POB Exam 2 Vocabulary

Photosynthesis

A process that transforms light energy into chemical energy — meaning the potential energy found in electrons that participate in covalent bonds, usually in sugars or other carbohydrates.

pigment

A molecule that absorbs specific wavelengths of light.

chlorophyll

The primary photosynthetic pigment in land plants and most algae.

photosystem ii

A complex of molecular machines that acquire electrons by oxidizing water, use the energy in sunlight to excite those electrons to a high-energy state, and pass them on to an electron carrier that feeds the electron transport chain, leading to ATP production by ATP synthase.

photosystem i

A complex of molecular machines that receive low-energy electrons at the end of the electron transport chain, use the energy in sunlight to excite those electrons to a high-energy state, and pass them on to electron carriers that either feed the electron transport chain or an enzyme that catalyzes the reduction of NADP⁺ to NADPH.

calvin cycle

A series of reactions that results in carbon from CO₂ being “fixed,” or reduced, and used to synthesize sugars.

rubisco

The enzyme that catalyzes the reduction of CO₂ and its incorporation into sugars.

stomata

Openings in stems and leaves that allow gas exchange via diffusion along their concentration gradients — most importantly, CO₂ to enter and O₂ to leave.

guard cells

Specialized epidermal cells that regulate the size of stomata depending on environmental conditions.

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.

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.

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.

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.

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.

non-template (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).

promoter

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

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.

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.

codon

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

start codon

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

stop codon

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

gene expression

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

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.

exon

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 chromosome.

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.

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.

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.

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.)

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.

deleterious mutation

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

gene

A segment of DNA that codes for a protein or RNA product. Genes comprise both structural and regulatory elements.

chromosome

A complex of DNA-binding proteins and DNA. Chromosomes are circular in most bacteria and archaea and linear in eukaryotes.

haploid number

The number of different types of chromosomes present in a cell. Haploid number is indicated with an n. Humans have 23 different types of chromosomes, so in that species n = 23.

ploidy

The number of each type of chromosome present in a cell. written as a number before the n that presents haploid number. Humans, for example, are 2n, meaning that they have two of each type of chromosomes.

haploid

Having one of each type of chromosome.

diploid

Having two of each type of chromosome.

Homologous chromosomes (or simply homologs)

Different versions of the same chromosome type.

replicated chromosomes

A chromosome comprised of two identical DNA molecules, joined together.

sister chromatids

The identical copies in a replicated chromosome.

mitosis

A process in eukaryotes that is responsible for distributing a copy of each chromosome to each daughter cell. It occurs after chromosomes have been replicated and prior to the physical division of the parent cell into two daughter cells.

m phase

The portion of the cell cycle when mitosis and cell division occur.

interphase

The portion of the cell cycle when growth and DNA replication occur.

prophase

The initial phase of mitosis, when replicated chromosomes condense and the nuclear envelope breaks down.

metaphase

The middle phase of mitosis, when replicated chromosomes move to the middle of the cell.

anaphase and telophase

The late phases of mitosis, when sister chromatids separate and one of each type of chromosome ends up at either end of the parent cell, then nuclear envelopes re-form around each set of chromosomes.

germ cells

Cells that directly give rise to sperm or eggs, or are sperm or eggs themselves.  Germ cells undergo meiosis to produce haploid daughter cells.

somatic cells

Cells that form the body, and that only undergo mitosis.

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.

kinase

An enzyme that catalyzes the addition of a phosphate group from ATP to a recipient molecule.

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

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.