Amino acids, mutations, and western blots

Question 1

How do peptide bonds form between amino acids?

Answer 1

Through hydrolysis, the bond occurs between COO and NH3

Question 2

Peptide bonds between amino acids form what?

Answer 2

Proteins

Question 3

Do proteins have directionality? If so, how?

Answer 3

Yes, they have a N terminal (amino NH3) end and C terminal (COO ) end

Question 4

What changes among amino acids structures? What consistent? Draw it

Answer 4

The carbon end COO and the amine end H3N are consistent, the R group changes among amino acids

Question 5

The genetic code is degenerate, what does that mean?

Answer 5

Means that multiple codons, code for the same thing

Question 6

How is the genetic codes degeneracy helping to buffer against mutations?

Answer 6

They buffer against transition SNPS, as CAU and CAC differ by one amino acid, but code for the same thing so if the T went to G in the original code it would still be fine

Question 7

What is the start codon?

Answer 7

AUG

Question 8

What defines the reading frame?

Answer 8

start codon

Question 9

Which terminal end is made first of proteins? Which is made last?

Answer 9

N terminal end made first, C terminal end made last

Question 10

How do amino acids get put together from mrna?

Answer 10

Trna

Question 11

What is the anticodon loop?

Answer 11

Is a loop in tRNA molecule which is complimentary to the mRNA, it recognizes a specific amino acid

Question 12

Where is the amino acid attached on the tRNA mlcl?

Answer 12

The 3’ end

Question 13

What is a charged tRNA?

Answer 13

A tRNA molecule that has the correct amino acid, (corresponding to the mRNA) attached

Question 14

What enzyme attached the amino acid to the tRNA?

Answer 14

the enzyme aminoacyl-tRNA synthetase

Question 15

What brings together the charged tRNA and mRNA?

Answer 15

ribosomes

Question 16

What are ribosomes made of? What do they look like structurally?

Answer 16

Made of 1/3 protein, and 2/d rRNA, contain a large and small subunit

Question 17

Ribosomes move across mRNA in what direction?

Answer 17

5’ to 3’

Question 18

What combines the amino acids brought in by the charged tRNA into peptides?

Answer 18

Peptidyl-transferase center

Question 19

What is the Shine-Dalgarno Sequence?

Answer 19

is a sequence in mRNA and that is recognized by rRNA in the small subunit of the ribosome, it helps position ribosomes upstream of the start codon

Question 20

What is the Kozak sequence?

Answer 20

does same function as shine dalgarno, but in eukaryotes

Question 21

SNPS in exons result in which 4 different outcomes?

Answer 21

NO mutation
silent mutations
missense mutation
nonsense mutations

Question 22

What is a silent mutation?

Answer 22

get same amino acid after change in nucleotide

Question 23

What is a missense mutation?

Answer 23

get chemically similar or different (nonconservative) amino acid

Question 24

whats a nonense mutation?

Answer 24

get a stop codon

Question 25

When can a silent mutation is have phenotypic effects?

Answer 25

Say the nucleotide changes which effects stability of mRNA and then causes less expressivity
or it can be near the end of an exon which might interfere with splicing

Question 26

What is Western blotting used for?

Answer 26

Used to detect a particular protein from a mixture of protein
* Can also determine the size of the protein and level of protein expression

Question 27

What gel are western blots done?

Answer 27

polyacrylamide gel

Question 28

How does western blotting work?

Answer 28

we boil samples and then add detergent to separate the proteins by size
then we use probes which bind to our proteins of interest to visualize them in gel

Question 29

what are the probes in western blotting? describe the structure of them and how they help to visualize proteins

Answer 29

these are antibodies that recognize specific proteins and bind to them (the primary antibody binds) and the antibody with the fluorescent label (called the secondary antibody) makes it so you can see it in the gel

Question 30

Say we have a STR in one gene will travel farther or shorter distance than the WT gene?

Answer 30

shorter

Question 31

Say we have a higher expression in one gene, what will it look like in the western blot?

Answer 31

it’ll be bigger as more of the proteins are being made