BIO Final Flashcards
what are the parts of the scientific method?
observe question/problem hypothesis experiment conclusion
Controls and variables in experiment
Variable
- a factor that influences a process
- the variable may be altered in an experiment to see its effect on the outcome Control
- the variable is not altered
- allows for comparison between the altered variable test and the unaltered variable test
structure of membranes
- phospholipidsarranged in a bilayer
- globular proteins inserted in the lipid bilayer
- fluid mosaic model- mosaic of proteins floats in or on the fluid lipid bilayer like boats on a pond. (tight junctions restrict this)
4 components of cellular membranes
- phospholipid bilayer
- transmembrane proteins
- interior protein network
- cell surface markers
phospholipid bilayer
- double layer of phospholipids that forms in water, with hydrophilic parts facing outwards and hydrophobic tails facing inwards
- glycerol- 3 carbon polyalcohol
- 2 fatty acids (inwards)
- phosphate group (outwards)
transmembrane proteins
- transporters
- enzymes
- cell-surface receptors
- cell-surface identity markers
- cell-to-cell adhesion proteins
- attachments to the cytoskeleton
Membrane pores
extensive nonpolar regions within a transmembrane protein, can create a pore through the membrane (beta barrel) with polar interior
Ion channels
hydrophilic when open, allows passage of ions. Open or close from a chemical or electrical stimulus
carrier proteins
helps transport both ions and other solutes, such as some sugars and amino acids. Requires a concentration gradient.
covalent bonds
- when atoms share 2 or more valence electrons
- results in no net charge, satisfies octet rule, no unpaired electrons
- strength of bond depends on the # of shared electrons
- can be more than one atom sharing
ionic bonds
- donation of an electron
* formed by the attraction of oppositely charged ions
hydrogen bonds
- individual bonds are weak
- caused by cohesion or adhesion
- can be formed b/w 2 polar covalent water molecules or a water molecule and a polar organic molecule
cohesion
allows molecule to be attracted to another of the same type
adhesion
allows molecule to be attracted to another of a different type
atomic number
number of protons
atomic mass
sum of protons and neutrons. Protons = electrons
Isotopes
Atoms of one element that vary only in the number of neutrons in the nucleus
pH: Acid
- 1-7
- any hydrophobic (non polar) substance that increases hydrogen
- the stronger the acid the more hydrogen and the lower the pH
pH: Base
- 7-14
- hydrophillic (polar)
- lowers the hydrogen
hydrolysis
breakdown of large molec. with the addition of water
dehydration synthesis
formation of large molecules by removal of water
structural components of amino acids
- primary
- secondary
- tertiary
- quaternary
primary structure
sequence of amino acids fastened together by peptide bonds
secondary structure
interaction of groups in the peptide backbone: alfa helix and beta sheet
tertiary structure
final folded shape of a globular protein. stabilized by number of forces. final level of structure for proteins consisting of only a single polypeptide chain. 3D shape
quaternary structure
arrangement of individual chains in a protein with 2 or more polypeptide chains interacting with eachother
structural components on nucleic acids
- nucleotides
- 5 carbon sugar+phosphate+nitrogenous base
- nucleotides connected by phosphodiester bonds
purines
adenine and guanine
pyrimidines
thymine and cytosine, and uracil
Basic building blocks of cells (4)
- Proteins (polymers of amino acids)
- Nucleic Acids (polymers of nucleotides)
- Polysaccharides (polymers of sugars)
- Lipids (polymers of hydrocarbons)
types of organelles: eukaryotic
nucleus, ribosomes, endomembrane system, ER, Golgi apparatus, lysosomes, microbodies, vacuoles, mitochondria, chloroplasts, cytoskeleton, centrosomes, ECM
Nucleus
- holds genetic info
* nucelolus- where rRNA synthesis takes place
ribosomes
- protein synthesis machinery
- links amino acids together through dehydration synthesis, forming peptide bonds and finally proteins
- rRNA protein complex
- may be free in cytoplasm or associated with internal membranes
Endomembrane system
divides cell into compartments
ER
- Rough- attachment of many ribosomes. Synthesis of proteins to be secreted, sent to lysosome or membrane
- smooth- few ribosomes. Synthesis, store calcium, and detox
Golgi apparatus
- flattened stacks of interconnected membranes
- packaging and distribution of molec. which vesicles then transport
- cis-face nucleus
- trans- faces plasma membrane
- produces glycoprotiens
lysosomes
- membrane bound digestive vesicles
- arise from GA
- enzymes catalyze breakdown of molec.
- phagocytosis: destroy foreign matter
microbodies
peroxisomes- vesicles that contain enzymes involved in oxidation of fatty acids
vacuoles
- in plants
- central- storage (starch)
- contractile- protists, pumps out water
- storage
mitochondria
- powerhouse of cell
- has own membrane
- has own DNA
- oxidative metabolism
cholorplasts
- in plants
- contains chlorophyll
- thylakoid membrane- sacs within the membrane
- grana- stacks of thylakoid membrane
cytoskeleton
- network of protein fibers found in eukaryotes. supports shape and keeps organelles fixed.
- microfilaments- (actin) contraction
- microtubules- largest, facilitate movement in cell
- intermediate filaments- stability
centrosomes
region surrounding centrioles
ECM
protein and other materials outside the plasma membrane that cell secretes out. forms protective layer.
prokayotic DNA
circular, only one origin of replication
eukaryotic DNA
linear, many origins of replication
prokaryotic cell
simple structure, nucleoid, small ribosomes, fission, small, simple flagella
eukaryotic cells
complex, nucleus, chromatin, large ribosomes, membrane bound organelles, large, complex flagella
active transport
- transport against gradient
- ATP required
- low to high
- highly selective carrier proteins
- sodium potassium pump
passive transport
- with the gradient
- high to low
- diffusion
- no ATP required
osmosis
- diffusion of water across a membrane
- high to low
- no ATP required
- drawn to high concentrations of solute
hypertonic solution
high solute concentration. Water moves toward this
hypotonic solution
has lower solute concentration. water moves away
isotonic solution
same osmotic concentration or equal
optimal conditions for enzymes
- high temp
- higher concentration
- high pH level (more basic)
4 types of cell signaling
- direct contact
- paracrine signaling
- endocrine signaling
- synaptic signaling
direct contact
molecules on the surface of one cell are recognized by receptors on the adjacent cell. cell development
paracrine signaling
- signal released from a cell has an effect on neighboring cells
- immune response
- secrete in localized area
endocrine signaling
- hormones released from a cell affect other cells throughout the body
- slow and small but long lasting
synaptic signaling
- nerve cells release the signal ( neurotransmitter ) which binds to receptors on nearby cells
- rapid and water soluble
- covers distances but cells never touch
- breaks down very quickly
- neurons
aerobic respiration
- final electron acceptor is oxygen
* C6H12O6+6O2=6CO2 + 6H2O
metabolism of fats
- fatty acids to glycerol
- glycerol can be modified into pyruvate and put into glycolysis
- beta oxidation: fatty acids converted into acetyl groups then put into Kreb cycle
oxidation of glucose
- glycolysis
- pyruvate oxidation
- Krebs Cycle
- ETC and chemiosmosis
glycolysis
- Converts 1 glucose (6 carbons) to 2 pyruvate (3 carbons)
- 10-step biochemical pathway
- Occurs in the cytoplasm
- Net production of 2 ATP molecules by substrate-level phosphorylation
- 2 NADH produced by the reduction of NAD +
pyruvate oxidation
• In the presence of oxygen, pyruvate is oxidized
– Occurs in the mitochondria in eukaryotes
• multienzyme complex called pyruvate dehydrogenase catalyzes the reaction
– Occurs at the plasma membrane in prokaryotes
krebs cycle
- Oxidizes the acetyl group from pyruvate
- Occurs in the matrix of the mitochondria
- Biochemical pathway of 9 steps in three segments
- Acetyl-CoA + oxaloacetate → citrate
- Citrate rearrangement and decarboxylation
- Regeneration of oxaloacetate
electron transport chain
- ETC is a series of membrane-bound electron carriers
- Embedded in the inner mitochondrial membrane
- Electrons from NADH and FADH 2 are transferred to complexes of the ETC
- Each complex
– A proton pump creating proton gradient
– Transfers electrons to next carrier
chemiosmosis
- Accumulation of protons in the intermembrane space drives protons into the matrix via diffusion
- Membrane relatively impermeable to ions
- Most protons can only reenter matrix through ATP synthase
– Uses energy of gradient to make ATP from ADP + P i
fermentation
- use of organic molec. as final electron acceptor
- Reduces organic molecules in order to regenerate NAD+
- ethanol and lactic acid
anaerobic respiration
- Use of inorganic molecules (other than O 2 ) as final electron acceptor
- methanogens or sulfur bacteria
carbon fixation
- the incorporation of CO2 into organic molecules
- uses rubisco
- calvin cycle
calvin cycle
- occurs in stroma
- glucose is not a direct product
- carbon fixation: Rubisco + CO2= 2 PGA
- reduction: PGA is reduced to G3P
- regeneration of Rubisco: G3P is used
photosystem 1
reaction center with weak absoption
photosystem 2
absorbs most light energy, start of photosynthesis
signal transduction
the event in the cell when ligand binds to a receptor
types of receptors
channel linked receptors – ion channel that opens in response to a ligand
- enzymatic receptors – receptor is an enzyme that is activated by the ligand
- G protein-coupled receptor – a G-protein (bound to GTP) assists in transmitting the signal
second messengers
a substance whose release within a cell is promoted by a hormone and that brings about a response by the cell. examples are cyclic AMP and calcium
DNA replication
• Requires 3 things
– Something to copy
• Parental DNA molecule
– Something to do the copying
• Enzymes
– Building blocks to make copy
• Nucleotide triphosphates
Steps of DNA replication (initiation, elongation, termination)
- remove DNA-associated proteins
- unwinde separate original (template) strands (DNA helicase)
- synthesize RNA primers (primase)
- extends primers with DNA polymerase III
- degrade RNA primers and fill gap with DNA polymerase I
- rewind new hybrid strands
transcription
•create 3 different RNA polymerases
– RNA polymerase I transcribes rRNA
– RNA polymerase II transcribes mRNA and some snRNA
– RNA polymerase III transcribes tRNA and some other small RNAs
translation: initiation
– Initiating amino acid is methionine
– More complicated initiation complex
– Lack of an RBS – small subunit binds to 5 ′ cap of mRNA
translation: elongation
Definition
– 2 nd charged tRNA can bind to empty A site
– Requires elongation factor called EF- Tu to bind to tRNA and GTP
– Peptide bond can then form
– Addition of successive amino acids occurs as a cycle
translation: termination
– Elongation continues until the ribosome encounters a stop codon
– Stop codons are recognized by release factors which release the polypeptide from the ribosome
chromosome structure
kinetichore: center of strand
centromere: binds sister chromatids
synaptonemal complex: binds homologous chromosomes
Template Strand
The nucleotide strand used for transcription. Read by RNA polymerase in 3-5 direction.
coding strand
complement of transcribed mRNA, runs 5 to 3 direction
structure of mature mRNA
Three big parts of eukaryotic mRNA: on the 5 prime end there will be a methylated g cap- a modied g nucleotide. 3 prime end has a poly A tail. Sequences in the DNA called introns and exons (in mature mRNA introns are cut out).
binary fission
- cell division of bacteria
- reproduction for bacteria
- a ring of DNA attached to the cell membrane of the bacteria duplicates
- cytokinesis occurs which splits the cell into two and creates two daughter cells each containing a ring of DNA
- no nucleus is divided (not mitosis)
cell cycle
interphase, mitosis, and cytokenesis
interphase
G1 (growth), Synthesis (DNA replication), G2 (chromosomes condense)
mitosis
Prophase, Metaphase, Anaphase, Telophase
cytokinesis
cleavage furrow or cell plate
Crossing-over
Exchange of genetic material between homologous chromosomes
Test Cross
- Determine genotype of individual showing dominant traits (homo or hetero)
- Individual crossed w/ homozygous recessive parent
- resulting offspring phenotype distribution tell what unknown parent is
Sex Linkage
A genetic trait whose allele has its locus on the X chromosome.
Exceptions to the chromosomal theory of inheritance
A. Mitochondrialgenes are inherited from the female parent. Both males and females are equallyaffected but males cannot pass it on.
B. Chloroplast genes mayalso be passed on uniparentally (usually maternal)
DNA structure
- 2 strands of nucletoides in double helix
- antiparallel
- bases inside, phosphates out
- opposing bases pair by H-bond
prokaryotic DNA replication
starts from a single point and proceeds in 2 directions until the entire chromosome is copied.
DNA repair
mismatch repair
base excision repair
nucleotide excision repair
direct repair
double strand break repair
recombination
Describe base excision repair
- a base is improperly paired (a deaminiated cytosine)
- Glycosylase removes the base
- AP endonuclease cleaves around along with phosphodiesterase
- DNA polymerase fills the gap
- ligase Re-connects backbone
nucleotide excision repair
- recognize damage site, excise small segment, fill in gap, ligase
- repair of “bulky” damage (e.g. dimers) that creates distortions in DNA
Mismatch Repair
Removes mismatched based using methylation patterns to determine parental DNA strand.
proofreading
Prokaryotic Transcription
- Operon
- RNA pol finds promotor
- Transcription ends at terminator
- transcription and translation happen simultaneously in prokaryotes
- mature mRNA
mRNA Splicing
- Non-coding segments (introns) are removed
- coding segments (exons) are spliced together
- splicesomes
Types of gene expression control
Transcriptional (slowest, most efficient) - onset of transcription
Translational - life span of mRNA, translation rate
Post-translational (fastest, least efficient) - Protein activation or inhibition
Control can be positive or negative
transcription factors
Definition
• General transcription factors
– Necessary for the assembly of a transcription apparatus and recruitment of RNA polymerase II to a promoter
– TFIID recognizes TATA box sequences
• Specific transcription factors
– Increase the level of transcription in certain cell types or in response to signals
promoter
• form the binding sites for general transcription factors
enhancers
• the binding site of the specific transcription factors
– DNA bends to form loop to position enhancer closer to promoter
Posttranscriptional Regulation
- Control of gene expression usually involves the control of transcription initiation
- Gene expression can be controlled after transcription with
– Small RNAs
• miRNA and siRNA
– Alternative splicing
– RNA editing
– mRNA degradation
miRNA/siRNA
Micro RNA/small interfering RNA , short ~22 nt RNA sequences that bind to 3’ UTR target mRNAs and result in silencing
(RISC)
RNA editing
Definition
• Creates mature mRNA that are not truly encoded by the genome
• Involves chemical modification of a base to change its base-pairing properties
protein degradation
- Proteins are produced and degraded continually in the cell
- Lysosomes house proteases for nonspecific protein digestion
- Proteins marked specifically for destruction with ubiquitin
- Degradation of proteins marked with ubiquitin occurs at the proteasome
DNA manipulation
• Enzymes that cleave DNA at specific sites
– Used by bacteria against viruses
• Restriction enzymes significant
– Allow a form of physical mapping that was previously impossible
– Allow the creation of recombinant DNA molecules (from two different sources)
3 types of restriction enzymes
- Type I and III cleave with less precision and are not used in manipulating DNA
- Type II
– Recognize specific DNA sequences
– Cleave at specific site within sequence
– Can lead to “sticky ends” that can be joined
• Blunt ends can also be joined
molecular cloning
- Clone – genetically identical copy
- Molecular cloning – isolation of a specific DNA sequence (usually protein-encoding)
– Sometimes called gene cloning
• The most flexible and common host for cloning is E. coli
– Vector – carries DNA in host and can replicate in the host
– Each host – vector system has particular uses
plasmids
types of vector
– Small, circular chromosomes
– Used for cloning small pieces of DNA
– 3 components
- Origin of replication – allows independent replication
- Selectable marker – allows presence of plasmid to be easily identified
- Multiple cloning site (MCS)
• Polymerase chain reaction (PCR)
- developed by Mullis
- replicates DNA strand without cell
- – Each PCR cycle involves three steps:
- Denaturation (high temperature)
- Annealing of primers (low temperature)
- DNA synthesis (intermediate temperature)
– Taq polymerase
DNA analysis
• Restriction maps
– Molecular biologists need maps to analyze and compare cloned DNAs
southern blotting
– Sample DNA is digested by restriction enzymes and separated by gel electrophoresis
– Double-stranded DNA denatured into single-strands
– Gel “blotted” with filter paper to transfer DNA
– Filter is incubated with a labeled probe consisting of purified, single-stranded DNA corresponding to a specific gene
northern blotting
mRNA
western blotting
with proteins
RFLP
you can cut a piece of DNA from different sources, with same enzyme, and you get different ladder patterns. not the exact same DNA cuts in the same places. detects repetitions or point mutations.
