Unit 3- Phylogeny, Metabolism, and Genetics Flashcards
Define parsimony
the shortest possible tree that explains the data is considered best
What is parsimony’s utility in the sciences generally
It helps ensure data is presented efficiently without filler or jargon
What are the 3 different types of secondary structures of proteins?
Random Coils, Alpha Helices, and Beta Pleated sheets
Uracil is found only in
RNA
Thymine is found only in
DNA
What is the direction DNA is replicated in?
5’ to 3’ on its respective strand
what is the Central Dogma of Biology?
DNA-> RNA-> Proteins
What are the different types of genomic DNA found in Eukaryotes?
Nuclear, Mitochondrial, Chloroplast
What is the purpose of the cladistic method and phylogenetic systematics
The cladistic method visually shows the evolutionary and phylogenetic history of organisms. It illustrates mutation and speciation events
Define Phylogeny
the natural relatedness between groups of living things
Distinguish between Character and Character-State
Characters are traits which help identify organisms, which can be phenotypic, genotypic, biochemical, or molecular. The character-state (0,1,2,3,4) Helps identify whether or not the trait is ancestral or derived (0 vs 1,2,3,4)
What is the difference between ancestral and derived character-states?
Ancestral states are those which are original to the common ancestor and not changed. Derived states (1, 2, etc.) are those which have changed from the common ancestor
What is the significance of an outgroup?
An outgroup shows one organism with all ancestral traits and is used as a means of mutation/speciation identification within a taxon data matrix
Define Monophyletic
A Group of organisms classified in the same taxon and share a common ancestor
Define Parsimony
The Simplest explanation for data is most likely to be correct
What is the difference between a character by taxon data matrix, a cladogram, and a Venn Diagram
a Taxon Data Matrix is a grid which represents character changes by evolutionary history with an outgroup and the corresponding speciation events A Cladogram shows in visual tree form, how organisms speciated from a common ancestor over time A Venn Diagram is a visual representation of comparing and contrasting traits for different organisms
Explain how mutations (nucleotide substitutions and insertions/deletions) change DNA sequences
Frameshift mutations could cause an early or late stop codon(Insertion/deletion) and a substitution could be a silent or missense mutation
What is the significance of R-Groups? How do they make Amino Acids different?
R Goups’ placement in a formula indicates that the group attached to that site varies from one compound to another
Protein’s Primary structure
Amino Acid Chains
Protein’s Secondary Structure
beta Pleated sheets, Alpha Helices, and Random coils
Protein Tertiary Structure
Secondary structures bonded by disulfide bonds (3D state)
Protein Quaternary Structure
More than 1 polypeptide, has subunits, and features the 1st 3 structure types
What is a protein’s native conformation?
3-D correct state of a protein. If it’s altered, it’s considered denatured
What is a protein subunit
A single protein molecule that assembles with other protein molecules to form a protein complex
What is the significance of active sites with regard to enzyme function?
Active site binds to the substrate to catalyze a reaction
What is the significance of Allosteric sites with regard to enzyme function?
The altered activity of an enzyme due to the bonding of a molecule to a region other than the active site
what effect do factors such as pH, temperature, salt concentration and the presence of activators or inhibitors have on enzyme function?
They all have the ability to denature the protein and cause loss of function
What is Enzyme/Protein denaturation?
Alteration of native conformation and function by breaking bonds
Define Cofactor
An Enzyme accessory, usually a metallic Ion
Define a Coenzyme
Serves as transient carriers of specific atoms or functional groups during metabolic reactions. They operate in conjunction with an enzyme
What is the difference between competitive/noncompetitive enzyme inhibitors
Competetive enzyme inhibitors bind to the active site Noncompetitive enzyme inhibitors bond off the active site, but change conformation of the protein
What is a spontaneous reaction?
A reaction that does not require an enzyme to catalyze it
What is a nonspontaneous reaction?
A reaction that requires an enzyme and ATP to catalyze the reaction
What is an endergonic reaction
A reaction that absorbs surrounding energy
What is an Exergonic reaction
A reaction that releases energy into the surroundings
Why are enzymes in an experiment not considered part of the reactants or products?
Because they catalyze the reaction and are not participating or being created.
how can the cell can perform energy requiring/consuming reactions through energy coupling
The Transfer of energy from endergonic to exergonic processes or by Catabolism to anabolism
What is the role of phosphorylation/dephosphorylation in metabolism?
Add a Phosphate group to ADP to make ATP Remove a phosphate group from ADP or ATP to make AMP or ADP
What is the function of ATP in a cell?
ATP is the energy currency in the cell
What is ATP’s Structure?
Adenosine and 3 Phosphate groups
Explain how ATP/ADP/AMP can gain or lose through phosphorylation and hydrolysis
Hydrolysis breaks off a phosphate group (AMP or ADP) and Phosphorylation adds a phosphate group (ADP or ATP)
Oxidation
A loss of electrons
Reduction
A gain of electrons
Describe the basic structure and functional role of NAD+ and contrast it with NADH
NAD+ is reduced, NADH is oxidized
Describe the basic structure and functional role of FAD and contrast it with FADH2
FAD is reduced, FADH2 is oxidized
Number of carbon atoms in glucose
6
Number of carbon atoms in pyruvate
3
Number of Carbon atoms in G3P
3
Number of Carbon atoms in Citric Acid
5
Where does the citric acid cycle occur in the cell?
Eukaryotic (Mitochondria) Cell Membrane (Prokaryotic)
How is a proton gradient created and how this gradient is used to synthesize ATP (by ATP synthase) by chemiosmosis
In the ETC, the proton gradient is used to oxidize and reduce each protein subunit to force an ADP and Phosphate group together at the ATP Synthase to generate ATP
What is the role of oxygen in Cellular respiration?
Oxygen allows substrate-level and oxidative phosphorylation to occur. Oxygen is also the final electron acceptor
Explain the difference between substrate-level and oxidative phosphorylation;
Substate Level- Citric Acid Cycle Oxidative- ETC/S
Explain the difference between substrate-level and oxidative phosphorylation;
Substate Level- Citric Acid Cycle Oxidative- ETC/S
Explain under what conditions it becomes necessary for a cell to switch to a fermentation pathway and the benefit of performing fermentation (as opposed to cellular respiration) under such conditions
Anaerobic conditions (No Oxygen) forces the cell into a fermentation pathway
Describe how other compounds (nitrates and carbonates) can be used as final electron acceptors in (anaerobic) respiration
Nitrates and carbonates all have oxygen in them and can suffice as final electron acceptors because of Oxygen’s electron affinity.
Complementary Base Pairing
A-T G-C
Sense Strand
The strand with the coding sequence for a specific gene
Antisense strand
the strand with the complement of the coding sequence for a specific gene
Triplet Code
the standard version of the genetic code, in which a sequence of three nucleotides in a DNA or RNA molecule codes for a specific amino acid in protein synthesis
Antiparallel strands
each strand runs in 5’ to 3’ direction oppositely
Degenerate code
The genetic code is degenerate because there are many instances in which different codons specify the same amino acid
What is the structure of DNA
Features Deoxyribose Double-Stranded Contains Thymine in base pairs Sugar-Phosphate backbone
What is the difference between Ribose and Deoxyribose
Ribose contains oxygen Deoxyribose does not contain oxygen
What does 5’ and 3’ mean?
The directionality of nucleic acids
mRNA (Messenger RNA)
Translated from the sense strand of DNA
rRNA
Make up ribosomal subunits for translation
tRNA
Hold the anticodons and amino acids for polypeptide chain synthesis
Central Dogma of Biology
DNA-> RNA-> Protein
What is a genome?
All DNA in a cell
What is a Proteome?
All Proteins in a cell
What is a Metabolome?
All DNA, RNA, and Protein data in a cell
Transcriptome?
All RNA in a cell
Define Gene
the site on a chromosome that provides the information for a certain cell function
Define Chromosome
Tightly coiled bodies within the cell, composed of DNA, and are primary locations for genetic material
Define Chromatin
Genetic material in the nucleus (uncoiled)
What is the nature of the chromosomes in prokaryotes?
Single, Circular chromosome
What is the nature of chromosomes in eukaryotes?
Multiple, tightly coiled chromosomes in a nucleus
What is the structure of bacterial ribosomes
Large and Small subunits
What is the structure of bacterial ribosomes
Large and Small subunits
What are the different types of genomic DNA found in eukaryotes?
Nuclear Mitochondria Chloroplast
Define Codon
Triplet code that corresponds with an amino acid
Define Anticodon
Anticodons are located on tRNA molecules and are complementary of the codon and adds to the amino acid chain
What is the role of RNA Polymerase in transcription
RNA Polymerase copies DNA and transcribes it into mRNA
What is the role of transcription factors in transcription
a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence
Sense Strand of DNA
contains the coding information for a particular gene
Antisense strand of DNA
is a complement of the sense strand and holds noncoding information for that gene
Purines
Nitrogenous bases Adenine and Guanine
Pyrimidines
Nitrogenous Bases Cytosine Thymine Guanine
Purines
(Adenine, Guanine)
Pyrimidines
RNA
Sugar-Phosphate Backbone
DNA
Electron Transport Chain
Citric Acid Cycle
Glycolysis
Pyruvate Dehydrogenase Complex
(Pyruvate/Pyruvic Acid converted into Acetyl CoA)
How many hydrogen bonds are between Adenine and Thymine?
2
How Many hydrogen bonds are beterrn Guanine and Cytosine?
3
Autorad (Autoradiography)
shows the sequences of nucleotides (each type located in a different lane) Gel electrophoresis
PCR
Polymerase Chain Reaction
Steps of PCR
Amplification, Specificity, and Sensitivity
Histones only occur in what type of cells?
Eukaryotic
Function of Insulator in Eukaryotic DNA
Prevents activity of a gene from influing its genetic neighbors
Repressor Function
Non-Coding segment
slows down transcription
Promoter function
Binding site for RNA Polymerase
RNA Polymerase
DNA Copying Enzyme
Exon
a segment of a DNA or RNA molecule containing information coding for a protein or peptide sequence.
Intron
a segment of a DNA or RNA molecule that does not code for proteins and interrupts the sequence of genes.
SNRP
small nuclear ribonucleoproteins, are RNA-protein complexes that combine with unmodified pre-mRNA and various other proteins to form a spliceosome, a large RNA-protein molecular complex upon which splicing of pre-mRNA occurs.
DHAP is converted into G3P by what enzyme?
Isomerase
Glycolysis results in how many ATP Molecules?
4 Total, 2 Net
How many NADH Molecules are produced in GLycolysis
2
ated in the Citric Acid Cycle
