Genetics Midterm 1

UCI bio sci 97

gene

• the physical unit for heredity

• composed of defined dna sequences that control dna transcription and contain the information needed to produc functional rna or protein

difference between chromosome structure of sexually reproducing animals and bacteria

sexually reproducing: usually diploid with homologus pairs of chromosomes (1 homolog from each parent). their gametes are haploid

bacteria: haploid with 1 circular chromosome, reproduce through binary fission

meiosis

cell goes from diploid —> haploid (2x as many daughter cells, so end up with 4 daughter cells)

mitosis

cell division in somatic cells producing genetically identical daughter cells

genotype

an organisms genetic composition

phenotype

the observable traits that result from the genotype and environment

are alleles part of a genotype or phenotype?

part of an organisms genotype

The central Dogma

flow of genetic information in a cell

DNA —> RNA —> Protein

why is DNAs double helix special?

the two strand are complementary, when they separate they can each serve as a template strand to build a new complementary strand

purpose for gel electrophoresis

• a method to separate DNA fragments based on their size

• DNA is negatively charged and an electric current pulls it towards the positive end

• smaller fragments —> move through gel more easily and travel farther

• larger fragments move slowly and dont travel as far

3 important properties of genetic material

1. precise replication: be able to copy itself with very few mistakes (DNA must be stable)

2. information: must be able to store lots of information compactly

3. mutation: must undergo mutagenesis at a low rate

dNMP (deoxyribonucleoside monophosphate) structure and function

• deoxyribose sugar

• 1 phosphate group

• 1 nitrogenous base (A,T,C,G)

• function: units that make up the DNA strand

dNTP ( deoxyribonucleoside triphosphate) structure and function

• deoxyribose sugar

• 1 nitrogenous base (A, T,C,G)

• 3 phosphate groups

• function: DNA building blocks to grow the strand (release 2 phosphate groups when its joined)

purines

• A and G

• two ring structure

pyrimidines

• T, C, and U

• 1 ring structure

how can you separate dna strands?

• can break hydrogen bonds between complementary bases using heat (denaturation)

how many hydrogen bonds are between A and T?

2 hydrogen bonds

how many hydrogen bonds are between G and C?

3 hydrogen bonds

which direction does polymerization ALWAYS occur?

5’ —> 3"‘

polymerization

join nucleotides together to form the DNA strand

helicase

unwinds/ unzips DNA during DNA replication

SSBs (single strand binding proteins)

keeps two DNA strands separated (prevents hydrogen bonds between base pairs to reform)

Gyrase

an enzyme that relieves the twisting and tension that builds up in DNA ahead of replication fork (relieve torsional stress)

RNA primase

an enzyme that makes a short RNA primer during DNA replication

DNA polymerase

an enzyme that builds new DNA strand during DNA replication

CAN ONLY ADD NUCLEOTIDES TO THE 3’ END

new DNA is synthesized 5’ —>3’

DNA ligase

seals ends

where does PCR DNA replication take place?

a test tube (doubles the amount of DNA with each cycle)

what is required for a PCR?

• template DNA

• 2 primers (short sequences that define where copying starts)

• DNA polymerase (usually Taq polymerase)

• dNTPS (the nucleotides used to build new strands)

Steps for PCR

1. denaturation: DNA is heated and strands separate

2. Annealing: primers bind to template

3. extension: DNA polymerase adds nucleotides

Semiconservative DNA replication

each new DNA molecule contains one original strand and one newly synthesized strand

antiparallel

dna runs antiparallel:1 strand is 5’ —> 3’ and the other runs 3’ —> 5’

chain terminating nucleotides (ddNTPs) structure and function

• stop DNA synthesis when added to a growing DNA strand

• lack the 3’OH group needed to continue synthesis

• used in sanger sequencing

Sanger sequencing

• method used to determine exact sequence of bases in a DNA strand

• use a template strand to make copies of DNA occasionally adding ddNTPs to create DNA fragments of different lengths

• fragments get seperated using gel electrophoesis and read shortest —> longest

• uses fluorescent dyes to label nucleotide bases

next generation sequencing

• can read millions of DNA fragments at the same time (faster than sanger)

• Cuts DNA into many small fragments

• all the fragments are copied and sequenced simultaneously

• a machine detects the bases being added

• a computer puts overlapping sequences together and reads them at the same time to put them back together

what gives us our phenotype?

proteins

which direction does RNA polymerase move?

5’ —> 3’

uracil

RNA ONLY, replace T when pairing with A

RNA polymerase

an enzyme that makes RNA from a DNA template during transcription

what does DNA need to be copied into before it becomes proteins?

messenger RNA (mRNA)

Promoter

• a specific DNA sequence where RNA polymerase binds to begin transcription (determines start and direction)

• Upstream on gene

common prokaryote promoter

-10 and -35 regions

Common eukaryote promoter

TATA box

where does transcription take place in prokaryotes?

the cytoplasm

where does transcription occur in eukaryotes?

the nucleus

true/ false: translation and transcrition can happen simultaneously in eukaryotes

FALSE, can occur simultaneously in prokaryotes ONLY, eukaryotes its seperate

+1 nucleotide

first nucleotide of RNA to be transcribed

Enhancer

• DNA sequence that INCREASES transcription of a gene

• binding site for activator proteins

• can be close or far (upstream or downstream)

Silencer

• DNA sequence that decreases/ prevents transscription of a gene

• binding site for repressor proteins

• can be located close/ far

splicing

• removing introns from pre-mRNA and joining remaining exons together to make mature mRNA

• eukaryotes

• occurs at site determined by consensus sequenced

Alternative splicing

• cell splices the same pre-mRNA in different ways, producing different combos of exons (getting different proteins)

• order of exons not altered, only number

3 essential ribosome tasks

1. bind mRNA - identify start codon where translation begins

2. bind tRNAs - hold tRNAs to facilitate complementary base pairing

3. form peptide bonds - join amino acids together to build growing protein

codon

group of 3 bases on mRNA that code for amino acids

anticodon

3 nucleotides on a tRNA that is complementary to mRNA codon

tRNA (transfer RNA)

type of RNA that brings the correct amino acid to the ribosome during translation

amino acid

small molecule that i the building block for proteins

peptide bond

chemical bond connecting 2 amino acids to each other

polypeptide

long chain of amino acids (make up enzymes, different proteins, and hormones)

explain the process on translation (3 steps)

1. initiation: ribosome binds to mRNA and reads its codons, a tRNA with the anticodon brings in correct amino acids

2. elongation: ribosome moves along mRNA one codon t a time slowly making peptide bonds and adding amino acids

3. termination: ribosome reaches stop codon

in which direction is a polypeptide synthesized?

N-terminus —> C- terminus

what is a UTR?

• untranslated region

• 5’ UTR before start codon

• 3’ UTR after stop codon

in which direction is mRNA translated?

5’ —> 3’

polycistronic mRNA

single mRNA molecule that contains instructions to make multiple proteins

synonymous codons

different codon that code for the same amino acid

third base wobble

refers to the fact that the third base of an mRNA codon can sometimes vary without changing the amino acid

how do the aminoacyl- tRNA synthetases “translate” the genetic code

an enzyme that matches the correct amino acid to the correct tRNA

point mutation

a single nucleotide in DNA is changed

silent mutation

DNA/ mRNA codon is changed but amino acid is the same

missense mutation

change in 1 nucleotide causing a different amino acid to be added

nonsense mutation

point mutation that changes a codon into a stop codon

frameshift mutation

nucleotides are added/ deleted NOT in a multiple of 3

regulatory mutation

mutation in DNA region that controls when, where, or how much a gene is expressed (ex: promoter)

forward mutation

change in gene from wild type —> mutant type

reverse mutation

changes a mutant gene back to wild type

terminator

DNA sequence that signals RNA polymerase to stop transcription

how many proteins does each eukaryotic mRNA code for?

one

to which terminus are amino acids added to on a peptide chain?

C- terminus (dehydration reaction joins amino acids together)

function of aminoacyl tRNA syntheses

attach amino acids to tRNAs

A site

location on ribosome where new tRNA enters carrying amino acid

P site

location on ribosome that holds the tRNA carrying the growing peptide chain

E site

location on ribosome that empty tRNA exists the ribosome

true/ false: a single mRNA can be translated multiple times

TRUE: the same mRNA can be used to make many copies of the same protein

polysomes

groups of multiple ribosomes simultaneously translating the same mRNA molecule

intragenic reversion

a second mutation within the same gene that restores the original function that was lost because of the first mutation

second-site reversion

a second mutation occurs at a different location from the original mutation and restores the genes normal function/ phenotype

what are the 3 key structural/ chemical differences between DNA and RNA?

1. different sugars

2. different bases (DNA uses T while RNA uses U)

3. structure: DNA is double stranded while RNA is single stranded

define mRNA

carries genetic message from DNA and translates into amino acids forming a polypeptide

define tRNA

transports specific amino acid to ribosome during translation

rRNA

forms the large and small subunits where translation of mRNA into polypeptides takes place

what are the three major differences in transcription between prokaryotes and eukaryotes

1. location: (prokaryotes = cytoplasm, eukaryotes = nucleus)

2. RNA polymerase (prokaryotes = mainly 1 RNA polymerase, eukaryotes= many RNA polymerase)

3. RNA processing: prokaryotes = little to none, eukaryotes = extensive processing

5’ cap

protects mRNA and helps it exit the nucleus after transcription

poly-A tail

protects mRNA and helps transport it out of the nucleus after transcription

which RNA polymerase makes mRNAs in eukaryotes

RNA polymerase 2

what is the role of a promoter in transcription

tells RNA polymerase where to start transcription

which strand of DNA is the promoter located on?

coding (non-template) strand

what is a consensus sequence

the most common DNA pattern of bases found at that region

intron

section of a gene that is transcribed into the pre-mRNA but removed during RNA splicing

exon

a section of a gene that remains in the mature mRNA after splicing

alternative promoter

• different promoter that can be used to start transcription of the same gene

• a gene can have multiple promoters to start transcription at differe locations

alternative polyadenylation

a cell can choose different sites to add the poly-A tail to the same pre-mRNAA

true/ false: Chromose number indicates how complex an organism is

FALSE: how many chromosomes an organism has has nothing to do with complexity