BIOMG 1350 - Vocabulary

Vocab for prelim one

What do all living things have in common

common origin (LUCA), similar DNA sequences, basic chemistry, fundamental processes

prokaryotes

archaea/bacteria, no nucleus, single celled, no membrane-bound organelles, evolutionary successful

eukaryotes

eukaryotes, cells have a nucleus, membrane bound organelles

Theory of Endosymbiosis

two prokaryotic cells merged to form a eukaryotic cell with a mitochondria (only happened once with plants and once with chloroplasts)

surface per cell volume

larger ratio (as in smaller cells) makes it more efficient as reactions are carried out on cell membranes

compartmentalization

cells complete many reactions that need to be separated (benefit of membrane-bound organelles)

molecule is fluorescent if…

it absorbs wavelength of one wavelength and emits light of a longer wavelength

Green Fluorescent Protein (GFP)

comes from jellyfish Aequoria Victoria, fluorescent green, fluoresces on its own, scientists have modified to have more colors, helps identify location of cell components

plasma membrane

separates cell from environment, mediates interactions with environment (signaling, nutrient uptake, endo- and exocytosis)

cytoplasm

everything in between plasma membrane and nucleus

Cytosol

soluble portion of cytoplasm outside of organelles, crowded with many chemical reactions (like protein synthesis)

nucleus

contains the genome, replication and transcription here, nucleolus

nucleolus

where ribosomes are assembled (darker region)

endoplasmic reticulum

primary site for synthesis of lipids and membrane proteins/secreted proteins

Golgi Apparatus/complex

modification of secretory proteins, sorting station for vesicle tracking

mitochondria

major site for ATP production (oxidative phosphorylation), production of major metabolites (amino acids and nucleotides)

Central Dogma of Molecular Biology

DNA sequence → mRNA sequence → protein sequence

macromolecules (biological polymers)

abundant in cells, signature of life, each one is a polymer constructed from monomers, formed by condensation

condensation/dehydration synthesis

a chemical reaction that joins smaller molecules together to form a larger molecule while releasing a water molecule as a byproduct

nucleic acids

DNA and RNA

DNA (deoxyribonucleic acid)

monomers are deoxynucleotides (use deoxyribose) form polymers by phosphodiester linkages, the genetic material

deoxyribose

2’ carbon carries a second hydrogen (instead of OH), effects on stability of DNA

deoxynucleotide polymer

base + 5-carbon sugar (deoxynucleoside) + phosphate

structure of DNA

double-stranded antiparallel double helix with sugar-phosphate backbones on the outside and complementary nitrogenous bases paired inside

complementary base pairing in DNA

adenine (A) pairs with thymine (T) via 2 hydrogen bonds; cytosine (C) pairs with (G) via 3 hydrogen bonds

antiparallel DNA strands

one strand runs 5’ → 3’ direction while the complementary strand runs in the 3’ → 5’ direction

phosphodiester bond

covalent linkage connecting the 3’ hydroxyl group of one sugar to the 5’ phosphate group of the adjacent nucleotide

purines vs. pyrimidines in DNA

purines (adenine and guanine) have a double-ring structure; pyrimidines (cytosine and thymine) have a single-ring structure

DNA replication

semiconservative process of copying a double-stranded DNA molecule to produce two identical DNA copies

semiconservative replication

mechanism where each newly synthesized DNA molecule contains one original parental strand and one newly synthesized strand

DNA helicase

enzyme that unwinds and separates the double-stranded DNA helix at the replication fork by breaking hydrogen bonds

primase

RNA polymerase that synthesizes a short RNA primer to supply a free 3’ hydroxyl group required by DNA polymerase—provide 3’ hydroxyl group required by DNA polymerase

short RNA molecule

RNA primer, provides the free 3’-OH group for DNA polymerase to start DNA synthesis

DNA polymerase

enzyme responsible for synthesizing new DNA strands in the 5’ → 3’ direction by adding complementary nucleotides

leading strand

DNA strand synthesized continuously toward the replication fork in the 5’ → 3’ direction

lagging strand

DNA strand synthesized discontinuously away from the replication fork in short segments

Okazaki fragments

short segments of newly synthesized DNA produced on the lagging strand during replication

DNA ligase

enzyme that seals nicks in the sugar-phosphate backbone by joining Okazaki fragments with phosphodiester bonds

end-replication problem

inability of DNA polymerases to completely replicate the extreme 5’ end of the lagging strand, causing linear chromosomes to shorten over repeated divisions

telomeres

repetitive, non-coding nucleotide sequences at the terminals of linear eukaryotic chromosomes that protect vital genetic information from degradation and prevent chromosome end fusion

telomerase

ribonucleoprotein enzyme that extends chromosome ends by synthesizing repetitive telomeric DNA using its own internal RNA template

replication bubbles and multiple origins

feature of eukaryotic chromosome duplication where replication initiates at many sites simultaneously, creating expanding open regions where bidirectional synthesis occurs to replicate large linear genomes efficiently

chromatin

complex of DNA and protein (mainly histones) that packages long DNA molecules into a compact structure inside eukaryotic nuclei

histones

positively charged proteins around which eukaryotic DNA wraps, forming nucleosomes to organize and package the genome

nucleosome

basic repeating structural unit of chromatin, consisting of a segment of DNA wound around an octamer of core histone proteins

genome

the sum of all genes (genetic information) of a given organism

ribose

the 5-carbon sugar in RNA; unlike DNA’s deoxyribose, it has an -OH group on the 2’ carbon

uracil

a nitrogenous base found in RNA that replaces thymine (T); it pairs with adenine

single-stranded

RNA is generally single-stranded, but it can fold back on itself through complementary base pairing to form complex 3D structures

gene

a segment of DNA containing the information needed to produce a functional RNA or protein

promoter

a DNA sequence where RNA polymerase and other transcription machinery bind to initiate transcription

template strand

the DNA strand that RNA polymerase reads 3’ → 5’ to make a complementary RNA strand

coding DNA

the DNA strand that has essentially the same sequence as the RNA transcript, except DNA has T where RNA has U

transcription

the process of making RNA from a DNA template

RNA nucleotide

made of ribose + phosphate group + nitrogenous base (A, U, C, or G)

complementary base pairing

during transcription, DNA bases determine the RNA sequence (A-U, T-A, C-G, G-C)

5’ → 3’ direction

the direction in which RNA is synthesizes; RNA polymerase adds new nucleotides to the 3’ end

transcription start site

The specific nucleotide in DNA where RNA synthesis begins, usually designated +1. It is located within/just downstream of the promoter region

elongation

the stage of transcription when RNA polymerase moves along the template DNA and adds RNA nucleotides to the growing RNA strand

termination

The transcription stage ends when RNA polymerase receives a termination signal, stops RNA synthesis, and releases the RNA transcript. Translation ends when a release factor binds to the stop codon

mRNA (messenger RNA)

an RNA molecule that carries the genetic information copied from DNA and can be used by a ribosome to make a protein

terminator

a DNA sequence that signals the end of transcription

advantages of cells making RNA

three different types of RNA (mRNA, tRNA, rRNA) work together in protein synthesis (translation)

genes can be encoded in both DNA strands

The promoter’s position and orientation determine where RNA synthesis starts and which strand serves as the template. Many RNA polymerases can transcribe a single gene simultaneously.

function of mRNA (messenger RNA)

protein coding

function of rRNA (ribosomal RNA)

protein synthesis (machinery), RNA that combines with proteins to form ribosomes and plays an important structural and catalytic role in translation

function of tRNA (transfer RNA)

protein synthesis (adaptors to mRNA), carries a specific amino acid to the ribosome during translation

what does transcription allow

amplification and regulation (can be regulated to change cell behavior)

intron

sequences of RNA that are removed during RNA splicing

exon

squences that remain in the mRNA after RNA splicing

RNA splicing

the process of removing introns and joining exons together to produce mature mRNA

5’ capping

Addition of a modified guanine nucleotide (5’ cap) to the 5’ end of a pre-mRNA. This protects the RNA and aids in nuclear export and translation, and helps ribosome recognize mRNA

polyadenylation

the addition of a poly (A) tail—a string of adenine nucleotides—to the 3’ end of a pre-mRNA it helps to increase mRNA stability and assists with nuclear export and translation

pre-mRNA

initial RNA transcript made from a protein-coding gene that has not yet undergone all of its processing

Mature mRNA

processed mRNA containing a 5’ cap, joined exons, and usually a 3’ poly (A) tail, ready to leave nucleus and be translated

modifications to mRNA (like poly A tail and 5’ cap) can affect…

how quickly mRNA is turned over (mRNA stability) and how efficiently mRNA is translated

spliceosome

a complex of snRNAs and proteins that removes introns and joins exons during RNA splicing

snRNA (small nuclear RNA)

small RNA molecules found in the nucleus that combine with proteins to form the spliceosome and help recognize and remove introns during RNA splicing

amino acid

The building blocks of proteins. During translation, amino acids are linked together to form a polypeptide/protein

codon

a sequence of 3 nucleotides on mRNA that specifies an amino acid or signals the end of translation, defined by 3 nucleotides

how many nucleotides define a codon?

3 nucleotides

how many possible codons are there

64 possible codons—61 code for amino acids and 3 are stop codons

start codon

AUG. signals beginning of translation (and codes for methionine)

stop codon(s)

UAA, UAG, or UGA (don’t have to memorize) signal the end of translation and do not code for amino acid

anticodon

a sequence of 3 nucleotides on tRNA that is complementary to an mRNA codon

anticodon loop

the region of a tRNA that contains its anticodon, which pairs with a complementary codon on mRNA

how is mRNA read during translation?

ribosome reads mRNA 5’ → 3’, one codon at a time

how does a codon determine an amino acid

a tRNA with a complementary anticodon binds the codon, bringing its attached amino acid to the ribosome

what are the monomers of proteins?

amino acids

aminoacyl-tRNA synthetase

an enzyme that attaches the correct amino acid to its corresponding tRNA, ensures that the correct amino acid is attached to each tRNA, helping connect mRNA codon sequence to the correct amino acid sequence

small ribosomal subunit

the smaller part of the ribosome that binds the mRNA and helps position it for translation

large ribosomal subunit

the larger part of the ribosome that contains the sites where tRNAs interact and peptide bonds are formed

ribosome

complex made of rRNA and proteins, consisting of a small subunit and a large subunit, it is the site of protein synthesis

what do peptide bonds do

covalent bonds that link amino acids together during translation to form a growing polypeptide

condensation reaction (dehydration synthesis)

a chemical reaction that joins to molecules together while removing a molecule of water (H₂O)

how does dehydration synthesis relate to proteins

amino acids are joined together by condensation reactions, forming polypeptide bonds and releasing water

what occurs chemically during peptide bond with two amino acids?

an -OH from the carboxyl group of one amino acid and an H from the amino group of another combine to form H₂O, leaving a peptide bond between the amino acids

hydrolysis

a reaction that breaks a chemical bond by adding water; is essentially the reverse of dehydration synthesis

amino group

a functional group found in amino acids containing nitrogen, typically written as -NH₂ or NH₃ (depending on pH). it is one of the two groups that make up the backbone of an amino acid