Biochemistry Week 2 Terms & Definitions for Biology

You receive a genetics report which states that protein X has a P47G change. This report means the primary structure of protein X has changed by having

glycine replace proline at position 47

Proteins with similar structures and functions are said to be

homologous

What dos the trans configuration of a peptide bond do?

aligns the permanent dipoles of the C-O and N-H bonds in the same direction

What does the resonance within the peptide bond result in?

It gives it a slightly double bound characteristic, limiting its ability to rotate freely, and restricts how polypeptides can fold

What limits the ability of the Ca and Na to rotate freely about their bonds?

Steric interactions between R groups

Size of one turn of alpha helice

5.4 A

Number of amino acids in one helical turn

3.6/3.7

What amino acid is not compatible with helical structure? What would happen if it were introduced?

proline; the helix would stop there or change its directionality by introducing a kink.

When a polypeptide is stretched, what happens to the R groups? How far apart are they?

The alternate every other residue into or out of the plane. R groups on the same side of the plan are 7 A apart.

What actually contributes to the shape of a helix?

H bonding between the carbonyl and amino group of two peptide bonds 4 AA removed.

What stabilizes beta sheets

H bonds between functional groups of the polypeptide backbone in different segments of sheet structure

Describe the structure and conformation of reverse turns

Involve four amino acid residues and are typically initiated by a proline. Residues in positions Ca2 and Ca3 are often occupied by small-ish polar residues, because reverse turns are usually founds at the extremities of a protein interacting with water

What does random structure mean

it alcks a specific type of geometric repeat unit observed in other types of secondary structure. (not a helix or beta sheet)

Which sequence when formed into an extended sheet structure would segregate its hydrophobic residues to a single surface?

D-L-K-V-S-A-N-F-Q

T-S-R-V-M-I-A-E

Q-V-I-W-K-F-D-S

T-R-E-S-N-D-H-L

M-C-D-V-M-A-H-K

D-L-K-V-S-A-N-F-Q

How would you create a helix with a hydrophobic face?

Place hydrophobic residues alternating every 3rd and 4th position in the polypeptide chain

What do chaperones do?

provide a protected environment for a protein to fold, reducing the likelihood of inappropriate rxns between proteins. However, in a non-competing environment, all that is needed is the proteins primary structure.

What do nucleic acids play an important role in?

reproduction, development, FUNCTION (organism maintainence), and genetic mutation/variation

What is the difference between DNA and RNA?

RNA has an OH group on the 2' C, where DNA has a H on the 2' C. RNA will also have the Uracil base in place of thymine.

Nucleic acids contain

pentose sugar, phosphate, base

what is in a nucleoside

sugar + base

what is in a nucleotide

sugar + base + phosphate

where does numbering of a pentos sugar carbons start?

at the C where the base is bound

where is the alpha phosphate?

bound closest to the 5' C

NTP =

nucleoside triphosphate (nucleotide)

What are the purines? what is their structure

A,G

two rings

What are the pyrimidines and what are their structure

C,U,T

one ring

free phosphate is located at the ___ end of a nucleic acid

5'

free hydroxyl is located at the ____ end of a nucleic acid

3'

what is the name of the group/bond that joins a 3' and 5' C?

phosphodiester linkage

What contributes to the negative charge of nucleic acids

the phosphate backbone

pKa of the phosphate group

about 1

what is a polymer of nucleotides

nucleic acids

DNA/RNA exhibit _____ and are conventionally written in the ________ direction

polarity; 5' -> 3'

which bases form a triple bond?

G and C

____ DNA is most common, which is ____ handed, with _____ base pairs in a full turn. bases are set _____ degrees apart from the previous base

B form

10

36

DNA strands run ____, and the strands are _____

anti-parallel

complementary

___ form DNA is left handed

Z

______ DNA is most flexible (can bend)

AT-rich

______ determines the helix form

solvent composition

Chargaffs rule

amount of purines = amount of pyrimidines

Double helix is held together by

H bonds

Why are AT rich regions present in start sites for transcription

they are more easily pulled apart for machinery to bind

What is occuring when DNA Anneals or "hybridizes"?

the double stranded form is energentically more favorable under mild conditions, so double helix reforms spontaneously. complementary strands reanneal

what process of nucleic acids play a large role in the efficacy of biotechnology?

hybridization

_____ affects melting temp

base composition

what is Tm

the temp at which half the DNA is dentatured to a single stranded state

hyperchromic effect

striking absorbance increases as DNA denatures or melts

Biological consequences and biotechnical utility of DNA structural properties

each strand is a template for another

DNA stroes, passes on, and disseminates info

nucleic acid sequences can be determined

What is the protein base unit around which DNA is wrapped?

nucleosome

nucleosome consists of ____

8 histones and 146 bp DNA

Core histone subtypes

H2A, H2B, H3,H4, and the linker H1

What enzymes supercoil DNA

topoisomerases

function of type I topoisomerase

break one strand to relax 1 strand of DNA

function of type II topoisimerase

break both strands to supercoil, requires ATP

Supercoiling of DNA starts with _____ but here are increasing levels to produce chromatin

nucleosomes

Base sequence of telomere repeating sequence and on what end

(TTAGGG)n, 3'

karyotype

chromosome makeup of a cell

Monomers of nucleic acids

nucleotides

What is meant by De novo biosynthesis

almost all organisms synthesize nucleotides

what is salvage

turnover or recycling of nucleic acids

PRPP synthetase:

enzyme responsible for the synthesis of activated ribose, which is necessary for de novo synthesis of purine and pyrimidine nucleotides

PRPP is required for _____ and _____

synthesis of both purines and pyrimidines AND nucleotide salvage

What rxn does PRPP synthetase catalyze?

addition of a phosphate from an ATP to a Ribose-5-phosphate in a process called "charging" to create PRPP

How do purine and pyrimidine synthesis differ

purine bases are added directlt to the PRPP, pyrimidines bases are built off site and added later

How many steps to create a purine? what is the result?

11, inosine monophosphate

Pathway to Adenosine monophosphate from IMP is dependent on ___ as an energy source

GTP

Pathway to Guanine monophosphate from IMP is dependent on ___ as an energy source

ATP

What determines if AMP or GMP from IMP?

concentration of GTP and ATP

What is kinase

enzyme that adds phosphate groups

Base specific _______ synthesize nucleoside diphosphates

nucleoside monophosphate kinases

Nucleoside diphosphate kinases convert _______. They do not _____

NDPs to NTPS

discriminate between ribose and deoxyribose

IMP pathway control points of purine nucleoside biosynthesis

used to maintain purine concentration

feedback inhibition by ADP and GDP

Allosteric activation by PRPP

Branch Point control of purine nucleotide biosynthesis

used to maintain a balance of each purine

Rates of AMP and GMP are coordinated

AMP and GMP are competetive inhibitors of IMP

Purines are synthesized by _____

assembling a purine base on PRPP

What is the first purine nucleotide synthesized

IMP

What converts AMP and GMP to ATP GTP

kinases

What 4 things are used to synthesize purines

PRPP, amino acids, folate, ATP

What provides Ns to purine biosynthesis

Amino Acids

What does orotate phosphoriboxyl transferase do

uses PRPP to attach orotate to a pentose sugar

Product of pyrimidine synthesis

Uridine monophosphate (UMP)

Commited step of pyrimidine synthesis

aspartate to carbamoylaspartate via aspartate transcarbamoylase

Product of PRPP acting on orotate

orotate monophosphate

Pyrimidine de novo biosynthesis ingredient list

glutamine, aspartate, bicarbonate, ATP, PRPP-activated sugar

CAD protein is a trifunctional enzyme in animal cells that ______

catalyzes the first three steps of pyrimidine biosynthesis, beginning with 2 ATP, Co2, and glutamine, and ending with orotate

What does ODCase do (OMP-decarboxylase)?

makes UMP from OMP in pyrimidine biosynthesis

OPM -> UMP -> ? via kinases

UTP

CTP is synthesized from ___ by _____

UTP; CTP synthase

When synthesizing CTP from UTP, where do animals and bacteria get the amino group from?

glutamine and ammonia, respectivelyy

In e. coli, how is PRPP regulation different

it leads to inhibition, not activation

Pyrimidine are synthesized by ____

placing an assembled pyrimidine base on PRPP

____ is the first pyrimidine nucleotide synthesized

OMP

____ convert UMP to UTP

kinases

Pyrimidine synthesis is regulated by what?

substrate, RRP, and ATP (activated), and product (UDP, UTP) (inhibited)

dDNA synthesis is catalyzed by ____. ___ is reduced at he 2' position to form the _____. ______ provides reducing power

ribonucleotide reductase

NDP

dNDP

NADPH

Goal of ribonucleotide reductase

produce correct rations of the 4 dNDPs

Nucleosides are absorbed through the intestine or further degraded by ______ and _____

nucleosidases

nucleoside phosphorylases

Nucleotidases and phosphatases yield ______

nucleosides

Nucleotides are ____ and cannot pass through

ionic

cell membranes

Purines are broken down into _____. Degredation proceeds by _____.

uric acid

removing base from nucleotides, then sugars

Pyrimidines are converted to _____ for catabolism

CoA derrivatives