Ap Bio Exam Flashcards
Linear Electron Flow (Photosystem II)
Photon of light strikes a pigment molecule. Light travels from pigment molecule to pigment molecule until it reaches P680. Electron is then transferred to primary electron acceptor and water is split (H+ is released into thylakoid space). Additionally, two oxygen atoms join together to form O2
Linear Electron Flow (Photosystem II to I)
Photoexcited electrons pass from the primary electron acceptor of Photosystem I to Photosystem II via an ETC. As electrons flow down, protons are pumped into the thylakoid space.
Linear Electron Flow (Photosystem I)
Electrons move from 0700 pair to Photosystem I’s primary electron acceptor. The electrons then go down a second electron transport chain, reducing NADP+ to NADPH
Cyclic Electron Flow
Takes place in PS I & generats ATP
Calvin Cycle (Carbon Fixation)
Carbon from Co2 molecule attaches to a five carbon sugar (RuBP), this six carbon intermediate is so unstable it needs to split into 2 3-carbon molecules
Calvin Cycle (Reduction)
Each 3 carbon molecule recieves a phosphate group from ATP and is reduced and loses a phosphate group to become G3P. For 3 molecules of CO2, six molecules of G3P are produced.
Calvin Cycle (Regeneration)
Only one G3P can be counted as net gain because the other five G3P molecules are used to regenerate 3 molecules of RuBP
Paracrine Signaling
A signaling cell acts on nearby target cells by secreting molecules of a local regulator
Endocrine Signaling
Specialized cells release hormones, where they reach target cells that can recognize and respond to them
RTKs
Binding molecules signal two receptor monomers to join and form a dimer. Each tyrosine kinase adds a phosphate group (from ATP) to the a tyrosine molecule part of the tail. Proteins can now bind to a specific phosphorylated tyrosine
GPCR
cell-surface transmembrane receptor that works with the help of a G protein, typically activating a single transduction pathway. G proteins are in an active state when they bind to GTP.
Where can signals for apoptosis come from?
From the ER when excessive protein misfolding occurs, from the nucleus when DNA has suffered irreparable damage, or when a cell sends a signal to another cell (extracellular)
Prophase
Parent cell duplicated chromosomes condense and mitotic spindle begins to form
Prometaphase
Nuclear envelope breaks down, microtubules grow outward from the centrosomes (which are moving apart) and connect to each chromosome at its kinetochore
Metaphase
Chromosomes align along with the cell equator. Each chromosome has at least two microtubules extending from its kinetochore.
Anaphase
Each chromosome’s sister chromatids separate and move to opposite poles of the cell
Telophase
Chromosomes arrive at the cell poles, mitotic spindle disassembles, and two nuclear envelopes form
Cytokinesis
Cleavage furrow is formed, allowing the cytoplasm to split into two genetically identical daughter cells
Cytokinesis in plant cells
Vesicles from the golgi move along microtubules to the middle of the cell, forming a cell plate. The cell plate expands as vesicles containing cell wall materials fuse, expanding outwards until two distinct daughter cells are formed.
Prokaryotes (division)
Go through binary fission - double their size and divide in half. Origins of replication move towards opposite ends of the cell
How do CDK and Cyclin monitor the cell cycle?
CDK is present at equal levels throughout the cell cycle. However, cyclin levels fluctuate. When cyclin combines with CDK, MPF is produced and when enough MPF accumulates, the cell passes the G2 checkpoint and begins mitosis.
Density-dependant inhibition
crowded cells stop dividing (binding of a cell-surface protein to its counterpart on an adjoining cell sends a signal to both that inhibits cell division.
Prophase 1 (meiosis)
Spindle forms, duplicated chromosomes start to move to opposite sides of the cell, crossing over occurs. Microtubules from one pole or the other attach to the kinetochores, one at the centromere of each homolog
Metaphase 1
Pair of homologous chromosomes arranged at the metaphase plate, each pair lining up independently of other pairs
Anaphase 1
Homologs move towards opposite poles guided by the spindle. The two chromatids of same chromosome move towards the same pole
Three events in meiosis that contribute to genetic diversity
Crossing over, random fertilization, and independent assortment
Crossing Over
DNA molecules of nonsister chromatids are broken and rejoined to each other
Law of segregation
The two alleles for each gene separate during gamete formation
Law of independent assortment
Alleles of genes on nonhomologous chromosomes assort independently during gamete formation
Inversion and Translocation
Inversion - chromosomal fragment reattaches to original chromosome but in reverse orientation. Translocation - chromosomal fragment joins a nonhomologous chromosome.
Genomic imprinting
Variation in phenotype depends on whether an allele is inherited from the male or female parent
Pleiotropic
A gene that influences two or more phenotypes
Epistasis
When one gene locus masks or modifies the phenotype of a second gene locus
5’ end vs 3’ end
5’ end has a phosphate group attached to it & the 3’ end has a hydroxyl group attached to it
Replication Fork
At the end of a replication bubble where the parental strands of DNA are being unwound
Helicases
Untwist the double helix at the replication forks
Single-strand binding proteins
bind to the unpaired DNA strands, keeping them apart
Topoisomerase
Relieves strain in DNA from untwisting of the double helix
Primase
Synthesizes a primer - a complementary RNA chain which is the first part of the replicated DNA
DNA Polymerase 3 vs 1
DNA Polymerase 1 removes the RNA from the primer and replaces it from DNA. DNA Polymerase 3 can proofread and adds DNA nucleotides to the RNA primer
Which way does DNA polymerase move
5’ to 3’ direction
What happens to fix errors in DNA replication
Nuclease cuts out strand containing the damage and resulting resulting gap is filled with nucleotides (from DNA polymerase), and DNA ligase then seals everything back up
Telomeres
Special nucleotide sequences at the end of eukaryotic chromosomal DNA to protect the DNA from getting eroded away
Heterochromatic vs euchromatin
Heterochromatin is compact (largely inaccessible to proteins responsible for transcribing the genetic info) and euchromatin is the opposite
RNA polymerase
Pries the two strands of DNA apart & joins together RNA nucleotides complementary to the DNA template strand
Initiation of Transcription
Once the transcription factors are attached to the promoter DNA & RNA polymerase is bound to them correctly, the enzyme unwinds the two DNA strands and begins translating (TATA box = promoter region of the DNA)
tRNA loop and 3’ end
The 3’ end acts as an attachment site for an amino acid, while the loop on the other end has the anticodon
How are anticodons conventionally written
Usually written 3’ to 5’ to align properly with codons written 5’ to 3’
Wobble
Less than 61 tRNAs - some are able to bind to more than one codon
Three binding sites in ribosome for tRNA
P site - holds the tRNA carrying the growing polypeptide chain
A site - holds the tRNA carrying the next amino acid
E site - where discharged tRNAs leave from
Three steps of translation
Initiation, elongation, termination
Termination in transcription vs translation
Transcription - after reaching the termination signal, enzymes chase RNA polymerase down
Translation - after reaching the stop codon, a water molecule is added to the polypeptide change, breaking the bond between the polypeptide and tRNA
Operon
The operator, promoter, and genes they control
Repressor (operon)
Binds to the operator, preventing RNA polymerase from transcribing the genes
Inducer (operon)
Specific small molecule that inactivates the repressor
Inducible vs Repressible enzymes (functioning in anabolic vs catabolic pathways)
Repressible enzymes generally function in anabolic pathways, while inducible enzymes usually function in catabolic pathways
Methylation vs Acetylation
addition of acetyl groups appears to promote transcription due to opening up chromatin structure while the addition of methyl groups does the opposite.
General transcription factors
Act at the promoter of all genes - essential for transcription of all protein-coding genes
How can gene expression be strongly decreased or increased
By the binding of specific transcription factors, either activators or repressors, to the control elements of enhancers
Mediator proteins
Interact w/ general transcription factors at the promotor after interacting w/ enhancers far from the promoter. Some activators add acetyl groups to histones, while some repressors add methyl groups to histones.
Eukaryotic genes are co-expressed (what does that mean)
The genes coding for the enzymes of a metabolic pathway are typically scattered over diff chromosomes. Transcription activators in the nucleus recognize the control elements and bind to them no matter where they are in the genome.
miRNAs
small, single-stranded RNA molecules capable of binding to complementary sequences in mRNA molecules
siRNAs
double stranded, similar to miRNAs, block/turn off gene expression
piRNAS (piwi-interacting)
Induce formation of heterochromatin, blocking expression of some parasitic DNA elements in the genome known as transposons.
lncRNAs
Turn certain genes off, such as the second X chromosome in females. Can also help condense chromatin or bring the enhancer of a gene together w/ mediator proteins & the gene’s promoter
Cytoplasmic determinants
Early mitotic divisions distribute the zygote’s cytoplasm into separate cells - the nucleus of these cells may be exposed to different cytoplasmic determinants
Master genes
Master regulatory genes have protein products that commit the cell to becoming a specific type of cell
Homeotic genes
Master regulatory genes that control placement & spatial organization of body parts in animals, plants, & fungi
Morphogen gradient hypothesis
Gradients of substances called morphogens establish an embryo’s axes & other features of its form
Mutations of what type of genes could lead to cancer?
Genes that normally regulate cell growth & division during the cell cycle
Tumor-suppressor genes
Encode for proteins to help prevent uncontrolled cell growth. Any mutation that decreases the activity of this protein may lead to cancer
Oncogenes
Converted from proto-oncogenes - normal version that codes for proteins that stimulate normal cell growth & division
Glycolysis
Glucose is split into two three carbon sugars (pyruvate). Net energy yield per glucose molecules is 2 ATP, 2 NADH, and 2 H+.
Pre Citric Acid Cycle
Pyruvate enters the mitochondrion through a transport protein & is processed by a complex of several enzymes (pyruvate dehydrogenase). Pyruvate then gets converted to Acetyl CoA.
Citric Acid Cycle
- One step produces an ATP by substrate level phosphorylation
- Two carbon molecules are released (as carbon dioxide)
- Electrons are carried off by 1 FADH2 molecule & 3 NADH molecules
Electron Transport Chain
Electrons are passed down carriers, releasing energy which is used to pump H+ across the intermembrane space. This creates a gradient, so as the hydrogen ions flow back they go through ATP synthase, causing it to spin and generate ATP
Glycosidic Bond
Between two sugars
Peptide bond
Between amino acids
Primary Structure
Particular number and sequence of amino acids making up the polypeptide
Secondary Structure
Parts of the polypeptide chain are coiled or folded, forming twists & corrugations
Tertiary Structure
Give a protein its overall 3D shape. This is due to interaction between R groups (ex. hydrophobic groups clustering in). Covalent bonding can help to solidify a tertiary structure
Quaternary Structure
Combination of two or more polypeptide subunits (stabilized the same way tertiary structures are)
Phosphodiester linkage
A phosphate group covalently linked to the sugars of two nucleotides
Saturated vs Unsaturated Fats
Saturated fats are solid at room temperature while unsaturated fats are liquids at room temperature.
What way does water potential move
from the system with a higher water potential to the system with a lower water potential.
Dehydration Reaction
Water molecule lost in the formation of new bond between two monomers
Hydrolysis
Adds a water molecule, breaking a bond and reverting polymers back to monomers
4 Emergent Properties of Water
Cohesive behavior, ability to moderate temperature, expansion upon freezing, and versatility as a solvent
Endotherms
Regulate their internal body temp independent of the outside environment temp
Ectotherms
Are reliant on the outside temperature to regulate their internal temperature
Chemosynthetic
Organisms that make food from chemical energy from their environment
Heterotrophic
Organisms that gain energy from consuming other organisms
Photosynthetic
Organisms that use the energy from sunlight to synthesize their own food
