Bio 171 Lecture 1: Characteristics of life, genetic material, 3 domains, and the tree of life

Amino acid:

Organic molecule containing a central carbon atom attached to a carboxyl group, amino group, hydrogen atom, and side chain. Building block (monomer) of proteins (polymers).

Anti-codon:

Sequence of 3 nucleotides in a tRNA molecule that bp w/ corresponding codon in mRNA molecule.

Archaea:

Domain of life. Consists of single-celled organisms w/ single circular chromosomes and lack membrane-bound nucleus. Divide by binary fission and differ from bacteria in many aspects of their cell/molecular bio.

Bacteria:

Domain of life. Consist of single-celled organisms w/o nucleus. Have a cell wall made of peptidoglycan, typically have a single circular chromosome and divide by binary fission.

Carbohydrate:

Organic molecule containing C/H/O atoms that provide energy source for metabolism and forms the starting point for synthesis of other organic molecules. Make up cell wall in bacteria/plants/algae.

Cell (Plasma) membrane:

Barrier that surrounds the cytoplasm of the living material within the cell from the non-living environment around it. Controls the movement of materials in/out cell.

Central dogma:

Observation that info in cell usually flows from DNA to RNA to protein.

Codon:

Group of 3 adjacent nucleotides in mRNA that specifies an amino acid in a protein/terminates protein synthesis.

Deoxyribonucleic Acid (DNA):

Double helix linear polymer made up of various sequences of bases A/T/G/C in all cellular organisms. Carries genetic info needed to specify amino acid sequence of all protein synthesized in organism. Transmits that info to generations w/ chromosomes. Deoxyribose sugar.

DNA replication:

Process of duplicating DNA molecule, during which the parental strands separate and new partner strands are made by creating new base pairs. Mistakes during replication cause mutations that alter DNA sequence.

Eukarya:

Domain of life. Eukaryote cells have nucleus and divide by mitosis.

Eukaryote:

Organism (animals/plants/fungi/protists) w/ cells that have nucleus.

Gene:

Unit of heredity affecting organism traits. Specific stretch of nucleotides in DNA sequence that corresponds to make specific RNA/protein. Genes are active only when “expressed” as RNA/proteins.

Gene expression:

Occurs in central dogma signaling if a gene product is on (RNA is translated into protein)/off (RNA functions in cell).

Genetic code:

Instructions for matches codons in an mRNA sequence and the amino acid added by the matching tRNA. 3 stop codons don’t have a corresponding tRNA and end protein synthesis (i.e., translation).

messenger RNA (mRNA):

RNA carrying genetic message from DNA in nucleus and combines w/ ribosome to direct protein synthesis. Contains 3 codons that base-pair with anti-codons on tRNA molecules. Each tRNA carries an amino acid, and all tRNA molecules with the same anticodon carry the same amino acid.

non-template DNA:

Untranscribed strand for RNA synthesis during transcription. Matches RNA sequence.

Nucleic acid:

Nucleotides polymer that encodes/transmits genetic info.

Nucleus (of a cell):

Compartment within cell that houses DNA in chromosomes.

Peptide bond:

Covalent bond that links carbon atom in carboxyl group of one amino acid to nitrogen atom in amino group of another amino acid.

Phospholipid:

Type of lipid and major component of cell membrane.

Phylogenetic tree:

Branching diagram representing hypothesis about evolutionary relationship among groups of organisms.

Prokaryote:

Organism (bacteria/archaea) whose cells doesn’t have a nucleus.

Protein:

Folded polymers of amino acids. Key structural/functional molecule that does the work of the cell, providing structural support/catlyzing chemical reactions.

ribosomal RNA (rRNA):

Noncoding RNA built in all ribosomes essential in translation.

Ribonucleic Acid (RNA):

Key in protein synthesis and gene expression. Ribose sugar. Bases A/U/G/C.

Ribosome:

Complex RNA and protein structure that synthesizes proteins from amino acids as directed by sequence of mRNA.

transfer RNA (tRNA):

Noncoding RNA that carries amino acids for use in growing polypeptide chain to ribosome during translation.

Template DNA:

In DNA replication, the parental strand whose sequence is used to synthesis a complementary daughter strand. In transcription, DNA strand whose sequence is used to synthesis a complementary mRNA molecule.

“tree of life”:

Evolutionary tree that shows evolutionary history/relationship of all extinct and living organisms.

Transcription:

RNA polymerase adds complementary base pairing (A:U & G:C) to transcribe template DNA (gene) to growing complementary RNA strand.

Translation:

mRNA uses genetic code/complementary bp to translate strand into polypeptide chain, synthesizing protein.

List the characteristics that all living organisms have; describe how biologists distinguish living organisms from non-living entities

Complexity, organization (at scale within a cell, the cell itself, communities of cells), abilities to respond to environment, metabolize (aerobic/anaerobic), reproduce, and capacity to evolve (life doesn’t arise spontaneously). Carbon and water based.

Give a reason why viruses might be considered living.

Contain genetic material (DNA/RNA). Evolve over time.

Give a reason why viruses might not be considered living.

Doesn’t have cellular characteristics. Unable to acquire energy/metabolize. Can’t respond to environmental stimuli. Require host cell to function (e.g. reproduce).

Describe what the "tree of life", and phylogenetic trees more generally, represent

Tree of life is the evolutionary relationships among all organisms while phylogenetic trees are for specific species of organisms.

Identify past and present on a phylogenetic tree, along with the root, tip and nodes on tree.

Time runs from root to tips. Root: Earliest common ancestor. Tip: Species currently alive. Nodes: MRCA. Groups are more closely related when their node is closest to present day.

Explain where prokaryotes and eukaryotes are found in the three contemporary domains of life: Bacteria, Archaea, and Eukarya

Bacteria and Archaea: prokaryotes (no nucleus, no membrane bound organelles)

Eukaryote: Eukarya

Identify the most recent common ancestor (MRCA) for two organisms on a phylogenetic tree.

The MRCA for humans and chimpanzees are gorillas.

Explain where prokaryotes and eukaryotes (animals/plants) are found in the three contemporary domains of life: Bacteria, Archaea, and Eukarya.

Prokaryotes: bacteria/archaea. Eukaryotes: eukarya.

Explain the relationship among nucleotides, DNA, genes, amino acids, proteins, and the genetic code

DNA is stored genetic info (genes) which have a genetic code, through the use of nucleotides in mRNA specify enzymes, in the central dogma know when translated what amino acids to use when building a protein.

Describe the central dogma using the following terms: DNA, RNA, protein, transcription, and translation.

The usual flow of genetic info from a separated template DNA transcribed w/ enzymes placing nucleotides into RNA as a code for the translation of amino acid sequence into a protein.

Describe the data used to construct the tree of life.

MRCA data is used. RNA is used because all living things are made up of RNA.

Apply the 3 requirements for evolution by natural selection to a new example.

1. Beetles pop. began w/ varied inherited traits. 2. Predators (birds) eliminated light shell beetles b/c easier to see and eat. 3. Reproduction of survivor (mostly dark shell beetles). 4. Increased frequency of traits that enhance survival and reproductive success.

What is an important difference between a eukaryote and a prokaryote?

Eukaryotes have a nucleus/membranebound organelles and prokaryotes don’t.

What does the tree showing the three domains of life tell us about how Eukarya, Archaea, and Bacteria are related to each other?

Everything stems from bacteria.

Which other domain are Archaea most closely related to?

Eukarya.

Which domain do animals belong to?

Eukarya.

Where do Archaea and Bacteria live?

Can be found in any environment.

What roles do Archaea and Bacteria play ecologically?

Play crucial roles proiding oxygen in atmosphere. Biogeochemical/nutrient cycles (nitrogen fixation, decomposition). Important mutualisms (create symbiotic relationships w/ eukaryotes).

What is the genetic material of all living organisms?

DNA.

What are four key characteristics of all living organisms?

Diversity of structure. Ability to replicate. Mutability. Gene expression (central dogma).

What allows for a diversity of structure in DNA?

There is no restriction on the sequence of bases along a strand. Length of DNA strands.

Why is it important to be able to replicate DNA?

DNA replication is essential for life b/c it ensures that each new cell receives an exact copy of the organism's genetic material during cell division. This process is crucial for growth, development, repair, and reproduction in living organism pops.

What needs to happen in order for DNA to replicate?

1. Initiation. 2. 2 strands of DNA separate (unwinding). 2. Each strand used as template (Primer binding). 3. Elongation. 4. Termination.

What is the end product of DNA replication?

Each DNA double helix has 1 old and 1 new strand that create 2 identical DNA molecules.

What does it mean to say there was a mutation?

A change in genetic info (nucleotides) in DNA.

What do mutations lead to?

No effect. Altered protein function. Genetic disorders/diseases. Beneficial effects. Genetic variation.

Are all mutations bad?

No some are harmful, neutral, and some are essential in the process of evolution allowing populations of organisms to change through time and adapt to their environment.

What does it mean to say that mutations are spontaneous and random?

Not dependent on what an organism wants. No specific cause/predictable pattern.

What regulates transcription?

Noncoding DNA. Promoters. Transcription factors. Enhancers/silencers. Epigenetic modifications.

What is a key enzyme that is part of transcription?

RNA polymerase.

What is different about base pairing in transcription as opposed to DNA replication?

Antiparallel. DNA template is read in opposite direction of RNA transcription synthesis. A:U instead of A:T.

How does the ribosome do translation?

Ribosome binds with mRNA at the site of translation to ensure the correct reading frame for codons in the mRNA to form string of amino acids. When ribosome reaches stop codon, end of genetic message is signaled and ribosome detached from mRNA relasing chain.

what is a ribosome made of?

rRNA and proteins

end product of translation

Chain of amino acids that eventually fold into protein.

Three kinds of RNA play roles in the central dogma: what are their names?

rRNA. tRNA. mRNA.

How do you use the table that contains the genetic code?

Use codon table to determine amino acid sequence produced from DNA/mRNA sequence. Use codon table to determine which amino acid will be carried by a tRNA, given anticodon sequence.

What process produced the diversity of life that we see all around us?

Descent w/ modification (evolution by natural selection).

What are the three requirements for evolution by natural selection?

1. Traits are variable within pop. 2. Trait variation is heritable. 3. Some individuals reproduce more than others (competition).

What are the tips of a phylogenetic tree?

Species/groups of organisms living today (MRCA).

How can you compare two phylogenetic trees to each other to tell if they are equivalent?

Same number of nodes.

Is the vast majority of life microscopic or macroscopic?

Microscopic.

Why are rRNA genes used to build the tree of life?

They are universal as the building blocks for ribosomes that create proteins that all living organisms need to evolve.