Bis 101 midterm 1

Chromosome

piece dsDNA (N)

Ploidy

xn

gene

sequence DNA in genome encodes info and direct synthesis of bio end product

somatic

any cell except gamete

gamete

sex cell

allele

gene varient

wild type

common

null type

non functioning

genome

entire gene set

gene expression

cellular pdocuction of biological molecules riven by info encoded in DNA sequence

Genetic material

Heritable, mutable, readable, stable

prokaryote DNA

circular

eukaryote DNA

double stranded linear

nucleotide

contains 5 carbon sugar, nitrogenous base, phosphate group

nucleoside

contains 5 carbon sugar, nitrogenous base

Nitrogenous base carbon

C1

phosphate carbon

C5

RNA

less stable, more reactive, single stranded, xtra OH on C2, transcription and translation

DNA

only OH on C3, more stable, less reactive, double stranded, DNA

watson crick double helix

anti parallel, double stranded, Nitrogenous bases in middle via h-bonds, Phosphate and OH bond C5 and C3 on outside via phosphodiester bond

chargaff

A=T (2 bonds) G=C (3 bonds)

pyridines

T and C

Purines

A and G

transcription

process of reading single stranded DNA and building RNA based off of it (reads 5-3 and made 3-5)

steps of transcription and translation

1. Initiation

2. elongation

3. terminate

transcription initiation

Protein recognizes gene 2 start, start via promoter (DNA sequence) upstream of start site recognized via proteins

sigma factor

(-35,-10) helps recognize promoter to recruit RNA Poly to bind (different sigma factor = different gene expression)

RNA polymerase

synthesize RNA at +1, no primar “de novo”, all or nothing if any change it won’t work

core enzyme

part of RNA polymerase weak promoter when alone

holoenzyme

recognizes promoter, unwinds transcription

promoter

specific region of DNA located upstream (5’) of a gene that acts as a binding site for RNA polymerase and transcription factors to initiate gene transcription (stregnth affects how it latches and matches)

DNA template

noncoding strand and complementary of RNA (1 strand = 1 template)

Non Template DNA

same as RNA but change T to U

termination sequence/termination

specific DNA sequence that signals the end of gene transcription and transcribed still

Transcription of prokaryotes

1 RNA polymerase, polytrinsic, simple, occur in cytoplasm, translation and transcription coupled, only make mRNA

transcription of Eukaryotes

3 RNA polymerase, complex + relaxed initiation, occur in nucleus, transcription and translation compartmentalized, have cap and tail, many different rnas, splicing, monotrinsic

RNA polymerase I

transcribed rrna

RNA polymerase II

transcribed mrna

RNA polymerase III

transcribed trna

polytrinsic

mrna strand can complete many different proteins

monotrinsic

mrna only transcribes 1 protein

exons

exit nucleus and is the ORF(in mrna)

introns

stay in nucleus (removed from prerna)

spliceosome

use functional rna and proteins to recognize mrna facilitate splicing

transcription unit

contiuous stretch

DNA encodes primary transcript

coding region, introns, and utr (always expressed and necessary)

transcription factors

proteins that bind to DNA to regulate transcription initiation, always expressed and necessary

general transcription factors

all transcription factors required 4 transcription initiation by rna polymerize it regulates, specific for each RNA poly, +

specific transcription factors

regulate transcription, initiate specific genes, set of genes, + or - depending on sequence binded to

coding region

portion transcription unit that determines primary sequence of protein based on coding region (ORF)

5’ cap

contains methylguanylate, extra guanine, protect + prevent degradation, UTR

poly A tail (3’)

contains a lot of a lot of A, added post transcriptionally

mature mrna

mrna after spliced start-stop codon(protein product)

translation

read 3-5 and made 5-3 (uses trna rrna and ribosomes)

steps of translation

A dds amino acid

P ut peptide bond together

E ribsome and protein exits

what helps match TRNA to according amino acid from mrna strand

aminoacyl trna synthase

shrine delgrano sequence

AGGAGGU helps ribosome bind prior to AUG

Initiation factors (IFs)

helps small unit bind (ex 5’ cap)

translation termination

stop codon and has release factor (protein) so no other amino acids bind to it as it’s recognized (2GPT = 2GDP + 2Pi)

mutation

any change in DNA sequence from base line is hertiable

point mutation

nonsense/missense/synonymous

frame shift

causes massive change and early start unless + or - 3 nucleotides, insertion and deletion

germ mutation

entire organism changes (carries mutation to offspring)

somatic mutation

certain part in body and doesn’t pass down

operon

clusters of genes that are linked covalently together and transcribed to single rna transcript (only in prokaryotes/very rare in eukaryotes)

(+) transcript regulation

activator binds to active binding site increasing RNA ability to find start site (b4 promotes) can use allosteric inhibition to remove it

allosteric inhibition for transcript regulation

add to activator to remove ability to bind to the active binding site decreasing ability for RNA polymerase to find it

(-) transcript regulation

inhibitor binds to promoter (after promoter) at operator blocking rna polymerase to build strand and use allosteric activation to remove it

allosteric activator for transcript regualation

gets added to inhibitor to remove ability for it to bind on operator causing transcription

effector

added to substrate to change configuration to make active site available

operator

cis acting meaning they only affect one

repressors

trans-acting means they are mobile and can act on multiple operators/promoters

cap

(+) regulator of lac operans transcription, when it binds it increases RNA polymerase and increases transcription of operon

cap binding site

where cap binds

Cap and CAMP

only when cap is bound from camp it can bind to activator to recruit RNA polymerase, (Camp is allosteric activator of Cap)

When there is a lot of glucose

inactive cap decreasing transcription

glucose and camp relationship

inversely proportional

regulation of gene expression in prokaryotes

respond quickly to environment, gene clustered in operons, + and - regulation of gene expression

genome of all cell types in an individual are identical

true, they are expressed differently

what is more related different cells types in the same individual or same cell types in different individuals

same individual as there have the same intial genome prior to differentiation

transcription factors binding

know where to bind through protein interactions from dna sequences

enhancers

dna sequences when bound and specific trna increases transcription initiation (sometimes they’re required for transcription initiation

silencers

dna sequences, when bound for specific transcription factors, decrease transcription initiation (even inhibitors)

similarity of both enhancers and silencers

upstream/downstream in a gene, act at a distance, TF bind here, cis acting, tissue/cell specific

Chromatin structure

Packaging of dna saves to genes for transcription

Transcription initiation (gene regulation)

Most control of gene expression is via regulation of transcription initiation and can be regulated by binding specific dna sequences

RNA splicing

Gene expression can be controlled by rate of pattern of splicing

Translation control

Gene silencing occurs by micro RNA’s blocking translation of mRNA and availability of translation machinery can regulate of protein synthesis

post translational

Chemical modifications to proteins alter their function and activity (phosphates, methyl, acetyl, ubiquitous which degrades proteins)

Micro rna

functional rna molecules encoded for in dna and can inhibit translation of some mRNA. Is anti // and complementary to target mRNAs 3utr that is regulates

Regulation of translation microrna

After mRNA transcription and extra processing that’s ss can change but pair with target mRNA (- regulates)

RNA binding proteins

Can affect rna stability binding to 3/5 Utr increasing stability. Can be chemical modifications to rna to increase/decrease stability

proto oncogene

Promotes cell growth

tumor suppressor genes

Inhibit cell growth

Epigenetics

Above genetics which is heritable stable dna in the gene in gene expression that occur due to alternatices in chromatin (can by dynamic and reversible and response to environment)

Epigenome

Collection of all epigenetic change in chemical shifts

Nucleosome

Basic unit of chromatin (histone portions and 1.67 turns of dna )

Euchromatin

Open chromatin, turns transcription on, loosely packed nucleosomes, high acceptability for transcription machinery

Heterochromatin

Closer chromatin, transcription off, densely packed nucleosomes, low accessibility

Histones

Tails and can be modified to alter chromatin stability, condensation, and accessibility of DNa (+ charge),