BSCI Unit 2 Midterm (copy)

Linkage through coupling

When dominant alleles are together on the same copy of each chromosome in a homologous pair. Works the same for recessive

Linkage through repulsion

When different alleles, dominant and recessive are together on the same chromosome of a homologous pair

Linkage groups

Series of genes that are linked

Linked Genes

Genes that are inherited together

Interference

When one recombination event affects the presence of another

STR

Short tandem repeats

Recessive non-wildtype

When the organism needs one wild type allele in order to be expressed

Dominant non-wildtype

When the organism needs 2 wildtype alleles to be expressed

Haploinsufficiency

One wild type copy is not enough

Incomplete Dominance

Intermediate phenotype 1:2:1 where heterozygote is intermediate of the 2 phenotypes

Codominance

When both alleles are expressed in the heterozygote, 1:2:1 ratio. Example of this is blood typing

Lethal Alleles

Recessive allele's that cause death during embryonic development. Can't be dominant because the allele's wouldn't be able to be passed onto offspring

Pleiotropy

Single gene affects numerous seemingly unrelated genes

Penetrance

Percentage of individuals with a genotype that express the related phenotypes

Expressivity

The degree to which a phenotype is expressed

Sex influenced trait

When one sex shows a higher degree of trait expression or higher incidence

Sex limited trait

Genotype is only expressed in one sex despite being autosomal

Environmentally dependent/conditional phenotype

Where the genotype causes the individual to be more susceptible to producing a phenotype when exposed to an environmental cue.

Heterogenic Trait

Where alleles in any one of many genes causes a phenotyppe

Complementation test

A cross between 2 mutant phenotype individuals to see if they express that phenotype because of mutations in the same gene.

Complementation occurs in a complementation cross

Alleles are in different genes and offspring are wild-type (Different from mutant parents)

No complementation occurs in complementation cross

Alleles are in the same gene and offspring are mutants like parents

Polygenic traits

Traits affected by many genes

Novel Phenotypes

Two genes each affecting the same trait. They act independently

Epistasis

2 genes interact and affect the presense of another

Recessive epistasis

Recessive genotype at one locus always always produces the same phenotype regardless of second locus.

Recessive Epistasis Ratio

9:3:4

Dominant Epistasis

Dominant genotype at one locus produces the same phenotype regardless of the second locus.

Dominant epistasis ratio

12:3:1

Duplicate Dominant Epistasis

Recessive genotype at EITHER locus produces the same phenotype

Duplicate Dominant Epistasis Ratio

9:7

Duplicate Recessive Epistasis

Dominant genotype at either locus produces the same phenotype

Duplicate Recessive Epistasis Ratio

15:1

Concordance

Proportion of twin sets in range from 0-1

Higher concordance in monozygotic twins

Possess genetic basis

Nontemplate/Coding/Sense Strand

Strand not use as a template for RNA production

Template/Anticoding/Nonsense

Used to make RNA

Components of the transcription unit

Transcriptional start site, RNA coding region, Transcription termination site

Initiation Stage

Promoter induces transcription.

Promoter in Bacteria

-10 and -35 Motif

Holoenzyme

Bind to promoter to form replication bubble

Sigma

Makes binding specific to promoter sequence. Distinguishes promoter

Core Enzyme

RNA polymerase

Elongation Stage

RNA polymerase polymerizes slowly without error correction while Sigma is released

Termination in Bacteria

Formation of a hairpin that physically blocks our RNA polymerase causing hybrid strand to separate

Rho-Dependent Termination

Rho binds to RNA and moves upstrand to hybrid to form a hairpin near the hybrid. Rho uses helicase activity to break the strand to release RNA

Rho Independent Termination

Hairpin forms in G-C dense regions while U-A dense regions in the hybrid are weak and eventually separate

Eukaryotic Core Promoter

Multiple consensus sequences. TATA box is most common

Most Common RNA polymerase that encodes for translation

RNA Polymerase II

Basal Transcription Factors

Bind polymerase to core promoters, similar to sigma in Prokaryotes.

Non-coding RNA

RNA that has been transcribed but will not be translated

Post transcription in Eukaryotes vs Prokaryotes

Prokaryotes immediately move on to translation meaning translation and transcription occur at the same time
Eukaryotic transcription is in nucleus while translation is in the cytoplasm. Modifications must be made to stabilize and export to cytoplasm

5' Cap

Guanine Triphosphate nucleoside in reverse orientation to triphosphate nucleoside in the first position of the transcribed pre-mRNA. Bond is then methylated. Increases stability and improves transcription efficiency.

3' Poly-A Tail

50-250 adenines to 3' end in order to stabilize mRNA. Positions ribosome along with 5' cap. Signals for export to the nucleus

Rat1

Digestive Enzyme that binds at 5' end on cleavage site to the RNA to stop transcription

mRNA Splicing

Removal of introns that interrupt coding sequence and must be removed to make mRNA mature.

Spliceosome

Proteins that bind at the splice sites in an intron, fold RNA, and cut intron off.

Alternative splicing

Keeping different exon combinations from the same gene to form different products.

Isoforms

Different protein products translated from alternative splicing.

Trans-splicing

Single mature mRNA is made of exons of more than one primary RNA

Degenerate Code

Amino acids that can be coded by numerous codons

Transfer RNA (tRNA)

Complementary to mRNA codons by using anticodon pairs to carry amino acids to attachment sites

Aminoacyl-tRNA synthetase

Loads amino acids onto correct tRNA

Wobble

Nonspecific pairing at third position on codon because there are enough tRNA's for each codon

Shine Dalgarno Sequence

Start site of translation that is complimentary to rRNA component of the small subunit and allows a start codon to be conditioned directly.

Ribosome Subunites

Large Subunit: 50s
Small Subunit: 30s

Initiation Factor 2

Step 1 of Elongation

Charged tRNA delivered to A site

Step 2 of Elongation

Creation of peptide bond between amino acids in A and P site, releasing the amino acid from the tRNA in the P position

Step 3 of Elongation

Translocation of the ribosome down stream 5' to 3' and A to P

E position

Exit point of tRNA

A Position

First position where tRNA is delivered

P Position

Where amino acid is released and where peptide bonds and chains form

Termination of translation

Stop codon in position A causes a release factor to bind instead of a tRNA causing nothing to attach to the polypeptide chain.

Do eukaryotes have shine dalgarno?

No

Eukaryotic Translation promotion

5' cap and 3' tail orient mRNA so that small subunit of ribosome begins at the 5' end. Ribosome assembly of large and small subunit once an AUG start codon is found in Kozak sequence.

Antibody Staining

Identify whether a particular protein is present in the cells of a tissue.

Proteomics

Extraction and categorization of proteins. Compares it to expressive proteins that may be produced.

Germ Line Cells

Lines of cells set aside during embryotic development so that it minimizes the mutations can be passed down to the gametes

De Novo

Occurrence of a mutation in germ line cells. May cause phenotypic affects on offspring that parents do not present.

Point Mutation

SNPs or INDELs that affect one or a few nucleotides

Chromosomal Mutations

Can affect multiple genes or an entire chromsome

Nucleotide Mutations

Effect on DNA sequence level

Amino Acid Mutations

Effect on transcription or translation

Substitution Mutations

Change in nucleotide sequence that does not affect nucleotide length

Transitions

Purine to Purine and Pyrimidine to Pyrimidine

Transversions

Purine to Pyrimidine or Vise Versa

INDELs

Addition or removal of a nucleotide. This actually affects length of sequence

Silent Mutation/Synonymous Mutation

Nucleotide alteration that has no affect on amino acid sequence due to degeneracy

Missense Mutations

Nonsynonymous mutation where a change in nucleotide sequence causes change in the amino acid sequence

Nonsense Mutations

Nonsynonomous mutation where change in the nucleotide sequence induces a premature stop codon by changing an amino acid codon.

Frameshift Mutation

INDEL Mutation causing the change in reading frame. Insertions of 1,2 change the downstream codons and INDELs of 3,6,9... are frame Insertions/Deletions that do not affects the sequence of remaining codons

Neutral Mutations

Amino acid sequence changes but phenotype remains the same

Loss of Function Mutation

Where a mutation causes a nonfunctional or less functional protein product

Gain of Function Mutation

Mutation causes protein product to take on a new function

Lethal Mutation

Cause embryonic or developmental lethality

Conditional Mutation

Causes a new phenotypic affect but only within certain conditions

Mutation Rate

Chance a specific base pair will change

Mutation Rate equations

Total number of mutations/Number of mutations in a gene
Or
Number of mutations in a gene/Total bases in a gene

Mutation Frequency

Chance a function altering mutation will occur (Non-neutral)