Mcat Biochem - Ch. 7

Front 1

gene

Back 1

- unit of DNA that encodes a specific protein or RNA molecule.

- expression is through transcription and translation

Front 2

Central dogma of molecular biology

Back 2

DNA -- (transcription) -- RNA -- (translation)-- Protein

RNA -- (reverse transcription)-- DNA

DNA -- (replication) -- DNA

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Messenger RNA

Back 3

- carries info specifying the amino acid sequence of the protein to the ribosome

- transcribed from DNA by RNA polymerase in the nucleus

- Eukaryotes = monocistronic

- prokaryotes = polycistronic

Front 4

codons

Back 4

- 3 nucleotide segments that are translated into amino acids

- written in the 5' to 3' direction

- on mRNA

- recognized by anti-codon on tRNA

- 3 nucleotides = reading frame

Front 5

transfer RNA

Back 5

- converts language of nucleic acids to language of amino acids and peptides

- contains anticodon

- can be charged/uncharged with an amino acid

- found in the cytoplasm

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aminoacyl-tRNA synthetase

Back 6

- different ones activate different amino acids

- requires two high-energy bonds from ATP

- transfers activated amino acid to the 3' end of the correct tRNA

Front 7

CCA nucleotide

Back 7

- on tRNA

- where the amino acid binds

Front 8

ribosomal RNA

Back 8

-synthesized in the nucleus

- used in protein assembly in the cytoplasm

- may function as ribozymes (enzymes made up of ribosomes instead of peptides)

- catalyzes formation of peptide bonds

-responsible in splicing out its own introns within the nucleus

Front 9

Starting/ending amino acid

Back 9

- methiomne

- start codon = AUG

- ending codon= UGA, UAA, UAG

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Wobble position

Back 10

- 3rd letter In the codon sequence

- mutations here are called silent or degenerate

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point mutation

Back 11

- when a mutation occurs and it affects one of the nucleotides in a codon

- expressed mutation

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missense mutation

Back 12

- type of expressed point mutation

- one amino acid substitutes for another

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nonsense mutation

Back 13

- type of expressed point mutation

- codon encodes for a premature stop codon

-"truncation mutation"

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frameshift mutation

Back 14

- when nucleotides are added or deleted from the mRNA sequence

Front 15

transcription

Back 15

- creation of mRNA from a DNA template

- synthesized by RNA polymerase (binds in the promoter region -- TATA box)

Front 16

RNA polymerases

Back 16

-1 : in the nucleus, synthesizes rRNA

-2 : in the nucleus, synthesizes hnRNA, & small nuclear RNA (snRNA)

-3 : in the nucleus, synthesizes tRNA and some rRNA

-travels in the 3' to 5' direction

- does not proofread

- thymine = uracil

Front 17

heterogeneous nuclear RNA

Back 17

-"hnRNA"

-primary transcript of RNA

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Splicing

Back 18

- of hnRNA

- removes introns (noncoding sequences) and keeps exons (ligate coding sequences)

- accomplished by splicesome

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5' cap

Back 19

- end of hnRNA

- 7-methylguanylate triphosphate cap is added

- recognized as binding site

- protects mRNA from degradation in cytoplasm

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3' Poly-A-Tail

Back 20

- protects against rapid degradation

- composed of adenine bases

Front 21

alternative splicing

Back 21

- primary transcript of hnRNA may be spliced together in different ways to produce multiple variants of proteins encoded by the same original gene.

Front 22

translation

Back 22

- starts when mRNA is in the cytoplasm

-converts the mRNA transcript into a functional protein

- 3 stages: initiation, elongation, and termination

Front 23

Ribosome

Back 23

- composed of proteins and rRNA

- functions to bring the mRNA message and the carged aminoacyl-tRNA together to create a protein

- 3 binding sites for tRNA = A, P, and E.

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Translation: initiation

Back 24

- small subunit binds to the shine-dalgarno sequence 5' end of mRNA

-charged initiator of tRNA binds to the AUG start codon

- large subunit binds to the small subunit (forms initiation complex)--- assisted by initiation factors

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Translation: Elongation

Back 25

- ribosome moves in 5' to 3' direction and synthesizes proteins from its amino to carboxyl terminus

Front 26

A site

Back 26

- holds incoming aminacyl-tRNA complex

Front 27

P site

Back 27

- holds tRNA that carries the growing polypeptide chain

-peptide bond is formed as polypeptide is passed from P to A site (with the help of peptidyl transferase and GTP)

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E site

Back 28

- where uncharged tRNA pauses before exiting the ribosome

Front 29

Elongation factors

Back 29

- locate and recruit aminoacyl-tRNA along with GTP

- removes GDP when the energy has been used

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Termination

Back 30

-when any of the 3 stop codons move into the A site

Front 31

Release Factor

Back 31

- protein that binds the termination codon and causes a water molecule to be added to the polypeptide chain

- released at the P site

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Chaperones

Back 32

-assist in the protein folding process

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Phosphorylation

Back 33

- addition of phosphates by protein kinases to activate or deactivate proteins

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Carboxylation

Back 34

- addition of carboxylic acid groups, usually to serve as calcium-binding sites

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Glycosylation

Back 35

- addition of oligosaccharides as proteins pass through the ER and Golgi apparatus to determine cellular destination

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Prenylation

Back 36

- addition of lipid groups to certain membrane-bound enzymes

Front 37

Operon

Back 37

- cluster of genes transcribed as a single mRNA

- 2 types: inducible and repressible

Front 38

Jacob- Monod Model

Back 38

- used to describe the structure and function of operons

- structural gene, operator site, promoter site, and regulator gene

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structural gene

Back 39

- codes for the protein of interest

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operator site

Back 40

- nonstranscribable region of DNA that is capable of binding a repressor protein

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promoter site

Back 41

-provides a place for RNA polymerase to bind

Front 42

regulator gene

Back 42

-codes for a protein known as the repressor

Front 43

Operon: inducible systems

Back 43

- repressor is bonded tightly to the operator system and acts as a road block

- RNA polymerase is unable to move from the promoter

Front 44

negative control

Back 44

- binding of a protein reduces transcriptional activity

Front 45

catabolite activator protein (CAP)

Back 45

- transcriptional activator used by E.coli when glucose levels are low to signal that alternative sources should be used.

Front 46

positive control mechanisms

Back 46

- binding of a molecule increases transcription of a gene

Front 47

Operon: repressible systems

Back 47

- allows constant production of a protein product until corepressor binds to the repressor to stop translation

- serves as a negative feedback

Front 48

corepressor

Back 48

- what the repressor binds to in order to activate

Front 49

Transcription factors

Back 49

- transcription-activating proteins that search the DNA looking for DNA-binding motifs

Front 50

DNA binding domain

Back 50

- Transcription factor

- binds to nucleotide sequence in the promoter region or a DNA response element

Front 51

activation domain

Back 51

- allows for the binding of several transcription factors important regulatory proteins

Front 52

Enhancers

Back 52

- allows for the control of ones genes expression by multiple signals

- transcription factor that binds to a specific DNA sequence

- Ex: enhancer binds to RNA polymerase at a signal promoter sequence and enables the RNA polymerase to transcribe the specific gene

Front 53

Gene duplication

Back 53

- in series on the same chromosome = many copies in a row of the same genetic info

- in parallel = by opening the gene with helicases and permitting DNA replication only of that gene

Front 54

Heterochromatin

Back 54

- tightly coiled DNA that appears dark under the microscope

- tight coiling makes it inaccessible to the transcription machinery so the genes are inactive

Front 55

Euchromatin

Back 55

- looser DNA and appears light under a microscope

- transcription machinery can access genes of interest

Front 56

histone acetylases

Back 56

- proteins involved in chromatin remodeling

Front 57

Acetylation

Back 57

- decreases the positive charge on lysine residues and weakens the interaction of the histone with DNA

- results in an open chromatin conformation that allows for easier access of the transcriptional machinery to the DNA

Front 58

Histone deacetylases

Back 58

proteins that function to remove acetyl groups from histones

- results in closed chromatin conformation

- decreases gene expression

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DNA Methylation

Back 59

- involved in chromatin remodeling and regulation of gene expression

- DNA Methylases add methyl groups to cytosine and adenine nucleotides

- linked with silencing of gene expression

Front 60

shRNA

Back 60

- targets mRNA to be degraded in the cytoplasm

- BINDS to hnRNA to induce splicing