Genetics Test 2

mitosis

Eukaryotic chromosomes are only visible during

10-100 million bp in length

several 100-1000 genes interspersed throughout

origin og rep ~100,000 bp apart

telomeres have repetitive sequences at both ends

other repetitve sequnces near centromere and interspersed throughout

Centromere

recognition site for kinetochore microtubules

condense

during metaphase, chromosomes ____ 10,000 fold

in human nucleus, which is 5-10um, 46 chromo contain enough DNA to extend to more than 2 meters

Cpoiled chromatin fibers are compacted further into a chromatin ~700nm in diameter

proteins, octamers

Linear DNA interacts with ___, which affect the degree of chromosome compaction

Linear 2x stranded DNA wrap around an ___ of 2 copies each of 4 histones to form nucleosomes

H2A, H2B, H3, H4 are core histones

Histones

Basic, + charged proteins that play a critical role in chromatin

have a globular domain and a charged, flexible Histone Tail

Non-histones

are less + charged proteins

also bind the linker region and aid in chromatin compaction

they also may affect gene expression

Nucleosomes

the repeating structural unit of chromatin and condense its structure by 7 fold

147 base pairs of DNA winds around histone otamer and resemble beads on a string

Histones have a globular domain and a charged, flexible Histone Tail

Closely associate with each other to form a 30nm solenoid that is compacted ~50fold

structure is characteristic of uncoiled chromatin fiber in interphase

going into metaphase, the 30nm structure folded into series of Loop Domains that are 300nm

H1

the linker histone that binds to spacer DNA between nucleosomes, but not as tightly as the core histones

nonhistone proteins also bind the linker region and aid in chromatin compaction

plays a key role in packing of chromatin

solenoid

Nucleosomes Closely associate with each other to form a 30nm ____ that is compacted ~50fold

structure is characteristic of uncoiled chromatin fiber in interphase

going into metaphase, the 30nm structure folded into series of Loop Domains that are 300nm

Euchromatin

NOT tightly coiled

less condensed regions of chromosomes are transcriptionally active

Heterochromatin

IS condensed

tightly compacted regions of chromosomes that are in general transcriptionally inactive

unique to eukaryotes

Replicates later during S phase than euchromatin

Important in maintaining the structural integrity of chromosomes

learned inactivated X chromo is condensed into heterochrmatic Barr body

Translocation of genes into heterochromatic regions can alter gene expression if too tightly wound, unable to be expressed

interphase

during ___ , eukaryotic chromosomes are not structurally uniform from end to end

Chromatin can be induced to change its struture via chromain remodoling

histone tails are targets for a variety of chem. modification that regulate chromatin folding and gene expression

• acetylation, methylation, phosphorlyation of amino acids in histone tails

repetitive

Most of the human genome consists of ___ DNA and its function is unknown

Tandem

Middle repetitive sequences include ___ repeats and interspersed retrotransposons

Tandem repeats include: mutiple copy genes, VNTRs, STRs

Multiple copy genes

rDNA

clustered on the short arm of acrocentric chromosomes (13,14,21,22)

Variable Number of Tandem Repeats (VNTRs)

15-100 bp repeated sequences within & between genes that extend for 1-20kb in length

clusters of ___ throughout the genome are called minisatellites

Short Tandem Repeats STRs

Di-, tri-, tetra-, penta repeats (2-6bp long)

clusters of __ throughout the genome are called microsatellites

most common is (CA)n where n is 5-50 repeats

often used in DNA profiling

Transposable

___ sequences are interspersed and can relocate within the genome

SINEs and LINEs

Short interspersed elements (SINEs)

make up ~13% of genome

<500bp long present in 50,000+ times in human genome

best characterized is the Alu family which are 200-300 bp long and make up 5+% of human genome

Alu family is a group of closely related DNA sequences arising from single ancestral sequence

Long interspersed elements (LINEs)

make up ~21% of the genome

~6 kb long and present ~850,000 times in human genome

Single Nucleotide Polymorphisms (SNPs)

are the most common type of genetic variation

occur once in every 500-1000 bp

• 10 mill SNPs in the human genome

Most are between genes and have been used to identify genes in the human genome

are also used for personalized genomic meds

common type of genetic variation where a single DNA building block—called a nucleotide—differs between individuals at a specific position in a genome

DNA replication

makes DNA copies that are transmitted from cell to cell and from parent to offspring

Chromosomal DNA

stores information in units called genes

DNA does NOT directly participate in translation (protein synthesis), DNA is the blue print and stays behind

Transcription

produces an RNA copy of a gene

1st step in gene expression

involves the sythesis of mRNA that is complementary to the sequence of 1 of the 2 strands of DNA

occurs in the NUCLEUS of eukaryotic cells

mRNA is transported to the cytoplasm for translation

genetic info stored in DNA is transferred to mRNA, which directs synthesis of proteins

DNA does NOT directly participate in translation (protein synthesis), DNA is the blue print and stays behind

Messenger RNA

contains information to make a polypeptide

product of transcription is a single stranded primary ___ transcrpit

• note the 5’-3’ orientation of the __ and nontemplate strand

• they will be exactly the same sequence except for the T to U change

Translation

produces a polypeptide using information in mRNA

__ of mRNA is the polymerization of amino acids into a polypeptide chain

occurs on RIBOSOMES in the cytoplasm, each ribosome with 2 subunits composed of RNA and protein

Polypeptide

becomes part of a functional protein that contributes to an organism’s traits

Genetic Code

ATCG

• written in linear form using ‘letters’ that designate the order of the purines/pyrimidines in mRNA

• each ‘word’ in mRNA is 3 ‘letters’ so its a triplet code

  • 3 letters make up a CODON that specifies 1 amino acid

• __ is unambiguous, non-overlapping & degenerate (multiple three-letter nucleotide combinations (codons) can code for the same single amino acid)

• contains 1 start and 3 stop codons that initiate and terminate translation, resp.

• ___ is universal with some exception in mtDNA, a triplet always builds the same amino acids

• no spaces between codons in reading frame

Degeneracy

3rd nucleotide in codon is in ‘wobble’ position

multiple 3 letter sequences can code for same amino acid

RNA polymerase

directs mRNA sythesis, using only 1 strand of DNA as a template

does NOT require a primer like DNA polymerase does during rep

Adds nucleotides in the 5’-3’ direction

promoter region is present

RNA polymerase I

transcribes genes that encodes rRNA

• genes clusters (rDNA) are moderately repetitve DNA sequences near the ends of chromosomes 13, 14, 15, 21, 22

RNA polymerase II

transcribes genes that encode mRNA and snRNA

transcribes 1 strand of the double helix to generate 1 mRNA at any one time

RNA polymerase III

transcribe genes that encode tRNA and 5S rRNA

• gene clusters are on chromosome 1

Template strand

DNA strand that is transcribed

Non-template/coding/sense/partner strand

DNA strand that is complement to strand transcribed, it is NOT transcribed

Chromatin remodeling

opening up of the genetic material

must occur so that RNA polymerase and transcription factors can bind to DNA

In addition to DNA sequences that code for the intended protein, eukaryotic genes have promoter sequences and regulatory elements in the 5’ and 3’ untranslated regions (UTR)

Promoters

sequences in the 5’ untranslated regions (UTRs) of genes that signal the inition of transcription

for most structural genes, __ include

• The transcrption start site TSS

• TATA box about 25 bases upstream from the TSS

• Proximal promoter elements are further upstream

CORE ___ includes the TATA box and the TSS

Core ___ is cis acting element

Regulatory elements

short DNA sequences that affect the ability of RNA polymerase to recognize the promoter

Proximal promoter elements in the 5’UTR influence the level of basal transcription

Enhancers stimulate and silencers inhibit transcription

• can be on either side of a gene or within a gene and quite distant from the start of transcpriton (100,000bp away)

• enhancers are needed for max transcription and some are responsible for time and tissue specific gene expression

Cis acting

___ elements are DNA sequences that are located in and around eukaryotic genes to which regulatory proteins bind

Initiation

Transcpriton

occurs when the DNA strands begin to seperate and exposes a single stranded DNA template that will be transcribed into mRNA

elongation

fter a short RNA sequence has been transcibed, RNA polymerase leaves the promoter and enters into the ___ stage

termination

elongation continues until ___, ___ DNA sequences are in the 3’UTR

Stabilizing

___ mRNA

WHy

• for safe travels out of the nucleus and into cytoplasm

How

• methyl cap on 5’

• Poly A tail on 3’

• splicing of introns (non coding regions of sequence)

methylated cap

mRNA have ___ on 5’ end

poly A tail

mRNA have a ___ on the 3’ end, not encoded by the gene

Ribonuclease cleaves the 3’ end at the sequence AAUAA before transcriptional termination

another enzyme adds 100-200 ribonucleotides containg adenine to 3’ end (__)

mRNA splicing

in eukaryotes, pre mRNA processing includes removing introns and linking exons together with phosphodiester bonds

Process is called ___

human dystrophin gene is an extreme example of ___ the largest known human gene

spliceosomes

In humans, excising introns requires ___

are large complexes composed of small nuclear riboproteins (snRNPs)

• include small nuclear RNA (snRNA) and a set of proteins

They bind to an intron and precisely recognize intron/exon boundaries, holding mRNA in correct configuration

Enzymatic reactions remove introns and covalently link exons

Alternative Splicing

increases the number of proteins that can be made from a single mRNA transcript

number of proteins an organism can make is called its proteome

humans produce several hundred thousand different proteins from approximately 20,00 genes in the haploid genome by ___

Gene

specific sequence of nucleotides that contains the information required to build a protein or RNA molecule

types of __

• structural __ encode proteins

• rDNA encode rRNA and tRNA

• Regulatory RNA control __ expression

are specific sequences of DNA bases (adenine, thymine, cytosine, and guanine) arranged on chromosomes.

• Function: They act as instructions or "recipes" telling cells how to make proteins, which perform vital body functions.

tRNA (transfer RNA)

molecule that matches a triplet codon with the correct amino acid

are short molecules with 75-90 base pairs

transcribed by RNA polymerase III

each __ has an anticodon complementary to a codon in mRNA

Charged __ have an amino acid covalently bound to the 3’ end

binding between the codon and anticodon of a charged __ directs the incorporation of amino acids into a growing polypeptide chain

3 levels of structure based on degree of folding,

• Primary: linear sequence that is 75-80 nucleotide sequence

• Secondary: cloverleaf shape with 3 stem loops is formed because of short complementary sequences within the __

• Tertiary: L shape formed by 3D folding

Named acording to the amino acid they carry

Charging

Before translation can start, the tRNA molecules must be chemically linked to their respective amino acids, this activation process is called ___

occurs under the direction of enzymes called

• aminoacyl tRNA sythetase

• each synthetase recognizes ONE amino acid and the structural features of its corresponding tRNA, including its anticodon

codon, anticodon

Base pairing between an mRNA ___ and a tRNA ___ determines which amino acid is added to a growing polypeptide

AUG, start

___ codon sets the reading frame for all remaining codons

Large and small

Ribosomes have a __ and __ subunits

different parts of a ribosome have different functions

Sm. subunit binds to mRNA

RNA in the lg. subunit has peptidyl transferase activity

• it is a ribozyme that catalyzes peptide bond formation between amino acids

3 distinct binding sites: E P and A sites

Initiation factors (IFs)

Translation begins with initiation in eukaryotes and requires proteins called ___

• __ bind to small subunit and 5’ untranslated leader sequences position the mRNA, which is scanned for the 1st AUG codon

• tRNA with complementary anticodon loop binds mRNA

• Large subunit joins the complec, positioing tRNA at P site

Peptide

During elongation, new tRNAs enter the A site and a __ bond is formed between the 1st and 2nd amino acids

Ribosomes move in a 5’ to 3’ direction along the mRNA

Elongation factors EFs are required

Uncharged tRNA to E site and the complex shifts for the tRNA containing hte polypeptide is now in the P site

Release factors

Termination occurs when a stop codon is in the A site

No tRNAs carry anticodons for stop codons

____ bind to the stop codon and the ribosomal subunits, mRNA, and polypeptide disassociate