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307 terms

Biology Final

STUDY
PLAY
Who discovered the structure of DNA?
Watson & Crick
Gregor Mendel
showed how traits passed from one generation to another
Frederick Griffith
showed that traits could be passed by the transfer of molecules
Frederick Griffith's Experiment with mice
-injected bacteria into mice
-2 types of streptococcus: smooth and rough
-smooth bacteria killed mice
-rough bacteria mice lived
-boiled smooth bacteria mice lived
-mixture of boiled smooth and living rough mice died
transforming factor
the dead cells from the smooth boiled bacteria transferred a trait to still living in the mice and killed them. Rough bacteria transferred to smooth
Hershey and Chase experiment
-used bacteriophage
-to determine what is being passed from one generation to another
Bacteriophage experiment
-phage injected then makes more phage
-original phage stays outside and injects phage
-protein- injects radioactive sulfer
-DNA- injects radioactive phosphate
-DNA found in the phage
base pairs
A-T
G-C
Pyrimidines
T & C
Purines
A & G
Ribose
H group
deoxyribose
no oxygen
What link nucleotides to each other in DNA?
phosphodiester bonds
hydrogen bonds
temporary and weak-impermanet
lots of them make strong
histomes
DNA wrap around this
Denaturation
denature strands of DNA (break apart)
The entire human genome is how big?
3.2 billion base pairs long
DNA replication
conservative: no change, copy
semiconservative: original strand, separated then copied to turn into daughter cells
dispersive: DNA copied in sections
build new strands of DNA
rule of complementary
A&T G&C
what is the original stand of DNA
template
The DNA is a nucleus is organized by being wrapped around histome proteins in a beads on a string structure known as...
nucleosome
5 prime
phosphate
3 prime
hydroxyl group (OH)
Which enzyme cannot synthesize a nucleic acid chain from scratch (without a primer)?
DNA polymerase
DNA polymerase
-moves in the 5 to 3 direction
-it needs a primer
what unwinds a DNA helix
Helicase
stabilize single stranded DNA and prevent the two strands at the replication fork from reforming double stranded DNA
single stranded binding proteins
avoids twisting of the DNA ahead of replication fork by cutting the DNA, turning the DNA on one side of the break in the direction opposite of that of the twisting force, and rejoining the two strands again
topoisomerase
(relaxes DNA)
synthesizes RNA primer in the 5 to 3 direction to initiate a new DNA strand
Primase
main replication enzyme in E.coli. extends the RNA primer by adding DNA nucleotides to it.
DNA polymerase III
tethers DNA polymerase III to the DNA template, making replication more efficient
sliding DNA clamp
seals nick left between adjacent fragments after RNA primers replaced with DNA
DNA ligase
leading strand of DNA synthesis
synthesized continuously
lagging strand of DNA synthesis
synthesized discontinuously
evolution
change in the genetic composition of a population from generation to generation
elements
composed of individual atomos
molecule
2 or more atoms of 1 element
atomic number
is the number of protons in the nucleus
atomic mass
sum of the protons and neutrons
4 most common elements
CHON
Carbon, Hydrogen, Oxygen, Nitrogen
trace elements
those required by an organism in small quantities
4 most important chemical linkages in biological molecules
chemical bonds
electrical attraction cation(-) and anion(+)
ionic bonds
electron sharing (polar & nonpolar)
covalent bonds
partially charged atoms. individual ones are weak, bond with oxygen, nitrogen and sulfur, weak unless there is a lot
hydrogen bonds
weak forces that develop over very short distances between nonpolar molecules (equal sharing)
Van der Waala Force
4 properties of water
1. cohesive behavior (allow ppl to walk on water)
2. ability to moderate temp
3. expansion upon freezing
4. versatility as a solvent
cohesion
hydrogen bonds hold water molecules together
adhesion
an attraction between different substances
(allow water to travel up the plants cell wall)
surface tension
is a measure of how hard it is to break the surface of a liquid
moderation of temperature
-water absorbs heat from warmer air and releases stored heat to cooler air
-water can absorb or release a large amount of heat with only a slight change in it own temp.
evaporation cooling
transforming from a liquid to a gas
heat of vaporization
how hot we have to get to sweat
is the heat a liquid must absorb to be converted to gas
hydration layer
water forms around the charged molecules
solvent
water
solute
is whats being dissolved
buffers
substances that neutralize acids and bases
tetravalence
carbon can form 4 covalent bonds with a variety of atoms
-valence is the number of covalent bonds that an atom can form
hydrocarbons
are organic molecules consisting of only carbon and hydrogen
enantiomers
mirror images fo each other, typically only one of the 2 can enter a reaction
structural isomers
same chemical formula but atoms are arranged different ways
isomers
2 or more molecules with the same chemical formula, but different molecular structures
polymer
long chains of monomers
monomers
carbohydrates, proteins, lipids, nucleic acids
dehydration reactions
2 monomers are covalently bonded through the loss of water molecule
hydrolysis
covalent bonds between 2 monomers are broken by the addition of water molecules
(broken down by adding water molecules)
neutral lipids
fatty acid: a single hydrocarbon chain with a carboxyl group
oils: are liquid at biological temperatures
fats: are semisolid
saturated: have no double bonds between individual carbon atoms of the fatty acid chain
unsaturated
at least one double bond. where double bonds are formed, hydrogen is eliminated (kinked)
phospholipids
primary lipids fo cell membranes
-hydrophobic tails and hydrophilic heads
-when added to water, they self assemble a bilayer, with the hydrophobic tail pointing toward the interior
steroids
lipids characterized by a carbon consisting of 4 fused rings
proteins
enzymes
structural support
storage
transport
cellular communication
movement
defense against foreign substances
amino acids
organic molecules with carboxyl and amino groups
peptide bonds
link amino acids through dehydration synthsis
primary structure
the unique sequence of amino acids
-determined by inherited genetic information
secondary structure
coils, folds, random coils and loops
-alpha helix and beta pleated sheet
tertiary structure
overall three dimensional shape or conformation
-interaction among various side chains (R group)
Quaternary structure
several proteins, how they bond
-protein consists of multiple polypeptides
protein conformation
-also depends no the physical and chemical conditions of the proteins environment
-pH
-salt concentration
-temperature
denaturation
occurs when a protein loses its native structure
-a denatured protein is biologically inactive
nucleic acids
nucleic acids store and transmit hereditary information
nucleotides
the monomer of nucleic acids, consists of 3 parts linked together by covalent bonds
RNA based catalysts are called..
ribozymes
catalysts
speed up the rates of reactions by many millions of times without the need for an increase in temperature
potential energy
energy of position
kinetic energy
energy of motion
chemical energy
potential energy of the body
all living organisms exchange energy (fact)
living organisms are open systems
2 laws of thermo dynamics
1. energy can be transferred or transformed but it cannot be created or destroyed
2. every energy transfer or transformation increases the disorder (entropy) of the universe
exothermic reaction
spontaneous, release energy
endothermic reaction
absorbs energy, NOT spontaneou
spontaneous reactions
delta G is NEGATIVE
organisms reach equilibrium
-when delta G = zero
they Die
catabolic pathways
-delta G = negative
-spontaneous (cat falling)
-break it down
-exergonic
anabolic pathways
-positive delta G
-requires energy
-Never spontaneous
-build stuff up
-endergonic
exergonic reaction
-energy outward
-spontaneous
-negative
-releases energy
endergonic reaction
-energy inward
-absorbs free energy
-not spontaneous
-positive
-needs energy
hydrolysis of ATP
adds water-break apart
ATP
3 phosphate
ADP
2 phosphate
energy coupling
use an exergonic reaction to drive an endergonic one
phosphorylation
add phosphate to make ATP
enzymes do what?
speed up metabolic reactions without heat
ATP is..
recycled in the cell
catalyst
speed up reactions
active site
where the substrate binds to and a chemical reaction occurs
substrate
is a molecule upon which an enzyme acts
enzyme substrate complex
a complex composed of a substrate bound to the active site of an enzyme
cofactor
is a non protein chemical compound that is bound to a protein and is required for the proteins biological activity
coenzyme
a substrate that enhances the action of an enzyme
reactant
used during a chemical reaction to make the product
products
the final total
enzymes reduce activation energy
-creates the hump in the graph
enzymes stabilize the transition state
1. enzymes bring the reacting molecules together
2. enzymes expose the reactant molecules to altered charge environments that promote catalysts
3. enzymes change the shape of the substrate molecules (induced fit)
competitive inhibitor
binds to the active site
noncompetitive inhibitor
binds somewhere else; changes shape
feedback inhibition
end product switches off the metabolic pathway
allosteric regulation
enzymes function at one site is affected by the binding of a regulatory molecule at another site
-activators and inhibitors
evolution
change in the genetic composition of a population generation to generation
Natural Selection, Darwin's 4 observation
1. variations in traits within populations
2. traits are inherited from parents to offspring
3. all species are capable of producing excess offspring
4. many of these offspring do not survive
microevolution
-fine details
-short period of time
-small scale genetic changes in populations
macroevolution
-large time scale (dinosaurs)
-larger scale evolutionary changes in species and more exclusive groups
natural selection
survival
mutation
changes in DNA (spontaneous)
migration
stuff moving and change
random genetic drift
different genes
phylogeny
-everything started from 1 thing
-evolutionary history
genetic code
all organisms have the same
monophyletic
consists of the ancestor species and all its descendants
paraphyletic
grouping consists of an ancestral species and some, but not all, of the descendants
polyphyletic
grouping consists of various species that lack a common ancestor
2 sources of the SARS disease
1. civets
2. horse shoes flies
earliest evidence of life
3.4 billion years ago
methanogens
swamp gas
extreme halophiles
salt loving organisms
extreme thermophiles
hot places or cold areas
archaea
share traits with bacteria and eukaryotes
cell surface structures
1.cell wall
-maintains shape
-provides physical protection
-prevents the cell from bursting in a hypotonic environment
2. eukaryote cell walls are made of cellulose
3. most bacterial cell walls contain peptidoglycan
what is peptidoglycan
proteins on sugar backbone
gram positive
turns purple
big peptidoglycan layer
gram negative
turns pink
capsid on top layer
chemoautotrophs
oxygen, use CO2
chemoheterotrophs
oxygen, eat stuff
photoautotrophs
uses light for energy, use CO2
photoheterotrophs
uses light for energy, eat stuff
obligate aerobes
require oxygen for cellular respiratoin
obligate anaerobes
are poisoned by oxygen and use fermentation or anaerobic respiration
facultative anaerobes
can survive with or without oxygen
nitrogen fixation
take nitrogen gas from atmosphere make ammonium build amino acids and nucleic
how does bacteria reproduce
binary fission-cell divides, grows, DNA replication
R plasmids
carry genes for antibiotic resistance
metabolic cooperation
enhance ability to survive
biofilm
surface coating colonies
Cell Theory (3)
1. all organisms are composed or one or more cells
2. the cell is the basic structure and functional unit of all living organisms
3. cells arise only from the division of preexisting cells
light microscopy
views living cells and individual cells
electron microscopy
looks at outside of cells
high resolution
looks at killed cells, fixed, covered sheet
phospholipid bilayer
all cells have this
-heads are hydrophilic
-tails are hydrophobic
is a capsule gram negative or positive
negative
smooth endoplasmic reticulum
make lipids
doesn't have proteins, no ribosomes
rough endoplasmic reticulum
make and package proteins
cis
Endoplasmic reticulum fuse here
trans
leave here (bud off)
microbodies
break apart fats and oils to produce sugar
lysosomes
digest stuff
in animal cells
work well acidic areas
endocytosis
which brings molecules into the cell from exterior
mitochondria
require oxygen, cellular respiration
centrioles
animal cells not plants
microfilaments
small in cell membrane
work with myosins
central vacuole
stores H2O
shape of plant
what are plant cell walls made of
cellulose
anchoring junction
holds cells together
tight junction
prevent water from leeking
gap protein
channels between cells of the same tissue type
plasma membrane
selectively permeable
defines shape of cell
cell communication
regulation of substrates
transport proteins
enzymes
voltage membrane potential
outside-positve
inside-negative
membrane
composed mainly of phospholipids
glycolipids and glycoproteins
outer surface of cell membrane
key for cell recognition
fluid mosaic model for membranes
fluid-phospholipid molecules constantly move and exchange places. laterally

mosaic-membrane proteins float individually in the lipid bilayer.
unsaturated fatty acids
kinks
saturated fatty acids
saturated with hydrogen
passive transport
-spontaneous
-no energy required
-high to low concentration
diffusion
-passive transport
-spontaneous
-no input of energy
-high to low concentration
osmosis
diffusion through water
passive transport
isotonic solution
water balance equal
hypertonic solution
water outside cell
hypotonic solution
water comes inside cell
facilitated diffusion
spontaneous
passive transport
no input energy
channel proteins
aquaporins-move water fast
gated channels- switch between open, closed, or intermediate states
carrier proteins
bind a specific single solute and transport it across the lipid bilayer
Active transport
requires energy
NOT spontaneous
low to high concentration
substances move across their concentration gradient
primary active transport
move positively charged ions across membranes also releases ATP

H+ pumps (proton pump)

sodium potassium pump. (animal cells)
moves 3 Na+ out of cell, moves 2 K+ into cell
secondary active transport
uses ATP and ions
pushes ion out while shooting another ion in

Symport (together, same)
antiport (against each other)
oxidation
OIL
breakdown-remove electrons
reduction
RIG
gains electrons
electron carriers
NAD+--NADH
FAD--FADH2
ATP synthesis
how ATP is made in and pyruvate glycolysis and citric acid cycle
cellular respiration (3 steps)
1. Glycolysis- release ATP
2. Pyruvate oxidation and the Citric acid cycle- in the mitochondrial matrix
3. Oxidative phosphorylation-in inner mitochondrial membrane
phosphofructokinase
tells that there is too much ATP
Glycolysis
takes place in the cytosol
sugar splitting
gets lots of energy
gains more
takes place even without CO2
Pyruvate oxidation and Citric Acid cycle
ATP present
CO2 present
active transport
prokaryotes: cytosol
eukaryotes: mitochondrial matrix
oxidation phosphorylation
oxygen added
eukaryotes: inner mitochondrial membrane
prokaryotes: plasma membrane
the first tRNA that binds to the ribosome is?
binds to the small ribosomal subunit (p side)
operons
unit of gene expression
controlled element of a group of genes in a regulated manner
found only in prokaryotes
allows quick response to environment
Trp repressor
works in trans
floats around
Trp operator
works in cis
fixed in place
negative control
repressor controls
positive control
activator controls
positive/negative control
activator and pressor control
what is the start point of a gene
TATA box/promoter
what binds to the initiator tRNA before binding to the cap of the mRNA
small ribosomal subunit
when are genes in a cell expressed
all the time or some of the time
coactivators
cause DNA to form a loop
form bridge between activators at the enhancer and proteins at the promoter and promoter proximal region
posttranslational regulation
controls availability of functional proteins in 3 ways:
-chemical modification
-processing
-degradation
the immediate source of energy for translation comes from the break down of
GTP
plasmids
are used as shuttles to move genes between bacteria and other organisms
restriction endonucleases
cut nucleic acids and DNA function as immune system for DNA
transcription
production of DNA to RNA
reverse transcriptase
RNA to DNA
polymerase chain reaction (PCR)
produces an extremely large number of copies of a specific DNA sequence
3 steps of PCR
Denaturation
Annealing
Extension
microarray
see what genes are being expressed
G-protein coupled receptors
responsible for your sense of smell
target proteins
phosphorolated by kinase
kinase adds phosphate
tyrosine kinase receptor can lead to what
cancer
mitogen activated protein triggers what
cell division
how do your turn off proteins
dephosphorolation
ligand gated ion channel receptor
-ion control
-controls body movement
-ligan/signal
-allows ion flow
-signal binds to receptor opens gate, allows ions in
photosynthesis equation
6CO2 + 12H2o --- C6H12O6 + 6O2 + 6H2O
light dependent reactions
energy of sunlight is absorbed and converted into chemical energy (ATP and NADPH)
light independent reactions
(calvin cycle)
electrons in NADPH are used as a source of energy to convert CO2 to organic form
where does photosynthesis take place
chloroplast
electromagnetic spectrum
gamma rays
x rays
ultraviolet radiation
near infrared radiation
infrared radiation
microwaves
radio waves
what is the main pigment in photosynthesis
chlorophyll a
chlorophylls
absorb photons and transfer excited electrons to primary acceptor molecules
carotenoids
absorb light energy and pass it on by inductive resonance to chlorophylls
the calvin cycle
phase 1- carbon fixation

phase 2- reduction

phase 3-regeneration of the CO2 acceptor
gene
a segment of DNA

molecular: transcribed and translated

mendelian: determines hereditary trait
who did the pea plant experiment
Mendel
test cross
? x homozygous recessive

genotype and phenotype ratios=always the same
incomplete dominance
a for of inheritance in which one allele for a specific trait is not completely dominant over the other allele
co dominance
occurs when the contributors of both alleles are visible in the phenotype
complete dominance
the dominant allele completely masks the effect of the recessive allele in heterozygous condition
multiple alleles
there are 3 or more forms of a gene for a trait
pleiotropy
one gene affects many traits
polygenic inheritance
many genes affect 1 trait
linkage group
chromosomes
linked groups
genes on same DNA
Mendel's 1st law
principle of segregation
Mendel's 2nd law
principle of independent assortment
self cross between 2 heterozygous, the expected genotypic ratio
1:2:1
tumor supressor genes could be accurately compared to?
brakes on a car
mendels most important contribution was to show heredity is?
discrete factors, that we all call genes
sickle cell anemia was given as an example of
pleiotropy
AaBb x aaBb-progeny will have the genotype aabb
1/8
what is a karyotype, taken by who
photo of chromosomes, Cytogeneticist
trisomy 21
down syndrome
PKU
autosomal recessive
high levels of phenyalanine
cystic fibrosis
plietrophy
autosomal recessive
leads to phenomena
sickle cell anemia
african americans are carriers
heterozygote advantage
advantage against malaria
duschine muscular dystrophy
x linked
progressive loss of muscle
rare
Huntington disease
dominant
later in life
genome
3 x 10^9 base pairs
1953
watson and crick DNA structure
1973
recombinant DNA "born"
1990
HGP formalized
2001
human draft sequence announced
1. HGP-francis collins
2. Celera-craig venter
e. coli
4.6 Mb
4,200 genes
humans
2,900 Mb
20,000 genes
method of prenatal diagnosis takes the fluid that bathes the fetus
Amniocentesis
_______ was the head of the Celera project to sequence the human genome
craig venter
True about Dolly
all nuclear DNA came from 1 parent
the immediate source of energy for translation comes from the break down of
GTP
negative control
the Trp operon is an example of
small ribosomal subunit binds to the initiate tRNA before binding to the cap of the mRNA
...
what sequence which when mutated can stop transcription of a gene
TATAAAA
RNA polymerase does NOT need_____ to transcribe a gene
start codon

-only on mRNA to start synthesis of protein
what makes PCR so specific. what allows you to specifically amplify single genes
the primers are specific for the gene genes
what do you use to make cDNA from mRNA?
reverse transcriptase
immune system
defends you against invaders
recognize bad things and kill it
innate immunity
always present in your body
very fast
not specific
responds to invaders
adaptive immunity
slower
attacks
specific
only vertebrates
2nd line of defense
adaptive
antimicrobal attack
mucus, tears
attack peptides
interferon
makes you feel bad when you get infection, your response
warn immune system
cytokines
tell immune cells that something is wrong
local inflammatory response: complementary system
reacts to antibodies, destroy bacteria cell wall, triggers inflammation by lysing
Toll Like Receptors
recognize pathogens
binds and activates
activate inflammation
dendritic cells
swallow pathogens, bridge between innate and adaptive
natural killer cells
look for cells that don't look normal, not specific
antibodies
not apart of innate immune system
B & T cells recognize
antigen specific region in epitope by receptors
B cells mature in...
bone marrow
t cells mature in..
thymis
MHC
present antigens to T cells
distinguish between self and non self
B cell receptors BCR
bind to specific intact antigens, stuck on surface of T cells
MHC, 2 types
MHCI: on every cell in cody CD8
MHCII: CD4 on immune cells
Helper T cells
CD4 binds the MCHII molecule, recognize foreign molecules
Antigen presenting cells
look for pathogens, swallow them and break them up
cytokines
active T & B cells
cytotoxic T cells
kill infected cells
apoptosis
form of cell suicide, break cells into vesicles
involved in cell mediated immunity and destroy virally infected cells are
cytotoxic T cells
B cells
activated by cytokines, secrete antibodies
memory cells
recognize the same antigen
plasma cells
float in blood
secretory cells, secrete antibodies that fight infection
one of the ways a bacterium will be destroyed after entering the body through a small cut in the skin is by?
being bound by a group
active immunity
develop a memory against that infection
passive immunity
inject antibodies from infection, short term protection
cell involved in innate immunity and a person lacking these cells may nave a high than normal chance of developing malignant tumors(cancer)
natural killer cells
(recognize cancer cells)