Biology final vocab

Physiology

The study of systems that allow organisms to fulfill functions such as processing food and waste, reproducing, and defending against disease.

Proximate causation

 Explanations that focus on the molecular and cellular mechanisms responsible for a function.

Ultimate causation

Explanations that focus on why structures and processes observed in an organism exist in terms of their evolutionary history and impact on fitness.

Cell

Membrane-bound structures that form the fundamental unit of life.

Tissue

Groups of cells that perform a common function.

Organ

Two or more tissues that create a structure with a specific function.

Herbivore

An animal that eats plant tissues.

Pathogen

 Any agent that causes disease—usually a fungus, virus, or bacterium.

System

Groups of organs that together perform an integrated function.

Stomata

Regulated openings in leaves where gas exchange occurs (the singular form of the term is stoma)

Fitness trade-off

An unavoidable conflict between maximizing the fitness benefits and minimizing the fitness costs in aspects of one or more traits.

Plasticity

The ability of the same genotype to produce different phenotypes in response to different environmental conditions.

Membrane voltage

In cells, an electrical potential created by a separation of charge across a membrane. Also called a transmembrane potential or a membrane potential

Electric current:

In cells, a flow of charge in the form of ions

Concentration gradient

A difference in the concentration of an ion or molecule in one area versus another, often across a cell membrane or organelle membrane. Substances move down their concentration gradients passively and spontaneously, via diffusion.

Electric potential gradient

A difference in charge carried by ions in one area versus another, almost always across a cell membrane or organelle membrane. Substances move down their electric potential gradients passively and spontaneously, toward unlike charges and away from like charges.

Electrochemical gradient

The overall gradient across a cell membrane or organelle membrane, produced by differences in concentration of substances combined with differences in the distribution of charge.

Hormone

A molecule that acts as a long-distance signal between cells in the same multicellular individual.

Ligand

Any molecule that binds to a receptor and triggers a response. Includes both long-distance and short-distance cell-to-cell signals as well as intracellular signals.

Signal transduction

A change in the form of a signal, for example from a hormone that binds to a receptor on the surface of a cell to a second messenger or phosphorylation cascade inside the cell.

Phosphorylation cascade

A chain reaction that amplifies the signal from a chemical messenger. It occurs when each kinase in a signaling network phosphorylates multiple target proteins, which each then go on to phosphorylate multiple target proteins, and so on.

Second messenger

An ion or small molecule that is released in response to a chemical messenger binding to a cell-surface receptor and acts as an intracellular signal

Homeostasis

Self-regulating biological processes that maintain stable conditions in the body in the face of changing external conditions. Critical for Health: Disruption of homeostasis is a root cause of many diseases (e.g., obesity, type 2 diabetes, coronary artery disease).

Positive feedback

A response by a physiological system that increases the amount that a regulated condition differs from the normal level. It is the opposite of a corrective, self-limiting step.

Negative feedback

A response by a physiological system that returns a regulated condition back to the normal and preferred level. It is a corrective, self-limiting step or event.

Set point

In a homeostatic system, the preferred value or range of an internal variable or condition.

Gene

A segment of DNA that contains the information required to produce a product that functions in the organism.

Alleles

Different versions of a gene that have slight variations in the DNA sequence found in other alleles of the same gene.

Transcription

The process that creates an RNA molecule from information stored in a gene.

Translation

The process that uses the information in messenger RNA (mRNA) to synthesize a protein.

Wild type

The typical or most common version of an allele or phenotype, as opposed to novel, unusual, or low-fitness forms.

Co-dominant alleles

Heterozygotes have the phenotype associated with both alleles present. 

Loss-of-function alleles

Alleles that lead to a protein or RNA product that cannot function normally or is completely absent.

Sext chromosome

A chromosome associated with the sext of the individual.

Autosome

Any chromosome that is not a sext chromosome. 

Sext-linked genes

Genes found on a sext chromosome.

Linked genes

Genes found on the same chromosome

Telomerase

 An enzyme that catalyzes the addition of deoxyribonucleotides to lagging strands at either end of a linear chromosome, thus helping to solve the end-replication problem.

Stem cells

A “professional divider” cell. After each round of mitosis and cell division, one daughter cell becomes a stem cell and the other becomes a specialized cell type that no longer divides. Different types of stem cells give rise to daughter cells which then mature into specific cell types.

DNA proofreading

 The ability of DNA polymerase to respond when it adds the wrong base by mistake by 1) pausing synthesis of the new strand, 2) removing the mismatched base with an exonuclease activity, and 3) adding the correct base.

DNA mismatch repair

Proteins and enzymes work on newly synthesized DNA molecules to recognize and repair mismatched bases.

DNA excision repair

 Proteins and enzymes work on DNA molecules long after replication is complete to recognize and repair damaged areas as they arise

DNA polymerase

An enzyme that catalyzes the formation of phosphodiester linkages between deoxyribonucleotides, forming the primary structure of DNA

DNA ligase

An enzyme that catalyzes the formation of phosphodiester linkages in gaps between two existing nucleotides in double-stranded DNA.

Origin of replication

A location (a point) where enzymes open the DNA double helix so replication can begin.

Replication fork

The y-shaped structure visible in micrographs of DNA during replication. This is the site where the replisome works, synthesizing the leading and lagging strands.

Primase

An enzyme that adds a short RNA primer to single-stranded DNA, so DNA polymerase can start adding complementary bases

Replisome

 The multi-molecular machine that works at the replication fork, copying DNA.

Helicase

An enzyme in the replisome that opens the DNA double helix, creating single-stranded template DNA for leading and lagging strand synthesis.

Topoisomerase

An enzyme that is important in DNA replication. It breaks and rejoins DNA to relieve the tension created when helicase continuously opens the double helix

DNA endonuclease

Nucleotides on the damaged strand are removed

Anticodon

A sequence of three bases found at one end of a tRNA that binds to a codon in mRNA during translation via complementary base pairing.

Release factor

A protein that fits into the A site of a ribosome, binds to a stop codon, and interacts with the ribosome to terminate translation

Reading frame

The sets of three-base codons in RNA or DNA that specify the primary sequence of amino acids in a protein; is set by the start codon, and identifies the subsequent sequence of codons.

Ribozyme

An RNA molecule that catalyzes a chemical reaction, analogous to enzymes, which are protein catalysts.

RNA polymerase

An enzyme that catalyzes the formation of phosophodiester linkages between ribonucleotides, forming an RNA product that is complementary to the sequences of bases in a DNA template.

Template strand

The strand in a DNA double helix that is “read” by RNA polymerase during transcription.

Positive control (over gene expression)

Mechanisms that increase the amount of active gene product available.

Negative control (over gene expression)

Mechanisms that decrease the amount of active gene product available.

Operon

A sequence of structural gene sequences whose products have related functions and that are under the control of the same promoter and other regulatory sequences, meaning that they are transcribed as a unit.

Transcription factors

Proteins that regulate transcription, often by binding to regulatory sequences in DNA.

Exons

 In eukaryotic genes, sections of the coding sequence code for amino acids found in a protein product.

Introns

 In eukaryotic genes, sections of the coding sequence that are transcribed but later removed before an mRNA is translated into a protein product.

Chromatin

The complex of DNA and histones that makes up a chromosom

Nucleosome

A group of four histone proteins that has DNA wrapped around it.

Histone proteins

Proteins that have an abundance of positively charged lysines and arginines in their primary structure, which interact with negative charges on the sugar-phosphate backbone of DNA to form nucleosomes

5′ cap

 A modified form of the nucleotide guanine (G) that is added to the 5′ end of a pre-mRNA in eukaryotes, during RNA processing that occurs prior to export from the nucleus.

Intron splicing:

Removing introns from pre-mRNAs and rejoining exons into a continuous strand, during RNA processing that occurs prior to export from the nucleus.

Poly-A tail:

A long series of adenine (A) nucleotides that is added to the 3′ end of a pre-mRNA in eukaryotes, during RNA processing that occurs prior to export from the nucleus.

Protein phosphorylation

The addition of a phosphate group or ATP to a protein.

Kinase

An enzyme that adds a phosphate group to other proteins.

Gene expression

The entire set of processes that results in using the information stored in a gene.

mutation

Any change in the genetic information in DNA

Missense mutation

A change in a single base that alters the mRNA codon and changes the amino acid at that position in the protein product.

Coding DNA strand	TAT TCT CGA GAC AAC ACC
Resulting protein	Tyr Ser Arg Asp Asn Thr

Nonsense mutation

A change in a single base that alters the mRNA codon to a new and premature stop codon in the mRNA, shortening the protein product.

Coding DNA strand	TA(A) TCT CGA GGC AAC ACC
Resulting protein	[STOP]

Silent mutation

 A change in a single base that alters the mRNA codon but does not change the amino acid at that position in the protein product. (Also called a synonymous substitution.)

Coding DNA strand	TAT TC(C) CGA GGC AAC ACC
Resulting protein	Tyr Ser Arg Gly Asn Thr

Frameshift mutation

A change in DNA that alters the reading frame of codons in an mRNA, resulting in altered codons in mRNA and altered amino acids in the protein product.

Coding DNA strand	TAT TCT CGA G(A)G CAA CAC C
Resulting protein	Tyr Ser Arg Glu Gln His

Deleterious mutation

Any mutation that decreases fitness; deleterious mutations that lead to early death are termed lethal.

 three main sources of mutation

1. Errors that occur when DNA is being copied prior to mitosis or meiosis

2. Physical or chemical damage to DNA

3. Errors that occur as chromosomes are being moved during mitosis or meiosis.

Cancer

A family of diseases all characterized by uncontrolled cell division as the underlying cause.

Metastasis

The process of tumor cells breaking away from a tumor, traveling to new locations, and starting new tumors.

Cell cycle:

An orderly, highly regulated, and precisely controlled sequence of events that occurs as cells grow and divide.

Cell cycle checkpoints

Intervals in the cell cycle when regulatory proteins check specific aspects of the cell for damage, especially DNA, and allow or prevent continued progress through the cycle.

Tumor suppressors

Genes whose protein products function as regulatory molecules at cell cycle checkpoints, preventing uncontrolled division of damaged cells.

Stop codon

A codon that signals where translation and thus protein synthesis ends. Usually UAA, UAG, and UGA.

Start codon

The codon that signals where translation and thus protein synthesis begins. Usually AUG and also codes for the amino acid methionine (Met).

Codon

 A group of three bases in an mRNA that codes for an amino acid. 

Genetic code

The set of relationships between the 64 possible codons in mRNA and the amino acids that are added to a newly synthesized protein.

Promoter

The regulatory sequence in a gene or operon where RNA polymerase initiates transcription.

Non-template strand (coding strand)

The strand in a DNA double helix that matches the sequence of bases in the RNA product of transcription, except that the DNA contains thymine (T) and the RNA contains uracil (U).