CELS191 Flashcards

Flashcards covering a range of topics from the CELS191 course.

Phylogenetic Tree

A branching diagram that represents the evolutionary relationships between different species or groups of organisms.

Three Domains of Life

Bacteria, Archaea, and Eukarya.

Cellular organization

How the components of a cell are arranged inside that cell.

Reproduction

The process of producing offspring (sexual or asexual reproduction).

Metabolism

The chemical reactions that occur within a cell to convert macromolecules into energy, building blocks, and waste products.

Homeostasis

Ability to maintain a constant state.

Heredity

The passing on of genetic information from one generation to the next.

Response to stimuli

Ability to sense and respond to changes in the environment.

Growth and Development

Increases in size and maturity over the life-span.

Adaptation through evolution

The process of an organism or species becoming better suited to its environment over generations.

The Tree of Life

A special phylogenetic tree that shows how all life is related to each other through evolution, grouped into three domains: Bacteria, Archaea, and Eukarya. DNA sequences were used to construct this tree.

Phylogenetic Trees

A diagram used to show relationships between species where lines on the diagram are called branches and the length of lines represents time (or number of differences) between species; points where lines split are called nodes that represent the last common ancestor between species and species that are closer together on the tree are more closely related.

Eukaryotes

Organisms from domain Eukarya that can be single-celled or multi-celled, large cell size (10 to 100 µm), have organelles (e.g. nucleus, golgi body, mitochondria), and photosynthetic eukaryotes have chloroplasts.

Prokaryotes

Organisms from Archaea and Bacteria domains that are single-celled, small cell size (1 to 5 µm), and lack organelles.

Common Cell Structures

All eukaryotic and prokaryotic cells have a cell or plasma membrane, cytosol (cellular fluid), ribosomes, and chromosome(s) (can be DNA or RNA). Some cell-types have a cell wall (can be prokaryotic or eukaryotic).

Endosymbiont Theory

The widely accepted theory that mitochondria and chloroplasts were originally derived from free-living prokaryotic cells. Mitochondria from proteobacteria (aerobic bacteria) and Chloroplasts from cyanobacteria (photosynthetic bacteria). Have their own DNA and ribosomes. Can synthesise some (but not all) of their own proteins.

Plasma membrane

Supramolecular structures surrounding the outside of both eukaryotic and prokaryotic cells made from three macromolecules: Lipids, Proteins, and Carbohydrates.

Lipids

Not polymeric, are heterogeneous, grouped together because they are hydrophobic, and examples include steroids, phospholipids, triacylglycerols. Phospholipids and cholesterol are key structural components in the cell membrane

Proteins

The molecules by which cells perform their functions that are diverse in function and abundant within the cell. They are polymeric where a monomer of a protein is an amino acid and 20 amino acids differ by their ‘R’ group (side chain).

Carbohydrates

Sugars and macromolecules of sugars that are involved in building structures, energy storage, and recognition.

Diffusion

Movement of liquids, solids, or gases from a region where they are more concentrated to a region where they are less concentrated.

Facilitated Diffusion

Movement of molecules across membranes down their concentration gradient, facilitated by proteins.

Active Transport

Requires energy (usually in the form of ATP) to pump substances in or out of cells/compartments against their concentration gradient.

Co-Transport

Coupling of diffusion of one substance (A) to the transport of another substance (B) that is going against its concentration gradient.

Bulk Transport

Cells use vesicles/vacuoles to move things in/out of the cell in these cases. Two forms: Exocytosis (out) and Endocytosis (in).

Exocytosis

Cellular secretion of biological molecules when vesicles fuse with the plasma membrane. Two types: Constitutive exocytosis and Regulated exocytosis

Endocytosis

Intake of biological molecules from outside the cell where the plasma membrane forms “fingers” that wrap around extracellular fluid/molecules. Three forms: Phagocytosis, Pinocytosis, and Receptor-mediated endocytosis

Chloroplasts

Convert light energy to chemical energy (glucose).

Mitochondria

Convert chemical energy to ATP (energy transfer molecule).

Photosynthesis

Converting light energy to chemical energy. Occurs in two stages and requires different compartments: The Light Reactions occur in the thylakoid and the Calvin cycle occurs in the stroma where the overall goal is creation of glucose.

Light Reactions

Light energy is captured by chlorophyl pigments in Photosystem II and two electrons are sent down the electron transport chain. The cytochrome complex pumps protons into the thylakoid space for ATP Synthase to use when making ATP

Calvin Cycle

Uses ATP and NADPH from the light reactions to build organic carbohydrates (sugars). Easy to think about “three turns” at once: Carbon Fixation, Reduction Phase, and Regeneration Phase

Cellular Respiration

Harvesting chemical energy from glucose. Occurs in three stages and requires different compartments: Glycolysis occurs in the cytosol, Citric acid cycle occurs in the mitochondrial matrix, and Oxidative phosphorylation occurs in the intermembrane space across the inner membrane where the overall goal is creation of ATP.

Energy Molecules: ATP and ADP

ATP (adenosine triphosphate) is our major energy transfer molecule where cellular respiration converts energy from glucose to ATP for our cells. Energy is released upon breaking of the phosphate bonds in ATP converting ATP to ADP (adenosine diphosphate).

Energy Molecules: NADH and FADH2

High energy electron carriers, electrons are added in the form of added H+. Involved in redox (reduction/oxidation) reactions where oxidation is the loss of electrons (or loss of hydrogen) and the reduced form: NADH or FADH2.

Glycolysis

In the cytosol, Glucose (sugar) is converted to two smaller molecules of pyruvate and generates a small amount of ATP (energy molecule) where electrons are transferred to the high energy electron carrier (NAD+), making NADH.

Pyruvate Oxidation and Citric Acid Cycle

In the mitochondrial matrix, Pyruvate is converted into Acetyl CoA (a 2-Carbon molecule) where Acetyl CoA enters the citric acid cycle. Generates a small amount of ATP (energy molecule) and high energy electron carriers NADH and FADH2.

Oxidative Phosphorylation

In the inner membrane of the mitochondrion and uses the intermembrane space. Two parts: 1. Electron transport chain: Energy from electrons inNADH and FADH2 used. 2. Chemiosmosis: ATP production

Transcription

Overall purpose is to make an RNA (messenger RNA = mRNA) copy of the coding strand of DNA. Transcribes the mRNA from the template strand is from the template strand, Occurs in the nucleus. Three stages:Initiation, Elongation, and Termination

Eukaryotic Genes

Eukaryotic genes have same basic structure that can be coded in either direction along a chromosome with a Promoter, 5’ UTR, “Coding Sequence”, and 3’ UTR

Transcription: Initiation

Transcription factors bind to a section of the DNA, called the promoter region.A eukaryotic promoter region commonly includes a TATA box where transcription initiation complex gets formed.

Transcription: Elongation

RNA polymerase moves along the DNA creating an mRNA copy of the sequence; It unwinds the double-stranded DNA; It “reads” the template DNA strand; It joins RNA nucleotides as they base-pair to the DNA template strand.

Transcription: Termination

The DNA strand contains a terminator signal sequence that signals the detachment of the pre-mRNA molecule. THIS IS THE END OF TRANSCRIPTION.

RNA Processing

In eukaryotes, the RNA transcript is modified before it is ready to leave the nucleus and mRNA is called a “pre-mRNA” before this processing.

RNA Processing: End Modifications

Modification of the 5’ end, 5’ G cap (a modified guanine) is added to the 5’ end of the pre-mRNA and Modification of the 3’ end, Poly-A tail (Made of ~200 Adenine nucleotides) is added to the 3’ end of the pre-mRNA

RNA Processing: Splicing

Areas of non-coding nucleic acid (called introns) are removed where the remaining segments of the RNA strand (called exons) are spliced (stuck) together. The exons are the part of the original gene that will be translated into amino acids.

Translation

Overall purpose is to make a polypeptide (protein) using the message encoded by mRNA where tRNA molecules are able to translate the message from nucleotides to amino acids. Occurs in the cytoplasm on ribosomes- free floating or bound to endoplasmic reticulum.

Ribosomes

Ribosomes are made up of ribosomal RNA (rRNA) and protein where rRNA made in the nucleolus and rRNA combines with proteins synthesized in the cytosol and imported back to the nucleus to make subunits.

Codons, tRNA, and Amino Acids

The mRNA is “read” in nucleotide triplets called a codon where The codons are interpreted by transfer RNAs (tRNAs). Each tRNA is attached to a specific amino acid.

Translation: Initiation

First, the small ribosomal subunit (with tRNA attached) binds to the 5’ end of the mRNA where the small ribosomal subunit scans along the mRNA until it reaches the start codon (AUG). Next, the large ribosomal subunit attaches and the mRNA, small ribosomal subunit, tRNA and large ribosomal subunit form the translation initiation complex.

Translation: Elongation

The very first tRNA docks in the P site and the next tRNA (and every other tRNA afterwards) docks in the A site.

Translation: Termination

A stop codon (UAG, UAA or UGA) is recognized where a protein called a release factor enters the A site, instead of a tRNA. The release factor prompts the polypeptide to detach from the tRNA in the P site.

Nucleic Acid Structure

Polymeric molecules are “macromolecules created by polymerization of monomers” Nucleic acids (DNA and RNA) are polymers of nucleotides.

Nucleotide Structure

Each nucleotide monomer consists of a phosphate group, pentose sugar, and nucleobase (or nitrogenous base).

DNA Structure

DNA is formed from two nucleic acid strands. Strands are anti-parallel – run in opposite directions.Backbones of strands are on the outside of the molecule. Bases point inwards, bound in pairs.

Nucleobases

Four bases in DNA: Adenine (A), cytosine (C), guanine (G), thymine (T). Cytosine and thymine are pyrimidines. Adenine and guanine are purines. Purines always pair (hydrogen bond) with pyrimidines. A = T (two hydrogen bonds) and G ≡ C (three hydrogen bonds).

DNA Replication

As DNA is anti-parallel, the two strands are replicated in slightly different ways. The leading strand is made continuously and the lagging strand is made in short fragments/same enzymes are involved in replicating both strands.

DNA Replication: Helicase

Unwinds parental DNA and begins to travel away from "origin of replication" . Creates a "replication fork" where DNA behind it is single-stranded (ready to be replicated) and DNA ahead of it is double-stranded (unable to be replicated yet).

DNA Replication: Single-Stranded Binding Proteins

Bind to and stabilize single-stranded DNA and prevent unwound DNA from winding back up again.

DNA Replication: Topoisomerase

Relieves stress and strain ahead of replication forks. Prevents DNA ahead of helicase from becoming too tightly wound.

DNA Replication: Primase

Makes an RNA primer to start DNA replication creating a double-strand by adding a primer at the 5’ end.

DNA Replication: DNA Polymerase III

Builds the new DNA strand and uses the unwound parental strand as a template while reading parental strand in 3' to 5' direction, builds new strand in 5' to 3' direction.

DNA Replication: DNA Polymerase I

Removes RNA nucleotides of primer and replaces them with DNA nucleotides.

DNA Replication: Ligase

Joins (ligates) DNA backbones of neighbouring fragments together. Joins Okazaki fragments of lagging strand.

DNA Replication Errors

Errors can be made when DNA is replicated and Errors can be fixed by exonuclease or endonuclease enzymes.

Exonuclease

DNA polymerase III has exonuclease abilities that fixes mistakes as it makes them giving DNA pol III extremely low error rate (~1 in 1 billion).

Endonuclease

Fix mistakes AFTER replication is complete where the Generic process = Removes a portion of DNA around error, DNA pol III replaces portion of DNA, and Ligase sticks new portion to rest of strand.

Cell Division: Mitosis

For growth and repair happens throughout the life-time of an organism where it Makes identical cells.

Cell Division: Meiosis

For producing gametes only happens in ovaries and testes that Makes non- identical cells.

Before Cell Division: Replicated Chromosome

Chromosome that consists of two sister chromatids where Sister chromatids are genetically identical.

Cell Division: Terminology-Haploid and Diploid

Haploid= One copy of each chromosome/ diploi= Two copies of each chromosome

Cell Division: Terminology-Homologous Chromosomes

Chromosomes come in pairs called a homologous pair where One chromosome in pair from each parent, the same length, and the same genes.

Cell Division: Terminology-Non-Sister Chromatids

Sister chromatids are two chromatids making up the same chromosome where Non-sister chromatids are chromatids that come from the other chromosome in the homologous pair and have the same length, genes, and position of the centromere.

Chromosomal Aberrations

Arise from errors in cell division and can happen either in mitosis or meiosis where Chromosomal aberrations in sperm/eggs contribute to infertility.

Chromosomal Aberrations: Numeric

Aneuploidy can cause too many or too few of a certain chromosome caused by non-disjunction: monosomy or trisomy

Cell Division: Terminology-Crossing Over

The reciprocal exchange of genetic material between non-sister chromatids only happens in Prophase 1 that Generates different combinations of genotypes.

Definitions of Mendelian Genetics-Phenotype

An observable physical, biological, or behavioural trait in an organism -Encoded for by alleles.

Definitions of Mendelian Genetics- Allele

The different versions of a gene- Result in different phenotypes between organisms

Exceptions to Mendel’s Laws- Sex-Linked Traits

Gene is located on a sex chromosome that changes the ratio of phenotypes between males and females.

Exceptions to Mendel’s Laws-Linked Genes

Cannot assort independently as they are on the same chromosome and can either be completely linked or incompletely linked that has parental or non-parental

The Human Genome Project

Large international collaborative research project that aimed to sequence entire human genome completed from 1990 to 2003.

Types of Human Variation: SNPs

Single nucleotide polymorphisms (SNPs): Single base change in genetic sequence where Up to four possible alleles (A, T, C, or G) across the human genome.

Types of Human Variation: STRs

STRs: Short tandem repeats: Short segments of repeated sequence:repeats of a 2 to 6 base pair long piece of sequence where each person gets two alleles (one from each parent).

Types of Human Variation: InDels

An insertion or deletion of nucleotide bases in the genome where It can cause frame-shifts.

Gene Therapy

The introduction of genes into an affected individual for therapeutic purposes

Stem Cells

Unspecialised cells that can divide to produce multiple different types of cells. Process of differentiation converts a cell from a stem cell to a specialized cell.

Bacterial Pathogens

Most bacteria are beneficial or have no effect on our health, but some bacteria are pathogenic (disease-causing).

Virulence Factors

Factors that help the bacterial with the 4 stages of microbial pathogenesis that are either Non-Toxic, Toxic, Endotoxins, or Exotoxins.

Horizontal Gene Transfer: Transformation

Competent cells can take up DNA from the environment that incorporate into bacterial chromosome or plasmids

Horizontal Gene Transfer: Transduction

Where Bacteriophage accidentally injects bacterial DNA into a new bacterial recipient cell.

Horizontal Gene Transfer: Conjugation

Is Direct transfer of plasmid DNA between two cells (same or different species) that are temporarily joined by a conjugation pilus

Viral Structures: Genome

All viruses have a nucleic acid genome: DNA or RNA, Single-stranded or double-stranded, Circular, linear, or segmented

Viral Structures: Capsid

All viruses have a protein coat (capsid) around their genome. Capsids have three general shapes: Helical, Icosahedral, and Complex.

Viral Structures: Envelope

Some viruses have an envelope surrounding the capsid.Viruses without an envelope are called “naked” viruses.

Viral Infections: 6 Steps

1.Attachment. 2. Penetration. 3. Uncoating. 4. Replication. 5. Assembly 6. Release