Cellular and Molecular principles of life Key terms

nucleic acid

macromolecule containing hydrogen, oxygen, nitrogen, carbon, and phosphorus

Amino Acid

compound with an amino group on one end and a carboxyl group on the other end and an R group

Essential Amino Acids

Amino acids that are needed, but cannot be made by the body; they must be eatin in foods

non-essential amino acids

amino acids that the body can synthesize on its own; does not need to get from dietary sources

amphiphilic

molecules possessing both hydrophobic (nonpolar) and a hydrophilic (polar) parts, forms bilayers

micro RNA

regulates gene expression

Mycoplasma

bacteria that lack cell wall

FECA

first eukaryote common ancestor, made from endosymbiosis of archaea and proteobacteria

Proteobacteria

Most diverse bacterial lineage

LECA

last eukaryotic common ancestor

Central Dogma

theory that states that, in cells, information only flows from DNA to RNA to proteins and not back the other way.

Watson and Crick

Developed the double helix model of DNA using x-ray crystallography

Nucleolus

Found inside the nucleus and produces ribosomes

Purines

Bases with a double-ring structure.

Adenine and Guanine

Pyrimidines

cytosine, thymine, uracil

phosphodiester bond

the type of bond that links the nucleotides in DNA or RNA. joins the phosphate group of one nucleotide to the hydroxyl group on the sugar of another nucleotide. strong covalent bonds

Double Helix

two strands of nucleotides wound about each other; structure of DNA

Transcription

synthesis of an RNA molecule from a DNA template

Translation

synthesis of a polypeptide using the information from mRNA

Histones

protein molecules around which DNA is tightly coiled in chromatin

Chromatin

Clusters of DNA, RNA, and proteins in the nucleus of a cell

Nucleosome

repeating subunit of chromatin fibers, consisting of DNA coiled around histones

Eurochromatin

loosely packed chromatin, open chromatin that allows DNA to be exposed

Heterochromatin

Eukaryotic chromatin that remains highly compacted during interphase and is generally not transcribed. closed chromatin

Chromatin Remodeling

the process of chemical changes to the DNA and histones that activate and inactivate gene expression

Histone post-translational modifications

modifications affect the histone's ability to associate with DNA and/or association with other proteins

modifying groups get added to the amino acids on the long protein tails

metacentric

centromere in middle of chromosome

submetacentric

centromere slightly off center

acrometacentric

centromere more off centre

Telecentric

Chromosome is rod shaped with a centromere at the proximal end.

Interphase

period of the cell cycle between cell divisions

Prophase

Chromosomes become visable, nuclear envelop dissolves, spindle forms

Metaphase

Chromosomes line up in the middle of the cell, the equator

mitotic spindle

a structure made of microtubules that controls chromosome movement during mitosis

Anaphase

Phase of mitosis in which the chromosomes separate and move to opposite ends of the cell

Telophase

After the chromosome seperates, the cell seals off, Final Phase of Mitosis.

Cytokinesis

division of the cytoplasm to form two separate daughter cells

FISH

fluorescent in situ hybridization to see chromosomes

semi-conservative replication

Each half of an original DNA molecule serves as a template for a new strand, and the two new DNA molecules each have one old and one new strand.

linear DNA replication

replicated bidirectionally

multiple initiation sites reduce time

initiator protein

binds to origin and separates strands of DNA to initiate replication

DNA helicase

An enzyme that breaks the double strand during DNA replication by breaking hydrogen bonds between the nitrogenous bases

Topoisomerase

Enzyme that functions in DNA replication, helping to relieve strain in the double helix ahead of the replication fork, unwinds the double helix

Primase

An enzyme that joins RNA nucleotides to make the primer using the parental DNA strand as a template.

Free dNTPs

The actual building blocks for DNA, free floating deoxy nucleoside triphosphates

DNA polymerase

Enzyme involved in DNA replication that joins individual nucleotides to produce a DNA molecule

Pyrosphosphate

in DNA replication, as each monomer of dNTP joins the DNA strand, it loses two phosphate groups as a molecule of pyrophosphate.

lagging strand

A discontinuously synthesized DNA strand that elongates by means of Okazaki fragments, each synthesized in a 5' to 3' direction away from the replication fork.

leading strand

The new continuous complementary DNA strand synthesized along the template strand in the mandatory 5' to 3' direction.

Exonuclease

removes RNA primers and replaces them with DNA dNTPs in DNA replication

DNA ligase

enzyme that chemically links DNA fragments together

Okazaki fragments

Small fragments of DNA produced on the lagging strand during DNA replication, joined later by DNA ligase to form a complete strand.

Telomeres

Repeated DNA sequences at the ends of eukaryotic chromosomes.

Erosion of genes

Loss of genetic material from chromosome ends, the shortening of telomeres

Telomerase

An enzyme that catalyzes the lengthening of telomeres in eukaryotic cells, to protect genetic data

Gene Expression

process by which a gene produces its product and the product carries out its function

intergenic regions

nontranscribed regions of DNA located between adjacent genes

Regulatory Regions

Dna nucleotide sequences that are concerned with the regulation of expression of the gene

Promoter

A specific nucleotide sequence in DNA that binds RNA polymerase and indicates where to start transcribing RNA.

Coding regions

sequences of DNA that serve as instructions for making proteins, exons

Introns

Noncoding segments of nucleic acid that lie between coding sequences, they are spliced out before the RNA is translated into a protein

Exons

Coding segments of eukaryotic DNA.

Dystrophin

the longest human gene

mRNA

messenger RNA; type of RNA that carries instructions from DNA in the nucleus to the ribosome

rRNA

ribosomal RNA; type of RNA that makes up part of the ribosome

transcription bubble

site where transcription begins

transcription unit

A region of DNA that is transcribed into an RNA molecule, contains the promoter, RNA coding region and a terminator

RNA polymerase II

transcribes mRNA, transcribes genes encoding proteins

basal apparatus

The complex of transcription factors that assembles at the promoter before RNA polymerase is bound

RNA pol II promoters

consist of a "core promoter" that can be composed of a number of elements, including the TATA box (TATA sequence upstream of start site)

TATA box

A promoter DNA sequence crucial in forming the transcription initiation complex.

TFIID

the first general transcription factor to bind the promoter, binds to the TATA box through the TATA binding protein (TBP). This bond leads to DNA bending and unwinding

regulatory promoter

located immediately upstream of the core promoter, bind to transcription factors and regulate the speed of the process of transcription

Mediator complex

A protein complex that acts as an adaptor that interacts with transcription factors bound to regulatory sites and with general initiation factors for RNA polymerase II-mediated transcription.

enhancers and silencers

speed up or slow down the rate of transcription

abortive initiation

checkpoint to regulate gene expression, a rate limiting control on gene activation. When the transcript is long enough, the RNA pol II leaves the promoter region to make space for the next round

Elongation

RNA nucleotides are added to the chain using RNA pol II

Termination

RNA pol continues synthesising, pre-mRNA is cleaved while this is happening. The extra RNA stretch is degraded by Rat 1. transcription stops when rat 1 reaches the polymerase

Pre-mRNA Cleavage

Separation of pre-mRNA from growing RNA chain.

Rat1

exonuclease that degrades mRNA being produced by RNA polymerase from 5' to 3' end, and when it catches up with the RNA polymerase, it causes the polymerase to fall off the template --> termination of transcription

Noncolinearity

Eukaryotic genes have interrupted coding sequences - presence of introns

5' cap

A modified form of guanine nucleotide and methylation added onto the nucleotide at the 5' end of a pre-mRNA molecule. the cap increases mRNA stability

Methylation

addition of a methyl group

poly-A tail

Modified end of the 3' end of an mRNA molecule consisting of the addition of some 50 to 250 adenine nucleotides.

consensus sequence

the most commonly occurring bases within a sequence element. required to indicate where splicing occurs

Splicing

the process of removing introns and reconnecting exons in a pre-mRNA

5' splice site

GU at the beginning of the intron

3' splice site

AG at end of intron

branch point sequence

- located 18-38 nucleotides upstream of 3' junction site

- it is a conserved sequence that always possesses an A nucleotide

splicosome

An enzyme that splices introns out of RNA.

ribonucleoprotein

made of protein and rRNA

lariat

during splicing, the intron is released in this shape

alternative splicing

same DNA molecule can be spliced in different ways to generate different mRNA products

Polydenylation

Adds a tail to mRNA and helps move molecules out of the nucleus

ribonucleoprotein complexes

Molecular assemblies of RNA and proteins.

Nuclear Export

Process of transporting RNA out of the nucleus.

nuclear pore complex

large protein channels embedded in nuclear envelope that allow RNA and other macromolecules to pass from nucleus to cytoplasm

export receptors

bind to RNPs and guide them to pores in the nucleus in order to release into cytoplasm

Nucleoporins

proteins that make up the nuclear pore complex which facilitate transport

Ran-GTP

a small GTPase that regulates the directionality of transport of macromolecules out of the nucleus