Exam 1 Study Guide Questions Pt. 1

What is the central dogma of genetic information

DNA → RNA → Protein

dsDNA

double stranded DNA

ssDNA

single strand DNA

why do we call mRNA a “positive sense strand”?

because it’s the one that info to make the protein

looking at a dsDNA gene and the resulting mRNA how would you identify the positive and negative sense DNA strands?

+sense DNA matches the sequence of the mRNA

-sense DNA was the template strand complementary to the mRNA

what 3 possible locations can ribosomes be found in the cell

ER membrane, on channel protein, in cytoplasm

For each location of a ribsome in cell where will the proteins they make end up

ER membrane - makes membrane protein (can be outside cell membrane)

Channel Protein - makes protein that ends up in lumen of ER and can be secreted (leaves)

Cytoplasm - cytoplasmic proteins

why are proteins in important in the cell, what funcitons do they perform

make structures and do jobs

what does semiconservative DNA replication mean

One strand remains original

what macromolecules are used by living cells

lipids, carbs, nucleic acids, proteins,

what does a lewis dot structure help us predict

the structure of a molecule/ bonding pattern

what is a valence shell

outer shell that bonds

which two columns of the period table can donate elections, which recive

donate - 1 and 2, receive - 16 and 17

covalent bond

sharing electrons

ionic bonds

attraction based on charge

how many bonds do carbon oxygen hydrogen and nitrogen like to form

4, 2,1, 3

what is a dipole

uneven sharing of electrons in a covalent bond

what is a hydrogen bond

H - F, O, N - F, O, N

can polar molecules from hydrogen bonds with nonpolar molecules

yes

Hydrophilic

Likes water, polar, can H bond

hydrophobic

doesnt like water, non polar, can not H bond

list the main atom-atom bonds/interactions in order from weakest to strongest

Vanderwall’s < dipole dipole < ionic < covalent

what makes van der Waals different from the other interactions

they are non polar, made by temporary dipoles in non polar molecules, they are different because they don’t have permanent dipoles

why are hydrophobic interactions significant for protein folding?

forces between amino acid R groups are how the protein folds and forms secondary/tertiary structures

what are the R groups of amino acids

dictate protein function

what kinds of R groups (hydrophobic/hydrophilic) would you anticipate to find on the surface of a protein floating in the cytoplasm?

hydrophilic

what R groups would you anticipate to find buried in the interior of the same protein in cytoplasm?

hydrophobic

what R groups would you expect to find in a transmembrane domain (interacting with phospholipid tails)

hydrophobic

what R groups would you expect to find exposed to the extracellular environment

hydrophilic

why are van der Waals interactions and hydrogen significant for DNA structure

Base - base = hydrogen bonds, base on top of base = van der Waals

what components make up a DNA nucleotide

Phosphate, Sugar, base

what is the difference between DNA and RNA nucleotides

Uracil instead of Thymine, RNA has oxygenated sugar

Which compontnets make up DNA backbone

phosphates and sugars

what type of covalent bond holds the backbone together

phosphodiester bond

what do the terms 5’ and 3’ refer too

5’ = phosphate side, 3’= OH side

why does DNA need to be compacted

because there is a lot of DNA in one nucleus

Nucloside

base + sugar

nucleotide

base + sugar + phosphate

whats a dNTP

deoxynucleotide triphosphate - DNA nucleotide

what charge does DNA have?

negative (phosphate backbone)

what its the structural difference between purines and pyrimidines

purines have two rings, pyrimidines have one ring

what are two common chemical modifications made to DNA bases

methylation (Adding a CH₃) and Amination (adding an NH₂)

How is ATP act like an energy source for biological reactions

ATP → ADP + Pi + energy (also reversable)

what is the transion site on a free energy diagram

where it reaches a peak

what is an enzyme and how dies it affect a chemcial reaciton

protein that lowers activation energy

what does + delta G mean

non spontaneous - requires energy

what are the two laws of thermodynamics

1 - energy can not be created or destroyed

2 - spontaneous reactions take place with an increase of disorder (entropy)

how can proteins be denatured

with pH changes and temperature

how is DNA melted

increase in temp to melt the H bonds between the base pairs

what is a buffer and why do we use it in lab

it resists pH change, it can control pH of a solution

wohy would a high content of G and C nucleotiedes require more energy to melt DNA

because they have3 H bonds between them while A and T only have 2

How does DNA move in gel electrophoresis and what do the bands created represent

move towards positive charge, larger moves more slowly, bands show different lengths of DNA

what is a nuclease

cut DNA

what is an endonuclease

cuts in the middle of DNA

what is an exonuclease

cuts the ends of DNA strands

why are restriction endonucleases special?

they cut DNA at specific sequences

what’s a conformational shift of a protein`

change in protein shape induced by some stimulus

what is a ligand

what binds to an enzyme

when is a ligand a substrate

substrates are ligands that are acted upon by an enzyme

how do proteins read and bind to a particular DNA sequence

the R groups of aminoa cids will bind to corresponding sites on the DNA

What is the function of DNA ligase

connect DNA by forming/reforming phosphodiester bonds

what do cofactors and what does it do

positive ions that help enzyme function by neutralizing negative charges (especially on backbone of DNA)

what’s a coenzyme

organic enzymes that help other enzymes function