Chapter 1: Genomes and the Flow of Biological Information Flashcards
the diversity of life is unified by 4 common themes; organisms must be:
- separate in some way from their environment
- able to store information in a stable way
- able to reliably replicate and pass information to the next generation
- able to extract energy from their surroundings
for an organism to be separate from its surroundings, it must be defined by a (1); this allows the organism to distinguish between (2)
- physical barrier
- self and non-self
all living organisms derive from a common original lie form referred to as (1) or (2)
- last universal common ancestor (LUCA)
- progenote
living organisms are constructed from 4 basic classes of ()
macromolecules
what is the basis of the theory that all life is derived from LUCA
when modern organisms are compared, the core building blocks of all organisms are the same (conserved)
nucleic acids are linear polymers of ()
nucleotides
a nucleotide is composed of:
- sugar molecule
- nitrogenous base
- phosphate group
main purpose of nucleic acids is to ()
store (DNA) and carry (RNA) information
proteins are linear polymers of ()
amino acids
an amino acid is composed of:
- amino group
- carboxyl group
- H atom
- side chain
workhorses of the cell
proteins
lipids are composed of ()
fatty acids
due to the (1) property of lipids, they can act as barriers for cells; separating them from their (2) environment
- hydrophobic
- aqueous
the 2 main parts of a fatty acid are:
- hydrophillic (polar) head
- hydrophobic tail
carbohydrates are polymers of ()
small sugars
main role of carbohydrates is to ()
store energy
because carbohydrates are hydrophilic, they can () of some proteins
increase the solubility
why is the storage and passage (flow) of biological information important for living organisms?
- faithful production of offspring
- proper tissue development/growth in multicellular organisms
the 4 nucleobases
guanine, cytosine, thymine, adenine
the 4 nucleosides
guanosine, cytidine, thymidine, adenosine
maintenance of life is based on the process of (1), both in the context of (2) and (3)
- reproduction
- growth of a specific tissue
- development of new offspring
properties of DNA
- double helix structure
- complementary base pairing
- antiparallel directionality
describe the double helix structure of DNA
phosphate backbone on the outside, complementary base pairs on the inside
describe the directionality of DNA
- nucleic acids have distinct ends (5’ and 3’)
- when 2 strands form DNA, 3’ aligns with 5’ (and vice versa)
properties of DNA that make it good for information storage
- stable (compared to RNA)
- 2 stranded structure allows for separation and copying of information
sequence of nucleotides in DNA of an organism; total DNA content of the cell
genome
why is the genome considered the blueprint for life?
it stores all the information needed to specify cellular function
give an overview of the transmission of the genome
- replication - accurate copying of information
- segregation - correct separation of copies
- transfer of copies into new cells
molecular machine responsible for synthesizing new DNA copies
DNA polymerase
the genome is composed of (1) and (2) regions in chromosomes
- genes (coding)
- intergenic (noncoding)
genes not only have instructions for a product but also instructions for ()
when and where a product should be made
all bacterial and some eukaryotic cells have (), which are small, circular DNA separate from chromosomes
plasmids
it is important to remember that organism complexity does not simply correlate with (1) or (2)
- genome size
- genome number
the process of making RNA by copying the sequence of a region in a gene; the first step in gene expression
transcription
in terms of usage, RNA is either (1) or (2)
- used directly by the cell
- used as information to direct manufacture of a particular protein
DNA : DNA polymerase :: RNA : ()
RNA polymerase
in RNA, A pairs with ()
uracil (U)
the initial product of a transcription event (RNA) is referred to as (); it is further reined into the final product
primary transcript
process of turning the information in mRNA into a protein is called ()
translation
coding RNAs that contain the information to produce a protein
messenger RNAs (mRNAs)
start codon in translation
Met (methionine)
each amino acid is represented (encoded) by 3 nucleotides in the mRNA molecule called a ()
codon
translation is performed by the (), which has protein and RNA components
ribosome
() interprets the information in mRNA into the protein sequence
transfer RNAs (tRNAs)
() allows for different proteins to emerge from a single gene
alternative splicing
ways to regulate gene expression
- concentrations of RNAs and proteins
- activity states (conformations) of RNAs and proteins
how can gene expression be regulated through the concentrations of RNAs and proteins
- certain RNAs and proteins can either promote or
inhibit the expression of genes - increased concentrations of these RNAs or proteins can affect expression of genes
gene expression is regulated in both (1) and (2), allowing the genome to express the correct genes when and where needed
- time
- space
temporal and spatial gene regulation can determine:
- tissue cell types during development
- cellular responses to environmental changes
main difference between prokaryotes and eukaryotes
eukaryotes have a nucleus while prokaryotes do not
components of cells are spatially organized into regions to ()
help facilitate functions
despite not having a nucleus, DNA in prokaryotes is concentrated in a region called ()
nucleoid
the non-specialized regions of a cell make up the ()
cytoplasm
examples of membrane-bound organelles in eukaryotes
- nucleus
- endoplasmic reticulum and Golgi apparatus
- mitochondria and chloroplasts
- lysosomes and peroxisomes
why is the nuclear membrane porous
to allow for molecular machines to interact with DNA for cellular processes
benefits of cellular compartmentalization
- compartmentalization facilitates biochemical reactions via the co-localization of materials
- physical separation provides an opportunity for regualtion
how does co-localization of materials aid in efficiency of cellular processes
- reactants are localized together -> more efficient biochemical rxns
- related processes with shared materials are localized together -> more efficient use and transport of materials
how does physical separation of processes help in regulation of cellular processes
processes cannot proceed unless certain regulatory conditions are met, preventing faulty products from being utilized
genes operate in (), where the activity of one gene affects the activity of another
networks
refers to the visual features and properties of an organism
phenotype
organisms have () - number of copies of its genome
ploidy
what is the advantage of diploid or polyploidy
presence of a ‘back-up’ version of a gene, in case one version is defective
() refer to the normal, typical organisms that occur most frequently in a natural population
wild-type
copies of a gene that are similar (have same function) but different (may express different phenotype); version of a gene
allele
explain the basis of forward genetics
mutant phenotype is observed and the gene that causes the phenotype is then discovered
explain the basis of reverse genetics
a gene of interest is disrupted, and the phenotype is observed to determine disrupted gene’s function
any change in the gene sequence
mutation
in diploids, mutations can be (1) or (2)
- dominant
- recessive
one mutant copy in heterozygotes is enough to produce a mutant phenotye
dominant mutation
phenotype of mutant version is masked by presence of wild-type allele; thus mutant phenotype is only expressed in homozygotes with this mutation
recessive mutation
kinds of gene mutations
- point mutations
- insertions
- deletions
- rearrangements
gene mutations can either alter the (1) of a protein or the (2) and change gene expression
- sequence and structure
- regulatory regions of a gene
mutations that result in a loss of the wild-type function are referred to as
null or loss-of-function mutations
mutations that result in a gain of a new abnormal function are referred to as
gain-of-function mutation
single nucleotide changes (point mutations) can have a variety of effects
- missense mutation
- nonsense mutation
- silent mutation
single nucleotide changes alter the encoded amino acid
missense mutations
single nucleotide changes introduce a premature stop codon
nonsense mutations
single nucleotide changes do not alter encoded amino acid
silent mutations
why are frameshift mutations (due to insertions or deletions) catastrophic
entire amino acid sequence can be disrupted/affected
() can lead to phenotypic changes without altering the underlying DNA
epigenetic changes
examples of epigenetic changes
regulation of the compactness of chromatin -> genes tightly wound around chromatin are inaccessible and thus not expressed
a mutation in a single gene causes a disease
monogenic diseases
diseases that result from changes in several genes
polygenic (multifactorial) diseases
percentage of people with the gene mutation that will develop the disease
penetrance of mutation
relatedness among organisms is indicated using a ()
phylogenetic tree
phylogenetic trees are typically based on comparisons of ()
multiple genes
in phylogenetic trees, the () indicates how related organisms are
length of the branch
characteristics of model organisms
- have fast generation times
- relatively small and cultivatable in a lab
- biochemically or genetically tractable
how do viruses provide insights into replication and gene expression mechanisms
viruses must infect and use a host cell’s cellular machinery to reproduce; studying how viruses reproduce allows for a closer look at how cellular machinery of the host cell works
