Foundations of Bio Test 4

central dogma

principle or set of principles laid down and currently true

central dogma of biology

the process of making proteins comes from information in DNA and can be analyzed on many different levels

DNA

holds the information to make proteins

proteins

determine a lot about how a cell or organism functions and looks

amino acids

monomers of proteins

nucleotides

monomers of nucleic acids

RNA

nucleic acid; mediates protein synthesis during transcription and translation by carrying protein-encoding information

4 steps of transcription

initiation, elongation, termination, processing

transpcription

mRNA copies of genes are made by RNA polymerase

chromatin

DNA + histones

histones

protein complexes responsible for packing DNA

euchromatin

open, loosely packed DNA easy to access by regulatory proteins; copied or used

heterochromatin

closed, tightly packed region of DNA hard to access by regulatory proteins; not copied or used

transcription factors (TFs) (x2)

proteins that bind to DNA and regulate gene expression; activators and repressors

activators

TF protein promoting transcription

repressors

TF protein stopping transcription

general transcription factors (GTFs)

proteins binding to DNA regulating gene expression; bind upstream of every gene needing transcribed in TATAA box

RNA polymerase

an enzyme making polymers of RNA using DNA as a template

sigma factor

protein binding to promotor DNA region to guide RNA polymerase to the correct location; GTF of prokaryotes

introns

removed from strand during alternative splicing; stay IN the nucleus

exons

join together on mRNA strand; EXit nucleus

protein variation

ability to get multiple protein variations from 1 gene; discredits the 1 gene = 1 protein hypothesis

properties of genetic code (x6)

triplet, non-overlapping, redundant, unambiguous, punctuated, universal

triplet property of genetic code

all “words” of the genetic language are 3 RNA nucleotides long

1 start codon in genetic code

AUG

3 stop codons in genetic code

UAA, UAG, UGA

redundant property of genetic code

most amino acids in genetic code are represented by more than one codon

unambiguous property of genetic code

codons are exclusive; each codon specifies only 1 amino acid

universal property of genetic code

the same codons specify the same amino acids and stop codons in all organisms

3 RNAs that mediate/ carry out translation

tRNA, rRNA, mRNA

tRNA synthases

attach amino acid to tRNA with the corresponding anticodon

3 tRNA binding sites on large ribosomal subunit

A (amino acyl tRNA), P (polypeptide/ pepitidyl), E (exit)

A (amino acyl tRNA) site

where anticodon of charged tRNA binds with its complementary codon in mRNA; access site

P (polypeptide/ peptidyl) site

where tRNA adds its amino acid to the growing chain (polymerization site)

E (exit) site

where tRNA sits before being released from the ribosome

phosphorylation

added phosphate groups; alters the shape of the protein

glycosylation

adding sugars; important for targeting and recognition

proteolysis

cleaving the polypeptide; allows the fragments to fold into different shapes

mutations

changes in the DNA/ nucleotide sequence of the genome; can change protein shape and function

causes of mutations

DNA replication, spontaneous chemical changes, mutagens

somatic mutations

occur in somatic (body) cells; may have consequences for the phenotype of an individual; not passed to offspring

germ line mutations

occur in germ line cells (gametes); passed to offspring; can have consequences for future generations

point mutations

changes to 1 nucleotide; classified by phenotypic effect

types of point mutations (6)

silent, missense (conservative/ non-conservative), nonsense, frameshift (insertion/ deletion)

silent mutation

change in DNA bases, but the amino acid stays the same; no impact on protein function

missense mutation

amino acid does change

conservative missense mutation

chemical property of a new amino acid is the same as the original; may not fold protein all the way/ halfway right

non-conservative missense mutation

chemical property of new amino acid is different from the original; closes up active site and loses function

nonsense mutation

amino acid changes to a stop codon (sentence ended early); results in loss of function

frameshift mutation

addition (insertion) or deletion of a DNA base changes how the mRNA is read; sometimes results in loss of function and sometimes gain; can have more significant effects on final protein

differential gene expression

a biochemical process that determines which genes respond to which signals or triggers depending on the condition; regulated at 3 levels

3 levels of gene expression

transcriptional, translational, and post-translational controls

negative control

regulatory protein shuts down transcription

positive control

regulatory protein triggers transcription

operon

a group of genes transcribed together and regulated by a shared promoter and operator

inducer

small molecule triggering transcription of a gene; goes with TF

operator

sequence of DNA a transcription factor binds to

catabolite activator protein (CAP)

activated when cAMP is present; when there is ample glucose outside the cell, there is no cAMP synthesis, and CAP doesn’t bind DNA to activate lac operon expression

lactose absent

repressor activated, operon not expressed

lactose present + glucose present

repressor inactivated, activator not activated, operon expressed at low levels

lactose present + glucose absent

repressor inactivated, CAP activated, operon expressed at higher levels

tryptophan

important amino acid; if prokaryote can’t get from the environment, it can express the enzymes to make its own

regulon

a set of separate genes and operons containing the same regulatory sequences and are controlled by a single type of regulatory protein

sos regulon

DNA damage control

nucleosome

8 histones and DNA wrapped around them; part of chromatin

epigenetics

duplicating the entire chromatin structure so DNA and chromatin-associated proteins are all duplicated

core promoter

binding site for GTFs and where RNA polymerase II binds

promoter- proximal elements

binding site for activator/ repressor proteins (TFs); close to promoter

distal- regulatory elements

DNA sequences farther away from protein coding DNA sequence; can be upstream or downstream of coding region; facilitate chromatin remodeling; where TFs bind

3 distal-regulatory elements

enhancer, silencer, insulator

enhancer

increases transcription; distal-regulatory element

silencer

decreases transcription; distal-regulatory element

insulator

stops heterochromatin from spreading and silencing gene; maintains transcription; distal-regulatory element

mediator protein

binds activating TFs to loop DNA and maintain open chromatin; binds GTFs which call over and bind RNA polymerase II to start transcription

preaxial polydactyly

point mutation in enhancer binding site leads to abnormal expression of gene; causes extra fingers