Biology Flashcards
What is the cell theory (5 points)
- all living things are composed of cells
- the cell is the basic functional unit of life
- the chemical reactions of life take place inside the cell
- cells arise from pre existing cells only
- cells carry genetic info as DNA.
what are the six kingdoms? what is monera
protists, fungi, plantae, animalia, bacteria, archaea
monera represented bacteria and archaea as a kingdom but was recently changed (it was THE prokaryotic kingdom)
carrier proteins
charged ions and larger charged molecules pass the membrane by carrier proteins
Histones
complexes with DNA to form chromosomes, dna wraps around histone proteins to make it more compact. Histones are involved in transcripition (tighten and loosen)
nucleolus
a dense structure in the nucleus where ribosomal RNA, (rRNA) synthesis occurs! Need this for protein synthesis at the ribosome
Ribosome
site of protein production. synthesized by the nucleolus. Free ribosomes are in the cytoplasm, but bound ribosomes line the outer membrane of the endoplasmic reticulum.
endoplasmic Reticulum smooth vs rough
Smooth: doesnt have ribosomes, not involved in protein synthesis but it helps metabolize and produce lipids.
Rough: plays important role in making proteins
Golgi Apparatus
receives vesicles and contents from smooth ER and then modifies them (processes such as glycosylation) repackages them into vesicles and distributes them to the cell surface for exocytosis.
mitochondria
Site of aerobic respiration in the cell. makes ATP. outer and inner phospholipid bilayer
cytoplasm, how do things move in it and what are its contents
cytosol ( the fluid part) and all the organelles. Transport within cytoplasm occurs by cyclosis- streaming movement within the cell
Vacuole vs vesicle
a vacuole is larger than a vesicle, more likely found in plant than animal cells. both involved in transport and storage of materials
centrioles
made of microtubules, involved in spindle organization during cell division. Not bound by any membrane. animal cells generally have a pair of centrioles oriented at right angles that lie in a region called the centrosome. The centrosome organizes microtubules and helps regulate the progression of the cell cycle. PLants do not have them!!
Lysosomes
what important cell process are they involved in?
contain hydrolytic enzymes for inracellular digestion. Self destructing occurs by rupturing lyossome and releasing the hydrolytic enzymes in a process called AUTOLYSIS
microtubules
hollow rods made of polymerized TUBULIN protein. radiates throughout the cell and provides it with support. Provides a framework for organelle movement within the cell. Centrioles (which direct the separation of chromosomes during cell division) are made of microtubules.
Cilia and flagella are arrangements of them (9 pairs surround 2 singlets) which extend from certain cells and are involved in cell motility and cytoplasmic movement.
Microfilaments
solid rods of ACTIN which are important in cell movement and support. muscle contraction (actin and myosin) they move materials across the plasma membrane. cleavage furrow, amoeba movement
Plasmolysis
when medium is hypertonic to the cell (outside is more solute, water will leave and the cell shrivels)
Three type of carrier proteins in active transport
antiporters; moves two or more ions or molecules in opposite direction across membrane
symporters; moves ‘’ in same direction across a membrane
(anti and symp are secondary active)
pump- requires atp (primary active)
Pinocytosis
Ingestion of fluids or small particles through endocytosis
phagocytosis
type of endocytosis where large particles are engulfed. may be receptor mediated
3 types of Intracellular circulation
-Brownian movement: kinetic energy spread ssmall suspended particles throughout the cytoplasm o the cell
Cytosis or streaming: the circular motion of cytoplasm around the cell transports molecules
Endoplasmic Reticulum: Network/direct passageway for plasma membrane to nuclear membrane
intermediate filaments
support for cell shape, keratin
two types of extracellular circulation
- diffusion- if cells are close enough to outside environment
- circulatory system
Cell Div : Interphase
a period of growth and chromosome replication. MOST of time is spent here. during this time, cell does normal stuff and each chromosome is replicated so that during division a complete copy of genome can be distributed to both daughter cells. throughout interphase the chromosomes are uncoiled as “chromatin” (not visible)
3 stages:
1. G1: active ggrowth. grows, makes proteins, length of g1 is VARIABLE
2. S: period of DNA synthesis
3. G2: prepares to divide. grows and makes proteins. next is M phase
Sister Chromatids
After replication, the chromosomes consist of two identical sister chromatids, held together at a central region called the centromere.
karyokinesis
nuclear division. it is followed by cell division, cytokinesis.
mitosis Prophase
During prophase, (first M stage) the chromosomes condense and the centriole pairs separate and move towards the opposite poles of the cell (in animals). the spindle apparatus forms between themand the nuclear membrane dissolves, allowing the spindle fibers to interact with the chromosomes
mitosis Metaphase
second (after prophase), the centriole pairs are now at opposite poles of the cell. the fibers of the spindle apparatus attach to each chromatid at its corresponding Kinetochore. the spindle fibers align the chromosomes at the center of the cell forming the metaphase plate.
kinetochore
the location at the centromere where the spindle tubule attaches
mitosis Anaphase
the centromeres split so each chromatid has its own distinct centromere. thus allowing sister chromatids to separate. the sisters are pulled toward opposite sides of cell by shortening spindle fibers. (microtubules)
mitosis Telophase
The spindle apparatus disappears. a nuclear membrane forms around each set of new chromosomes. chromosomes uncoil, resuming interphase form. towards the end of telophase, cytokinesis occurs
cytokinesis
near end of telophase, the cytoplasm divides into two daughter cells, each with a complete nucleus and its own organelles. in animal cells, a cleavage furrow (microfilament) forms and the cell membrane indents along the equator of the cell, pinching through the cell and separating the nuclei.
interphase of meiosis
the parents cells chromosomes are replicated , resulting in 2N sister chromatids
what is the first meiotic division
produces two intermediate daughter cells with N chromosomes and sister chromatids.
Prophase I
Chromatin condenses into chromosomes, the spindle apparatus forms, and the nucleoli and nuclear membrane disappear. homologous chromosomes (which code for the same traits) come together and intertwine in a process called SYNAPSIS. since this is two sister chromatid pairs, its four chromatids – called a TETRAD. sometimes chromatids of homologous chromatids break and have cross over. the points of contact where crossing over can occur are chiasmata. (sister chromatids not identical anymore..)
when does a tetrad form? what is synapsis?
tetrad forms in prophase I when two homologus chromosome pairs of sister chromatids come together in the process called synapsis
Metaphase I
homologous pairs (tetrads) align at the equatorial plane and each pair attaches to a separate spindle fiber at the kinetochore.
Anaphase I
The homologous pairs are pulled to opposite poles of the cell. this is called DISJUNCTION. the maternal/paternal chromosomes separate and either chromosome can end up in either daughter cel. the distribution of homologous chromosomes to the two intermediate daughter cells is random with respect to parental origin. Each daughter cell has a unique pool of genes from a random mix.
nondisjunction
occurs when cells don’t separate correctly in meiosis anaphase I -
Telophase I
nuclear membrane forms around each new nucleus. Each chromosome still consists of sister chromatids joined at the centromere.
-spindle apparatus dissapears
second meiotic division
essentially the same as MITOSIS except it is not preceded by chromosomal replication (meiosis I was tho) . in prophase II the nuclear membrane dissolves and spindle apparatus forms. metaphase II the chromosomes align, anaphase II separate and move to opposite poles. in telophase II get new nuclear membrane. the new cells have haploid number of chromosomes. in women only one of the daughter cells becomes a functional gamete, the other two or three are destroyed by the body.
Central Dogma
describes the two step process- transcription and translation. where information in genes flows from DNA-> RNA -> Protein
DNA structural units (pyrimidine and Purine)
DNA is made of nucleotides. A nucleotide includes a deoxyribose (5 carbon sugar), a nitrogenous base, and a phosphate group attached to the sugar.
Purines: Adenine and Guanine. larger than pyrimidines because two ring nitrogenous base.
Pyrimidine: Thymine, Cytosine, uracil. (one ring)
— A:T (AU in RNA) (2 H bonds)
—- G:C (3 h bonds)
watson crick (with rosalind franklins help) dna model; antiparallel 5’ next to 3’ end
topoisomerase
uncoils the dna strands as they get separated by dna helicase (for DNA rep)
DNA helicase
breaks the H bonds between nitrogenous bases in order for DNA replication to occur. makes replication fork
semiconservative dna rep
result is one parent strand one new stand
DNA polymerase
reads parent dna strand and makes a complementary antiparallel daughter one. Always reads 3->5!! writes 5 to 3.
why is the genetic code redundant?
there are 64 possible combos of the 4 nucleotides into a codon (of three), but it only codes for 20 amino acids so most amino acids have more than one combo coding for them
tRNA
whats the anticodon?
what is the aminoacyl trna complex?
a small RNA molecule in cytoplasm, it assists the translation of mRNA into a sequence of amino acids. by bringing the amino acids coded for in the mRNA sequence to the ribosomes during protein synthesis!! It recognizes both the mRNA codon and its corresponding amino acid. it has a 3d structure and one end has a three nucleotide sequence- the ANTICODON which is complementary to one of the mRNA codons. the other end is the site of attachment of the corresponding amino acid. each amino acid has its own aminoacyl-tRNA synthetase which has an active site that bids to the amino acid and its tRNA, thereby atttaching them to form the aminoacyl trna complex.
(theres at least one type of trna for each amino acid, about 40 total)
Transcription
mRNA is synthesized in the nucleus through transcription. RNA much shorter than dna, just a segment of dna. rna polymerase binds to the dna at the PROMOTER REGION- a short dna sequence found upstream from the site where transcription of a specific RNA is going to take place. (TATA box)
-transcription factors then help RNA polymerase bind to the DNA molecule and initiate transcription. (like with dna replication, it surrounds dna after being opened by dna helicase and topoisomerase) the rna then recruits complementary RNA nucleotides based on DNA sequence. As with DNA polymerase, RNA polymerase reads DNA in the 3 to 5 direction making it 5 to 3.
Post Transcriptional Processing
after transcription is done. mRNA is processed. un processed mrna is called hetero nuclear mRNA (pre mrna).
- a pre mrna has extra sequences called INTRONS. EXONS are the ones that are needed. so the introns are spliced out by the spliceosome, leaving just exons.
- also a guanine cap and a series of adenines (the polyA tail) are aded to provide protection from enzyme degradaion once RNA leaves the nucleus.
Translation
describe the 3 stages
occurs in the cytoplasm.
- Initiation begins when ribosome binds the mRNA near its 5’ end. The ribosome scans the mRNA until it binds to a start codon (AUG). the initiatior aminoacyl tRNA complex, methionine tRNA (UAC) base pairs with the start codon!
- Elongation - the hydrogen bonds form between the mRNA codon in the A site of the ribosome and its complementary anticodon on the incoming aminoacyl trna complex. A peptide bond is formed between the amino acid attached to the tRNA in the A site and the amino acid attached to the tRNA in the P site of the ribosome. after the bond forms the P site trna is uncharged and no longer has the amino acid whereas the A site contains peptidyl tRNA. next in TRANSLOCATION, the ribosome moves over three nucleotides and as this happens the tRNA from the P site is expelled ( E site then leaves) , and the peptidyl tRNA from the A site moves into the P site. A site is empty for new stuff
- TERMINATION: when one of the three special mRNA termination codons/ stop codons arrives in the A site the synthesis stops. it codes the ribosome to stop translation ( they dont code for amino acids)
what is a polyribosome
the term for when numerous ribosomes simultaneously translate a single mRNA molecule
Ribosome
made of rRNA and proteins. the two subunits (one small one large) bind only during protein synthesis. They have three sites for trna, A p and e. In the A site (aminoacyl trna) the codon binds to the next incoming trna, which is then transferred to the p site (peptidyl trna) where the trna contributes its amino acid to the growing peptide chain. finally the E (exit site)
catabolic and anabolic reactions
catabolism: catabolic reactions break down large chemicals and release energy
anabolic reactions: build up large chemicals and require energy (aka synthesis)
What is respiration
the consumption of oxygen by the body. cells use oxygen to convert glucose into ATP, a ready source of energy for cellular activities
-conversion of chemical energy in molecular bonds into the usable energy needed to drive the processes of living cells. oxidation of feul molecules ultimately.
external respiration; entrance of air into lungs and gas exchange between alveoli and blood. internal respiration- exchange of gas between the blood and the cells and the intracell process of respiration
what is irritability
the ability to respond to a stimulus as part of regulation of physiological activities
what is dehydrogenation
during respiration, high energy hydrogen atoms are removed from organic molecules (the ch bond is high energy). it is the OXIDATION part of feuls (preferable carbs or fats)
this requires energy input
electron transport chain
reductions steps of respiration where oxygen is the final acceptor and gets reduced. energy released by this reduction stage (it makes an H gradient) is used to form a high energy phosphate bond making ATP
Aerobic vs Anaerobic glygolysis
aerobic glycolysis :
- decarboxylation of pyruvate
- Krebs cycle (CAC)
- Electron Transport Chain
Anaerobic: FERMENTATION
Glyclolysis
the first stage of glucose catabolism (breakdown) is glycolysis. its a series of reactions that leads to the oxidative breakdown of glucose into two molecules of pyruvate, the production of ATP (2 atp used, 4 made- net of 2 per glucose), and the reduction of NAD+ to NADH (2 NADH are made per glucose) . this all occurs in the cytoplasm, mediated by specific enzymes.
-glucose reacts with hexokinase to form glucose 6 phosphate. this reacts with phosphoglucose isomerase and makes fructose 6 phosphate. this then interacts with phosphofructokinase t make fructose 1,6 biphosphate. aldolase makes it into glyceraldehyde 3 phosphate. but its first split into two molecules of three carbons - glyceraldehyde 3 phosphate and dihydroxyacetone phosphate. the latter is isomerized into glyceraldehyde 3 phosphate (PGAL) so it can be used, so we have two PGAL which enter the energy releasing steps of glycolysis eventually making pyruvate.
substrate level phosphorylation
ATP synthesis is directly coupled with the degradation of glucose (no intermediate molecule like NAD+)
Fermentation
In the absence of O2, NAD+ must be regenerated in order for glycolysis to continue making ATP. this can be accomplished by reducing pyruvate into lactic acid or ethanol. Fermentation makes just two ATP per glucose.
where does Alcohol Fermentation occur
occurs in yeast and some bacteria. the pyruvate produced in glycolysis is converted into ethanol, regenerating NAD+
where does Lactic Acid Fermentation occur
occurs in certain fungi, bacteria, and human muscle cells during strenuous activity. When the oxygen supply to muscle cells lags behind the rate of glucose catabolism, the pyruvate generated is reduced to lactic acid. The NAD+ is regenerated
Cellular Respiration: Pyruvate Decarboxylation
First stage
-the pyruvate made in glycolysis is transported into the mitochondrial matrix where it loses a CO2 (decarboxylated), the acetyl group that remains is transferred to coenzyme A making acetyl CoA. In this process, 1 NAD+ is reduced to NADH, 1 CO2 is made per pyruvate.
Krebs cycle
second stage of cell respiration
acetyl combines with oxaloacetate making a six carbon citrate. in a series of reactions, two CO2 are released, and oxaloacetate is regenerated for another cycle. Each turn of the CAC makes one ATP by substrate level phosphorylation via a GTP intermediate. In addition 3 NADH are made and 1 FADH2 (per cycle, so double these per glucose). these coenzymes (NADH and FADH2) then transport the electrons to the e transport chain , where more ATP is produced via oxidative phosphorylation
PRODUCTS PER GLUCOSE: 6 NADH, 2 FADH2, 4 CO2, 2 GTP, 2 CoA
electron transport chain
oxidative phosphorylation step (3rd) of cell respiration
-ETC is a complex carrier mechanism in the innter mitochondrial membrane. ATP is produced when high energy potential electrons are transferred from ANDH and FADH2 to oxygen by a series of carrier molecules in the membrane. As the electrons are transferred from carrier to carrier, free energy is released which is used to form ATP.
Throughout this process hydrogen ions are pumped from the matrix into the intermembrane space, makiing a concentration gradient. At the end of the ETC they pass through channels along their gradient , in this process energy is released to make ADP into ATP.
Most molecules of the ETC are cytochromes- electron carriers that resemble hemoglobin in their active site. contains a central iron atom that can undergo a reversible redox reaction. each carrier is reduced as it accepts an electron and is oxidized when it passes it to the next carrier. the last carrier passes it t o the final electron acceptor, O2, which picks up a pair of hydrogen ions from the surrounding medium as well, making H2O.
cytochrome
Most molecules of the ETC are cytochromes- electron carriers that resemble hemoglobin in their active site. contains a central iron atom that can undergo a reversible redox reaction. each carrier is reduced as it accepts an electron and is oxidized when it passes it to the next carrier.
how many ATP are made by substrate level phosphorylation as glucose is metabolized ?
degradation of one glucose yields a NET of two ATP from glycolysis by substrate level phosphorylation. In addition to this one ATP for each CAC turn is made, so this is a net of FOUR ATP by sub level
how many ATP are made by oxidative phosphorylation?
-Each FADh2 makes 2 ATP, and each NADH makes 3 except for the two NADH which were made in glycolysis (these cant cross the inner mitochondrial membrane, must transfer their electrons to an intermediate carrier molecule, which uses 1 ATP. so these two NADH generate only two ATP per glucose each.
-the two NADH from glycolysis yield a total of FOUR ATP. The other EIGHT (6 from CAC, 2 from decarb pyruv) make 24 ATP
24 + 4 + 4 = 32 ATP via oxidative phosphorylation!
TOTAL IS 36 ! 32 from ox plus 2 from glycolysis and 2 from CAC (substrate level)
When do carbohydrates, fats and proteins enter for energy consumption
- carbs are the first preference after glucose and they either are converted into glucose or enter glycolysis as an intermediate. glycogen from liver can be used as an intermediate for instance
- fats are second in line, they make most Atp per gram. they are hydrolyzed by lipases to fatty acids and glycerol when needed, carried by blood to other tissue for oxidation. Glycerol can be converted into PGAL, a glycolytic intermediate. But a fatty acid needs to first be activated in cytoplasm, requiring two ATP. once activated it is transported into the mitochondria and converted into acetyl coA.
- proteins are used when there isnt enough fat or carbs. Most amino acids undergo a transamination reaction where they lose an amino group to make an alpha keto acid. the carbon atoms of most amino acids are made into acetyl coa, pyruvate, or an intermediate in the CAC.
oxidative deamination
removes an ammonia directly from an amino acid. Ammonia is toxic in vertebrates, fish can excrete it but insects and birds make it into uric acid. mammals convert it to urea for excretion
Coenzyme
a type of cofactor that is organic
Vmax
maximum velocity of a reaction , substrate concentration is saturated
Competitive inhibition impact on vmax
competitive inhibition doesnt change the vmax but requires a higher concentration of substrate in order to get there
noncompetitive inhibition and vmax
noncompetitive inhibition lowers the Vmax but has the same concentration of substrate needed to get there. aka allosteric inhibition
- cofactor
2. prosthetic group
many enzymes need a nonprotein molecule called a cofactor to be active. they can be metal cations such as Zn or Fe, or small organic groups called coenzymes. most coenzymes are obtained from the diet as vitamin derivatives. Cofactors that bind to enzymes by strong covalent bonds are called prosthetic groups
Mendel’s Four principles of inheritence
- Genes exist in alternative forms (now alleles) a gene controls a specific trait in an organism
- an organism has two alleles for each inherited trait, one inherited from each parent. (law of independent assortment!)
- the two alleles segregate during meiosis, resulting in gametes that cary out only one allele in any given inerited trait
- if two alleles in an individual organism are different, only one will be fully expressed, the other sient. (dominant ) Mendel’s Law of Dominance.
What is a monohybrid cross
a cross where only one trait is being studied in a mating. purple flower PP and white pp. This makes completely heterozygous chidlren Pp. but all are purple.
Testcross
diagnostic tool to determine a genotype. You need a completely recessive phenotype to get accurately. If the dominant phenotype is expressed its either hetero or homo.
-this can be used to determine the unknown genotype with a dominant phenotype by crossing a dominant color with recessive. If the dominant is Aa, half the progeny will be Aa and half will be aa. if all are dominant, it was homo.
Mendel’s Law of Independent Assortment
mendel postulated that the inheritence of one trait is completely independent of any other trait. however we know this isnt completely true because genes on a chromosome generally stay together unless there is crossing over in meiosis
dihybrid cross
a cross looking for two traits crossing TTPP with ttpp makes TtPp in all offspring. if cross TtPp with TtPp it makes four phenotypes- tall purple, tall white, dwarf purple, dwarf white. 9:3:3:1 ratio. (9 is tall purple, 3 is tall white, 3 is dwarf purple, and 1 is dwarf white)
what are the non mendelian inheritance patterns?
- incomplete dominance
- codominance (ABO)
- Sex Determination (sex linked genes on X or Y chromosome, usually on X vs autosomes). generally only impact men because a man has one X chromosome so a recessive becomes dominant for them
autosomes
all humans have 22 pairs of autosomes and then a pair of sex chromosomes, xy or xx
nondisjunction
can have more or less copies of a particular chromosome if segregation doesnt happen correctly. if homologous chromosomes dont separate properly in meiosis I , or if sister chromatids dont separate right in meiosis II. trisomy (downs syndrome of chrom 21) and monosomy
Point Mutation, 3 possible impacts
a nucleic acid is replaced by another nucleic acid. involve usually 1-3 nucleotides. three possible effects on the codon;
- may code for the same amino acid (a silent mutation)
- May code for a different amino acid (a missense mutation) this may or may not cause a problem in the protein
- may be a stop codon (a nonsense mutation). usually these are lethal or severel inhibit functioning of the protein which can cause lots of issues for the organism.
Frameshift Mutation
nucleic acids are deleted or inserted into the genome sequence. Often this is lethal. the insertion or deletion throws off the entire sequence of codons from that point because the genome is read in groups of three. this also changes the length of the genome
Episome
plasmids that are capable of integration into the bacterial genome
Transformation
a foreign chromosome fragment (plasmid) is incorporated into the bacterial chromosome via recombination, making a new inheritable genetic combo
Conjugation, F+ and F-
“sexual mating” in bacteria. transfer of genetic material between two bacteria that temporarily join. a bridge pilus is formed between them and the donor F+ transfers genetic material to the F- type. Only bacteria containing plasmids called sex factors can conjugate. During conjugation between an F+ and F- cell, the F+ cell replicates its F factor an donates a copy to the recipient , converting the F- into an F+ cell. Genes that code for other characteristics may be found on the plasmids and transferred in too.
Hfr cells
sometimes in conjugation the sex factor is integrated into the bacterial genome, and the entire bacterial chromosome replicates and starts to move from donor to recipient. The bridge normally breaks before the whole thing can be transferred but the genes that enter the recipient cell can easily recombine with the genes present to form novel genetic combinations (it gets inserted into the new bacterial genome).. (HFR is high frequency of recombination)
Transduction
a bacteriophage is a virus that infects host bacterium by attaching to it, making a hole in its cell wall and injecting its viral DNA while its protein coat is attached to the wall. It happens when fragments of bacterial chromosome get packaged into the viral progeny in a viral infection. The virion can infect other bacteria and bring new genetic arrangements through recombination with the new host cells DNA.
what is the operon structure and how is it set up for transcription regulatioin
based on RNA polymerase accessibility to the genes it will transcribe. its directed by an operon which has structural genes, an operator region and a promoter region on DNA that is before the protein coding genes. Structural genes have the dna sequence for coding proteins. the operator is non transcribable dna, and it is the repressor binding site. The promoter is a noncoding sequence of DNA that serves as the initial binding site for RNA polymerase.
-regulator gene codes for synthesis of a repressor molecule that binds to the operator and blocks RNA polymerase from transcribing
rna polymerase must move past the operator to transcribe the genes.. regulation can occur by inducible or repressible systems
inducible system (transcription regulation in bacteria)
requires presence of an inducer for transcription to occur. in this system a repressor binds to an operator, forming a barrier that prevents RNA polermase from transcribing the structural genes. In order for transcription to happen, a inducer needs to bind to the repressor, forming an inducer repressor complex- this cannot bind to the operator so the barrier is removed. the proteins made are thus said to be inducible (induced by an inducer which stops a repressor from repressing)
–state is repressed until inducer comes
repressible system (transcription regulation in bacteria)
the repressor is inactive until it combines with the corepressor. The repressor can bind to the operator only when its formed repressor corepressor complex. These corepressor are often end products of the biosynthetic pathways that they control ( a signal to stop) proteins are said to be repressible, because normally theyre made until synthesis is stopped
- constitutive operons are ones that are mutated and syntheis does not stop, always being made
