNA
A
U
C
G
DNA is a double-stranded Helix
A-T & C-G purine-pyrimidine H-bonds
DNA Replication
5'---> 3'
Enzymes
DNA polymerase
DNA ligase
Okazaki fragments
The flow of Genetic Information from DNA to RNA to Protein
Gene Expression
Transcription
Translation
Synthesis of RNA under the direction of DNA
Transcription of a gene
Initiation
Elongation
Termination
Terminator
RNA polymerase
Promoter
DNA
Transcription
RNA
Translation
Polypeptide
tRNA
Anticodon
Specific amino acid attachment
Initiation
Elongation
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mRNA + SSU + initiator tRNA (start codon)
LSU & initiator tRNA --> P site
mRNA
Addition of cap and tail
Introns removed
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Genetic information is written in codons and is translated into amino acid sequences
Triplet Code
Codons
Amino acid
Ribosomes build polypeptides
rRNA + proteins
Binding sites for tRNA & mRNA
Mutations can affect genes
Mutations
Mutagens
Point mutations
Silent
Missense
Nonsense
Frameshift mutations
Insertion
Deletion
The Genetics of Viruses and Bacteria
Virus
Capsid
The phage injects its DNA
The phage DNA circularizes
Lysogenic cycle
Phage DNA inserts into the bacterial chromosome
The lysogenic bacterium replicates normally, copying the prophage at each cell division
Many cell divisions
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Lytic cycle
New phage DNA and proteins are synthesized
The cell lyses, releasing phages
New phages assemble
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Emerging viruses threaten human health
HIV
AIDS
Makes DNA on an RNA template
Retrovirus
Reverse transcriptase
Prions are infectious proteins
Bacteria can transfer DNA
Transformation
Transduction
Conjugation
Bacterial plasmids can serve as carriers for gene transfer
F factor
Gene on chromosome or plasmid
R plasmid
Antibiotic resistance
CHAPTER 11:
How Genes are controlled
Control of Gene Expression
Gene expression
Gene regulation
Operons
Promoter
Operator
Enzyme
Lac Operon
Other types of Operon
Trp operon
Activator
Inducible
Repressible
Regulatory proteins
Repressor
Eukaryotes gene expression mechanism
DNA unpacking
Transcription
Splicing
Addition of a cap and tail
Flow through nuclear envelope
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Chromosome structure and Chemical modifications
Cells differentiate
Epigenetic inheritance
X Chromosome inactivation
Barr Body
DNA packing
Histones
Nucleosomes
Eukaryotic transcription
Activators
Transcription factors
Proteins assisting RNA polymerase
Gene transcription
Enhancers
DNA-bending protein
RNA polymerase
Bending of DNA
Transciption
mRNA
Alternative RNA splicing
Other forms of regulation
Breakdown of mRNA
Initiation of Translation
Regulatory proteins for translation
Protein processing
Noncoding RNAs
Functional RNAs
miRNAs
Degrade complementing mRNAs
Block translation of partially complementing mRNAs
siRNAs
RNA interference of translation
Formation of centromere
Methylation for gamete formation
Cell Signaling and Waves of gene expression direct animal development
Homeotic gene
Animal development controlled by series of RNAs and protein
Monitoring gene expression
Nucleic acid hybridization
DNA microarray
Signal transduction pathways
Signaling cell
Extracellular fluid
Receptor protein
Plasma membrane
Signal transduction pathway
Relay proteins
Cloning of Plants and Animals
Cloning plants
Totipotent cells
Regeneration
Fragmentation
Growth medium
Cloning Animals
Nuclear Transplantation
Reproductive cloning
Therapeutic cloning
Embryonic stem cells
Adult stem cells
Ex Viro gene therapy in humans
The Genetic basis of Cancer
Cancer results from mutations in genes that control cell division
Proto-oncogene
Oncogene
Tumor-suppressor genes
Tumor-suppressor gene
Normal growth-inhibiting protein
Cell division under control
Mutated tumor-suppressor gene
Defective, nonfunctioning protein
Cell division not under control
Faulty proteins can interfere with normal signal transduction pathways
Affects cell cycle control system
Carcinogens
CHAPTER 12:
DNA Technology and Genomics
Gene cloning and Editing
Recombinant plasmids
Biotechnology
DNA technology
Genetic engineering
GMOs
Recombinant DNA
Gene Cloning
Bacterial plasmids (vector) with recombinant DNA
Enzymes are used to "cut and paste" DNA
Restriction enzymes and restriction fragments
DNA ligase
Nucleic acid probe can label specific DNA segments
Reverse transcriptase can help make genes for cloning
Complimentary DNA (cDNA)
New technique allow a specific gene to be edited
CRISPR-Cas9 system
target a gene in a living cell for removal or editing
Genetically Modified Organisms
Recombinant cells and organisms can mass-produce gene products
Bioengineering in the farm
DNA technology has changed the pharmaceutical industry and medicine
Treating Diseases
Human insulin production
Preventing Diseases
Vaccines
Diagnosing Diseases
Genetically modified organisms are transforming agriculture
GMOs
Transgenic organism
Gene therapy may someday help treat a variety of diseases
Ex Viro gene therapy in human
Use of GMO raises questions and concerns
Human Safety
Labeling
Environmental Safety
DNA Profiling
DNA fingerprinting
DNA sequences
PCR method
primers
Gel electrophoresis
sorts DNA molecules by size
Repetitive DNA
Short Tandem repeats (STRs)
Genomics and Bioinformatics
Small segments of DNA can be sequenced directly
Third-generation sequencing machines
3 hours
Next-generation sequencing
Genomics
Human Genome Project (HGP)
Whole-genome shotgun sequencing
Field of Bioinformatics is expanding our understanding of genomes
Bioinformatics
Proteomics
Genomes hold clues to human evolutions
Databases
GenBank
Polymers:
Cells make most of their macromolecules by joining smaller molecules into chains called polymers
Building blocks of polymers are called
monomers
Cells link monomers together to form polymers by a
dehydration reaction
; a reaction removes a molecule of water as two molecules become bonded together
Both Dehydration and Hydrolysis require the help of
Enzymes
Monosaccharides
Simple Sugars
Glucose, Fructose, Galactose
Cells construct a
Disaccharide
from two monosaccharide monomers by a dehydration reaction
Amino acid
Amino group
Carboxyl group
H atom
R group
Amino acid monomers linked together by dehydration reaction, called
peptide
bond
Creates chain of amino acids called
polypeptide
Nucleotides
Sugar, Phosphate group, Nitrogenous base
Breaking of cells is
Hydrolysis
Polysaccharides
Starch and Gylcogen
Chitin
is the structural polysaccharide found in insect exoskeletons and fungal cell wall
Cellulose
is the structural component found in plant cell wall
Protein/polypeptide
polynucleotide
Prophase II
Prometaphase II
Metaphase II
Anaphase II
Telophase II
Cytokinesis II
Meiosis II