bicd 100 exam 1

what is the study of genetics

the study of heredity and variation of inherited characteristics in individuals and populations

phenotype

often thought of as what is seen

more accurately, a composite of an organism’s observable and measurable traits or characteristics

chromosome

sister chromatids

two pieces of DNA joined at the centromere

homologous chromosomes

two of the same unjoined chromosomes in a cell

most likely one from the sperm and one from the egg

same genes in same locations, but may have different alleles of these genes

when do chromosomes have a centromere

always, even when unjoined

karyotype

all the chromosomes from a single cell

gene

section of DNA that codes for a functional gene product such as a messenger RNA, protein, transfer RNA, microRNA, etc etc

do all genes have start and stop codons

no, because not all genes code for proteins

locus

location of a gene

allele

version of a gene

wild type

functional gene product, does not mean it is always dominant

mutant

not functional

so could be non functional, partially functional, etc

what makes two alleles different? what makes them similar?

they have different DNA sequences but they still code for the same gene which could result in different products between the two of them

what is gene expression

can be thought of as the gene getting turned on

when a gene is expressed then it is being transcribed

are codons involved in transcription or translation

always translation since they are coding for amino acids

hemizygous

individual with only 1 allele of this instead of 2

example XY individuals who have necessary genes that are only on the X chromosome that they have 1 copy of

gel electrophoresis

separates DNA by size

charge difference makes negatively charged DNA molecules move towards the positive end of the gel

shorter molecules move faster through the gel and are lower down

what terminology do we use to talk about the size of RNA

length of RNA is the same as the number of bases it has

note that it is bases and not base pairs because it is single stranded

what do restriction enzymes do

cut dsDNA at a specific sequence

how would the gel of a heterozygous individual look

it doesn’t matter if the allele is dominant or not because these are just pieces of DNA

northern blot

for RNA analysis

very similar to gel electrophoresis

is looking for specific sequences of RNA like

western blot

for protein analysis

antibody is added so that specific proteins can be seen

the human genome has how many chromosomes

23 chromosomes

every nucleus has 2 sets of the entire genome in it

germ cells

haploid

23 chromosomes total, only 1 set of chromosomes instead of 2

sex cells like sperm and egg

somatic cells

diploid

2 sets of chromosomes so 46 total

cells that the body is made up of

if you look at a singular nucleotide what side is 3’ and 5’

if you look at the carbon ring then the carbon attached to phosphate is the 5’ end and the carbon with an OH group on it is the 3’ end

what are the steps of how DNA is condensed into chromosomes

dsDNA strand > nucleosomes consisting of DNA wrapped around histones > chromatin fiber consists of coiled nucleosomes > chromatin condenses further into loops> a chromosome is made of condensed chromatin fiber

which bases pair up with each other and why

A>T and C>G because they are held together in the double stranded structure by H bonds

the actual shape of the molecules determines if they can H bond together

hybridizing

another way to say that bases are paired with each other

when DNA and RNA pair up what orientation do they have to be in

they are also antiparallel just like dsDNA

transcription vs translation

transcription is copying info from DNA to RNA, think the base pair language of DNA is being copied over to RNA base pair language

translation is taking info from RNA and turning into protein, think the base pair language of RNA has to be translated into the protein amino acid language

what is the centromere made of and how does that affect its function

the centromere is a DNA sequence

it is necessary for mitosis and meiosis

microtubules can attach to it, so if it mutated then sister chromatids will not properly separate

roughly describe how DNA turns into protein

DNA is transcribed into pre-mRNA

the pre-mRNA is spliced and exons are joined together, making mRNA

the mRNA is translated into protein by a ribosome

splicing in simple terms

pre-mRNA is turned into mRNA by removing introns and joining exons

DNA and RNA are read in what direction

when DNA is being synthesized and RNA is being translated into protein it is read 5’ to 3’

when RNA is being transcribed it is read 3’ to 5’

stop codon

codon that stops protein synthesis

it is not translated into an amino acid

transcription still continues past here, it just stops translation

exons and introns

exons stay in the mRNA, intros get spliced out of the pre-mRNA

what is the UTR and where are they

UTR stands for untranslated regions, they are still transcribed into mRNA but not translated into amino acids

regulates translation and RNA processing and is a binding site for various proteins and regulatory RNAs

at the 5’ and 3’ end of the region that is being read

ribosome binding/recognition site (RBS)

a sequence of nucleotides somewhere in the 5’ UTR near the start codon where the big subunit of the ribosome binds

is transcribed but not translated

start codon

is the start of translation

it is the first amino acid that is transcribed

methionine

origins of replication

the sequence in the DNA where replication starts

it is not transcribed but it still has the above function

enhancer

regions of DNA near the promoter that activators/transcription factors bind to that make it more likely for the gene to be transcribed into RNA/boosts the rate of transcription

it is usually not transcribed

so for the purpose of this class anything that regulates the amount of transcription thats not the promoter

promoter

region of DNA on the coding strand that transcription factors and RNA polymerase bind to

it initiates transcription

it is usually not transcribed

terminator region

is the end of transcription

tricky to discuss whether it is transcribed or not transcribed

what are the ways that transcription can be affected by a mutation

expression is not just turning a gene on or off, usually the level of transcription is the thing that is affected

RNA abundance: how many pieces of RNA are made

RNA length: number of nucleotides

RNA sequence

structure of a gene

at the 5’ end>enhancer > promoter > TSS> 5’ UTR > intron/exon/intron/exon………> 3’ UTR > poly A site > terminator

coding vs template strand

coding strand matches the RNA

template strand is what is read to make the RNA since it is complementary to it

transcription factors

proteins that regulate genes by increasing or decreasing expression

these bind to enhancers and promoters and also interact with RNA polymerase

poly adenylation (poly a) signal

this is not the terminator

it is the end of the 3’ UTR

adds a protective tail of aaaaaaaaaa and signals for cleavage

splicing

the process of spliceosomescutting out introns and joining exons

the process of turning pre-mRNA into mRNA

ligate

the enzyme ligase ligates together exons by forming phosphodiester bonds btwn 2 pcs of DNA

what end of the intron is recognized first by the spliceosome

5’ end

isoform

different protein made from the same gene

created through alternative splicing

a mutation in an intron is detrimental when

it affects splicing

so it could cause an exon to be excluded or an intron to be included in translation

what would happen to the resulting protein if an intron was not spliced out of a gene

the most likely scenario would be a shorter protein

an intron is about 10 times longer than an exon so there is a higher chance of it having a stop codon

5’ UTR

ribosome binding site

kozak sequence

kozak sequence

required for the big subunit of the ribosome to bind

the kozak sequence is considered to be a part of the 5’ UTR and also includes the start codon and an extra G

3’ UTR

poly A signal (cleavage)

proteins bind to it which recruit exosomes that cause mRNA destabilization (less translation)

motor proteins walk on microtubules and more the RNA to specific places (localization)

code for micro RNAs that bind to other RNAs, when these microRNAS bind you get mRNA degradation post-transcription

where is the open reading frame

the ribosome reads btwn the start and stop codon

the start codon determines the reading frame since the ribosome starts there, then the rest of it consists of consecutive, non-overlapping triplets

silent mutation

a nucleotide is substituted, but there is no change to the amino acid

missense mutation

a nucleotide is changed which results in the amino acid being changed

nonsense mutation

makes a stop codon earlier in the sequence

frameshift mutation

changes the reading frame resulting from indels that are not a multiple of 3

insertion/deletion mutation

causes frameshift mutation if it is not a multiple of 3 and if it is inside the reading frame

so not all indels cause frameshifts

when/where is a change to the DNA sequence a mutation

any change to the DNA sequence is a mutation

coding, non-coding, in genes, outside of genes

when and where do mutations occur

they occur in the DNA, not in the RNA

mutations occur during replication bc DNA polymerase does not proofread perfectly

mutations occur because of environmental mutagens: UV rays, radiation

mutations in what cell types will be passed onto the next generation

gametes

where in the genome is it likely for a mutation to occur

non-coding regions

this is because non-coding regions are a lot longer than coding regions

describe when/where the subunits of the ribosome bind

the small subunit of the ribosome binds on the 5’ cap and scans until it finds the kozak sequence, then the large subunit binds and translates

what are some possible results of a mutation in the kozak sequence

• there is decreased ribosome binding so there is decreased protein production

• the ribosome recognizes a different/wrong start codon downstream which could lead to a shorter or non-functional protein if there is a frameshift

what is a theory for how an indel in the 5’ UTR could cause a frameshift

it creates a premature start codon

what are ways to indicate a gene is wild type

WT or +

LOF and GOF alleles

• loss of function allele is usually recessive if the other functional allele is enough to compensate (aka the functional allele will be dominant if it is haplosufficient)

• gain of function allele is usually dominant (if it masks or overrides the effect of the wild type allele then it will be dominant or partially dominant)

haplosufficient

one copy of an allele is enough to make a normal/wild type phenotype

constitutive

always on/ active

what are the types of intermediate phenotypes

codominance, partial dominance, incomplete dominance

what does a circle mean on a pedigree

female

what does a square mean on a pedigree

male

what does a diamond mean on a pedigree

sex is unknown

which individuals on a pedigree are affected and unaffected

affected are shaded, unaffected are unshaded

what do two lines connecting individuals on a pedigree mean

parents that are related to each other

the offspring of parents are shown in what order on a pedigree

birth order

autosomal dominant trait in a pedigree

• only need 1 copy of the allele to express the trait

• one of the parents expresses the trait

• male to male transmission (this rules out X-linked inheritance )

• traits do not skip a generation but not all offspring have to have the trait

autosomal recessive trait in a pedigree

need 2 copies of the allele to express the trait

parents may or may not express the trait

X-linked recessive trait on a pedigree

• trait is more common in males

• if a mother is affected then the trait will be passed to all sons

• affected males will only pass it to daughters if the mother is affected or a carrier

• affected males cannot pass it to their sons

X-linked dominant trait on a pedigree

• female parent can pass trait to both daughters and sons

• male parent can pass trait to all daughters but no sons

incomplete penetrance/variable penetrance

not everyone with the mutation has the phenotype

penetrance

the percentage of ppl with a genotype that exhibit the expected phenotype

variable expressivity

variation in phenotype

all people with the genotype have a change in phenotype, but they present it in different ways

epigenetics

(temporarily) inherited changes in gene expression that cannot be explained by differences in the DNA sequence

so it can be inherited through generations or the changes can be inherited cell by cell

what are the three mechanisms of epigenetics

histone acetylation, DNA methylation

RNA interference through micro RNAs

DNA methylation

cytosines in the DNA can get methylated which will decrease gene expression

since DNA replication is semi-conservative (meaning that replicated DNA is made of one “old strand” and one “new strand”) this means that methylation can be passed on/inherited

histone acetylation

acetyl groups are added to histones and nucleosomes become less compact which leads to more expression

what can affect the epigenetic state of the genome

environmental factors such as nutrition, temperature, stress

null allele

does not form a functional product

phosphorylation

a post-translation modification to a protein that can either activate or inactivate it

ubiquitination

a type of post-translational modification to protein where ubiquitin are added to protein and it gets targeted for degradation

protease

a type of post-translational modification to protein

a signal or protein that tells the cell to degrade a protein by using protease enzyme which can activate or inactivate an protein

it is useful for all cells to be genetically identical because

• embryos develop through mitosis, so all the genes can be passed on to every cell

• every cell has the potential to be differentiated into the required tissue during embryonic development or to replace dead/damaged cells